Bioinformatics operations, data types, formats, identifiers and topics

IRI:
http://edamontology.org
Authors:
Hervé Ménager
Jon Ison
Matúš Kalaš
Contributors:
Veit Schwämmle
Other visualisation:
Ontology source

Table of Content

  1. Classes
  2. Object Properties
  3. Annotation Properties
  4. Namespace Declarations

Classes

.nibc back to ToC or Class ToC

IRI: http://edamontology.org/format_3010

has super-classes
Binary formatc
Raw sequence formatc

1 or morec back to ToC or Class ToC

IRI: http://edamontology.org/data_2178

has super-classes
deprecated classc

18O labelingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3640

has super-classes
Labeled quantificationc

2 or morec back to ToC or Class ToC

IRI: http://edamontology.org/data_2180

has super-classes
deprecated classc

2bitc back to ToC or Class ToC

IRI: http://edamontology.org/format_3009

has super-classes
Binary formatc
Raw sequence formatc

2D PAGE datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2363

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
deprecated classc

2D PAGE experimentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3521

has super-classes
deprecated classc

2D PAGE gel reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2965

has super-classes
deprecated classc

2D PAGE imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_0942

has super-classes
Raw imagec
has topicop some Proteomicsc

2D PAGE reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2364

has super-classes
deprecated classc

2D PAGE spot reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2372

has super-classes
deprecated classc

3D EM Mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_3805

has super-classes
Structurec
has topicop some Structural biologyc

3D EM Maskc back to ToC or Class ToC

IRI: http://edamontology.org/data_3806

has super-classes
Structurec
has topicop some Structural biologyc

3D profile generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0297

has super-classes
Structure analysisc
Generationc
has outputop some Structural profilec
has inputop some Structure alignmentc
has inputop some Structurec

3D profile-to-3D profile alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0299

has super-classes
deprecated classc

3D profile-to-3D profile alignment (pairwise)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0513

has super-classes
deprecated classc

3D-1D scoring matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_1499

has super-classes
Protein sequence-structure scoring matrixc

3D-1D scoring matrix formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2064

has super-classes
Matrix formatc
is format ofop some 3D-1D scoring matrixc

3D-1D scoring matrix generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2239

A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments.
has super-classes
Protein property calculationc
Generationc
has topicop some Structure analysisc
has outputop some 3D-1D scoring matrixc

A2Mc back to ToC or Class ToC

IRI: http://edamontology.org/format_3281

has super-classes
FASTA-like (text)c
Alignment format (text)c

aaindexc back to ToC or Class ToC

IRI: http://edamontology.org/format_1504

has super-classes
Amino acid index formatc
Textual formatc

AAindex IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1128

has super-classes
Amino acid index IDc
Accessionc

Ab initio structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0476

has super-classes
Protein structure predictionc

Ab initio structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0174

has super-classes
deprecated classc

Ab-initio gene predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3662

has super-classes
Gene predictionc

AB1c back to ToC or Class ToC

IRI: http://edamontology.org/format_3000

AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF).
has super-classes
Sequence trace formatc
Binary formatc

ABCD formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3708

has super-classes
Biodiversity data formatc
is format ofop some Biodiversity datac

ABIc back to ToC or Class ToC

IRI: http://edamontology.org/format_1628

has super-classes
Sequence trace formatc
Binary formatc

ABS IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2741

has super-classes
Accessionc
Promoter IDc

Abstractc back to ToC or Class ToC

IRI: http://edamontology.org/data_2849

has super-classes
Text datac

Accessible surface calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0384

Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
has super-classes
Molecular surface analysisc
has outputop some Protein solvent accessibilityc

Accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2091

has super-classes
Identifierc
has sub-classes
AAindex IDc, ABS IDc, ACLAME IDc, ASTD IDc, ATC codec, AraC-XylS IDc, ArachnoServer IDc, BIND accession numberc, BRENDA ontology concept IDc, BRENDA organism IDc, BindingDB Monomer IDc, BioCyc IDc, BioGRID interaction IDc, BioModel IDc, BioNumbers IDc, BioPax concept IDc, Blattner numberc, BlotBase blot IDc, Brite hierarchy IDc, CABRI accessionc, CAS numberc, CATH identifierc, CCAP strain numberc, CDD IDc, CDD PSSM-IDc, COGEME EST IDc, COGEME unisequence IDc, COSMIC IDc, Cell type ontology IDc, ChEBI IDc, ChEBI concept IDc, ChemSpider IDc, Chemical registry number (Beilstein)c, Chemical registry number (Gmelin)c, CleanEx entry namec, Clone ID (IMAGE)c, Compound ID (3DMET)c, Compound ID (BioCyc)c, Compound ID (ChEMBL)c, Compound ID (ChemIDplus)c, Compound ID (HMDB)c, ConsensusPathDB entity IDc, DBD IDc, DIP IDc, DOIc, DPVweb IDc, DiProDB IDc, Disease ID (PharmGKB)c, Drug ID (KEGG)c, Drug ID (PharmGKB)c, Drug ID (TTD)c, DrugBank IDc, EC numberc, EGA accessionc, EMAGE IDc, EMAP concept IDc, EMBL/GenBank/DDBJ IDc, EMDB IDc, EPD IDc, Ensembl IDc, Ensembl gene IDc, Ensembl gene tree IDc, Ensembl protein IDc, Ensembl transcript IDc, Enzyme ID (BioCyc)c, Enzyme ID (CAZy)c, Enzyme ID (MEROPS)c, FIG IDc, FMA concept IDc, FlyBase IDc, GEO accession numberc, GI numberc, GO concept IDc, Gene ID (CGD)c, Gene ID (DictyBase)c, Gene ID (EcoGene)c, Gene ID (FlyBase)c, Gene ID (GeneDB)c, Gene ID (GeneFarm)c, Gene ID (Genolist)c, Gene ID (Gramene)c, Gene ID (HGNC)c, Gene ID (JCVI)c, Gene ID (KOME)c, Gene ID (MIPS)c, Gene ID (MfunGD)c, Gene ID (NCBI)c, Gene ID (PlasmoDB)c, Gene ID (SGD)c, Gene ID (SGN)c, Gene ID (VBASE2)c, Gene ID (VectorBase)c, Gene ID (Virginia microbial)c, Gene ID (WormBase)c, Gene ID (Xenbase)c, Gene ID (ZFIN)c, Gene ID (miRBase)c, Gene3D IDc, GeneSNP IDc, GenomeReviews IDc, GermOnline IDc, GlycoMap IDc, GlycomeDB IDc, Gramene identifierc, HAMAP IDc, HGMD IDc, HGNC concept IDc, HGVbase IDc, HIT IDc, HIX IDc, HMMER hidden Markov model IDc, HPA antibody idc, ICD identifierc, IMGT/HLA IDc, IPI protein IDc, ISBNc, IntAct accession numberc, InterPro accessionc, JASPAR profile IDc, KEGG Glycan IDc, KEGG object identifierc, LGICdb identifierc, LIPID MAPS IDc, Linucs IDc, LipidBank IDc, Locus ID (AGI)c, Locus ID (ASPGD)c, Locus ID (CGD)c, Locus ID (CMR)c, Locus ID (DictyBase)c, Locus ID (EntrezGene)c, Locus ID (MGG)c, Locus ID (MMP)c, Locus ID (MaizeGDB)c, Locus ID (PseudoCAP)c, Locus ID (SGD)c, Locus ID (Tropgene)c, Locus ID (UTR)c, MGED concept IDc, MGI accessionc, MINT IDc, MIRIAM URIc, MIRIAM identifierc, MMDB IDc, MaizeDB IDc, MatrixDB interaction IDc, MeSH concept IDc, Medline UIc, ModelDB IDc, MonosaccharideDB IDc, Mutation IDc, NCBI Genome Project IDc, NCBI genetic code IDc, NCBI genome accessionc, NCBI locus tagc, NCBI taxonomy IDc, NCBI versionc, NeuroMorpho IDc, NeuronDB IDc, OMIM IDc, ORF IDc, Orpha numberc, PDB IDc, PIR identifierc, PIRSF IDc, PRINTS codec, Pathway ID (BioCyc)c, Pathway ID (BioSystems)c, Pathway ID (CPDB)c, Pathway ID (ConsensusPathDB)c, Pathway ID (DQCS)c, Pathway ID (INOH)c, Pathway ID (KEGG)c, Pathway ID (NCI-Nature)c, Pathway ID (PATIKA)c, Pathway ID (Panther)c, Pathway ID (PharmGKB)c, Pathway ID (SMPDB)c, Pathway ID (Unipathway)c, Pathway ID (WikiPathways)c, Pathway ID (reactome)c, PeptideAtlas IDc, Pfam accession numberc, Pfam clan IDc, PharmGKB IDc, Plant Ontology concept IDc, ProDom accession numberc, Protein ID (CORUM)c, Protein ID (ConoServer)c, Protein ID (CuticleDB)c, Protein ID (DisProt)c, Protein ID (EMBL/GenBank/DDBJ)c, Protein ID (EcID)c, Protein ID (LGICdb)c, Protein ID (PeroxiBase)c, Protein ID (TopDB)c, Protein family ID (GeneFarm)c, Protein family ID (PANTHER)c, PubChem IDc, PubMed IDc, REBASE enzyme numberc, REDIdb IDc, RESID IDc, RFAM accessionc, RGD IDc, RNA central IDc, RNAVirusDB IDc, Reaction ID (BioCyc)c, Reaction ID (MACie)c, Reaction ID (Rhea)c, Reaction ID (SABIO-RK)c, RefSeq accessionc, SCOP domain identifierc, SGD IDc, SISYPHUS IDc, SMART accession numberc, STRING IDc, Sequence alignment IDc, Sequence cluster ID (COG)c, Sequence cluster ID (CluSTr)c, Sequence cluster ID (SYSTERS)c, Sequence cluster ID (UniGene)c, Sequence cluster ID (UniRef)c, Sequence feature ID (SwissRegulon)c, Signaling Gateway protein IDc, Spot ID (HSC-2DPAGE)c, Spot serial numberc, Stock number (TAIR)c, Superfamily hidden Markov model numberc, T3DB IDc, TAIR accessionc, TCDB IDc, TCIDc, TIGR identifierc, TIGRFam IDc, TRANSFAC accession numberc, Target ID (TTD)c, Taverna workflow IDc, TreeBASE study accession numberc, TreeFam accession numberc, UMLS concept IDc, UNITE accessionc, UTR accessionc, UniParc accessionc, UniProt accessionc, UniSTS accessionc, Unimod IDc, WormBase wormpep IDc, cPath IDc, dbEST accessionc, dbProbe IDc, dbSNP IDc, iHOP organism IDc, iHOP symbolc, iRefIndex IDc, mFLJ/mKIAA numberc, myGrid concept IDc

ACEc back to ToC or Class ToC

IRI: http://edamontology.org/format_3001

has super-classes
Sequence assembly formatc
Textual formatc

acedbc back to ToC or Class ToC

IRI: http://edamontology.org/format_1923

has super-classes
Sequence record format (text)c

ACLAME IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2631

has super-classes
Accessionc
Mobile genetic element IDc

Acronymc back to ToC or Class ToC

IRI: http://edamontology.org/data_1879

has super-classes
deprecated classc

Active site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3896

has super-classes
Binding site predictionc

affymetrixc back to ToC or Class ToC

IRI: http://edamontology.org/format_1639

has super-classes
Sequence cluster format (nucleic acid)c
Textual formatc

Affymetrix probe sets information library filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1643

has super-classes
deprecated classc

Affymetrix probe sets library filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1642

has super-classes
deprecated classc

affymetrix-expc back to ToC or Class ToC

IRI: http://edamontology.org/format_1641

has super-classes
Microarray experiment data formatc
Textual formatc

afgc back to ToC or Class ToC

IRI: http://edamontology.org/format_3582

has super-classes
Textual formatc
Sequence assembly format (text)c

Aggregationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3436

has super-classes
Data handlingc

AGPc back to ToC or Class ToC

IRI: http://edamontology.org/format_3693

has super-classes
Sequence assembly formatc
Textual formatc

Agricultural sciencec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3810

has super-classes
Biologyc

Aligned sequence orderc back to ToC or Class ToC

IRI: http://edamontology.org/data_1396

has super-classes
deprecated classc

Alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1916

has super-classes
Datac
has sub-classes
Secondary structure alignmentc, Sequence alignmentc, Sequence signature matchesc, Sequence-structure alignmentc, Structural (3D) profile alignmentc, Structure alignmentc

Alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2928

has super-classes
Operationc
Generationc
has sub-classes
Fold recognitionc, Sequence alignmentc, Structure alignmentc

Alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0083

has super-classes
deprecated classc

Alignment analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2946

has super-classes
deprecated classc

Alignment datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2083

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Alignment datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2539

This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles.
has super-classes
deprecated classc

Alignment formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1921

has super-classes
Format (by type of data)c
is format ofop some Sequence alignmentc
has sub-classes
ARBc, Alignment format (XML)c, Alignment format (pair only)c, Alignment format (text)c, BioJSON (BioXSD)c, BioJSON (Jalview)c, BioYAMLc, MSAMLc, RNAMLc

Alignment format (pair only)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2920

has super-classes
Alignment formatc
is format ofop some Pair sequence alignmentc
has sub-classes
BAMc, CRAMc, EBI Application Result XMLc, LAVc, PSLc, Pileupc, SAMc, axtc, proBAMc, srspairc

Alignment format (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2554

has super-classes
Alignment formatc
has sub-classes
A2Mc, BLCc, ClustalW formatc, DIALIGN formatc, EMBOSS simple formatc, FASTAc, FASTA-alnc, GCG format variantc, HMMER-alnc, MAFc, POc, Phylip format variantc, Stockholm formatc, T-Coffee formatc, TreeCon-seqc, XMFAc, csfastac, dafc, debugc, markx0 variantc, matchc, mega variantc, nexus-seqc, nexusnonc, pairc, scores formatc, selexc, srs formatc

Alignment format (XML)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2555

has super-classes
Alignment formatc
has sub-classes
BioXSD (XML)c, HSAMLc

Alignment processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2951

has super-classes
deprecated classc

Alignment score or penaltyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1394

has super-classes
Scorec
has sub-classes
Drop off scorec, Gap penaltyc, Match reward scorec, Mismatch penalty scorec

Allele frequency distribution analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0554

Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait.
has super-classes
Phylogenetic analysisc

Allergy, clinical immunology and immunotherapeuticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3400

has super-classes
Medicinec

Alpha diversity datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3737

has super-classes
Biodiversity datac

Alternative splicing predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0264

has super-classes
Splicing analysisc
has topicop some Gene structurec

aMAZE entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1653

has super-classes
deprecated classc

AMBER frcmodc back to ToC or Class ToC

IRI: http://edamontology.org/format_3888

has super-classes
Textual formatc
FF parameter formatc

AMBER offc back to ToC or Class ToC

IRI: http://edamontology.org/format_3889

has super-classes
Textual formatc
FF parameter formatc

AMBER topc back to ToC or Class ToC

IRI: http://edamontology.org/format_3881

version 7 is written to distinguish it from old versions of AMBER Prmtop. Similarly to HDF5, it is a completely different format, according to AMBER group: a drastic change to the file format occurred with the 2004 release of Amber 7 (http://ambermd.org/prmtop.pdf)
has super-classes
Tertiary structure formatc
Textual formatc
Topology formatc

ambiguousc back to ToC or Class ToC

IRI: http://edamontology.org/format_2097

has super-classes
Textual formatc
Raw sequence formatc
has sub-classes
consensusc

Amino acid annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0894

has super-classes
deprecated classc

Amino acid comparison matrix (floats)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1453

has super-classes
deprecated classc

Amino acid comparison matrix (integers)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1452

has super-classes
deprecated classc

Amino acid frequencies tablec back to ToC or Class ToC

IRI: http://edamontology.org/data_1267

has super-classes
Sequence composition reportc
Matrixc

Amino acid identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0994

has super-classes
Compound identifierc
is identifier ofop some Amino acid propertyc
has sub-classes
Amino acid namec

Amino acid identifier formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2562

has super-classes
deprecated classc

Amino acid indexc back to ToC or Class ToC

IRI: http://edamontology.org/data_1501

has super-classes
Amino acid propertyc
Matrixc
has sub-classes
Amino acid index (White-Wimley data)c, Amino acid index (chemical classes)c, Amino acid index (hydropathy)c, Amino acid index (molecular weight)c, Amino acid index (van der Waals radii)c

Amino acid index (chemical classes)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1502

has super-classes
Amino acid indexc

Amino acid index (hydropathy)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1506

has super-classes
Amino acid indexc

Amino acid index (molecular weight)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1505

has super-classes
Amino acid indexc

Amino acid index (van der Waals radii)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1508

has super-classes
Amino acid indexc

Amino acid index (White-Wimley data)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1507

has super-classes
Amino acid indexc

Amino acid index formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2017

has super-classes
Matrix formatc
is format ofop some Amino acid indexc
has sub-classes
aaindexc

Amino acid index IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1073

has super-classes
Identifier (by type of data)c
Matrix identifierc
is identifier ofop some Amino acid indexc
has sub-classes
AAindex IDc

Amino acid namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1006

has super-classes
Amino acid identifierc
has sub-classes
Amino acid name (full name)c, Amino acid name (single letter)c, Amino acid name (three letter)c

Amino acid name (full name)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2565

has super-classes
Amino acid namec

Amino acid name (single letter)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2563

has super-classes
Amino acid namec

Amino acid name (three letter)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2564

has super-classes
Amino acid namec
has sub-classes
PDB residue namec

Amino acid pair-wise contact potentialsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1503

has super-classes
Amino acid propertyc

Amino acid propertyc back to ToC or Class ToC

IRI: http://edamontology.org/data_2016

has super-classes
Molecular propertyc
has sub-classes
Amino acid indexc, Amino acid pair-wise contact potentialsc, Comparison matrix (amino acid)c

Amino acid word frequencies tablec back to ToC or Class ToC

IRI: http://edamontology.org/data_1268

has super-classes
Sequence composition reportc
Matrixc

Anaesthesiologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3402

has super-classes
Medicinec

Analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2945

This excludes non-analytical methods that read and write the same basic type of data (for that, see 'Data handling').
has super-classes
Operationc
has sub-classes
Enrichment analysisc, Expression analysisc, Genetic variation analysisc, Image analysisc, Network analysisc, Pathway analysisc, Phylogenetic analysisc, Protein function predictionc, Sequence analysisc, Spectral analysisc, Structure analysisc, Text miningc, Transmembrane protein analysisc

Analytical chemistryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3370

has super-classes
Chemistryc

Anatomyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3067

has super-classes
Biomedical sciencec

Ancestral reconstructionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3745

Ancestral reconstruction is often used to recover possible ancestral character states of ancient, extinct organisms.
has super-classes
Phylogenetic analysisc

Animal studyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3679

has super-classes
Laboratory animal sciencec
Experimental design and studiesc

Annotated textc back to ToC or Class ToC

IRI: http://edamontology.org/data_3779

has super-classes
Text datac
Textc

Annotated text formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3780

has super-classes
Format (by type of data)c
is format ofop some Annotated textc
has sub-classes
BioCc, BioNLP Shared Task formatc, OSCAR formatc, Open Annotation formatc, PubAnnotation formatc, PubTator formatc

Annotated URIc back to ToC or Class ToC

IRI: http://edamontology.org/data_1883

has super-classes
Data referencec

Annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2018

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Annotationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0226

This is a broad concept and is used a placeholder for other, more specific concepts.
has super-classes
Operationc
has inputop some Ontologyc
has topicop some Ontology and terminologyc
has sub-classes
Image annotationc, Phylogenetic tree annotationc, Sequence annotationc, Sequence tag mappingc, Text annotationc

Annotation processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2407

has super-classes
deprecated classc

Annotation retrievalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1774

Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations.
has super-classes
deprecated classc

Annotation retrieval (sequence)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0229

has super-classes
deprecated classc

Annotation trackc back to ToC or Class ToC

IRI: http://edamontology.org/data_3002

has super-classes
Sequence featuresc

Anonymisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3283

has super-classes
Data handlingc

Antimicrobial resistance predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3482

has super-classes
Sequence analysisc
Prediction and recognitionc
has topicop some Microbiologyc

Applied mathematicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3569

has super-classes
Mathematicsc

Arabidopsisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0786

has super-classes
deprecated classc

AraC-XylS IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2742

has super-classes
Accessionc
Transcription factor accessionc

ArachnoServer IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2578

has super-classes
Accessionc
Toxin accessionc

ARBc back to ToC or Class ToC

IRI: http://edamontology.org/format_3830

has super-classes
Alignment formatc
Binary formatc

arffc back to ToC or Class ToC

IRI: http://edamontology.org/format_3581

This file format is for machine learning.
has super-classes
Textual formatc

ArrayExpress accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1144

has super-classes
Experiment annotation IDc

ArrayExpress entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1640

has super-classes
deprecated classc

Articlec back to ToC or Class ToC

IRI: http://edamontology.org/data_0971

has super-classes
Text datac
Textc

Article analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2947

has super-classes
deprecated classc

Article comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3437

has super-classes
Comparisonc
has topicop some Literature and languagec
has sub-classes
Document clusteringc, Document similarity calculationc

Article formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2020

has super-classes
Format (by type of data)c
is format ofop some Articlec
has sub-classes
medlinec, pmcc

Article IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1088

has super-classes
Identifier (by type of data)c
is identifier ofop some Articlec
has sub-classes
DOIc, Medline UIc, PubMed IDc

Article metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_2857

has super-classes
deprecated classc

Article reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2954

has super-classes
deprecated classc

ASN.1 sequence formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1966

has super-classes
Textual formatc
Sequence record format (text)c

Assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3433

has super-classes
deprecated classc

ASTD IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2367

has super-classes
Sequence accession (nucleic acid)c
Accessionc
Identifier (hybrid)c
has sub-classes
ASTD ID (exon)c, ASTD ID (intron)c, ASTD ID (polya)c, ASTD ID (tss)c

ASTD ID (exon)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2368

has super-classes
ASTD IDc

ASTD ID (intron)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2369

has super-classes
ASTD IDc

ASTD ID (polya)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2370

has super-classes
ASTD IDc

ASTD ID (tss)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2371

has super-classes
ASTD IDc

ATC codec back to ToC or Class ToC

IRI: http://edamontology.org/data_3103

has super-classes
Accessionc
Drug accessionc

Atom IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_0983

has super-classes
Identifier (by type of data)c
has sub-classes
Atom namec

Atom namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1757

has super-classes
Atom IDc
Namec
has sub-classes
PDB atom namec

Atomic coordinatec back to ToC or Class ToC

IRI: http://edamontology.org/data_1743

has super-classes
Atomic propertyc

Atomic data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1918

has super-classes
deprecated classc

Atomic occupancyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1857

The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0.
has super-classes
Atomic propertyc

Atomic propertyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1917

has super-classes
Molecular propertyc
has sub-classes
Atomic coordinatec, Atomic occupancyc, Isotropic B factorc

Atomic x coordinatec back to ToC or Class ToC

IRI: http://edamontology.org/data_1744

has super-classes
deprecated classc

Atomic y coordinatec back to ToC or Class ToC

IRI: http://edamontology.org/data_1745

has super-classes
deprecated classc

Atomic z coordinatec back to ToC or Class ToC

IRI: http://edamontology.org/data_1746

has super-classes
deprecated classc

Author IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1881

has super-classes
Person identifierc
has sub-classes
DragonDB author identifierc

axtc back to ToC or Class ToC

IRI: http://edamontology.org/format_3013

has super-classes
Textual formatc
Alignment format (pair only)c

Backbone modellingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0479

Methods might require a preliminary C(alpha) trace.
has super-classes
Protein modellingc

Backbone torsion angle calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1825

has super-classes
deprecated classc

BacMap gene card formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1809

has super-classes
deprecated classc

BAIc back to ToC or Class ToC

IRI: http://edamontology.org/format_3327

has super-classes
Binary formatc
Data index formatc
is format ofop some Data indexc

BAMc back to ToC or Class ToC

IRI: http://edamontology.org/format_2572

has super-classes
Sequence trace formatc
Binary formatc
Alignment format (pair only)c

Base frequencies tablec back to ToC or Class ToC

IRI: http://edamontology.org/data_1265

has super-classes
Sequence composition reportc
Matrixc

Base pairing probability matrix dotplotc back to ToC or Class ToC

IRI: http://edamontology.org/data_1595

Such as generated by the Vienna package.
has super-classes
DNA base structural datac
Plotc

Base position variability plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_1263

has super-classes
Sequence composition reportc

Base position variability plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0287

has super-classes
Codon usage analysisc
Sequence visualisationc
has topicop some Gene structurec
has outputop some Base position variability plotc

Base word frequencies tablec back to ToC or Class ToC

IRI: http://edamontology.org/data_1266

has super-classes
Sequence composition reportc
Matrixc

Base-callingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3185

has super-classes
Sequence generationc
has topicop some Sequencingc

BCFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3020

has super-classes
Binary formatc
Sequence variation annotation formatc

BcFormsc back to ToC or Class ToC

IRI: http://edamontology.org/format_3951

BcForms is related to http://edamontology.org/format_3909. (BcForms uses BpForms to describe subunits which are DNA, RNA, or protein polymers.) However, that format isn't the parent of BcForms. BcForms is similarly related to SMILES (http://edamontology.org/data_2301).
has super-classes
Chemical data formatc
Protein report formatc
Textual formatc

BCMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3689

has super-classes
Biological pathway or network formatc
XMLc

BDMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3690

has super-classes
XMLc

BEASTc back to ToC or Class ToC

IRI: http://edamontology.org/format_3843

has super-classes
XMLc
Sequence record format (XML)c

BEDc back to ToC or Class ToC

IRI: http://edamontology.org/format_3003

BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track).
has super-classes
Textual formatc
Sequence annotation track formatc
has sub-classes
bedstrictc, chrominfoc

bed12c back to ToC or Class ToC

IRI: http://edamontology.org/format_3586

Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12
has super-classes
bedstrictc

bed6c back to ToC or Class ToC

IRI: http://edamontology.org/format_3585

Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6
has super-classes
bedstrictc
has sub-classes
ENCODE peak formatc

bedgraphc back to ToC or Class ToC

IRI: http://edamontology.org/format_3583

Holds a tab-delimited chromosome /start /end / datavalue dataset.
has super-classes
Textual formatc
Sequence annotation track formatc

bedstrictc back to ToC or Class ToC

IRI: http://edamontology.org/format_3584

Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.
has super-classes
BEDc
has sub-classes
bed12c, bed6c

BELc back to ToC or Class ToC

IRI: http://edamontology.org/format_3691

has super-classes
Textual formatc

Beta diversity datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3738

has super-classes
Biodiversity datac

bgzipc back to ToC or Class ToC

IRI: http://edamontology.org/format_3615

BAM files are compressed using a variant of GZIP (GNU ZIP), into a format called BGZF (Blocked GNU Zip Format).
has super-classes
Binary formatc
Image formatc

Bibliographic reference formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2848

has super-classes
Format (by type of data)c
is format ofop some Citationc
is format ofop some Abstractc
has sub-classes
CiteXplore-allc, CiteXplore-corec, Medline Display Formatc, PubMed XMLc, PubMed citationc

Bibliographyc back to ToC or Class ToC

IRI: http://edamontology.org/data_3505

has super-classes
Text datac

Bibliography generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3349

has super-classes
Generationc
has outputop some Bibliographyc

bigBedc back to ToC or Class ToC

IRI: http://edamontology.org/format_3004

has super-classes
Binary formatc
Sequence annotation track formatc

bigWigc back to ToC or Class ToC

IRI: http://edamontology.org/format_3006

has super-classes
Binary formatc
Sequence annotation track formatc

Binary formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2333

Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004.
has super-classes
Formatc
has sub-classes
.nibc, 2bitc, AB1c, ABIc, ARBc, BAIc, BAMc, BCFc, BMPc, BTrackc, BinPosc, COMBINE OMEXc, CRAMc, DICOM formatc, GIFc, HDFc, HDF5c, IDATc, JPGc, K-mer countgraphc, MSAMLc, OME-TIFFc, PCAzipc, PDFc, PNGc, SCFc, SFFc, SQLite formatc, SRA formatc, SRFc, TIFFc, TNGc, Tabix index file formatc, Thermo RAWc, VDBc, WIFF formatc, Waters RAWc, XTCc, ZTRc, Zarrc, bgzipc, bigBedc, bigWigc, ebwtc, ebwtlc, ibdc, imc, mshc, netCDFc, niic, pbmc, pcdc, pcxc, pgmc, ppmc, proBAMc, psdc, rastc, rgbc, snpeffdbc, tabixc, xbmc, xlsxc, xpmc
is disjoint with
Textual formatc, HTMLc, XMLc

BIND accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1129

has super-classes
Protein interaction IDc
Accessionc

BIND entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1568

has super-classes
deprecated classc

Binding site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2575

has super-classes
Protein function predictionc
Protein feature detectionc
has topicop some Protein interactionsc
has sub-classes
Active site predictionc, Ligand-binding site predictionc, Metal-binding site predictionc, Nucleic acids-binding site predictionc, Protein-protein binding site predictionc

BindingDB Monomer IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2580

has super-classes
Accessionc
Compound accessionc

BinPosc back to ToC or Class ToC

IRI: http://edamontology.org/format_3885

It is basically a translation of the ASCII atom coordinate format to binary code. The only additional information stored is a magic number that identifies the BinPos format and the number of atoms per snapshot. The remainder is the chain of coordinates binary encoded. A drawback of this format is its architecture dependency. Integers and floats codification depends on the architecture, thus it needs to be converted if working in different platforms (little endian, big endian).
has super-classes
Binary formatc
Trajectory format (binary)c

Biobankc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3337

has super-classes
Sample collectionsc

BioCc back to ToC or Class ToC

IRI: http://edamontology.org/format_3782

has super-classes
XMLc
Annotated text formatc

Biochemistryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3292

has super-classes
Biologyc
Chemistryc

BioCyc enzyme report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2322

has super-classes
deprecated classc

BioCyc IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2104

has super-classes
Accessionc
Identifier (hybrid)c
has sub-classes
Compound ID (BioCyc)c, Enzyme ID (BioCyc)c, Pathway ID (BioCyc)c, Reaction ID (BioCyc)c

Biodiversityc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3050

has super-classes
Ecologyc

Biodiversity datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3707

has super-classes
Datac
Ecological datac
has sub-classes
Alpha diversity datac, Beta diversity datac, Gamma diversity datac

Biodiversity data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3706

has super-classes
Format (by type of data)c
is format ofop some Biodiversity datac
has sub-classes
ABCD formatc, BIOM formatc, MCPDc

Bioengineeringc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3398

has super-classes
Biotechnologyc

BioGRID interaction IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2628

has super-classes
Protein interaction IDc
Accessionc

Bioimagingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3383

has super-classes
Imagingc

Bioinformaticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0091

This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation.
has super-classes
Informaticsc

BioJSON (BioXSD)c back to ToC or Class ToC

IRI: http://edamontology.org/format_3772

has super-classes
Sequence record formatc
Sequence feature annotation formatc
Alignment formatc
Raw sequence formatc
JSONc
is format ofop some Experimental measurementc
is format ofop some Sequence alignmentc
is format ofop some Sequence featuresc
is format ofop some Sequencec
is format ofop some Scorec

BioJSON (Jalview)c back to ToC or Class ToC

IRI: http://edamontology.org/format_3774

has super-classes
Sequence feature annotation formatc
Alignment formatc
JSONc
is format ofop some Sequence alignmentc
is format ofop some Sequence featuresc

Biological databasesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3071

has super-classes
Informaticsc
has sub-classes
Data acquisitionc, Data architecture, analysis and designc, Data governancec, Data identity and mappingc, Data integration and warehousingc, Data quality managementc, Data securityc, Data submission, annotation and curationc, Database managementc, Workflowsc

Biological model accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2891

has super-classes
Biological model IDc
has sub-classes
BioModel IDc, Brite hierarchy IDc, ModelDB IDc

Biological model formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2034

has super-classes
deprecated classc

Biological model IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1085

has super-classes
Identifier (by type of data)c
is identifier ofop some Mathematical modelc
has sub-classes
Biological model accessionc, Biological model namec

Biological model namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1170

has super-classes
Biological model IDc
Namec

Biological pathway mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_0947

has super-classes
deprecated classc

Biological pathway or network formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2013

has super-classes
Format (by type of data)c
is format ofop some Pathway or networkc
has sub-classes
BCMLc, BioPAXc, COMBINE OMEXc, CellMLc, CopasiMLc, GMLc, GPMLc, KGMLc, SBGN-MLc, SBMLc, SBtabc, VisMLc, sifc

Biological pathway or network report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3166

has super-classes
Format (by type of data)c
is format ofop some Pathway or network reportc
has sub-classes
CopasiMLc, SBRMLc

Biological system modellingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3075

has super-classes
deprecated classc

Biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3070

has super-classes
Topicc
has sub-classes
Agricultural sciencec, Biochemistryc, Biomarkersc, Biophysicsc, Biotechnologyc, Cell biologyc, Chemical biologyc, Developmental biologyc, Ecologyc, Environmental sciencec, Evolutionary biologyc, Freshwater biologyc, Geneticsc, Human biologyc, Marine biologyc, Microbiologyc, Model organismsc, Molecular biologyc, Plant biologyc, Structural biologyc, Synthetic biologyc, Systems biologyc, Virologyc, Zoologyc

BIOM formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3746

BIOM is a recognised standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc.
has super-classes
Textual formatc
Biodiversity data formatc

Biomarkersc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3360

has super-classes
Biologyc

Biomaterialsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3368

has super-classes
Biotechnologyc

Biomedical sciencec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3344

has super-classes
Topicc
has sub-classes
Anatomyc, Immunologyc, Laboratory animal sciencec, Medicines research and developmentc, Neurobiologyc, Nutritional sciencec, Parasitologyc, Pharmacologyc, Regenerative medicinec, Sample collectionsc

BioModel IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1171

has super-classes
Accessionc
Biological model accessionc

BioModel mathematical model formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1666

Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
has super-classes
deprecated classc

Biomolecular simulationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3892

This includes methods such as Molecular Dynamics, Coarse-grained dynamics, metadynamics, Quantum Mechanics, QM/MM, Markov State Models, etc.
has super-classes
Computational biologyc
has sub-classes
Molecular dynamicsc

BioNLP Shared Task formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3785

has super-classes
Textual formatc
Annotated text formatc

BioNumbers IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2660

has super-classes
Accessionc

BioPAXc back to ToC or Class ToC

IRI: http://edamontology.org/format_3156

has super-classes
Biological pathway or network formatc

BioPax concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1175

has super-classes
Ontology concept IDc
Accessionc

BioPax termc back to ToC or Class ToC

IRI: http://edamontology.org/data_1715

has super-classes
deprecated classc

Biophysicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3306

has super-classes
Biologyc
Physicsc

Biosafety classificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_3719

has super-classes
Biosafety reportc

Biosafety reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3716

has super-classes
Reportc
has sub-classes
Biosafety classificationc, Pathogenicity reportc

Biotechnologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3297

has super-classes
Biologyc
has sub-classes
Bioengineeringc, Biomaterialsc, Genetic engineeringc, Medical biotechnologyc, Metabolic engineeringc, Synthetic biologyc

Biotherapeuticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3374

has super-classes
Medicines research and developmentc

BioXSD (XML)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2352

has super-classes
Sequence record formatc
Sequence feature annotation formatc
XMLc
Alignment format (XML)c
Raw sequence formatc
is format ofop some Scorec
is format ofop some Sequencec
is format ofop some Experimental measurementc
is format ofop some Sequence featuresc
is format ofop some Sequence alignmentc

BioYAMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3773

has super-classes
Sequence record formatc
Sequence feature annotation formatc
Alignment formatc
Raw sequence formatc
YAMLc
is format ofop some Sequencec
is format ofop some Sequence featuresc
is format ofop some Experimental measurementc
is format ofop some Sequence alignmentc
is format ofop some Scorec

Bisulfite mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3186

Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected.
has super-classes
Physical mappingc
Methylation analysisc

Bit scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_2335

Bit scores are normalised with respect to the scoring system and therefore can be used to compare alignment scores from different searches.
has super-classes
Sequence similarityc

BLAST resultsc back to ToC or Class ToC

IRI: http://edamontology.org/format_1333

This includes score data, alignment data and summary table.
has super-classes
Database hits (sequence) formatc
Textual formatc
has sub-classes
BLAST XML results formatc, BLAST XML v2 results formatc

BLAST sequence alignment typec back to ToC or Class ToC

IRI: http://edamontology.org/data_1121

has super-classes
deprecated classc

BLAST XML results formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3331

has super-classes
BLAST resultsc
XMLc

BLAST XML v2 results formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3836

has super-classes
BLAST resultsc
XMLc

Blattner numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1886

has super-classes
Accessionc
Gene IDc

BLCc back to ToC or Class ToC

IRI: http://edamontology.org/format_3313

has super-classes
Alignment format (text)c

Blind peptide database searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3647

has super-classes
Peptide database searchc

Blot IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2587

has super-classes
Identifier (by type of data)c
has sub-classes
BlotBase blot IDc

BlotBase blot IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2588

has super-classes
Accessionc
Blot IDc

BMPc back to ToC or Class ToC

IRI: http://edamontology.org/format_3592

Although it is based on Windows internal bitmap data structures, it is supported by many non-Windows and non-PC applications.
has super-classes
Binary formatc
Image formatc

Book IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2633

has super-classes
Identifier (by type of data)c
has sub-classes
ISBNc

Box-Whisker plot plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2943

has super-classes
Visualisationc

BpFormsc back to ToC or Class ToC

IRI: http://edamontology.org/format_3909

has super-classes
Chemical formula formatc
Textual formatc
Raw sequence formatc
is format ofop some Sequence featuresc

BRENDA enzyme report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1512

has super-classes
deprecated classc

BRENDA ontology concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3769

has super-classes
Ontology concept IDc
Accessionc

BRENDA organism IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2593

has super-classes
Accessionc
Organism accessionc

Brite hierarchy IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2591

has super-classes
Accessionc
Biological model accessionc

BSMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3487

has super-classes
XMLc
Sequence record format (XML)c

BTrackc back to ToC or Class ToC

IRI: http://edamontology.org/format_3776

has super-classes
Sequence feature annotation formatc
Binary formatc
Sequence feature table formatc
Sequence annotation track formatc

C-alpha tracec back to ToC or Class ToC

IRI: http://edamontology.org/data_1470

C-beta atoms from amino acid side-chains may be included.
has super-classes
Protein structurec

CABRI accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2380

has super-classes
Accessionc
Identifier (hybrid)c

CABRI catalogue namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2597

has super-classes
Namec
Catalogue IDc

CAFc back to ToC or Class ToC

IRI: http://edamontology.org/format_1630

has super-classes
Textual formatc
Sequence assembly format (text)c

Calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3438

has super-classes
Operationc
has sub-classes
Dimensionality reductionc, Isotopic distributions calculationc, Nucleic acid property calculationc, Protein property calculationc, Rarefactionc, Retention time predictionc, Sequence composition calculationc, Statistical calculationc

Cancer typec back to ToC or Class ToC

IRI: http://edamontology.org/data_2592

has super-classes
deprecated classc

Carbohydrate accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2900

has super-classes
Carbohydrate identifierc
Molecule accessionc
has sub-classes
GlycoMap IDc, GlycomeDB IDc, KEGG Glycan IDc, Linucs IDc

Carbohydrate conformational mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_2753

has super-classes
Carbohydrate propertyc

Carbohydrate identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2663

has super-classes
Compound identifierc
is identifier ofop some Carbohydrate structurec
is identifier ofop some Carbohydrate reportc
has sub-classes
Carbohydrate accessionc

Carbohydrate propertyc back to ToC or Class ToC

IRI: http://edamontology.org/data_3425

has super-classes
Molecular propertyc
has sub-classes
Carbohydrate conformational mapc

Carbohydrate reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2313

has super-classes
Structure reportc

Carbohydrate structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_1462

has super-classes
Structurec
has topicop some Carbohydratesc
has topicop some Lipidsc

Carbohydratesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0152

has super-classes
Structure analysisc

Cardinalityc back to ToC or Class ToC

IRI: http://edamontology.org/data_2176

has super-classes
deprecated classc

Cardiologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3335

has super-classes
Medicinec

CAS numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1002

has super-classes
Chemical registry numberc
Accessionc
Drug accessionc

CAS numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_3102

has super-classes
deprecated classc

Catalogue IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2596

has super-classes
Identifier (by type of data)c
has sub-classes
CABRI catalogue namec

CATH architecturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1557

has super-classes
deprecated classc

CATH chain report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1760

The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain.
has super-classes
deprecated classc

CATH classc back to ToC or Class ToC

IRI: http://edamontology.org/data_1556

has super-classes
deprecated classc

CATH domain IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1040

has super-classes
CATH identifierc

CATH domain reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1762

The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.
has super-classes
deprecated classc

CATH domain report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3100

The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links.
has super-classes
Protein domain classification formatc

CATH domain sequences (ATOM)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1766

has super-classes
deprecated classc

CATH domain sequences (COMBS)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1767

has super-classes
deprecated classc

CATH functional categoryc back to ToC or Class ToC

IRI: http://edamontology.org/data_1561

has super-classes
deprecated classc

CATH homologous superfamilyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1559

has super-classes
deprecated classc

CATH identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2700

has super-classes
Protein domain IDc
Accessionc
has sub-classes
CATH domain IDc, CATH node IDc

CATH nodec back to ToC or Class ToC

IRI: http://edamontology.org/data_1553

The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links.
has super-classes
deprecated classc

CATH node IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1043

has super-classes
CATH identifierc
has sub-classes
CATH node ID (family)c

CATH node ID (family)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2701

has super-classes
CATH node IDc

CATH PDB report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1761

The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file.
has super-classes
deprecated classc

CATH representative domain sequences (ATOM)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1764

has super-classes
deprecated classc

CATH representative domain sequences (COMBS)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1765

has super-classes
deprecated classc

CATH structurally similar groupc back to ToC or Class ToC

IRI: http://edamontology.org/data_1560

has super-classes
deprecated classc

CATH topologyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1558

has super-classes
deprecated classc

CATH version informationc back to ToC or Class ToC

IRI: http://edamontology.org/data_1672

has super-classes
deprecated classc

CCAP strain numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_2778

has super-classes
Accessionc
Strain accessionc

CD spectrac back to ToC or Class ToC

IRI: http://edamontology.org/data_0939

has super-classes
Protein structure raw datac

CDD IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2666

has super-classes
Protein domain IDc
Accessionc

CDD PSSM-IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2714

has super-classes
Sequence profile IDc
Accessionc

cdsxmlc back to ToC or Class ToC

IRI: http://edamontology.org/format_2184

has super-classes
EMBL format (XML)c

celc back to ToC or Class ToC

IRI: http://edamontology.org/format_1638

has super-classes
Gene expression report formatc
Textual formatc
is format ofop some Raw microarray datac

Cell and tissue culturec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0608

has super-classes
deprecated classc

Cell biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2229

has super-classes
Biologyc

Cell culture collectionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3340

has super-classes
Sample collectionsc

Cell cyclec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0612

has super-classes
deprecated classc

Cell line namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2316

has super-classes
Strain namec
has sub-classes
Cell line name (assonant)c, Cell line name (exact)c, Cell line name (no punctuation)c, Cell line name (truncated)c

Cell line name (assonant)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2320

has super-classes
Cell line namec

Cell line name (exact)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2317

has super-classes
Cell line namec

Cell line name (no punctuation)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2319

has super-classes
Cell line namec

Cell line name (truncated)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2318

has super-classes
Cell line namec

Cell line reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0963

has super-classes
Organism reportc

Cell migration analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3446

has super-classes
Image analysisc
has topicop some Cell biologyc

Cell migration track imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_3449

has super-classes
Imagec
has topicop some Cell biologyc

Cell type accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2893

has super-classes
Cell type identifierc
has sub-classes
Cell type ontology IDc, NeuroMorpho IDc, NeuronDB IDc

Cell type identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2655

has super-classes
Identifier (by type of data)c
has sub-classes
Cell type accessionc, Cell type namec

Cell type namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2892

has super-classes
Namec
Cell type identifierc

Cell type ontology IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3238

has super-classes
Ontology concept IDc
Accessionc
Cell type accessionc

CellMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3240

has super-classes
Biological pathway or network formatc
XMLc

Cellular process pathwaysc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3527

has super-classes
deprecated classc

Cellular process pathways reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1660

has super-classes
deprecated classc

CGD gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1605

has super-classes
deprecated classc

Chado-XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3844

has super-classes
XMLc
Sequence record format (XML)c

CHARMM rtfc back to ToC or Class ToC

IRI: http://edamontology.org/format_3887

There is currently no tool available for conversion between GROMACS topology format and other formats, due to the internal differences in both approaches. There is, however, a method to convert small molecules parameterized with AMBER force-field into GROMACS format, allowing simulations of these systems with GROMACS MD package.
has super-classes
Tertiary structure formatc
Textual formatc
Topology formatc

ChEBIc back to ToC or Class ToC

IRI: http://edamontology.org/data_1724

has super-classes
deprecated classc

ChEBI concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1184

has super-classes
Ontology concept IDc
Accessionc

ChEBI entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1703

ChEBI includes an ontological classification defining relations between entities or classes of entities.
has super-classes
deprecated classc

ChEBI IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1174

has super-classes
Accessionc
Compound accessionc

Chemical biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3369

has super-classes
Biologyc
Synthetic chemistryc

Chemical data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2030

has super-classes
Format (by type of data)c
is format ofop some Small molecule reportc
has sub-classes
BcFormsc, HET group dictionary entry formatc, Mol2c, Molfilec, SDFc

Chemical formulac back to ToC or Class ToC

IRI: http://edamontology.org/data_0846

has super-classes
Molecular property (general)c
has sub-classes
SMILES stringc

Chemical formula formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2035

has super-classes
Format (by type of data)c
is format ofop some Chemical formulac
has sub-classes
BpFormsc, InChIc, InChIKeyc, SMILESc, mfc

Chemical identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0986

has super-classes
deprecated classc

Chemical name (brand)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1000

has super-classes
Compound namec

Chemical name (ChEBI)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0997

This is the recommended chemical name for use for example in database annotation.
has super-classes
Compound namec

Chemical name (INN)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0999

has super-classes
Compound namec

Chemical name (IUPAC)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0998

has super-classes
Compound namec

Chemical name (synonymous)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1001

has super-classes
Compound namec

Chemical redundancy removalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3564

has super-classes
Structure comparisonc

Chemical registry numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_0991

has super-classes
Compound accessionc
has sub-classes
CAS numberc, Chemical registry number (Beilstein)c, Chemical registry number (Gmelin)c

Chemical registry number (Beilstein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1003

has super-classes
Chemical registry numberc
Accessionc

Chemical registry number (Gmelin)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1004

has super-classes
Chemical registry numberc
Accessionc

Chemical similarity enrichmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3502

has super-classes
Enrichment analysisc
has topicop some Function analysisc

Chemical structure imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1712

The molecular identifier and formula are typically included.
has super-classes
Structure imagec

Chemical structure sketchc back to ToC or Class ToC

IRI: http://edamontology.org/data_3490

Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software.
has super-classes
deprecated classc

Cheminformaticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2258

has super-classes
Informaticsc
has sub-classes
Chemometricsc

Chemistryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3314

has super-classes
Topicc
has sub-classes
Analytical chemistryc, Biochemistryc, Computational chemistryc, Drug discoveryc, Synthetic chemistryc

Chemometricsc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3931

has super-classes
Cheminformaticsc

ChemSpider entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1702

has super-classes
deprecated classc

ChemSpider IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1173

has super-classes
Accessionc
Compound accessionc

Chimera detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0450

A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles.
has super-classes
Nucleic acid sequence analysisc

ChIP-on-chipc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3179

has super-classes
Immunoprecipitation experimentc

ChIP-seqc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3169

has super-classes
Sequencingc
Immunoprecipitation experimentc

CHPc back to ToC or Class ToC

IRI: http://edamontology.org/format_1644

has super-classes
Gene expression report formatc
Textual formatc
is format ofop some Processed microarray datac

Chromatogram visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3203

has super-classes
Visualisationc

Chromatographic alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3628

has super-classes
Spectral analysisc
has inputop some Mass spectrumc

chrominfoc back to ToC or Class ToC

IRI: http://edamontology.org/format_3587

Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not.
has super-classes
Textual formatc
BEDc

Chromosome annotation (aberration)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1853

has super-classes
deprecated classc

Chromosome conformation capturec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3940

has super-classes
Laboratory techniquesc

Chromosome namec back to ToC or Class ToC

IRI: http://edamontology.org/data_0987

has super-classes
Molecule namec
Nucleic acid identifierc
is identifier ofop some Chromosome reportc
has sub-classes
Chromosome name (BioCyc)c

Chromosome name (BioCyc)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2706

has super-classes
Chromosome namec

Chromosome reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0919

This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc.
has super-classes
Nucleic acid reportc

Chromosomesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0624

has super-classes
deprecated classc

CIP strain data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2211

has super-classes
deprecated classc

cis-regulatory element predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0441

Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand from which the element was transcribed. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. They also occur in RNA sequences, e.g. a riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity.
has super-classes
Transcriptional regulatory element predictionc

Citationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0970

A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available.
has super-classes
Text datac

CiteXplore-allc back to ToC or Class ToC

IRI: http://edamontology.org/format_1737

has super-classes
Textual formatc
Bibliographic reference formatc

CiteXplore-corec back to ToC or Class ToC

IRI: http://edamontology.org/format_1736

has super-classes
Textual formatc
Bibliographic reference formatc

Cladisticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3944

has super-classes
Sequence analysisc
Phylogenyc

Classificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2990

has super-classes
Operationc
has sub-classes
Sequence classificationc, Single particle alignment and classificationc, Structure classificationc

Classificationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2230

has super-classes
deprecated classc

Classification reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2987

This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on.
has super-classes
deprecated classc

CleanEx dataset codec back to ToC or Class ToC

IRI: http://edamontology.org/data_2710

has super-classes
Experiment annotation IDc

CleanEx entry namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2709

has super-classes
Gene expression report IDc
Accessionc

Clinical trial reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3558

has super-classes
Reportc

Clone IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1855

has super-classes
Transcript IDc
has sub-classes
Clone ID (IMAGE)c, Clone ID (RefSeq)c, EST accessionc

Clone ID (IMAGE)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2704

has super-classes
Clone IDc
Accessionc

Clone ID (RefSeq)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2803

has super-classes
RefSeq accessionc
Clone IDc

Clone libraryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3341

has super-classes
Sample collectionsc

clustal sequence formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1924

has super-classes
deprecated classc

ClustalW dendrogramc back to ToC or Class ToC

IRI: http://edamontology.org/format_1424

has super-classes
Textual formatc
Phylogenetic tree format (text)c

ClustalW formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1982

has super-classes
Textual formatc
Alignment format (text)c

Cluster textual view generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2934

has super-classes
deprecated classc

Clustered expression profilesc back to ToC or Class ToC

IRI: http://edamontology.org/data_3768

has super-classes
Expression datac
has sub-classes
Heat mapc

Clusteringc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3432

has super-classes
Operationc
has sub-classes
Document clusteringc, Expression profile clusteringc, Sequence clusteringc, Structure clusteringc

Clustering profile plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2935

has super-classes
Expression data visualisationc

codatac back to ToC or Class ToC

IRI: http://edamontology.org/format_1925

has super-classes
Textual formatc
Sequence record format (text)c

Coding regionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1313

has super-classes
deprecated classc

Coding region predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0436

has super-classes
Gene predictionc
has sub-classes
Translation initiation site predictionc

Coding RNAc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0655

has super-classes
deprecated classc

Codon adaptation indexc back to ToC or Class ToC

IRI: http://edamontology.org/data_1599

has super-classes
deprecated classc

Codon namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1024

has super-classes
deprecated classc

Codon numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_2216

has super-classes
Sequence positionc

Codon usagec back to ToC or Class ToC

IRI: http://edamontology.org/data_2927

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Codon usage analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0286

has super-classes
Nucleic acid sequence analysisc
has inputop some Nucleic acid sequencec
has outputop some Codon usage datac
has inputop some Codon usage tablec
has topicop some Gene expressionc
has outputop some Codon usage tablec
has sub-classes
Base position variability plottingc, Codon usage bias calculationc, Codon usage fraction calculationc, Codon usage table comparisonc, Codon usage table generationc, DNA substitution modellingc, Ecological modellingc, Genetic code predictionc

Codon usage biasc back to ToC or Class ToC

IRI: http://edamontology.org/data_2865

has super-classes
Codon usage datac

Codon usage bias calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2962

has super-classes
Codon usage analysisc
has outputop some Codon usage biasc

Codon usage bias plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_1600

has super-classes
Codon usage datac

Codon usage bias plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2963

has super-classes
deprecated classc

Codon usage datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0914

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Datac
has topicop some Gene expressionc
has sub-classes
Codon usage biasc, Codon usage bias plotc, Codon usage fraction differencec, Codon usage tablec, Genetic codec

Codon usage data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2493

has super-classes
deprecated classc

Codon usage fraction calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2964

has super-classes
Codon usage analysisc
has outputop some Codon usage fraction differencec

Codon usage fraction differencec back to ToC or Class ToC

IRI: http://edamontology.org/data_1602

has super-classes
Codon usage datac

Codon usage tablec back to ToC or Class ToC

IRI: http://edamontology.org/data_1597

A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table.
has super-classes
Codon usage datac
has topicop some Gene expressionc

Codon usage table comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0285

has super-classes
Codon usage analysisc
Nucleic acid comparisonc

Codon usage table formattingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0563

has super-classes
deprecated classc

Codon usage table generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0284

has super-classes
Codon usage analysisc
Generationc
has outputop some Codon usage tablec

Codon usage table IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2111

has super-classes
Identifier (by type of data)c
is identifier ofop some Codon usage tablec
is identifier ofop some Genetic codec
has sub-classes
Codon usage table namec

Codon usage table namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1076

has super-classes
Namec
Codon usage table IDc
is identifier ofop some Genetic codec
is identifier ofop some Codon usage tablec

Codon usage table processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2433

has super-classes
deprecated classc

COG sequence cluster formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1247

has super-classes
deprecated classc

COGEME EST IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2729

has super-classes
Accessionc
EST accessionc

COGEME unisequence IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2730

A unisequence is a single sequence assembled from ESTs.
has super-classes
Accessionc
EST accessionc

ColiCard report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1810

has super-classes
deprecated classc

Collapsing methodsc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3791

Genome-wide association studies (GWAS) analyse a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. Traditional association techniques can lack the power to detect the significance of rare variants individually, or measure their compound effect (rare variant burden). "Collapsing methods" were developed to overcome these problems.
has super-classes
Genetic variation analysisc

Colorc back to ToC or Class ToC

IRI: http://edamontology.org/data_2151

has super-classes
deprecated classc

COMBINE OMEXc back to ToC or Class ToC

IRI: http://edamontology.org/format_3686

An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. OMEX is one of the standardised formats within COMBINE (Computational Modeling in Biology Network).
has super-classes
Biological pathway or network formatc
Binary formatc
Experiment annotation formatc

Comparative genomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0797

has super-classes
Genomicsc

Comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2424

has super-classes
Operationc
has sub-classes
Article comparisonc, Database comparisonc, ID mappingc, Nucleic acid comparisonc, Ontology comparisonc, Phylogenetic tree comparisonc, Protein comparisonc, Sample comparisonc, Sequence alignment comparisonc, Sequence comparisonc, Sequence feature comparisonc, Structure comparisonc

Comparison matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_0874

The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats).
has super-classes
Matrixc
has sub-classes
Comparison matrix (amino acid)c, Comparison matrix (nucleotide)c

Comparison matrix (amino acid)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1449

has super-classes
Comparison matrixc
Amino acid propertyc

Comparison matrix (floats)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1447

has super-classes
deprecated classc

Comparison matrix (integers)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1446

has super-classes
deprecated classc

Comparison matrix (nucleotide)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1448

has super-classes
Comparison matrixc

Comparison matrix identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1069

has super-classes
Matrix identifierc
is identifier ofop some Comparison matrixc
has sub-classes
Comparison matrix namec

Comparison matrix namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1126

See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.
has super-classes
Comparison matrix identifierc
Namec
is identifier ofop some Comparison matrixc

Comparison matrix typec back to ToC or Class ToC

IRI: http://edamontology.org/data_1125

For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used.
has super-classes
deprecated classc

Complementary medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3423

has super-classes
Medicinec

completely unambiguousc back to ToC or Class ToC

IRI: http://edamontology.org/format_2566

has super-classes
Textual formatc
Raw sequence formatc
has sub-classes
completely unambiguous purec

completely unambiguous purec back to ToC or Class ToC

IRI: http://edamontology.org/format_2567

has super-classes
purec
completely unambiguousc
has sub-classes
completely unambiguous pure dnac, completely unambiguous pure nucleotidec, completely unambiguous pure proteinc, completely unambiguous pure rna sequencec

completely unambiguous pure dnac back to ToC or Class ToC

IRI: http://edamontology.org/format_2569

has super-classes
dnac
completely unambiguous purec

completely unambiguous pure nucleotidec back to ToC or Class ToC

IRI: http://edamontology.org/format_2568

has super-classes
nucleotidec
completely unambiguous purec

completely unambiguous pure proteinc back to ToC or Class ToC

IRI: http://edamontology.org/format_2607

has super-classes
proteinc
completely unambiguous purec

completely unambiguous pure rna sequencec back to ToC or Class ToC

IRI: http://edamontology.org/format_2570

has super-classes
rnac
completely unambiguous purec

Compound accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2894

has super-classes
Compound identifierc
Molecule accessionc
has sub-classes
BindingDB Monomer IDc, ChEBI IDc, ChemSpider IDc, Chemical registry numberc, Compound ID (3DMET)c, Compound ID (BioCyc)c, Compound ID (ChEMBL)c, Compound ID (ChemIDplus)c, Compound ID (HMDB)c, Compound ID (KEGG)c, PubChem CIDc

Compound ID (3DMET)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2635

has super-classes
Accessionc
Compound accessionc

Compound ID (BioCyc)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2105

has super-classes
Accessionc
BioCyc IDc
Compound accessionc

Compound ID (ChEMBL)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2646

has super-classes
Accessionc
Compound accessionc

Compound ID (ChemIDplus)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2658

has super-classes
Accessionc
Compound accessionc

Compound ID (HMDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2622

has super-classes
Accessionc
Compound accessionc

Compound ID (KEGG)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2605

has super-classes
KEGG object identifierc
Compound accessionc

Compound identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1086

has super-classes
Molecule identifierc
is identifier ofop some Small molecule reportc
has sub-classes
Amino acid identifierc, Carbohydrate identifierc, Compound accessionc, Compound namec, Drug identifierc, Monosaccharide identifierc, Nucleotide identifierc, Toxin identifierc, UNIIc

Compound libraries and screeningc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3343

has super-classes
Drug discoveryc

Compound namec back to ToC or Class ToC

IRI: http://edamontology.org/data_0990

has super-classes
Molecule namec
Compound identifierc
has sub-classes
Chemical name (ChEBI)c, Chemical name (INN)c, Chemical name (IUPAC)c, Chemical name (brand)c, Chemical name (synonymous)c, Drug namec, HET group namec, Nucleotide codec

Computational biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3307

This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology).
has super-classes
Topicc
has sub-classes
Biomolecular simulationc, Function analysisc, Molecular geneticsc, Molecular interactions, pathways and networksc, Nucleic acidsc, Phylogenyc, Proteinsc, Sequence analysisc, Sequence sites, features and motifsc, Structure analysisc

Computational chemistryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3332

has super-classes
Chemistryc
Computer sciencec

Computer sciencec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3316

has super-classes
Topicc
has sub-classes
Computational chemistryc, Data miningc, Data visualisationc, Machine learningc, Natural language processingc, Software engineeringc

Concentrationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2140

has super-classes
Molecular property (general)c

consensusc back to ToC or Class ToC

IRI: http://edamontology.org/format_1209

has super-classes
unpurec
ambiguousc

Consensus tree constructionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0555

Methods typically test for topological similarity between trees using for example a congruence index.
has super-classes
Phylogenetic tree constructionc
Phylogenetic tree comparisonc

Consensus-based sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0498

has super-classes
deprecated classc

ConsensusPathDB entity IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2776

has super-classes
Accessionc
ConsensusPathDB identifierc

ConsensusPathDB entity namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2777

has super-classes
Namec
ConsensusPathDB identifierc

ConsensusPathDB identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2917

has super-classes
Identifier (hybrid)c
has sub-classes
ConsensusPathDB entity IDc, ConsensusPathDB entity namec, Pathway ID (ConsensusPathDB)c

consensusXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3832

has super-classes
XMLc
Mass spectrometry data formatc

Conserved transcription regulatory sequence identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0242

has super-classes
deprecated classc

Constrained sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0497

has super-classes
deprecated classc

Contact map calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0392

has super-classes
Protein distance matrix calculationc
has outputop some Protein contact mapc

Conversionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3434

has super-classes
Operationc
has sub-classes
Sequence alignment conversionc, Sequence conversionc, Sequence coordinate conversionc

CopasiMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3239

has super-classes
Biological pathway or network formatc
XMLc
Biological pathway or network report formatc

Copy number estimationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3233

Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number).
has super-classes
DNA testingc

Core datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3031

Core data entities typically have a format and may be identified by an accession number.
has super-classes
deprecated classc

Correlationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3465

has super-classes
Operationc
has topicop some Proteomicsc
has sub-classes
Expression correlation analysisc, Sequence alignment analysis (site correlation)c

COSMIC IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3264

has super-classes
Accessionc
Sequence variation IDc

Count matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_3917

has super-classes
Matrixc

cPath IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2637

These identifiers are unique within the cPath database, however, they are not stable between releases.
has super-classes
Accessionc
Identifier (hybrid)c
Pathway or network accessionc

CPDB entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1654

has super-classes
deprecated classc

CpG island and isochore detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0430

An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence.
has super-classes
Nucleic acid feature detectionc
has topicop some Sequence composition, complexity and repeatsc

CpG island and isochoresc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1304

has super-classes
deprecated classc

CRAMc back to ToC or Class ToC

IRI: http://edamontology.org/format_3462

has super-classes
Binary formatc
Alignment format (pair only)c

Critical care medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3403

has super-classes
Medicinec

Cross-assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3730

has super-classes
Sequence assemblyc

csfastac back to ToC or Class ToC

IRI: http://edamontology.org/format_3589

FASTA format extended for color space information.
has super-classes
FASTA-like (text)c
Alignment format (text)c

CSVc back to ToC or Class ToC

IRI: http://edamontology.org/format_3752

has super-classes
DSVc

CTc back to ToC or Class ToC

IRI: http://edamontology.org/format_3309

has super-classes
RNA secondary structure formatc
Textual formatc

Cultivation parameterc back to ToC or Class ToC

IRI: http://edamontology.org/data_3724

has super-classes
Experimental measurementc

customtrackc back to ToC or Class ToC

IRI: http://edamontology.org/format_3588

Used for tracks/track views within galaxy.
has super-classes
Textual formatc
Sequence annotation track formatc

CWLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3857

has super-classes
Workflow formatc
YAMLc

Cysteine bridge detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1829

has super-classes
Protein cysteine and disulfide bond assignmentc

Cysteine torsion angle calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1827

has super-classes
deprecated classc

Cytoband formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3235

Reflects a UCSC Browser DB table.
has super-classes
Sequence range formatc
Textual formatc
is format ofop some Cytoband positionc

Cytoband positionc back to ToC or Class ToC

IRI: http://edamontology.org/data_3236

Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on.
has super-classes
Sequence coordinatesc

Cytogenetic mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1283

This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms.
has super-classes
Physical mapc
has sub-classes
Deletion mapc

Cytometryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3934

has super-classes
Laboratory techniquesc

Cytoscape input file formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3477

has super-classes
Gene expression report formatc
Textual formatc

dafc back to ToC or Class ToC

IRI: http://edamontology.org/format_1393

The format is clustal-like and includes annotation of domain family classification information.
has super-classes
Textual formatc
Alignment format (text)c

DaliLite hit tablec back to ToC or Class ToC

IRI: http://edamontology.org/data_1495

The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given.
has super-classes
deprecated classc

DaliLite log filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1679

has super-classes
deprecated classc

DAS formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1967

has super-classes
XMLc
Sequence record format (XML)c

DAS sequence feature annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_1269

has super-classes
deprecated classc

dasdnac back to ToC or Class ToC

IRI: http://edamontology.org/format_1968

The use of this format is deprecated.
has super-classes
XMLc
Sequence record format (XML)c

DASGFFc back to ToC or Class ToC

IRI: http://edamontology.org/format_1978

has super-classes
XMLc
Sequence feature table format (XML)c

datc back to ToC or Class ToC

IRI: http://edamontology.org/format_1637

has super-classes
Gene expression report formatc
Textual formatc
is format ofop some Microarray spots imagec

Datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0006

has sub-classes
Alignmentc, Biodiversity datac, Codon usage datac, Data indexc, Data referencec, Database search resultsc, Ecological datac, Evidencec, Experimental measurementc, Expression datac, Hierarchyc, Identifierc, Imagec, Keywordc, Mapc, Map datac, Mathematical modelc, Matrixc, Molecular propertyc, Molecular simulation datac, Ontology datac, Over-representation datac, Pathway or networkc, Phylogenetic datac, Plotc, Query scriptc, Reaction datac, Regular expressionc, Reportc, Scorec, Sequencec, Sequence attributec, Sequence coordinatesc, Sequence featuresc, Sequence features metadatac, Sequence setc, Sequence signature datac, Sequence variationsc, Simulationc, Spectrumc, Structural profilec, Structurec, Taxonomyc, Text datac, Training materialc
is in domain of
has formatop, has identifierop, is input ofop, is output ofop
is in range of
has inputop, has outputop, is format ofop, is identifier ofop
is disjoint with
Formatc, Operationc, Topicc, deprecated classc

Data acquisitionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3077

has super-classes
Biological databasesc

Data architecture, analysis and designc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3365

has super-classes
Biological databasesc

Data governancec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3571

has super-classes
Biological databasesc

Data handlingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2409

has super-classes
Operationc
has topicop some Database managementc
has sub-classes
Aggregationc, Anonymisationc, Depositionc, Editingc, Filteringc, Format detectionc, Formattingc, Parsingc, Query and retrievalc, Sortingc, Splittingc

Data handlingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2427

has super-classes
deprecated classc

Data identity and mappingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3345

has super-classes
Biological databasesc

Data indexc back to ToC or Class ToC

IRI: http://edamontology.org/data_0955

has super-classes
Datac
has topicop some Database managementc
has sub-classes
Genome indexc

Data index analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0228

has super-classes
deprecated classc

Data index datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2540

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Data index formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3326

has super-classes
Format (by type of data)c
is format ofop some Data indexc
has sub-classes
BAIc, Tabix index file formatc, ebwtc, ebwtlc, snpeffdbc

Data index processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2412

has super-classes
deprecated classc

Data index reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0956

has super-classes
Reportc
has topicop some Database managementc

Data integration and warehousingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3366

has super-classes
Biological databasesc

Data miningc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3473

has super-classes
Computer sciencec

Data quality managementc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3572

has super-classes
Biological databasesc

Data referencec back to ToC or Class ToC

IRI: http://edamontology.org/data_2093

A list of database accessions or identifiers are usually included.
has super-classes
Datac
has sub-classes
Annotated URIc, Database cross-mappingc, ID listc, Ontology mappingc

Data resource definitionc back to ToC or Class ToC

IRI: http://edamontology.org/data_0948

has super-classes
deprecated classc

Data resource definition accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2902

has super-classes
Data resource definition IDc
has sub-classes
MIRIAM URIc, MIRIAM identifierc

Data resource definition IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1084

has super-classes
Identifier (by type of data)c
has sub-classes
Data resource definition accessionc, Data resource definition namec

Data resource definition namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2253

has super-classes
Data resource definition IDc
Namec
has sub-classes
MIRIAM data type namec

Data resource identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0975

has super-classes
deprecated classc

Data retrievalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2422

has super-classes
Query and retrievalc
Information retrievalc
has inputop some Identifierc

Data retrieval (codon usage table)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2434

has super-classes
deprecated classc

Data retrieval (database cross-reference)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0225

has super-classes
deprecated classc

Data retrieval (database metadata)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0516

has super-classes
deprecated classc

Data retrieval (feature table)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0254

has super-classes
deprecated classc

Data retrieval (gene annotation)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2472

has super-classes
deprecated classc

Data retrieval (genotype and phenotype annotation)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2473

has super-classes
deprecated classc

Data retrieval (identifier)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2265

has super-classes
deprecated classc

Data retrieval (ontology annotation)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2222

has super-classes
deprecated classc

Data retrieval (ontology concept)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2224

has super-classes
deprecated classc

Data retrieval (pathway or network)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2264

has super-classes
deprecated classc

Data retrieval (phylogenetic tree)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2468

has super-classes
deprecated classc

Data retrieval (protein annotation)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2467

has super-classes
deprecated classc

Data retrieval (protein family annotation)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2470

has super-classes
deprecated classc

Data retrieval (protein interaction annotation)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2469

has super-classes
deprecated classc

Data retrieval (restriction enzyme annotation)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0280

has super-classes
deprecated classc

Data retrieval (RNA family annotation)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2471

has super-classes
deprecated classc

Data retrieval (sequence alignment)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0257

has super-classes
deprecated classc

Data retrieval (sequence profile)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2237

This includes direct retrieval methods that retrieve a profile by, e.g. the profile name.
has super-classes
deprecated classc

Data retrieval (tool metadata)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0515

has super-classes
deprecated classc

Data securityc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3263

has super-classes
Biological databasesc

Data submission, annotation and curationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0219

has super-classes
Biological databasesc

Data types and objectsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0770

has super-classes
deprecated classc

Data visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0092

has super-classes
Computer sciencec

Databankc back to ToC or Class ToC

IRI: http://edamontology.org/data_2831

has super-classes
deprecated classc

Databasec back to ToC or Class ToC

IRI: http://edamontology.org/data_0581

has super-classes
deprecated classc

Database category namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2149

has super-classes
deprecated classc

Database comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3561

has super-classes
Comparisonc
Mappingc

Database cross-mappingc back to ToC or Class ToC

IRI: http://edamontology.org/data_0954

The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc.
has super-classes
Data referencec

Database entryc back to ToC or Class ToC

IRI: http://edamontology.org/data_0843

has super-classes
deprecated classc

Database entry identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1062

This concept is required for completeness. It should never have child concepts.
has super-classes
deprecated classc

Database entry metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_2193

has super-classes
Resource metadatac

Database entry version informationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2090

has super-classes
deprecated classc

Database field namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2219

has super-classes
Namec

Database hits (sequence) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2066

has super-classes
Format (by type of data)c
is format ofop some Sequence search resultsc
has sub-classes
BLAST resultsc, EBI Application Result XMLc, FASTA search results formatc, InterPro hits formatc, Smith-Waterman formatc, dhfc, lhfc, mspcrunchc

Database IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1048

has super-classes
Identifier (by type of data)c
is identifier ofop some Database metadatac
has sub-classes
Database namec

Database managementc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3489

This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature. It covers the management and manipulation of digital documents, including database records, files and reports.
has super-classes
Biological databasesc

Database metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_0957

has super-classes
Resource metadatac

Database namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1056

has super-classes
Database IDc
Namec

Database name (CMD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2747

has super-classes
deprecated classc

Database name (Osteogenesis)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2748

has super-classes
deprecated classc

Database name (SwissRegulon)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2735

has super-classes
deprecated classc

Database searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2421

Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database.
has super-classes
Query and retrievalc
has outputop some Database search resultsc
has sub-classes
Literature searchc, Peptide database searchc, Sequence database searchc, Structure database searchc

Database search (by sequence)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3093

has super-classes
deprecated classc

Database search resultsc back to ToC or Class ToC

IRI: http://edamontology.org/data_2080

has super-classes
Datac
has sub-classes
Sequence search resultsc

Database version informationc back to ToC or Class ToC

IRI: http://edamontology.org/data_1670

has super-classes
deprecated classc

Datec back to ToC or Class ToC

IRI: http://edamontology.org/data_2156

has super-classes
deprecated classc

DBD IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2716

has super-classes
Accessionc
Transcription factor accessionc

dbEST accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1105

has super-classes
Accessionc
GenBank accessionc
EST accessionc

dbGaP formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3729

The Database of Genotypes and Phenotypes (dbGaP) is a National Institutes of Health (NIH) sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype.
has super-classes
Textual formatc

dbidc back to ToC or Class ToC

IRI: http://edamontology.org/format_1926

has super-classes
FASTA-like (text)c

dbProbe IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2719

has super-classes
Accessionc
Oligonucleotide IDc

dbSNP IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1106

has super-classes
Accessionc
Sequence variation IDc

dbSNP polymorphism report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1620

has super-classes
deprecated classc

DDBJ accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2916

has super-classes
EMBL/GenBank/DDBJ IDc

de Novo sequencingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3644

has super-classes
Sequence generationc
Peptide identificationc

De-novo assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0524

De-novo assemblers are much slower and more memory intensive than mapping assemblers.
has super-classes
Sequence assemblyc

debugc back to ToC or Class ToC

IRI: http://edamontology.org/format_1983

has super-classes
Textual formatc
Alignment format (text)c

debug-featc back to ToC or Class ToC

IRI: http://edamontology.org/format_1979

has super-classes
Sequence feature annotation formatc
Textual formatc

debug-seqc back to ToC or Class ToC

IRI: http://edamontology.org/format_1969

has super-classes
Textual formatc
Sequence record format (text)c

Deisotopingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3629

Deisotoping is commonly done to reduce complexity, and done in conjunction with the charge state deconvolution.
has super-classes
Spectral analysisc
has inputop some Mass spectrumc

Deletion mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1859

A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel.
has super-classes
Cytogenetic mapc

Demonstrationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2246

has super-classes
deprecated classc

Demultiplexingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3933

NGS sequence runs are often performed with multiple samples pooled together. In such cases, an index tag (or "barcode") - a unique sequence of between 6 and 12bp - is ligated to each sample's genetic material so that the sequence reads from different samples can be identified. The process of demultiplexing (dividing sequence reads into separate files for each index tag/sample) may be performed automatically by the sequencing hardware. Alternatively the reads may be lumped together in one file with barcodes still attached, requiring you to do the splitting using software. In such cases, a "mapping” file is used which indicates which barcodes correspond to which samples.
has super-classes
Sequence read processingc

Dendrogram visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2938

has super-classes
Expression data visualisationc

Dendrograph plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2936

has super-classes
deprecated classc

Dentistryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3405

has super-classes
Medicinec

Depositionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3431

For non-analytical operations, see the 'Processing' branch.
has super-classes
Data handlingc

Dermatologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3404

has super-classes
Medicinec

Designc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2430

has super-classes
Operationc
has sub-classes
Microarray probe designc, Nucleic acid designc

Developmental biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3064

has super-classes
Biologyc
has sub-classes
Embryologyc

dhfc back to ToC or Class ToC

IRI: http://edamontology.org/format_1336

The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database.
has super-classes
Database hits (sequence) formatc
Textual formatc

DIALIGN formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1392

has super-classes
Textual formatc
Alignment format (text)c

DICOM formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3548

has super-classes
Binary formatc
Image formatc

DictyBase gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1604

has super-classes
deprecated classc

Differential binding analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3677

has super-classes
Nucleic acid feature detectionc

Differential gene expression analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3223

Differential gene expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups.
has super-classes
Nucleic acid comparisonc
has sub-classes
Differential protein expression analysisc

Differential gene expression analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3742

has super-classes
deprecated classc

Differential protein expression analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3741

has super-classes
Protein comparisonc
Differential gene expression analysisc

Diffraction data analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3445

has super-classes
Structure analysisc
has sub-classes
Diffraction data integrationc, Diffraction data reductionc, Phasingc

Diffraction data integrationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3453

has super-classes
Diffraction data analysisc

Diffraction data reductionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3447

has super-classes
Diffraction data analysisc

Dimensionality reductionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3935

has super-classes
Calculationc
has topicop some Proteomicsc
has inputop some Mass spectrumc
has sub-classes
Feature extractionc, Feature selectionc

Dimethylc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3642

has super-classes
Labeled quantificationc

Dinucleotide propertyc back to ToC or Class ToC

IRI: http://edamontology.org/data_2720

has super-classes
DNA base structural datac

DIP IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2616

has super-classes
Protein interaction IDc
Accessionc

DiProDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2721

has super-classes
Accessionc
Oligonucleotide IDc

Directory metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_0583

has super-classes
deprecated classc

Directory namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1049

has super-classes
Namec

Dirichlet distributionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1347

has super-classes
Mathematical modelc

Dirichlet distribution formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2074

has super-classes
Format (by type of data)c
is format ofop some Dirichlet distributionc
has sub-classes
HMMER Dirichlet priorc, MEME Dirichlet priorc

Discrete entity identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0978

has super-classes
deprecated classc

Disease (specific)c back to ToC or Class ToC

IRI: http://edamontology.org/topic_2847

has super-classes
deprecated classc

Disease genes and proteinsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2813

has super-classes
deprecated classc

Disease IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1150

has super-classes
Disease identifierc
has sub-classes
Disease ID (PharmGKB)c, ICD identifierc, Orpha numberc

Disease ID (PharmGKB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2651

has super-classes
Disease IDc
Accessionc
PharmGKB IDc

Disease identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_3667

has super-classes
Identifier (by type of data)c
is identifier ofop some Disease reportc
has sub-classes
Disease IDc, Disease namec

Disease namec back to ToC or Class ToC

IRI: http://edamontology.org/data_3668

has super-classes
Namec
Disease identifierc

Disease pathway or network reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1661

has super-classes
deprecated classc

Disease pathwaysc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3528

has super-classes
deprecated classc

Disease reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1622

For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on.
has super-classes
Genotype/phenotype reportc
has topicop some Pathologyc

Distance matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_2855

has super-classes
Matrixc
has sub-classes
Protein distance matrixc, Sequence distance matrixc, Structural distance matrixc

Disulfide bond predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0471

has super-classes
Protein feature detectionc

DMR identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3809

has super-classes
Methylation analysisc

dnac back to ToC or Class ToC

IRI: http://edamontology.org/format_1212

has super-classes
nucleotidec
has sub-classes
completely unambiguous pure dnac, pure dnac, unambiguous pure dnac

DNAc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0654

The DNA sequences might be coding or non-coding sequences.
has super-classes
Nucleic acidsc
has sub-classes
DNA binding sitesc, DNA mutationc, DNA packagingc, DNA polymorphismc, DNA replication and recombinationc, DNA structural variationc

DNA back-translationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2510

has super-classes
Sequence conversionc
has topicop some Protein expressionc

DNA barcodingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3200

has super-classes
Nucleic acid sequence analysisc

DNA base pair stacking energies datac back to ToC or Class ToC

IRI: http://edamontology.org/data_1588

has super-classes
DNA base structural datac

DNA base pair twist angle datac back to ToC or Class ToC

IRI: http://edamontology.org/data_1589

has super-classes
DNA base structural datac

DNA base structural datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2088

has super-classes
Nucleic acid propertyc
has sub-classes
Base pairing probability matrix dotplotc, DNA base pair stacking energies datac, DNA base pair twist angle datac, DNA base trimer roll angles datac, Dinucleotide propertyc

DNA base trimer roll angles datac back to ToC or Class ToC

IRI: http://edamontology.org/data_1590

has super-classes
DNA base structural datac

DNA binding site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3903

has super-classes
Nucleic acids-binding site predictionc

DNA binding sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3125

This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes), restriction enzyme recognition sites (restriction sites) etc.
has super-classes
DNAc
Nucleic acid sites, features and motifsc
has sub-classes
Transcription factors and regulatory sitesc

DNA featuresc back to ToC or Class ToC

IRI: http://edamontology.org/data_2882

has super-classes
deprecated classc

DNA linear map renderingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0577

has super-classes
deprecated classc

DNA mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2520

has super-classes
Mappingc
has outputop some Mapc
has topicop some Mappingc
has topicop some Sequence assemblyc
has sub-classes
Genetic mappingc, Physical mappingc, Sequence tag mappingc

DNA methylationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3171

has super-classes
deprecated classc

DNA mutationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2533

has super-classes
Genetic variationc
DNAc

DNA packagingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3176

has super-classes
DNAc

DNA polymorphismc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2885

Includes microsatellite polymorphism in a DNA sequence. A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine.
has super-classes
Genetic variationc
DNAc

DNA profilingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3894

has super-classes
Nucleic acid sequence analysisc

DNA replication and recombinationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3127

has super-classes
DNAc

DNA sense specificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0853

The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used.
has super-classes
deprecated classc

DNA sequencec back to ToC or Class ToC

IRI: http://edamontology.org/data_3494

has super-classes
Nucleic acid sequencec

DNA sequence (raw)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3497

has super-classes
deprecated classc

DNA structural variationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3175

has super-classes
Genetic variationc
DNAc

DNA structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_1464

has super-classes
Nucleic acid structurec

DNA structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_3924

has super-classes
Nucleic acid structure alignmentc

DNA structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2442

has super-classes
Nucleic acid structure predictionc
has outputop some DNA structurec

DNA substitution modelc back to ToC or Class ToC

IRI: http://edamontology.org/data_1439

has super-classes
Mathematical modelc

DNA substitution modellingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0550

has super-classes
Codon usage analysisc
Modelling and simulationc
has topicop some Phylogenyc
has outputop some DNA substitution modelc

DNA testingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3920

This can include indirect methods which reveal the results of genetic changes, such as RNA analysis to indicate gene expression, or biochemical analysis to identify expressed proteins.
has super-classes
Nucleic acid sequence analysisc
has topicop some Genomicsc
has sub-classes
Copy number estimationc, Recombination detectionc

DNA transcriptionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0372

has super-classes
Sequence conversionc
has topicop some Gene expressionc

DNA transduction mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1284

has super-classes
Genetic mapc

DNA translationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0371

has super-classes
Sequence conversionc
has topicop some Protein expressionc

DNA vaccine designc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0560

has super-classes
Nucleic acid designc
has topicop some Immunologyc

DNA variationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0918

has super-classes
deprecated classc

DNA-binding protein predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3900

has super-classes
Protein-nucleic acid interaction analysisc
has outputop some Protein interaction datac
has topicop some Protein interactionsc

DNA-Seqc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3177

has super-classes
deprecated classc

doc2loc document informationc back to ToC or Class ToC

IRI: http://edamontology.org/data_1738

The doc2loc output includes the url, format, type and availability code of a document for every service provider.
has super-classes
deprecated classc

Document clusteringc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3279

has super-classes
Clusteringc
Article comparisonc

Document formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3507

has super-classes
Format (by type of data)c
has sub-classes
PDFc, docxc, latexc, xlsc, xlsxc

Document similarity calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3278

has super-classes
Article comparisonc

Document, record and content managementc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0220

has super-classes
deprecated classc

Documentation and helpc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3061

has super-classes
deprecated classc

docxc back to ToC or Class ToC

IRI: http://edamontology.org/format_3506

has super-classes
XMLc
Document formatc

DOIc back to ToC or Class ToC

IRI: http://edamontology.org/data_1188

has super-classes
Article IDc
Accessionc

Domain-domain interaction (indirect)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2360

has super-classes
deprecated classc

Domain-domain interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/data_2359

has super-classes
deprecated classc

Domain-nucleic acid interaction reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2358

has super-classes
deprecated classc

Domainatrix 3D-1D scoring matrix formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1500

has super-classes
deprecated classc

Domainatrix signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1368

has super-classes
deprecated classc

Dot plot plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0490

Dot plots are useful when having not too many (e.g. 20) data points for each category. Example: draw a dotplot of sequence similarities identified from word-matching or character comparison.
has super-classes
Sequence word comparisonc
Sequence visualisationc
has outputop some Dotplotc

Dot-bracket formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1457

has super-classes
RNA secondary structure formatc
Textual formatc
has sub-classes
Vienna local RNA secondary structure formatc

Dotplotc back to ToC or Class ToC

IRI: http://edamontology.org/data_0862

has super-classes
Sequence alignment reportc

DPVweb IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2836

has super-classes
Accessionc
Virus IDc

DragonDB author identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1882

has super-classes
Author IDc

DragonDB gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1606

has super-classes
deprecated classc

DRCAT resourcec back to ToC or Class ToC

IRI: http://edamontology.org/data_2875

has super-classes
deprecated classc

Drop off scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_1403

has super-classes
Alignment score or penaltyc

Drug accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2895

has super-classes
Drug identifierc
has sub-classes
ATC codec, CAS numberc, Drug ID (KEGG)c, Drug ID (PharmGKB)c, Drug ID (TTD)c, DrugBank IDc

Drug developmentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3373

has super-classes
Medicines research and developmentc

Drug discoveryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3336

This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.
has super-classes
Chemistryc
Medicines research and developmentc
has sub-classes
Compound libraries and screeningc, Medicinal chemistryc

Drug ID (KEGG)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2609

has super-classes
KEGG object identifierc
Accessionc
Drug accessionc

Drug ID (PharmGKB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2652

has super-classes
Accessionc
PharmGKB IDc
Drug accessionc

Drug ID (TTD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2653

has super-classes
Accessionc
Drug accessionc

Drug identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0993

has super-classes
Compound identifierc
is identifier ofop some Drug structurec
has sub-classes
Drug accessionc, Drug namec

Drug metabolismc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3375

has super-classes
Medicines research and developmentc

Drug namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2899

has super-classes
Compound namec
Drug identifierc

Drug reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1696

has super-classes
Small molecule reportc
has topicop some Small moleculesc

Drug structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_2851

has super-classes
Small molecule structurec

Drug structure relationship mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1662

has super-classes
deprecated classc

DrugBank IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2326

has super-classes
Accessionc
Drug accessionc

Drugs and target structuresc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0620

has super-classes
deprecated classc

dsspc back to ToC or Class ToC

IRI: http://edamontology.org/format_1454

The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format.
has super-classes
Protein secondary structure formatc
Textual formatc

DSSP secondary structure assignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1847

has super-classes
deprecated classc

DSVc back to ToC or Class ToC

IRI: http://edamontology.org/format_3751

has super-classes
Textual formatc
has sub-classes
CSVc, TSVc

dtac back to ToC or Class ToC

IRI: http://edamontology.org/format_3652

Each file contains one header line for the known or assumed charge and the mass of the precursor peptide ion, calculated from the measured *m*/*z* and the charge. This one line was then followed by all the *m*/*z*, intensity pairs that represent the spectrum.
has super-classes
Mass spectrometry data formatc

DTDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2249

has super-classes
deprecated classc

E-valuec back to ToC or Class ToC

IRI: http://edamontology.org/data_1667

An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score.
has super-classes
Statistical estimate scorec

Ear, nose and throat medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3406

has super-classes
Medicinec

EBI Application Result XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3157

has super-classes
Database hits (sequence) formatc
XMLc
Alignment format (pair only)c

ebwtc back to ToC or Class ToC

IRI: http://edamontology.org/format_3484

has super-classes
Binary formatc
Data index formatc
is format ofop some Genome indexc

ebwtlc back to ToC or Class ToC

IRI: http://edamontology.org/format_3491

has super-classes
Binary formatc
Data index formatc
is format ofop some Genome indexc

EC numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1011

has super-classes
Accessionc
Enzyme IDc

Echographyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3954

has super-classes
Imagingc

EcoCyc gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1607

has super-classes
deprecated classc

Ecological datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3736

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Datac
has sub-classes
Biodiversity datac

Ecological modellingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3946

has super-classes
Codon usage analysisc
Modelling and simulationc
has outputop some DNA substitution modelc
has topicop some Phylogenyc

Ecologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0610

has super-classes
Biologyc
has sub-classes
Biodiversityc, Metagenomicsc, Microbial ecologyc

Editingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3096

has super-classes
Data handlingc
has sub-classes
Phylogenetic tree editingc, Sequence alignment editingc, Sequence editingc, Structure editingc

EGA accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2383

has super-classes
Accessionc
Genotype experiment IDc

ELAND formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3818

has super-classes
Textual formatc
Sequence assembly format (text)c

Electron density mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_0937

has super-classes
Protein structure raw datac

Electron microscopyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0611

has super-classes
Structural biologyc
Imagingc

Electron microscopy modelc back to ToC or Class ToC

IRI: http://edamontology.org/data_0941

has super-classes
deprecated classc

Electron microscopy model formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2045

has super-classes
deprecated classc

Electron microscopy model IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1079

has super-classes
Identifier (by type of data)c
is identifier ofop some 3D EM Mapc
has sub-classes
EMDB IDc

Electronic health recordc back to ToC or Class ToC

IRI: http://edamontology.org/data_3861

has super-classes
Reportc

ELM IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1116

has super-classes
Sequence motif identifierc

EM Micrographc back to ToC or Class ToC

IRI: http://edamontology.org/data_3808

has super-classes
Raw imagec
has topicop some Structural biologyc

EM Moviec back to ToC or Class ToC

IRI: http://edamontology.org/data_3807

has super-classes
Raw imagec
has topicop some Structural biologyc

EMAGE IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1149

has super-classes
Gene expression report IDc
Accessionc

Email addressc back to ToC or Class ToC

IRI: http://edamontology.org/data_1691

has super-classes
User IDc

EMAPc back to ToC or Class ToC

IRI: http://edamontology.org/data_1723

has super-classes
deprecated classc

EMAP concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1183

has super-classes
Ontology concept IDc
Accessionc

EMBASSY domain classificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_1555

has super-classes
deprecated classc

EMBL accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2290

has super-classes
EMBL/GenBank/DDBJ IDc

EMBL featurec back to ToC or Class ToC

IRI: http://edamontology.org/format_1980

has super-classes
deprecated classc

EMBL feature locationc back to ToC or Class ToC

IRI: http://edamontology.org/format_1248

has super-classes
Sequence range formatc
Textual formatc

EMBL formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1927

has super-classes
EMBL-like (text)c
Sequence feature table format (text)c

EMBL format (XML)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2204

This is a placeholder for other more specific concepts. It should not normally be used for annotation.
has super-classes
EMBL-like (XML)c
has sub-classes
EMBLXMLc, cdsxmlc, insdxmlc

EMBL-HTMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_2311

has super-classes
HTMLc
EMBL-like formatc

EMBL-like (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2181

This concept may be used for the many non-standard EMBL-like text formats.
has super-classes
Textual formatc
EMBL-like formatc
has sub-classes
EMBL formatc, geneseqc

EMBL-like (XML)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2558

This concept may be used for the any non-standard EMBL-like XML formats.
has super-classes
XMLc
EMBL-like formatc
has sub-classes
EMBL format (XML)c

EMBL-like formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2543

This concept may be used for the many non-standard EMBL-like formats.
has super-classes
Sequence record formatc
has sub-classes
EMBL-HTMLc, EMBL-like (XML)c, EMBL-like (text)c

EMBL/GenBank/DDBJ IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1103

has super-classes
Sequence accession (nucleic acid)c
Accessionc
has sub-classes
DDBJ accessionc, EMBL accessionc, GenBank accessionc

EMBLXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_2183

has super-classes
EMBL format (XML)c

EMBOSS database resource definitionc back to ToC or Class ToC

IRI: http://edamontology.org/data_0952

has super-classes
deprecated classc

EMBOSS domainatrix log filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1683

has super-classes
deprecated classc

EMBOSS graphc back to ToC or Class ToC

IRI: http://edamontology.org/data_2142

has super-classes
deprecated classc

EMBOSS listfilec back to ToC or Class ToC

IRI: http://edamontology.org/data_1111

has super-classes
deprecated classc

EMBOSS megamerger log filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1686

has super-classes
deprecated classc

EMBOSS repeatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1297

has super-classes
Sequence features (repeats) formatc
Textual formatc

EMBOSS reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2143

has super-classes
deprecated classc

EMBOSS sequence patternc back to ToC or Class ToC

IRI: http://edamontology.org/format_1357

has super-classes
Sequence motif formatc
Textual formatc

EMBOSS sequence typec back to ToC or Class ToC

IRI: http://edamontology.org/data_1110

See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes.
has super-classes
deprecated classc

EMBOSS simple formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2001

has super-classes
Textual formatc
Alignment format (text)c

EMBOSS sites log filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1684

has super-classes
deprecated classc

EMBOSS supermatcher error filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1685

has super-classes
deprecated classc

EMBOSS Uniform Feature Objectc back to ToC or Class ToC

IRI: http://edamontology.org/data_1023

has super-classes
Namec
Sequence feature identifierc

EMBOSS Uniform Sequence Addressc back to ToC or Class ToC

IRI: http://edamontology.org/data_1095

has super-classes
Sequence identifierc
Namec

EMBOSS vectorstrip log filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1688

has super-classes
deprecated classc

EMBOSS whichdb log filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1687

has super-classes
deprecated classc

EMBOSS wordfinder log filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1682

has super-classes
deprecated classc

Embryo reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2724

has super-classes
deprecated classc

Embryologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3065

has super-classes
Developmental biologyc

EMDB entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1645

has super-classes
deprecated classc

EMDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1146

has super-classes
Electron microscopy model IDc
Accessionc

Emission matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_3355

Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state.
has super-classes
Matrixc

ENCODE broad peak formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3614

has super-classes
ENCODE peak formatc

ENCODE narrow peak formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3613

Format that covers both the broad peak format and narrow peak format from ENCODE.
has super-classes
ENCODE peak formatc

ENCODE peak formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3612

Format that covers both the broad peak format and narrow peak format from ENCODE.
has super-classes
bed6c
has sub-classes
ENCODE broad peak formatc, ENCODE narrow peak formatc

Endocrinology and metabolismc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3407

has super-classes
Medicinec

Enrichment analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3501

Categories from a relevant ontology can be used. The input is typically a set of genes or other biological objects, possibly represented by their identifiers, and the output of the analysis is typically a ranked list of categories, each associated with a statistical metric of over-/under-representation within the studied data.
has super-classes
Analysisc
has outputop some Over-representation datac
has sub-classes
Chemical similarity enrichmentc, Gene-set enrichment analysisc

Ensembl gene IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1033

has super-classes
Accessionc
Gene IDc
Ensembl IDc

Ensembl gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1603

has super-classes
deprecated classc

Ensembl gene tree IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3270

has super-classes
Phylogenetic tree IDc
Accessionc
Ensembl IDc

Ensembl IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2610

has super-classes
Accessionc
Identifier (hybrid)c
has sub-classes
Ensembl gene IDc, Ensembl gene tree IDc, Ensembl protein IDc, Ensembl transcript IDc

Ensembl ID ("Ornithorhynchus anatinus")c back to ToC or Class ToC

IRI: http://edamontology.org/data_2690

has super-classes
deprecated classc

Ensembl ID ('Bos taurus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2672

has super-classes
deprecated classc

Ensembl ID ('Canis familiaris')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2673

has super-classes
deprecated classc

Ensembl ID ('Cavia porcellus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2674

has super-classes
deprecated classc

Ensembl ID ('Ciona intestinalis')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2675

has super-classes
deprecated classc

Ensembl ID ('Ciona savignyi')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2676

has super-classes
deprecated classc

Ensembl ID ('Danio rerio')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2677

has super-classes
deprecated classc

Ensembl ID ('Dasypus novemcinctus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2678

has super-classes
deprecated classc

Ensembl ID ('Echinops telfairi')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2679

has super-classes
deprecated classc

Ensembl ID ('Erinaceus europaeus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2680

has super-classes
deprecated classc

Ensembl ID ('Felis catus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2681

has super-classes
deprecated classc

Ensembl ID ('Gallus gallus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2682

has super-classes
deprecated classc

Ensembl ID ('Gasterosteus aculeatus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2683

has super-classes
deprecated classc

Ensembl ID ('Homo sapiens')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2684

has super-classes
deprecated classc

Ensembl ID ('Loxodonta africana')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2685

has super-classes
deprecated classc

Ensembl ID ('Macaca mulatta')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2686

has super-classes
deprecated classc

Ensembl ID ('Monodelphis domestica')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2687

has super-classes
deprecated classc

Ensembl ID ('Mus musculus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2688

has super-classes
deprecated classc

Ensembl ID ('Myotis lucifugus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2689

has super-classes
deprecated classc

Ensembl ID ('Oryctolagus cuniculus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2691

has super-classes
deprecated classc

Ensembl ID ('Oryzias latipes')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2692

has super-classes
deprecated classc

Ensembl ID ('Otolemur garnettii')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2693

has super-classes
deprecated classc

Ensembl ID ('Pan troglodytes')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2694

has super-classes
deprecated classc

Ensembl ID ('Rattus norvegicus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2695

has super-classes
deprecated classc

Ensembl ID ('Spermophilus tridecemlineatus')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2696

has super-classes
deprecated classc

Ensembl ID ('Takifugu rubripes')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2697

has super-classes
deprecated classc

Ensembl ID ('Tupaia belangeri')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2698

has super-classes
deprecated classc

Ensembl ID ('Xenopus tropicalis')c back to ToC or Class ToC

IRI: http://edamontology.org/data_2699

has super-classes
deprecated classc

Ensembl ID (Homo sapiens)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2671

has super-classes
deprecated classc

Ensembl protein IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2398

has super-classes
Accessionc
Ensembl IDc
Protein accessionc

Ensembl transcript IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2725

has super-classes
Accessionc
Ensembl IDc
Transcript IDc

Ensembl variation file formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3499

has super-classes
Textual formatc
Sequence variation annotation formatc

Entity collection identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0980

has super-classes
deprecated classc

Entity feature identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0979

has super-classes
deprecated classc

Entity identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0974

has super-classes
deprecated classc

Enumerated file namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1058

has super-classes
File namec

Environmental information processing pathway reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1658

has super-classes
deprecated classc

Environmental information processing pathwaysc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3529

has super-classes
deprecated classc

Environmental sciencec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3855

has super-classes
Biologyc

ENZYME enzyme report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2323

has super-classes
deprecated classc

Enzyme IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2321

has super-classes
Enzyme identifierc
Protein accessionc
has sub-classes
EC numberc, Enzyme ID (BioCyc)c, Enzyme ID (CAZy)c, Enzyme ID (MEROPS)c, REBASE enzyme numberc

Enzyme ID (BioCyc)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2107

has super-classes
Accessionc
BioCyc IDc
Enzyme IDc

Enzyme ID (CAZy)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2702

has super-classes
Accessionc
Enzyme IDc

Enzyme ID (MEROPS)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2629

has super-classes
Accessionc
Enzyme IDc

Enzyme identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1010

has super-classes
Protein identifierc
has sub-classes
Enzyme IDc, Enzyme namec

Enzyme kinetics calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0334

has super-classes
Protein property calculationc
has outputop some Enzyme kinetics datac
has topicop some Enzymesc

Enzyme kinetics datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2024

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Protein propertyc
Reaction datac
has sub-classes
Hanes Woolf plotc, Kmc, Michaelis Menten plotc, Vmaxc

Enzyme kinetics report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2027

has super-classes
Format (by type of data)c
is format ofop some Enzyme kinetics datac
has sub-classes
findkmc

Enzyme namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1012

has super-classes
Protein namec
Enzyme identifierc
has sub-classes
Restriction enzyme namec

Enzyme reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1509

has super-classes
deprecated classc

Enzymesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0821

has super-classes
Proteinsc

EPD IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2386

has super-classes
Accessionc
Promoter IDc

Epigeneticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3295

This includes sub-topics such as histone modification and DNA methylation (methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.)
has super-classes
Geneticsc
has sub-classes
Epigenomicsc

Epigenomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3173

Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation.
has super-classes
Genomicsc
Epigeneticsc

Epitope mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0416

Epitope mapping is commonly done during vaccine design.
has super-classes
Mappingc
Protein feature detectionc
has topicop some Immunologyc

Epitope mapping (MHC Class I)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0423

has super-classes
deprecated classc

Epitope mapping (MHC Class II)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0424

has super-classes
deprecated classc

EPSc back to ToC or Class ToC

IRI: http://edamontology.org/format_3466

has super-classes
PSc

Errorc back to ToC or Class ToC

IRI: http://edamontology.org/data_2192

has super-classes
deprecated classc

Essential dynamicsc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3891

Principal Component Analysis (PCA) is a multivariate statistical analysis to obtain collective variables and reduce the dimensionality of the system.
has super-classes
Simulation analysisc
Nucleic acid structure analysisc

EST accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2728

has super-classes
Clone IDc
has sub-classes
COGEME EST IDc, COGEME unisequence IDc, MaizeDB IDc, dbEST accessionc

EST and cDNA sequence analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0317

For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts.
has super-classes
deprecated classc

EST assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0526

Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification.
has super-classes
Sequence assemblyc

est2genome formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1316

has super-classes
Gene annotation formatc
Textual formatc

Eukaryotesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2818

The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes.
has super-classes
deprecated classc

Evidencec back to ToC or Class ToC

IRI: http://edamontology.org/data_2042

has super-classes
Datac

Evolutionary biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3299

has super-classes
Biologyc
has sub-classes
Molecular evolutionc, Phenomicsc, Phylogenyc, Taxonomyc

Exactly 1c back to ToC or Class ToC

IRI: http://edamontology.org/data_2177

has super-classes
deprecated classc

Exactly 2c back to ToC or Class ToC

IRI: http://edamontology.org/data_2179

has super-classes
deprecated classc

Exome assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3229

has super-classes
Sequence assemblyc

Exome sequencingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3676

Exome sequencing is considered a cheap alternative to whole genome sequencing.
has super-classes
Sequencingc

Exonic splicing enhancer predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0446

An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA.
has super-classes
Promoter predictionc
has topicop some Gene structurec

Exonsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2397

has super-classes
deprecated classc

EXPc back to ToC or Class ToC

IRI: http://edamontology.org/format_1631

has super-classes
Textual formatc
Sequence assembly format (text)c

Experiment annotation formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3167

has super-classes
Format (by type of data)c
is format ofop some Protocolc
has sub-classes
COMBINE OMEXc, GCDMLc, GelMLc, ISA-TABc, Microarray experiment data formatc, PRIDE XMLc, SED-MLc, qcMLc, spMLc

Experiment annotation IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1078

has super-classes
Identifier (by type of data)c
is identifier ofop some Protocolc
has sub-classes
ArrayExpress accession numberc, CleanEx dataset codec, Gene Expression Atlas Experiment IDc, PRIDE experiment accession numberc, ProteomeXchange IDc

Experiment report (genotyping)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2381

has super-classes
deprecated classc

Experimental datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2028

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
deprecated classc

Experimental data (proteomics)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2838

has super-classes
deprecated classc

Experimental design and studiesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3678

has super-classes
Topicc
has sub-classes
Animal studyc, GWAS studyc, Preclinical and clinical studiesc

Experimental measurementc back to ToC or Class ToC

IRI: http://edamontology.org/data_3108

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
Datac
has sub-classes
Cultivation parameterc, Mass spectrometry datac, Morphology parameterc, Physiology parameterc, Protein interaction raw datac, Protein structure raw datac, RH scoresc, Raw microarray datac, Sequence tracec, Volume mapc

Expressed gene listc back to ToC or Class ToC

IRI: http://edamontology.org/data_2579

has super-classes
deprecated classc

Expression analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2495

has super-classes
Analysisc
has topicop some Gene expressionc
has sub-classes
Expression data visualisationc, Expression profile comparisonc, Expression profile pathway mappingc, Gene expression QTL analysisc, Gene regulatory network analysisc, Gene regulatory network predictionc, Gene-set enrichment analysisc, RNA-Seq analysisc, miRNA expression analysisc

Expression correlation analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3463

has super-classes
Expression profile comparisonc
Correlationc

Expression datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2603

has super-classes
Datac
has topicop some Gene expressionc
has sub-classes
Clustered expression profilesc, Gene expression matrixc, Gene expression profilec, Microarray hybridisation datac, Microarray metadatac, Microarray spots imagec

Expression data visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0571

has super-classes
Visualisationc
Expression analysisc
has inputop some Microarray hybridisation datac
has sub-classes
Clustering profile plottingc, Dendrogram visualisationc, Heat map generationc, Proximity map plottingc, Treemap visualisationc

Expression profile clusteringc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0313

has super-classes
Expression profile comparisonc
Clusteringc
has outputop some Processed microarray datac

Expression profile comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0315

has super-classes
Expression analysisc
has sub-classes
Expression correlation analysisc, Expression profile clusteringc

Expression profile pathway mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0533

has super-classes
Mappingc
Expression analysisc
Pathway analysisc
has outputop some Pathway or network reportc

Expression signalsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3123

has super-classes
deprecated classc

Family namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2732

has super-classes
Taxonc

Family name (virus)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2734

has super-classes
deprecated classc

FASTAc back to ToC or Class ToC

IRI: http://edamontology.org/format_1929

has super-classes
FASTA-like (text)c
Alignment format (text)c

FASTA search results formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1332

This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.)
has super-classes
Database hits (sequence) formatc
Textual formatc

FASTA-alnc back to ToC or Class ToC

IRI: http://edamontology.org/format_1984

has super-classes
FASTA-like (text)c
Alignment format (text)c

FASTA-HTMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_2310

has super-classes
HTMLc
FASTA-likec

FASTA-likec back to ToC or Class ToC

IRI: http://edamontology.org/format_2546

This concept may be used for the many non-standard FASTA-like formats.
has super-classes
Sequence record formatc
has sub-classes
FASTA-HTMLc, FASTA-like (text)c

FASTA-like (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2200

This concept may also be used for the many non-standard FASTA-like formats.
has super-classes
Textual formatc
FASTA-likec
has sub-classes
A2Mc, FASTAc, FASTA-alnc, HMMER-alnc, NCBI formatc, Pearson formatc, XMFAc, csfastac, dbidc, giFASTA formatc

FASTGc back to ToC or Class ToC

IRI: http://edamontology.org/format_3823

It is called FASTG, like FASTA, but the G stands for ‘graph’.
has super-classes
Textual formatc
Sequence assembly format (text)c

FASTQc back to ToC or Class ToC

IRI: http://edamontology.org/format_1930

has super-classes
FASTQ-like format (text)c

FASTQ-illuminac back to ToC or Class ToC

IRI: http://edamontology.org/format_1931

has super-classes
FASTQ-like format (text)c
has sub-classes
qualilluminac

FASTQ-like formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2545

This concept may be used for non-standard FASTQ short read-like formats.
has super-classes
Sequence trace formatc
has sub-classes
FASTQ-like format (text)c

FASTQ-like format (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2182

This concept may be used for non-standard FASTQ short read-like formats.
has super-classes
Textual formatc
FASTQ-like formatc
has sub-classes
FASTQc, FASTQ-illuminac, FASTQ-sangerc, FASTQ-solexac, qualc

FASTQ-sangerc back to ToC or Class ToC

IRI: http://edamontology.org/format_1932

has super-classes
FASTQ-like format (text)c

FASTQ-solexac back to ToC or Class ToC

IRI: http://edamontology.org/format_1933

has super-classes
FASTQ-like format (text)c
has sub-classes
qualsolexac

Fate mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1713

has super-classes
Imagec
has topicop some Embryologyc

Feature extractionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3937

has super-classes
Dimensionality reductionc
has topicop some Proteomicsc
has inputop some Mass spectrumc

Feature selectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3936

has super-classes
Dimensionality reductionc
has inputop some Mass spectrumc
has topicop some Proteomicsc

Feature tablec back to ToC or Class ToC

IRI: http://edamontology.org/data_1270

has super-classes
Sequence featuresc

Feature table processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2453

has super-classes
deprecated classc

Feature table queryc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0255

has super-classes
deprecated classc

featureXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3833

has super-classes
XMLc
Mass spectrometry data formatc

FF parameter formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3884

Many different file formats exist describing force field parameters. Tipically, each MD package or simulation software works with their own implementation (e.g. GROMACS itp, CHARMM rtf, AMBER off / frcmod).
has super-classes
Format (by type of data)c
is format ofop some Topology datac
has sub-classes
AMBER frcmodc, AMBER offc, GROMACS itpc

Fickett testcode plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_2160

has super-classes
Plotc

FIG IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2737

A FIG ID consists of four parts: a prefix, genome id, locus type and id number.
has super-classes
Accessionc
Gene IDc

File base namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1060

A file base name is the file name stripped of its directory specification and extension.
has super-classes
File namec

File format namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2129

has super-classes
Namec
Format identifierc
has sub-classes
OBO file format namec

File namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1050

has super-classes
Namec
has sub-classes
Enumerated file namec, File base namec, File name extensionc

File name extensionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1059

A file extension is the characters appearing after the final '.' in the file name.
has super-classes
File namec

Filteringc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3695

has super-classes
Data handlingc

findkmc back to ToC or Class ToC

IRI: http://edamontology.org/format_1582

has super-classes
Enzyme kinetics report formatc
Textual formatc

Fingerprintc back to ToC or Class ToC

IRI: http://edamontology.org/data_1365

has super-classes
Position-specific scoring matrixc

Fishc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0210

has super-classes
deprecated classc

fitch programc back to ToC or Class ToC

IRI: http://edamontology.org/format_1934

has super-classes
Textual formatc
Sequence record format (text)c

Fliesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0211

has super-classes
deprecated classc

Flow cell identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_3733

A flow cell is used to immobilise, amplify and sequence millions of molecules at once. In Illumina machines, a flowcell is composed of 8 "lanes" which allows 8 experiments in a single analysis.
has super-classes
Sequencing metadata namec

Fluxomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3955

The "fluxome" is the complete set of metabolic fluxes in a cell, and is a dynamic aspect of phenotype.
has super-classes
Omicsc

FlyBase gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1608

has super-classes
deprecated classc

FlyBase IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1089

has super-classes
Accessionc
Identifier (hybrid)c
has sub-classes
FlyBase primary identifierc, FlyBase secondary identifierc

FlyBase primary identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2112

has super-classes
FlyBase IDc

FlyBase secondary identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2174

Secondary identifier are used to handle entries that were merged with or split from other entries in the database.
has super-classes
FlyBase IDc

FMAc back to ToC or Class ToC

IRI: http://edamontology.org/data_1722

Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.
has super-classes
deprecated classc

FMA concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1182

Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.
has super-classes
Ontology concept IDc
Accessionc

Fold recognitionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0303

Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
has super-classes
Protein structure analysisc
Protein sequence analysisc
Alignmentc
Protein comparisonc
Protein feature detectionc
has sub-classes
Protein threadingc

Forcefield parameterisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3893

has super-classes
Modelling and simulationc
has topicop some Phylogenyc
has outputop some DNA substitution modelc

Forcefield parametersc back to ToC or Class ToC

IRI: http://edamontology.org/data_3871

has super-classes
Simulationc

Formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1915

The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.
has sub-classes
Binary formatc, Format (by type of data)c, HTMLc, JSONc, RDF formatc, Textual formatc, XMLc, YAMLc
is in domain of
is format ofop
is in range of
has formatop
is disjoint with
Datac, Operationc, Topicc, deprecated classc

Format (by type of data)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2350

This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches.
has super-classes
Formatc
has sub-classes
Alignment formatc, Annotated text formatc, Article formatc, Bibliographic reference formatc, Biodiversity data formatc, Biological pathway or network formatc, Biological pathway or network report formatc, Chemical data formatc, Chemical formula formatc, Data index formatc, Database hits (sequence) formatc, Dirichlet distribution formatc, Document formatc, Enzyme kinetics report formatc, Experiment annotation formatc, FF parameter formatc, Gene annotation formatc, Gene expression report formatc, Graph formatc, HMM emission and transition counts formatc, Image formatc, Individual genetic data formatc, Linked data formatc, Map formatc, Mass spectrometry data formatc, Matrix formatc, NLP formatc, NMR data formatc, Nucleic acid features (primers) formatc, Nucleic acid features (restriction sites) formatc, Ontology formatc, Phylogenetic character data formatc, Phylogenetic tree formatc, Phylogenetic tree report (tree distances) formatc, Protein domain classification formatc, Protein family report formatc, Protein interaction formatc, Protein report formatc, Protein secondary structure formatc, Protein structure report (quality evaluation) formatc, Query languagec, RNA annotation formatc, RNA secondary structure formatc, Raw microarray data formatc, Raw sequence formatc, Sequence assembly formatc, Sequence cluster formatc, Sequence distance matrix formatc, Sequence feature annotation formatc, Sequence features (repeats) formatc, Sequence motif formatc, Sequence profile formatc, Sequence quality report format (text)c, Sequence range formatc, Sequence record formatc, Sequence variation annotation formatc, Sequence-profile alignment formatc, Tertiary structure formatc, Text mining report formatc, Topology formatc, Trajectory formatc, Workflow formatc

Format detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3357

'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology.
has super-classes
Data handlingc
has outputop some Format identifierc
has inputop some Datac

Format identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_3358

has super-classes
Identifier (by type of data)c
has sub-classes
File format namec

Format validationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0336

has super-classes
Validationc

Formattingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0335

has super-classes
Data handlingc

Frameshift detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0265

Methods include sequence alignment (if related sequences are available) and word-based sequence comparison.
has super-classes
Sequencing error detectionc
Variant callingc
has topicop some Sequencingc

Free cysteine detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1830

A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal.
has super-classes
Protein cysteine and disulfide bond assignmentc

Freshwater biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3573

has super-classes
Biologyc

FSSP entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1581

has super-classes
deprecated classc

Full torsion angle calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1826

has super-classes
deprecated classc

Function analysisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1775

has super-classes
Computational biologyc
has sub-classes
Functional genomicsc

Functional clusteringc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3459

has super-classes
Sequence clusteringc
has topicop some Function analysisc

Functional genomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0085

has super-classes
Genomicsc
Function analysisc

Functional mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0486

This can involve characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).
has super-classes
deprecated classc

Functional profilingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0316

has super-classes
deprecated classc

Functional, regulatory and non-coding RNAc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0659

Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA).
has super-classes
RNAc
Gene structurec

Fungic back to ToC or Class ToC

IRI: http://edamontology.org/topic_0782

The resource may be specific to a fungus, a group of fungi or all fungi.
has super-classes
deprecated classc

Fungi annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2395

has super-classes
deprecated classc

Fungi annotation (anamorph)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2396

has super-classes
deprecated classc

G protein-coupled receptors (GPCR)c back to ToC or Class ToC

IRI: http://edamontology.org/topic_0151

has super-classes
deprecated classc

Gamma diversity datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3739

has super-classes
Biodiversity datac

Gap extension penaltyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1398

has super-classes
Gap penaltyc
has sub-classes
Terminal gap extension penaltyc

Gap extension penalty (float)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1407

has super-classes
deprecated classc

Gap extension penalty (integer)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1406

has super-classes
deprecated classc

Gap opening penaltyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1397

has super-classes
Gap penaltyc
has sub-classes
Terminal gap opening penaltyc

Gap opening penalty (float)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1405

has super-classes
deprecated classc

Gap opening penalty (integer)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1404

has super-classes
deprecated classc

Gap penaltyc back to ToC or Class ToC

IRI: http://edamontology.org/data_2137

has super-classes
Alignment score or penaltyc
has sub-classes
Gap extension penaltyc, Gap opening penaltyc, Gap separation penaltyc

Gap separation penaltyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1399

has super-classes
Gap penaltyc

Gap separation penalty (float)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1409

has super-classes
deprecated classc

Gap separation penalty (integer)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1408

has super-classes
deprecated classc

Gastroenterologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3409

has super-classes
Medicinec

GCDMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3163

has super-classes
XMLc
Experiment annotation formatc

GCGc back to ToC or Class ToC

IRI: http://edamontology.org/format_1935

GCG SSF (single sequence file) file format.
has super-classes
Textual formatc
GCG format variantc

GCG format variantc back to ToC or Class ToC

IRI: http://edamontology.org/format_3486

has super-classes
Textual formatc
Sequence record format (text)c
Alignment format (text)c
has sub-classes
GCGc, GCG MSFc, RSFc

GCG MSFc back to ToC or Class ToC

IRI: http://edamontology.org/format_1947

has super-classes
GCG format variantc

GCT/Res formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3709

has super-classes
Gene expression report formatc
Textual formatc

GDEc back to ToC or Class ToC

IRI: http://edamontology.org/format_3312

has super-classes
Textual formatc
Sequence record format (text)c

Gel IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2790

has super-classes
Identifier (by type of data)c
has sub-classes
Reference map name (SWISS-2DPAGE)c

GelMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3249

has super-classes
XMLc
Experiment annotation formatc

Gemini SQLite formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3622

has super-classes
Sequence variation annotation formatc
SQLite formatc

GENc back to ToC or Class ToC

IRI: http://edamontology.org/format_3812

has super-classes
Textual formatc
Sequence annotation track formatc

GenBank accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2292

has super-classes
EMBL/GenBank/DDBJ IDc
has sub-classes
dbEST accessionc

Genbank common namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1874

has super-classes
Organism namec

GenBank featurec back to ToC or Class ToC

IRI: http://edamontology.org/format_1981

has super-classes
deprecated classc

GenBank formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1936

has super-classes
GenBank-like format (text)c
Sequence feature table format (text)c

GenBank-HTMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_2532

has super-classes
HTMLc
GenBank-like formatc

GenBank-like formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2559

This concept may be used for the non-standard GenBank-like formats.
has super-classes
Sequence record formatc
has sub-classes
GenBank-HTMLc, GenBank-like format (text)c

GenBank-like format (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2205

This concept may be used for the non-standard GenBank-like text formats.
has super-classes
Textual formatc
GenBank-like formatc
has sub-classes
GenBank formatc, genpeptc

Gender medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3410

has super-classes
Medicinec

Gene and protein familiesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0623

A protein families database might include the classifier (e.g. a sequence profile) used to build the classification.
has super-classes
Proteinsc
Molecular geneticsc
has sub-classes
Immunoproteins and antigensc

Gene and transcript structure (report)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1300

has super-classes
deprecated classc

Gene annotation formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2031

has super-classes
Format (by type of data)c
is format ofop some Gene reportc
has sub-classes
OrthoXMLc, est2genome formatc

Gene classificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0917

has super-classes
deprecated classc

Gene clusterc back to ToC or Class ToC

IRI: http://edamontology.org/data_2198

has super-classes
deprecated classc

Gene cluster formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2175

has super-classes
deprecated classc

Gene component predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0426

Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
has super-classes
deprecated classc

Gene expressionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0203

This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on.
has super-classes
Molecular geneticsc
has sub-classes
Gene regulationc, Metatranscriptomicsc, RNA splicingc, Transcription factors and regulatory sitesc, Transcriptomicsc

Gene expression analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2410

has super-classes
deprecated classc

Gene expression and microarrayc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0629

has super-classes
deprecated classc

Gene Expression Atlas Experiment IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3568

has super-classes
Experiment annotation IDc

Gene expression data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3476

has super-classes
deprecated classc

Gene expression matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_3112

This combines data from all hybridisations.
has super-classes
Matrixc
Expression datac

Gene expression profilec back to ToC or Class ToC

IRI: http://edamontology.org/data_0928

has super-classes
Expression datac
has sub-classes
Sequence tag profilec

Gene expression profile analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0532

has super-classes
deprecated classc

Gene expression profile processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2435

has super-classes
deprecated classc

Gene expression profilingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0314

has super-classes
deprecated classc

Gene expression QTL analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3232

has super-classes
Expression analysisc

Gene expression report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2058

has super-classes
Format (by type of data)c
is format ofop some Expression datac
has sub-classes
CHPc, Cytoscape input file formatc, GCT/Res formatc, IDATc, ISA-TABc, Loomc, MAGE-MLc, MAGE-TABc, MTXc, Zarrc, celc, datc, rccc

Gene expression report IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1080

has super-classes
Identifier (by type of data)c
is identifier ofop some Processed microarray datac
has sub-classes
CleanEx entry namec, EMAGE IDc, GEO accession numberc, GermOnline IDc

Gene family reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3148

This includes reports on on gene homologues between species.
has super-classes
Nucleic acid reportc
has sub-classes
RNA family reportc

Gene features (coding region) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2159

has super-classes
deprecated classc

Gene features (exonic splicing enhancer)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1309

has super-classes
deprecated classc

Gene features (SECIS element)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1314

has super-classes
deprecated classc

Gene findingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0109

This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
has super-classes
deprecated classc

Gene functional annotationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3672

has super-classes
Sequence annotationc

Gene homology (report)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3269

has super-classes
deprecated classc

Gene IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2295

has super-classes
Gene identifierc
Locus IDc
has sub-classes
Blattner numberc, Ensembl gene IDc, FIG IDc, Gene ID (CGD)c, Gene ID (DictyBase)c, Gene ID (EcoGene)c, Gene ID (FlyBase)c, Gene ID (GeneDB)c, Gene ID (GeneFarm)c, Gene ID (Genolist)c, Gene ID (Gramene)c, Gene ID (HGNC)c, Gene ID (JCVI)c, Gene ID (KOME)c, Gene ID (MIPS)c, Gene ID (MfunGD)c, Gene ID (NCBI)c, Gene ID (PlasmoDB)c, Gene ID (SGD)c, Gene ID (SGN)c, Gene ID (VBASE2)c, Gene ID (VectorBase)c, Gene ID (Virginia microbial)c, Gene ID (WormBase)c, Gene ID (Xenbase)c, Gene ID (ZFIN)c, Gene ID (miRBase)c, HIX IDc, TAIR accession (gene)c, TIGR identifierc, iHOP symbolc, mFLJ/mKIAA numberc

Gene ID (CGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1031

has super-classes
Accessionc
Gene IDc

Gene ID (DictyBase)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1032

has super-classes
Accessionc
Gene IDc

Gene ID (ECK)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2297

has super-classes
Gene ID (EcoGene)c

Gene ID (EcoGene)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1795

has super-classes
Accessionc
Gene IDc
has sub-classes
Gene ID (ECK)c

Gene ID (FlyBase)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1796

has super-classes
Accessionc
Gene IDc

Gene ID (GeneDB Glossina morsitans)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1797

has super-classes
deprecated classc

Gene ID (GeneDB Leishmania major)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1798

has super-classes
deprecated classc

Gene ID (GeneDB Plasmodium falciparum)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1799

has super-classes
deprecated classc

Gene ID (GeneDB Schizosaccharomyces pombe)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1800

has super-classes
deprecated classc

Gene ID (GeneDB Trypanosoma brucei)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1801

has super-classes
deprecated classc

Gene ID (GeneDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1035

has super-classes
Accessionc
Gene IDc

Gene ID (GeneFarm)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1885

has super-classes
Accessionc
Gene IDc

Gene ID (Genolist)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2739

has super-classes
Accessionc
Gene IDc

Gene ID (Gramene)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1802

has super-classes
Accessionc
Gene IDc

Gene ID (HGNC)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2298

has super-classes
Accessionc
Gene IDc

Gene ID (JCVI)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2774

has super-classes
Accessionc
Gene IDc

Gene ID (KOME)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1907

has super-classes
Accessionc
Gene IDc

Gene ID (MfunGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2799

has super-classes
Accessionc
Gene IDc

Gene ID (MIPS Maize)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1887

has super-classes
deprecated classc

Gene ID (MIPS Medicago)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1888

has super-classes
deprecated classc

Gene ID (MIPS)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2285

has super-classes
Accessionc
Gene IDc

Gene ID (miRBase)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2642

has super-classes
Accessionc
Gene IDc

Gene ID (NCBI)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1027

has super-classes
RefSeq accessionc
Accessionc
Gene IDc

Gene ID (PlasmoDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1794

has super-classes
Accessionc
Gene IDc

Gene ID (SGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1034

has super-classes
Accessionc
Gene IDc
SGD IDc

Gene ID (SGN)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1804

has super-classes
Accessionc
Gene IDc

Gene ID (VBASE2)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2835

has super-classes
Accessionc
Gene IDc

Gene ID (VectorBase)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2759

has super-classes
Accessionc
Gene IDc

Gene ID (Virginia microbial)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1803

has super-classes
Accessionc
Gene IDc

Gene ID (WormBase)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1805

has super-classes
Accessionc
WormBase identifierc
Gene IDc

Gene ID (Xenbase)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2738

has super-classes
Accessionc
Gene IDc

Gene ID (ZFIN)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2643

has super-classes
Accessionc
Gene IDc

Gene identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1025

has super-classes
Identifier (by type of data)c
is identifier ofop some Gene reportc
has sub-classes
Gene IDc, Gene namec

Gene identifier (Entrez)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1030

has super-classes
deprecated classc

Gene identifier (NCBI RefSeq)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1028

has super-classes
deprecated classc

Gene identifier (NCBI UniGene)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1029

has super-classes
deprecated classc

Gene mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1285

has super-classes
Sequence mapc

Gene methylation analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3207

has super-classes
Methylation analysisc

Gene namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2299

has super-classes
Gene identifierc
Namec
has sub-classes
Gene symbolc

Gene name (AceView)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2296

has super-classes
deprecated classc

Gene name (Arabidopsis)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1890

has super-classes
deprecated classc

Gene name (ASPGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1783

has super-classes
deprecated classc

Gene name (Bacillus subtilis)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1793

has super-classes
deprecated classc

Gene name (CGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1784

has super-classes
deprecated classc

Gene name (CGSC)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1790

has super-classes
deprecated classc

Gene name (dictyBase)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1785

has super-classes
deprecated classc

Gene name (DragonDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1889

has super-classes
deprecated classc

Gene name (EcoGene primary)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1786

has super-classes
deprecated classc

Gene name (GeneFarm)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1892

has super-classes
deprecated classc

Gene name (Genolist)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2740

has super-classes
deprecated classc

Gene name (HGNC)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1791

has super-classes
deprecated classc

Gene name (HUGO)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2743

has super-classes
deprecated classc

Gene name (KEGG GENES)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2103

has super-classes
deprecated classc

Gene name (MaizeGDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1787

has super-classes
deprecated classc

Gene name (MGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1792

has super-classes
deprecated classc

Gene name (NCBI)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2300

has super-classes
deprecated classc

Gene name (SGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1788

has super-classes
deprecated classc

Gene name (TGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1789

has super-classes
deprecated classc

Gene orderc back to ToC or Class ToC

IRI: http://edamontology.org/data_3479

Such data are often used for genome rearrangement tools and phylogenetic tree labeling.
has super-classes
Matrixc

Gene predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2454

Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
has super-classes
Nucleic acid sequence analysisc
has topicop some Gene structurec
has outputop some Gene reportc
has sub-classes
Ab-initio gene predictionc, Coding region predictionc, Homology-based gene predictionc, Operon predictionc, SECIS element predictionc, Splicing analysisc, Transcriptional regulatory element predictionc, tRNA gene predictionc

Gene regulationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0204

has super-classes
Gene expressionc

Gene regulatory network analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1781

has super-classes
Expression analysisc
Network analysisc
has topicop some Molecular interactions, pathways and networksc

Gene regulatory network predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2437

has super-classes
Prediction and recognitionc
Expression analysisc
Network analysisc

Gene regulatory network processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2496

has super-classes
deprecated classc

Gene regulatory network reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2961

has super-classes
deprecated classc

Gene regulatory networksc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2846

has super-classes
deprecated classc

Gene reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0916

This includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s).
has super-classes
Nucleic acid reportc

Gene resourcesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2816

has super-classes
deprecated classc

Gene set testingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3224

has super-classes
deprecated classc

Gene structurec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0114

This incudes operons (operators, promoters and genes) from a bacterial genome. For example the operon leader and trailer gene, gene composition of the operon and associated information.
has super-classes
Molecular geneticsc
has sub-classes
Functional, regulatory and non-coding RNAc, Gene transcriptsc, Mobile genetic elementsc

Gene symbolc back to ToC or Class ToC

IRI: http://edamontology.org/data_1026

has super-classes
Gene namec

Gene symbol annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2768

has super-classes
deprecated classc

Gene synonymc back to ToC or Class ToC

IRI: http://edamontology.org/data_1806

has super-classes
deprecated classc

Gene transcript reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3134

This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).
has super-classes
Nucleic acid featuresc

Gene transcriptionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2399

has super-classes
deprecated classc

Gene transcriptsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3512

This includes Introns, and protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. Also expressed sequence tag (EST) or complementary DNA (cDNA) sequences.
has super-classes
RNAc
Gene structurec

Gene treec back to ToC or Class ToC

IRI: http://edamontology.org/data_3271

has super-classes
Phylogenetic treec

Gene tree constructionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0553

Gene trees can provide evidence for gene duplication events, as well as speciation events. Where sequences from different homologs are included in a gene tree, subsequent clustering of the orthologs can demonstrate evolutionary history of the orthologs.
has super-classes
Phylogenetic tree constructionc
has outputop some Gene reportc
has topicop some Phylogenomicsc

Gene-set enrichment analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2436

The Gene Ontology (GO) is typically used, the input is a set of Gene IDs, and the output of the analysis is typically a ranked list of GO concepts, each associated with a p-value.
has super-classes
Expression analysisc
Enrichment analysisc
has outputop some GO-term enrichment datac
has topicop some Function analysisc

Gene3D entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1572

has super-classes
deprecated classc

Gene3D IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1135

has super-classes
Accessionc
Protein family accessionc

GeneCards gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2329

has super-classes
deprecated classc

GeneDB gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1615

has super-classes
deprecated classc

GeneIlluminator gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1808

This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation.
has super-classes
deprecated classc

genePredc back to ToC or Class ToC

IRI: http://edamontology.org/format_3011

genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables.
has super-classes
Textual formatc
Sequence annotation track formatc

Generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3429

For non-analytical operations, see the 'Processing' branch.
has super-classes
Operationc
has sub-classes
3D profile generationc, 3D-1D scoring matrix generationc, Alignmentc, Bibliography generationc, Codon usage table generationc, Heat map generationc, Phylogenetic tree constructionc, Probabilistic data generationc, RNA secondary structure alignmentc, RNA structure covariance model generationc, Scaffoldingc, Sequence checksum generationc, Sequence clusteringc, Sequence distance matrix generationc, Sequence generationc, Sequence profile generationc

Genes and proteins resourcesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3078

has super-classes
deprecated classc

geneseqc back to ToC or Class ToC

IRI: http://edamontology.org/format_2186

has super-classes
EMBL-like (text)c

GeneSNP IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2805

has super-classes
Accessionc
Sequence variation IDc

Genetic codec back to ToC or Class ToC

IRI: http://edamontology.org/data_1598

A genetic code need not include detailed codon usage information.
has super-classes
Codon usage datac

Genetic code identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2127

has super-classes
Identifier (by type of data)c
is identifier ofop some Genetic codec
has sub-classes
Genetic code namec, NCBI genetic code IDc

Genetic code namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2128

has super-classes
Namec
Genetic code identifierc

Genetic code predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0489

has super-classes
Codon usage analysisc
Prediction and recognitionc
has outputop some Genetic codec

Genetic codes and codon usagec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0107

has super-classes
deprecated classc

Genetic engineeringc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3912

has super-classes
Geneticsc
Biotechnologyc

Genetic information processing pathway reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1657

has super-classes
deprecated classc

Genetic information processing pathwaysc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3530

has super-classes
deprecated classc

Genetic linkage reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0927

This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome).
has super-classes
Nucleic acid reportc

Genetic mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1278

A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms.
has super-classes
Mapc
has sub-classes
DNA transduction mapc, Haplotype mapc, QTL mapc

Genetic mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0282

This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs).
has super-classes
Linkage analysisc
DNA mappingc
has outputop some Genetic mapc
has sub-classes
Haplotype mappingc

Genetic mapping and linkagec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0796

has super-classes
deprecated classc

Genetic marker identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0281

A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc.
has super-classes
deprecated classc

Genetic organisationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3062

has super-classes
deprecated classc

Genetic variationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0199

has super-classes
Molecular geneticsc
has sub-classes
DNA mutationc, DNA polymorphismc, DNA structural variationc

Genetic variation analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3197

Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.
has super-classes
Analysisc
has sub-classes
Collapsing methodsc, Genotypingc, Reference identificationc, Structural variation detectionc, Variant callingc, Variant classificationc, Variant pattern analysisc, Variant prioritisationc

Geneticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3053

has super-classes
Biologyc
has sub-classes
Epigeneticsc, Genetic engineeringc, Genotype and phenotypec, Human geneticsc, Immunogeneticsc, Molecular geneticsc, Population geneticsc

Genome accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2903

has super-classes
Genome identifierc
has sub-classes
GenomeReviews IDc, NCBI Genome Project IDc, NCBI genome accessionc

Genome alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3182

has super-classes
Sequence alignmentc
Genome analysisc

Genome analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3918

has super-classes
Nucleic acid sequence analysisc
has topicop some Genomicsc
has sub-classes
Genome alignmentc, Genome annotationc, Genome assemblyc, Genome comparisonc, Genome feature comparisonc, Genome indexingc, Genome visualisationc, Whole genome methylation analysisc

Genome annotationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0362

has super-classes
Sequence annotationc
Genome analysisc

Genome annotationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0222

has super-classes
deprecated classc

Genome assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0525

has super-classes
Sequence assemblyc
Genome analysisc

Genome assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3440

has super-classes
deprecated classc

Genome build identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2340

has super-classes
Genome identifierc

Genome comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3209

has super-classes
Sequence comparisonc
Genome analysisc

Genome feature comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3194

Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on.
has super-classes
Sequence feature comparisonc
Genome analysisc

Genome identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2749

has super-classes
Identifier (by type of data)c
has sub-classes
Genome accessionc, Genome build identifierc

Genome indexc back to ToC or Class ToC

IRI: http://edamontology.org/data_3210

Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment.
has super-classes
Data indexc

Genome indexingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3211

Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. A suffix array consists of the lexicographically sorted list of suffixes of a genome.
has super-classes
Indexingc
Genome analysisc
has outputop some Genome indexc

Genome indexing (Burrows-Wheeler)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3212

The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm.
has super-classes
deprecated classc

Genome indexing (suffix arrays)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3213

A suffix array consists of the lexicographically sorted list of suffixes of a genome.
has super-classes
deprecated classc

Genome mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1288

has super-classes
Sequence mapc

Genome reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2711

has super-classes
Organism reportc

Genome resequencingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3923

Ultra-deep sequencing
has super-classes
Sequencingc

Genome version informationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2041

has super-classes
deprecated classc

Genome visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3208

has super-classes
Sequence visualisationc
Genome analysisc

GenomeReviews IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2751

has super-classes
Accessionc
Genome accessionc

Genomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0622

has super-classes
Omicsc
has sub-classes
Comparative genomicsc, Epigenomicsc, Functional genomicsc, Metagenomicsc, Paleogenomicsc, Pharmacogenomicsc, Phylogenomicsc, Population genomicsc, Proteogenomicsc, Structural genomicsc, Transcriptomicsc

Genotype and phenotypec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0625

has super-classes
Geneticsc
has sub-classes
Molecular evolutionc, Phenomicsc, Quantitative geneticsc

Genotype and phenotype annotation formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2059

has super-classes
deprecated classc

Genotype and phenotype annotation IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1081

has super-classes
Identifier (by type of data)c
is identifier ofop some Genotype/phenotype reportc
has sub-classes
HGVbase IDc, OMIM IDc

Genotype and phenotype datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2602

has super-classes
deprecated classc

Genotype experiment IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2382

has super-classes
Identifier (by type of data)c
is identifier ofop some Protocolc
has sub-classes
EGA accessionc

Genotype/phenotype reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0920

has super-classes
Reportc
has sub-classes
Disease reportc, Pharmacogenomic test reportc

Genotypingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3196

Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on.
has super-classes
Genetic variation analysisc
has sub-classes
Multilocus sequence typingc

Genotyping experimentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3516

has super-classes
Laboratory techniquesc

genpeptc back to ToC or Class ToC

IRI: http://edamontology.org/format_1937

Currently identical to refseqp format
has super-classes
GenBank-like format (text)c

Genus namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1870

has super-classes
Taxonc

Genus name (virus)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2733

has super-classes
deprecated classc

GEO accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1147

has super-classes
Gene expression report IDc
Accessionc

Geographic locationc back to ToC or Class ToC

IRI: http://edamontology.org/data_3720

has super-classes
Isolation reportc

Geotemporal metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_3105

has super-classes
deprecated classc

Geriatric medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3399

has super-classes
Medicinec

GermOnline IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1148

has super-classes
Gene expression report IDc
Accessionc

GFFc back to ToC or Class ToC

IRI: http://edamontology.org/format_2305

has super-classes
Sequence feature table format (text)c
Textual formatc
has sub-classes
GFF2c, GFF3c, GTFc

GFF2c back to ToC or Class ToC

IRI: http://edamontology.org/format_1974

has super-classes
GFFc
has sub-classes
GFF2-seqc

GFF2-seqc back to ToC or Class ToC

IRI: http://edamontology.org/format_1938

has super-classes
GFF2c
Sequence record format (text)c

GFF3c back to ToC or Class ToC

IRI: http://edamontology.org/format_1975

has super-classes
GFFc
has sub-classes
GFF3-seqc, GVFc, mirGFF3c

GFF3-seqc back to ToC or Class ToC

IRI: http://edamontology.org/format_1939

has super-classes
GFF3c
Sequence record format (text)c

GI numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_2314

Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.
has super-classes
Accessionc
Sequence accession (hybrid)c
has sub-classes
GI number (protein)c

GI number (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2327

Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.
has super-classes
GI numberc

GIFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3467

has super-classes
Binary formatc

giFASTA formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1940

has super-classes
FASTA-like (text)c

Global alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0496

Global alignment methods identify similarity across the entire length of the sequences.
has super-classes
Sequence alignmentc

Global structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0510

Global alignment methods identify similarity across the entire structures.
has super-classes
Structure alignmentc

GlobPlot domain imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1294

has super-classes
deprecated classc

GlycoMap IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2752

has super-classes
Accessionc
Carbohydrate accessionc

GlycomeDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2664

has super-classes
Accessionc
Carbohydrate accessionc

GMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3822

has super-classes
Biological pathway or network formatc
Textual formatc

GOc back to ToC or Class ToC

IRI: http://edamontology.org/data_1716

has super-classes
deprecated classc

GO (biological process)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1727

Data Type is an enumerated string.
has super-classes
deprecated classc

GO (cellular component)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1729

Data Type is an enumerated string.
has super-classes
deprecated classc

GO (molecular function)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1728

Data Type is an enumerated string.
has super-classes
deprecated classc

GO concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1176

has super-classes
Ontology concept IDc
Accessionc
has sub-classes
GO concept ID (biological process)c, GO concept ID (cellular component)c, GO concept ID (molecular function)c

GO concept ID (biological process)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2582

has super-classes
GO concept IDc

GO concept ID (cellular component)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2705

has super-classes
GO concept IDc

GO concept ID (molecular function)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2583

has super-classes
GO concept IDc

GO concept namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2581

has super-classes
deprecated classc

GO concept name (biological process)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3026

has super-classes
deprecated classc

GO concept name (cellular component)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2584

has super-classes
deprecated classc

GO concept name (molecular function)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3027

has super-classes
deprecated classc

GO-term enrichment datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3754

has super-classes
Over-representation datac
has topicop some Function analysisc

GPCR analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0473

has super-classes
deprecated classc

GPCR classificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2456

has super-classes
deprecated classc

GPCR coupling selectivity predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2457

has super-classes
deprecated classc

GPCR predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0472

has super-classes
deprecated classc

GPMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3657

has super-classes
Biological pathway or network formatc
XMLc

GPRc back to ToC or Class ToC

IRI: http://edamontology.org/format_3829

has super-classes
Textual formatc
Raw microarray data formatc

Gramene gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1609

has super-classes
deprecated classc

Gramene identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2915

has super-classes
Sequence accession (protein)c
Accessionc
has sub-classes
Gramene primary identifierc, Gramene secondary identifierc

Gramene primary identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1102

has super-classes
Gramene identifierc

Gramene secondary identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2293

has super-classes
Gramene identifierc

Graph formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3617

has super-classes
Format (by type of data)c
has sub-classes
K-mer countgraphc, xgmmlc

GROMACS itpc back to ToC or Class ToC

IRI: http://edamontology.org/format_3883

GROMACS itp files are used also to define position restrictions on the molecule, or to define the force field parameters for a particular ligand.
has super-classes
Tertiary structure formatc
Textual formatc
Topology formatc
FF parameter formatc

GROMACS topc back to ToC or Class ToC

IRI: http://edamontology.org/format_3880

There is currently no tool available for conversion between GROMACS topology format and other formats, due to the internal differences in both approaches. There is, however, a method to convert small molecules parameterized with AMBER force-field into GROMACS format, allowing simulations of these systems with GROMACS MD package.
has super-classes
Tertiary structure formatc
Textual formatc
Topology formatc

GSuitec back to ToC or Class ToC

IRI: http://edamontology.org/format_3775

has super-classes
Sequence feature annotation formatc
Textual formatc

GTFc back to ToC or Class ToC

IRI: http://edamontology.org/format_2306

has super-classes
GFFc

GTrackc back to ToC or Class ToC

IRI: http://edamontology.org/format_3164

has super-classes
Sequence feature table format (text)c
Textual formatc
Sequence annotation track formatc

GVFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3019

has super-classes
GFF3c
Sequence variation annotation formatc

GWAS reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3231

has super-classes
deprecated classc

GWAS studyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3517

has super-classes
Experimental design and studiesc

Gynaecology and obstetricsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3411

has super-classes
Medicinec

Haematologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3408

has super-classes
Medicinec

HAMAP IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2766

has super-classes
Accessionc
Protein family accessionc

Hanes Woolf plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_2026

has super-classes
Enzyme kinetics datac

Haplotype mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1863

has super-classes
Genetic mapc

Haplotype mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0487

Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimisation such as minimum error correction (MEC) model, expectation-maximisation algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).
has super-classes
Genetic mappingc
has outputop some Haplotype mapc

HDFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3873

HDF is currently supported by many commercial and non-commercial software platforms such as Java, MATLAB/Scilab, Octave, Python and R.
has super-classes
Binary formatc
Trajectory format (binary)c

HDF5c back to ToC or Class ToC

IRI: http://edamontology.org/format_3590

An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. Currently supported by the Python MDTraj package.
has super-classes
Binary formatc
Trajectory format (binary)c
has sub-classes
Loomc

Heat mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1636

has super-classes
Imagec
Clustered expression profilesc

Heat map generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0531

The heat map usually uses a coloring scheme to represent expression values. They can show how quantitative measurements were influenced by experimental conditions.
has super-classes
Expression data visualisationc
Generationc
has outputop some Heat mapc

Helical netc back to ToC or Class ToC

IRI: http://edamontology.org/data_2163

Useful for highlighting amphipathicity and other properties.
has super-classes
Protein secondary structure imagec

Helical wheelc back to ToC or Class ToC

IRI: http://edamontology.org/data_2162

has super-classes
Protein secondary structure imagec

Helical wheel drawingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2485

has super-classes
Structure visualisationc
has outputop some Helical wheelc

hennig86c back to ToC or Class ToC

IRI: http://edamontology.org/format_1941

has super-classes
Textual formatc
Sequence record format (text)c

Hepatic and biliary medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3412

has super-classes
Medicinec

HET group detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1846

A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output.
has super-classes
deprecated classc

HET group dictionary entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1705

has super-classes
Chemical data formatc
Textual formatc

HET group namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1005

has super-classes
Compound namec

Heterogen annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2240

has super-classes
deprecated classc

HGMD IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3265

has super-classes
Accessionc
Sequence variation IDc

HGNCc back to ToC or Class ToC

IRI: http://edamontology.org/data_1718

has super-classes
deprecated classc

HGNC concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1178

has super-classes
Ontology concept IDc
Accessionc

HGNC vocabularyc back to ToC or Class ToC

IRI: http://edamontology.org/data_0832

has super-classes
deprecated classc

HGVbase entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1624

has super-classes
deprecated classc

HGVbase IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1151

has super-classes
Genotype and phenotype annotation IDc
Accessionc

Hidden Markov modelc back to ToC or Class ToC

IRI: http://edamontology.org/data_1364

has super-classes
Mathematical modelc
has sub-classes
Profile HMMc

Hidden Markov modelc back to ToC or Class ToC

IRI: http://edamontology.org/data_3356

has super-classes
deprecated classc

Hidden Markov model formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2072

has super-classes
Sequence profile formatc
is format ofop some Hidden Markov modelc
has sub-classes
HMMER formatc, MEME background Markov modelc

Hierarchyc back to ToC or Class ToC

IRI: http://edamontology.org/data_2589

has super-classes
Datac

Hierarchy identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2590

has super-classes
deprecated classc

High-throughput sequencingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2842

has super-classes
deprecated classc

Histogramc back to ToC or Class ToC

IRI: http://edamontology.org/data_3905

has super-classes
Plotc

HIT IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2770

has super-classes
Accessionc
Transcript IDc

Hit sort orderc back to ToC or Class ToC

IRI: http://edamontology.org/data_1695

has super-classes
deprecated classc

HIVDB entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1625

has super-classes
deprecated classc

HIVDB identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1152

has super-classes
deprecated classc

HIX IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2771

has super-classes
Accessionc
Gene IDc

HMM emission and transition countsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1348

has super-classes
deprecated classc

HMM emission and transition counts formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2075

has super-classes
Format (by type of data)c
is format ofop some Emission matrixc
is format ofop some Transition matrixc
has sub-classes
HMMER emission and transitionc

HMMER Dirichlet priorc back to ToC or Class ToC

IRI: http://edamontology.org/format_1349

has super-classes
Dirichlet distribution formatc
Textual formatc

HMMER emission and transitionc back to ToC or Class ToC

IRI: http://edamontology.org/format_1351

has super-classes
HMM emission and transition counts formatc
Textual formatc

HMMER formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1370

has super-classes
Hidden Markov model formatc
Textual formatc
has sub-classes
HMMER2c, HMMER3c

HMMER hidden Markov model IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1118

has super-classes
Sequence profile IDc
Accessionc
is identifier ofop some Hidden Markov modelc

HMMER NULL hidden Markov modelc back to ToC or Class ToC

IRI: http://edamontology.org/data_1371

has super-classes
deprecated classc

HMMER profile alignment (HMM versus sequences)c back to ToC or Class ToC

IRI: http://edamontology.org/format_1422

has super-classes
Sequence-profile alignment formatc
Textual formatc

HMMER profile alignment (sequences versus HMMs)c back to ToC or Class ToC

IRI: http://edamontology.org/format_1421

has super-classes
Sequence-profile alignment formatc
Textual formatc

HMMER synthetic sequences setc back to ToC or Class ToC

IRI: http://edamontology.org/data_1237

has super-classes
deprecated classc

HMMER-alnc back to ToC or Class ToC

IRI: http://edamontology.org/format_1391

has super-classes
FASTA-like (text)c
Textual formatc
Alignment format (text)c

HMMER2c back to ToC or Class ToC

IRI: http://edamontology.org/format_3328

has super-classes
HMMER formatc

HMMER3c back to ToC or Class ToC

IRI: http://edamontology.org/format_3329

has super-classes
HMMER formatc

Homology modellingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0175

has super-classes
deprecated classc

Homology-based gene predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3663

has super-classes
Gene predictionc

Hopp and Woods plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_2957

has super-classes
Peptide immunogenicity datac
Plotc

Hopp and Woods plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2932

has super-classes
deprecated classc

HPA antibody idc back to ToC or Class ToC

IRI: http://edamontology.org/data_2772

has super-classes
Accessionc
Protein accessionc

HSAMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3845

has super-classes
XMLc
Alignment format (XML)c

hsspc back to ToC or Class ToC

IRI: http://edamontology.org/format_1455

has super-classes
Protein secondary structure formatc
Textual formatc

HTMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_2331

has super-classes
Formatc
is format ofop some Reportc
has sub-classes
EMBL-HTMLc, FASTA-HTMLc, GenBank-HTMLc, MHTMLc, iHOP formatc
is disjoint with
Binary formatc

Human biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2815

has super-classes
Biologyc

Human diseasec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0803

has super-classes
deprecated classc

Human geneticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3574

has super-classes
Geneticsc

HumanCyc entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1649

has super-classes
deprecated classc

Hybrid sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1385

Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA.
has super-classes
Sequence alignmentc

Hybrid sequence alignment (pair)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1388

has super-classes
deprecated classc

Hybrid sequence alignment constructionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0293

has super-classes
deprecated classc

Hydrogen bond calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0394

The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy.
has super-classes
Residue interaction calculationc
has outputop some Protein hydrogen bondsc

Hydrogen bond calculation (inter-residue)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2491

has super-classes
deprecated classc

ibdc back to ToC or Class ToC

IRI: http://edamontology.org/format_3839

imzML data is recorded in 2 files: '.imzXML' is a metadata XML file based on mzML by HUPO-PSI, and '.ibd' is a binary file containing the mass spectra.
has super-classes
Binary formatc
Mass spectrometry data formatc

ICD identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2611

has super-classes
Disease IDc
Accessionc
is identifier ofop some Disease reportc

ID listc back to ToC or Class ToC

IRI: http://edamontology.org/data_2872

has super-classes
Data referencec

ID mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3282

The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence.
has super-classes
Comparisonc
Mappingc

ID retrievalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3289

has super-classes
deprecated classc

IDATc back to ToC or Class ToC

IRI: http://edamontology.org/format_3578

has super-classes
Gene expression report formatc
Binary formatc
is format ofop some Raw microarray datac

Identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0842

has super-classes
Datac
is identifier ofop some Datac
has sub-classes
Accessionc, Identifier (by type of data)c, Identifier (hybrid)c, Namec, URIc
is in domain of
is identifier ofop
is in range of
has identifierop
is disjoint with
Reportc

Identifier (by type of data)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0976

This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.
has super-classes
Identifierc
has sub-classes
Amino acid index IDc, Article IDc, Atom IDc, Biological model IDc, Blot IDc, Book IDc, Catalogue IDc, Cell type identifierc, Codon usage table IDc, Data resource definition IDc, Database IDc, Disease identifierc, Electron microscopy model IDc, Experiment annotation IDc, Format identifierc, Gel IDc, Gene expression report IDc, Gene identifierc, Genetic code identifierc, Genome identifierc, Genotype and phenotype annotation IDc, Genotype experiment IDc, Job identifierc, Locus IDc, Map identifierc, Matrix identifierc, Mobile genetic element IDc, Molecular property identifierc, Molecule identifierc, Mutation identifierc, ORF identifierc, Ontology concept identifierc, Ontology identifierc, Organism identifierc, Pathway or network identifierc, Person identifierc, Phylogenetic tree IDc, Promoter IDc, Protein domain IDc, Protein family identifierc, Protein interaction IDc, Protein modification IDc, PubChem bioassay IDc, RNA family identifierc, Reaction IDc, Sample IDc, Sequence alignment IDc, Sequence feature identifierc, Sequence identifierc, Sequence motif identifierc, Sequence profile IDc, Sequence set IDc, Sequence variation IDc, Spot IDc, Stock numberc, Structural (3D) profile IDc, Structure alignment IDc, Structure identifierc, Tool identifierc, Transcription factor identifierc, Workflow IDc

Identifier (hybrid)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2109

This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.
has super-classes
Identifierc
has sub-classes
ASTD IDc, BioCyc IDc, CABRI accessionc, ConsensusPathDB identifierc, Ensembl IDc, FlyBase IDc, KEGG object identifierc, MGI accessionc, Pathway ID (WikiPathways)c, PharmGKB IDc, PubChem IDc, RGD IDc, SGD IDc, TAIR accessionc, TIGR identifierc, WormBase identifierc, cPath IDc, iHOP symbolc

Identifier with metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_2767

has super-classes
deprecated classc

idXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3764

has super-classes
XMLc
Mass spectrometry data formatc

igc back to ToC or Class ToC

IRI: http://edamontology.org/format_1942

has super-classes
Textual formatc
Sequence record format (text)c

igstrictc back to ToC or Class ToC

IRI: http://edamontology.org/format_1943

has super-classes
Textual formatc
Sequence record format (text)c

iHOP formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1740

has super-classes
Text mining report formatc
HTMLc
XMLc

iHOP organism IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1873

has super-classes
Accessionc
Organism accessionc

iHOP symbolc back to ToC or Class ToC

IRI: http://edamontology.org/data_1891

has super-classes
Accessionc
Identifier (hybrid)c
Gene IDc
Protein accessionc

imc back to ToC or Class ToC

IRI: http://edamontology.org/format_3593

IFUNC library reads and writes most uncompressed interchange versions of this format.
has super-classes
Binary formatc
Image formatc

Imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_2968

has super-classes
Datac
has sub-classes
Cell migration track imagec, Fate mapc, Heat mapc, Phylogenetic tree imagec, Protein imagec, RNA secondary structure imagec, Raw imagec, Sequence alignment imagec, Sequence imagec, Structure imagec

Image analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3443

has super-classes
Analysisc
has topicop some Imagingc
has sub-classes
Cell migration analysisc, Neurite measurementc, Single particle analysisc

Image annotationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3553

has super-classes
Annotationc

Image formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3547

has super-classes
Format (by type of data)c
is format ofop some Imagec
has sub-classes
BMPc, DICOM formatc, JPGc, OME-TIFFc, PNGc, SVGc, TIFFc, bgzipc, imc, mhdc, niic, nrrdc, pbmc, pcdc, pcxc, pgmc, ppmc, pptxc, psdc, rastc, rgbc, tabixc, xbmc, xpmc

Image metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_3546

This can include basic provenance and technical information about the image, scientific annotation and so on.
has super-classes
Reportc

Imagingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3382

This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure.
has super-classes
Laboratory techniquesc
has sub-classes
Bioimagingc, Echographyc, Electron microscopyc, Light microscopyc, MRIc, Medical imagingc, NMRc, Neutron diffractionc, Tomographyc, X-ray diffractionc

IMGT/HLA IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2773

has super-classes
Accessionc
Protein accessionc

Immunogen designc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0332

has super-classes
deprecated classc

Immunogeneticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3930

This involves the study of often complex genetic traits underlying diseases involving defects in the immune system. For example, identifying target genes for therapeutic approaches, or genetic variations involved in immunological pathology.
has super-classes
Immunologyc
Geneticsc

Immunogenicity predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0559

has super-classes
deprecated classc

Immunoinformaticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3948

This involves the study of often complex genetic traits underlying diseases involving defects in the immune system. For example, identifying target genes for therapeutic approaches, or genetic variations involved in immunological pathology.
has super-classes
Informaticsc
Immunologyc

Immunologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0804

has super-classes
Biomedical sciencec
has sub-classes
Immunogeneticsc, Immunoinformaticsc, Immunoproteins and antigensc

Immunoprecipitation experimentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3656

has super-classes
Laboratory techniquesc
has sub-classes
ChIP-on-chipc, ChIP-seqc, Methylated DNA immunoprecipitationc, RNA immunoprecipitationc

Immunoproteins and antigensc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2830

This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc."
has super-classes
Gene and protein familiesc
Immunologyc

Imputationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3557

has super-classes
Statistical calculationc

imzML metadata filec back to ToC or Class ToC

IRI: http://edamontology.org/format_3682

imzML data are recorded in 2 files: '.imzXML' is a metadata XML file based on mzML by HUPO-PSI, and '.ibd' is a binary file containing the mass spectra. This entry is for the metadata XML file
has super-classes
XMLc
Mass spectrometry data formatc

In vitro selectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3795

has super-classes
Nucleic acid designc

InChIc back to ToC or Class ToC

IRI: http://edamontology.org/format_1197

has super-classes
Chemical formula formatc
Textual formatc

InChIKeyc back to ToC or Class ToC

IRI: http://edamontology.org/format_1199

An InChIKey identifier is not human- nor machine-readable but is more suitable for web searches than an InChI chemical structure specification.
has super-classes
Chemical formula formatc
Textual formatc

Incident curve plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3503

has super-classes
Visualisationc

Indel detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0452

Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.
has super-classes
Variant callingc

Index formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3623

has super-classes
deprecated classc

Indexingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0227

has super-classes
Operationc
has outputop some Data indexc
has sub-classes
Genome indexingc

Individual genetic data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3287

has super-classes
Format (by type of data)c
has sub-classes
PED/MAPc

Infectious diseasec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3324

has super-classes
Pathologyc

Infectious tropical diseasec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3413

has super-classes
deprecated classc

Informaticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0605

has super-classes
Topicc
has sub-classes
Bioinformaticsc, Biological databasesc, Cheminformaticsc, Immunoinformaticsc, Laboratory information managementc, Medical informaticsc, Ontology and terminologyc

Information content matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_1363

has super-classes
Position-specific scoring matrixc

Information extractionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3907

has super-classes
Text miningc
has sub-classes
Named-entity and concept recognitionc

Information retrievalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3908

has super-classes
Text miningc
has sub-classes
Data retrievalc

Information retrievalc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0090

has super-classes
deprecated classc

Inhibitor annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2726

has super-classes
deprecated classc

INOH entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1650

has super-classes
deprecated classc

insdxmlc back to ToC or Class ToC

IRI: http://edamontology.org/format_2185

has super-classes
EMBL format (XML)c

IntAct accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1130

has super-classes
Protein interaction IDc
Accessionc

IntAct entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1569

has super-classes
deprecated classc

Integrated gene predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0434

has super-classes
deprecated classc

IntEnz enzyme report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1511

IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.
has super-classes
deprecated classc

InterPro accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1133

Every InterPro entry has a unique accession number to provide a persistent citation of database records.
has super-classes
Accessionc
Protein family accessionc
is identifier ofop some Protein signaturec
has sub-classes
InterPro secondary accessionc

InterPro architecture imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1292

The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein.
has super-classes
deprecated classc

InterPro compact match imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1290

The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.
has super-classes
deprecated classc

InterPro detailed match imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1291

The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself.
has super-classes
deprecated classc

InterPro entry abstract formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1571

References are included and a functional inference is made where possible.
has super-classes
deprecated classc

InterPro entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1570

This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.
has super-classes
deprecated classc

InterPro entry namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1132

has super-classes
Protein family namec
is identifier ofop some Protein signaturec

InterPro hits formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1341

has super-classes
Database hits (sequence) formatc
Textual formatc
has sub-classes
InterPro match table formatc, InterPro protein view report formatc

InterPro match table formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1343

The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated.
has super-classes
InterPro hits formatc

InterPro protein view report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1342

The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group.
has super-classes
InterPro hits formatc

InterPro secondary accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1134

has super-classes
InterPro accessionc
is identifier ofop some Protein signaturec

InterProScan XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3846

has super-classes
XMLc
Protein domain classification formatc

Intronsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2754

has super-classes
deprecated classc

Invertebratesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2819

The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates.
has super-classes
deprecated classc

Ion countingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3704

has super-classes
Label-free quantificationc

ipic back to ToC or Class ToC

IRI: http://edamontology.org/format_2189

has super-classes
deprecated classc

IPI protein IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2384

has super-classes
Sequence accession (protein)c
Accessionc

iRefIndex IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2668

has super-classes
Protein interaction IDc
Accessionc

ISA-TABc back to ToC or Class ToC

IRI: http://edamontology.org/format_3687

ISA-TAB is based on MAGE-TAB. Other than tabular, the ISA model can also be represented in RDF, and in JSON (compliable with a set of defined JSON Schemata).
has super-classes
Gene expression report formatc
Textual formatc
Experiment annotation formatc

ISBNc back to ToC or Class ToC

IRI: http://edamontology.org/data_2634

has super-classes
Accessionc
Book IDc

Isolation reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3717

has super-classes
Reportc
has sub-classes
Geographic locationc, Isolation sourcec

Isolation sourcec back to ToC or Class ToC

IRI: http://edamontology.org/data_3721

has super-classes
Isolation reportc

Isotope-coded protein labelc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3705

has super-classes
Labeled quantificationc

Isotopic distributions calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3632

has super-classes
Calculationc
has inputop some Mass spectrumc
has topicop some Proteomicsc

Isotropic B factorc back to ToC or Class ToC

IRI: http://edamontology.org/data_1858

has super-classes
Atomic propertyc

iTRAQc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3639

has super-classes
Labeled quantificationc

jackkniferc back to ToC or Class ToC

IRI: http://edamontology.org/format_1944

has super-classes
Textual formatc
Sequence record format (text)c

jackknifernonc back to ToC or Class ToC

IRI: http://edamontology.org/format_1970

has super-classes
Textual formatc
Sequence record format (text)c

JASPAR formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1367

has super-classes
Sequence profile formatc
Textual formatc

JASPAR profile IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1119

has super-classes
Sequence profile IDc
Accessionc

JCAMP-DXc back to ToC or Class ToC

IRI: http://edamontology.org/format_3859

JCAMP-DX is an ASCII based format and therefore not very compact even though it includes standards for file compression.
has super-classes
Textual formatc
Mass spectrometry data formatc

Job IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1676

has super-classes
deprecated classc

Job identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2098

has super-classes
Identifier (by type of data)c

Job metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_0959

has super-classes
deprecated classc

Job statusc back to ToC or Class ToC

IRI: http://edamontology.org/data_1675

Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed).
has super-classes
deprecated classc

Job typec back to ToC or Class ToC

IRI: http://edamontology.org/data_1677

has super-classes
deprecated classc

JPGc back to ToC or Class ToC

IRI: http://edamontology.org/format_3579

Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.
has super-classes
Binary formatc
Image formatc

JSONc back to ToC or Class ToC

IRI: http://edamontology.org/format_3464

has super-classes
Formatc
YAMLc
has sub-classes
BioJSON (BioXSD)c, BioJSON (Jalview)c, JSON-LDc, PubAnnotation formatc

JSON-LDc back to ToC or Class ToC

IRI: http://edamontology.org/format_3749

has super-classes
RDF formatc
JSONc
Linked data formatc
has sub-classes
Open Annotation formatc

K-mer countgraphc back to ToC or Class ToC

IRI: http://edamontology.org/format_3665

has super-classes
Binary formatc
Graph formatc

k-mer countingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3472

k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads.
has super-classes
Sequence composition calculationc

KEGG COMPOUND entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1698

has super-classes
deprecated classc

KEGG DISEASE entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1626

has super-classes
deprecated classc

KEGG DRUG entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1706

has super-classes
deprecated classc

KEGG ENZYME enzyme report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1514

has super-classes
deprecated classc

KEGG GENES gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1610

has super-classes
deprecated classc

KEGG GLYCAN entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1700

has super-classes
deprecated classc

KEGG Glycan IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2613

has super-classes
KEGG object identifierc
Accessionc
Carbohydrate accessionc

KEGG LIGAND entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1697

has super-classes
deprecated classc

KEGG object identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1154

has super-classes
Accessionc
Identifier (hybrid)c
has sub-classes
Compound ID (KEGG)c, Drug ID (KEGG)c, KEGG Glycan IDc, KEGG organism codec, Pathway ID (KEGG)c, Reaction ID (KEGG)c

KEGG organism codec back to ToC or Class ToC

IRI: http://edamontology.org/data_2102

has super-classes
KEGG object identifierc
Organism namec

KEGG PATHWAY entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1647

has super-classes
deprecated classc

KEGG PLANT entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1699

has super-classes
deprecated classc

KEGG REACTION enzyme report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1513

has super-classes
deprecated classc

Keywordc back to ToC or Class ToC

IRI: http://edamontology.org/data_0968

Boolean operators (AND, OR and NOT) and wildcard characters may be allowed.
has super-classes
Datac
has sub-classes
UniProt keywordc

KGMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3847

has super-classes
Biological pathway or network formatc
XMLc

Kinase namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2775

has super-classes
Protein namec

Kinetic modelc back to ToC or Class ToC

IRI: http://edamontology.org/data_3241

has super-classes
Mathematical modelc

Kingdom namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1044

has super-classes
Taxonc

Kmc back to ToC or Class ToC

IRI: http://edamontology.org/data_0910

has super-classes
Enzyme kinetics datac

KNIME datatable formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3765

has super-classes
Workflow formatc

KRSS2 Syntaxc back to ToC or Class ToC

IRI: http://edamontology.org/format_3254

This format is used in Protege 4.
has super-classes
Ontology formatc
Textual formatc

Label-free quantificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3634

has super-classes
Protein quantificationc
has sub-classes
Ion countingc, Spectral countingc

Labeled quantificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3635

has super-classes
Protein quantificationc
has sub-classes
18O labelingc, Dimethylc, Isotope-coded protein labelc, Metabolic labelingc, SILACc, TMT-tagc, iTRAQc

Laboratory animal sciencec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3386

has super-classes
Biomedical sciencec
has sub-classes
Animal studyc

Laboratory information managementc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0607

has super-classes
Informaticsc

Laboratory techniquesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3361

has super-classes
Topicc
has sub-classes
Chromosome conformation capturec, Cytometryc, Genotyping experimentc, Imagingc, Immunoprecipitation experimentc, Microarray experimentc, PCR experimentc, Protein interaction experimentc, Proteomics experimentc, RNAi experimentc, Sequencingc, Simulation experimentc

Lane identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_3734

has super-classes
Sequencing metadata namec

latexc back to ToC or Class ToC

IRI: http://edamontology.org/format_3817

uses the TeX typesetting program format
has super-classes
Textual formatc
Document formatc

LAVc back to ToC or Class ToC

IRI: http://edamontology.org/format_3014

has super-classes
Textual formatc
Alignment format (pair only)c

LGICdb identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2647

has super-classes
Accessionc
Protein accessionc

lhfc back to ToC or Class ToC

IRI: http://edamontology.org/format_1337

The hits are putative ligand-binding sequences and are found from a search of a sequence database.
has super-classes
Database hits (sequence) formatc
Textual formatc

Ligand identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0992

has super-classes
deprecated classc

Ligand-binding site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3897

has super-classes
Binding site predictionc

Light microscopyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3385

has super-classes
Imagingc

Linkage analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0283

For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc.
has super-classes
Nucleic acid sequence analysisc
has outputop some Genetic linkage reportc
has topicop some Mappingc
has sub-classes
Genetic mappingc, Linkage disequilibrium calculationc

Linkage disequilibrium (report)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1634

has super-classes
deprecated classc

Linkage disequilibrium calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0488

Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes.
has super-classes
Linkage analysisc
has outputop some Genetic linkage reportc

Linked data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3748

has super-classes
Format (by type of data)c
has sub-classes
JSON-LDc, RDF formatc

Linucs IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2796

has super-classes
Accessionc
Carbohydrate accessionc

Lipid accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2905

has super-classes
Lipid identifierc
Molecule accessionc
has sub-classes
LIPID MAPS IDc, LipidBank IDc

Lipid identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2812

has super-classes
Molecule identifierc
is identifier ofop some Lipid structurec
is identifier ofop some Lipid reportc
has sub-classes
Lipid accessionc

LIPID MAPS IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2625

has super-classes
Accessionc
Lipid accessionc

Lipid reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2879

has super-classes
Structure reportc

Lipid structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_2850

has super-classes
Structurec

LipidBank IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2665

has super-classes
Accessionc
Lipid accessionc

Lipidsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0153

has super-classes
Structure analysisc

Lipoproteinsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2232

has super-classes
deprecated classc

Listfile processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2120

has super-classes
deprecated classc

Literature analysisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0217

has super-classes
deprecated classc

Literature and languagec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3068

This includes the documentation of resources such as tools, services and databases, user support, how to get help etc.
has super-classes
Topicc
has sub-classes
Natural language processingc

Literature data resourcesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0606

has super-classes
deprecated classc

Literature searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0305

has super-classes
Database searchc
has topicop some Literature and languagec

Local alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0495

Local alignment methods identify regions of local similarity.
has super-classes
Sequence alignmentc

Local structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0509

Local alignment methods identify regions of local similarity, common substructures etc.
has super-classes
Structure alignmentc

Localisation scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_3756

has super-classes
Scorec

Localised reassemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3183

has super-classes
Sequence assemblyc

LocARNA PPc back to ToC or Class ToC

IRI: http://edamontology.org/format_3728

Format for multiple aligned or single sequences together with the probabilistic description of the (consensus) RNA secondary structure ensemble by probabilities of base pairs, base pair stackings, and base pairs and unpaired bases in the loop of base pairs.
has super-classes
Textual formatc

Locus annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2763

has super-classes
deprecated classc

Locus IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1893

has super-classes
Identifier (by type of data)c
is identifier ofop some Sequence coordinatesc
has sub-classes
Gene IDc, Locus ID (AGI)c, Locus ID (ASPGD)c, Locus ID (CGD)c, Locus ID (CMR)c, Locus ID (DictyBase)c, Locus ID (EntrezGene)c, Locus ID (MGG)c, Locus ID (MMP)c, Locus ID (MaizeGDB)c, Locus ID (PseudoCAP)c, Locus ID (SGD)c, Locus ID (Tropgene)c, Locus ID (UTR)c, NCBI locus tagc, ORF IDc

Locus ID (AGI)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1895

has super-classes
Locus IDc
Accessionc

Locus ID (ASPGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1896

has super-classes
Locus IDc
Accessionc

Locus ID (CGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1898

has super-classes
Locus IDc
Accessionc

Locus ID (CMR)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1899

has super-classes
Locus IDc
Accessionc

Locus ID (DictyBase)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1903

has super-classes
Locus IDc
Accessionc

Locus ID (EntrezGene)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1904

has super-classes
Locus IDc
Accessionc

Locus ID (MaizeGDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1905

has super-classes
Locus IDc
Accessionc

Locus ID (MGG)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1897

has super-classes
Locus IDc
Accessionc

Locus ID (MMP)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1902

has super-classes
Locus IDc
Accessionc

Locus ID (PseudoCAP)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2744

has super-classes
Locus IDc
Accessionc

Locus ID (SGD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1901

has super-classes
Locus IDc
Accessionc
SGD IDc

Locus ID (Tropgene)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1908

has super-classes
Locus IDc
Accessionc

Locus ID (UTR)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2745

has super-classes
Locus IDc
Accessionc

Logical operatorc back to ToC or Class ToC

IRI: http://edamontology.org/data_2133

has super-classes
Namec

Loomc back to ToC or Class ToC

IRI: http://edamontology.org/format_3913

has super-classes
Gene expression report formatc
HDF5c
is format ofop some Sequence tag profilec
is format ofop some Gene expression matrixc

Loop modellingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0481

has super-classes
Protein modellingc

Low complexity sequencesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0642

has super-classes
deprecated classc

LSIDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1055

LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>]
has super-classes
URNc

Machine learningc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3474

has super-classes
Computer sciencec

MAFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3008

Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format.
has super-classes
Textual formatc
Alignment format (text)c
Sequence annotation track formatc

MAGE-MLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3161

has super-classes
Gene expression report formatc
XMLc
is format ofop some Processed microarray datac

MAGE-TABc back to ToC or Class ToC

IRI: http://edamontology.org/format_3162

has super-classes
Gene expression report formatc
TSVc
is format ofop some Processed microarray datac

MaizeDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2798

has super-classes
Accessionc
EST accessionc

MaizeGDB gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1611

has super-classes
deprecated classc

Mammalsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3048

has super-classes
deprecated classc

Manchester OWL Syntaxc back to ToC or Class ToC

IRI: http://edamontology.org/format_3253

This format was influenced by the OWL Abstract Syntax and the DL style syntax.
has super-classes
OWL formatc
Textual formatc

Mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1274

has super-classes
Datac
has topicop some Mappingc
has sub-classes
Genetic mapc, Physical mapc

MAPc back to ToC or Class ToC

IRI: http://edamontology.org/format_3285

has super-classes
PED/MAPc

Map accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2904

has super-classes
Map identifierc

Map annotationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2466

has super-classes
deprecated classc

Map datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2019

has super-classes
Datac
has topicop some Mappingc

Map datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2522

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Map data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2521

has super-classes
deprecated classc

Map drawingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0573

has super-classes
Visualisationc
has inputop some Mapc
has sub-classes
Operon drawingc, Plasmid map drawingc, Restriction map drawingc

Map featurec back to ToC or Class ToC

IRI: http://edamontology.org/data_1865

Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info.
has super-classes
deprecated classc

Map formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2060

has super-classes
Format (by type of data)c
is format ofop some Mapc
has sub-classes
PlasMapper TextMapc

Map identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2117

has super-classes
Identifier (by type of data)c
is identifier ofop some Mapc
has sub-classes
Map accessionc

Map set datac back to ToC or Class ToC

IRI: http://edamontology.org/data_1864

has super-classes
deprecated classc

Map typec back to ToC or Class ToC

IRI: http://edamontology.org/data_1866

Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info.
has super-classes
deprecated classc

Mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2429

has super-classes
Operationc
has sub-classes
DNA mappingc, Database comparisonc, Epitope mappingc, Expression profile pathway mappingc, ID mappingc

Mappingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0102

This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome.
has super-classes
Sequence analysisc

Mapping assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0523

The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers.
has super-classes
Sequence assemblyc

Marine biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3387

has super-classes
Biologyc

markx0c back to ToC or Class ToC

IRI: http://edamontology.org/format_1985

has super-classes
markx0 variantc

markx0 variantc back to ToC or Class ToC

IRI: http://edamontology.org/format_2922

has super-classes
Textual formatc
Alignment format (text)c
has sub-classes
markx0c, markx1c, markx10c, markx2c, markx3c

markx1c back to ToC or Class ToC

IRI: http://edamontology.org/format_1986

has super-classes
markx0 variantc

markx10c back to ToC or Class ToC

IRI: http://edamontology.org/format_1987

has super-classes
markx0 variantc

markx2c back to ToC or Class ToC

IRI: http://edamontology.org/format_1988

has super-classes
markx0 variantc

markx3c back to ToC or Class ToC

IRI: http://edamontology.org/format_1989

has super-classes
markx0 variantc

Mascot .dat filec back to ToC or Class ToC

IRI: http://edamontology.org/format_3713

has super-classes
Textual formatc
Mass spectrometry data formatc

mase formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1945

has super-classes
Textual formatc
Sequence record format (text)c

Mass spectra calibrationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3627

has super-classes
Spectral analysisc
has inputop some Mass spectrumc

Mass spectrometryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0134

has super-classes
deprecated classc

Mass spectrometry datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2536

has super-classes
Experimental measurementc
has sub-classes
Mass spectrumc, Peptide mass fingerprintc

Mass spectrometry data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3245

has super-classes
Format (by type of data)c
is format ofop some Mass spectrometry datac
has sub-classes
JCAMP-DXc, MGFc, MSFc, Mascot .dat filec, MaxQuant APL peaklist formatc, PRIDE XMLc, SEQUEST .out filec, TIDE TXTc, Thermo RAWc, TraMLc, WIFF formatc, Waters RAWc, X!Tandem XMLc, consensusXMLc, dtac, featureXMLc, ibdc, idXMLc, imzML metadata filec, mzDatac, mzIdentMLc, mzMLc, mzQuantMLc, mzTabc, mzXMLc, netCDFc, pepXMLc, pklc, protXMLc, qcMLc

Mass spectrometry experimentc back to ToC or Class ToC

IRI: http://edamontology.org/data_3147

has super-classes
deprecated classc

Mass spectrumc back to ToC or Class ToC

IRI: http://edamontology.org/data_0943

has super-classes
Mass spectrometry datac
has topicop some Proteomicsc

Mass spectrum visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3694

has super-classes
Visualisationc

MATc back to ToC or Class ToC

IRI: http://edamontology.org/format_3626

has super-classes
Matrix formatc
is format ofop some 3D-1D scoring matrixc

matchc back to ToC or Class ToC

IRI: http://edamontology.org/format_1990

has super-classes
Textual formatc
Alignment format (text)c

Match reward scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_1401

has super-classes
Alignment score or penaltyc

Mathematical modelc back to ToC or Class ToC

IRI: http://edamontology.org/data_0950

has super-classes
Datac
has topicop some Computational biologyc
has sub-classes
DNA substitution modelc, Dirichlet distributionc, Hidden Markov modelc, Kinetic modelc

Mathematical modellingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3545

has super-classes
deprecated classc

Mathematicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3315

has super-classes
Topicc
has sub-classes
Applied mathematicsc, Pure mathematicsc, Statistics and probabilityc

Matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_2082

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Datac
has sub-classes
Amino acid frequencies tablec, Amino acid indexc, Amino acid word frequencies tablec, Base frequencies tablec, Base word frequencies tablec, Comparison matrixc, Count matrixc, Distance matrixc, Emission matrixc, Gene expression matrixc, Gene orderc, Position-specific scoring matrixc, Protein sequence-structure scoring matrixc, Structural transformation matrixc, Transition matrixc

Matrix formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3033

has super-classes
Format (by type of data)c
is format ofop some Matrixc
has sub-classes
3D-1D scoring matrix formatc, Amino acid index formatc, MATc, MTXc, Zarrc

Matrix identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_3036

has super-classes
Identifier (by type of data)c
is identifier ofop some Matrixc
has sub-classes
Amino acid index IDc, Comparison matrix identifierc

Matrix/scaffold attachment sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1308

has super-classes
deprecated classc

MatrixDB interaction IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2636

has super-classes
Protein interaction IDc
Accessionc

Maximum occurence analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3560

has super-classes
Protein structure validationc

MaxQuant APL peaklist formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3714

has super-classes
Textual formatc
Mass spectrometry data formatc

MCPDc back to ToC or Class ToC

IRI: http://edamontology.org/format_3777

has super-classes
Textual formatc
Biodiversity data formatc
is format ofop some Reference sample reportc
is format ofop some Sample annotationc
is format ofop some Organism reportc

mdcrdc back to ToC or Class ToC

IRI: http://edamontology.org/format_3878

has super-classes
Tertiary structure formatc
Textual formatc
Trajectory format (text)c

Medical biotechnologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3576

has super-classes
Biotechnologyc

Medical imagingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3384

has super-classes
Imagingc

Medical informaticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3063

has super-classes
Informaticsc

Medical toxicologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3415

has super-classes
Medicinec

Medicinal chemistryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0209

This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.
has super-classes
Drug discoveryc
Synthetic chemistryc

Medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3303

has super-classes
Topicc
has sub-classes
Allergy, clinical immunology and immunotherapeuticsc, Anaesthesiologyc, Cardiologyc, Complementary medicinec, Critical care medicinec, Dentistryc, Dermatologyc, Ear, nose and throat medicinec, Endocrinology and metabolismc, Gastroenterologyc, Gender medicinec, Geriatric medicinec, Gynaecology and obstetricsc, Haematologyc, Hepatic and biliary medicinec, Medical toxicologyc, Musculoskeletal medicinec, Neurologyc, Oncologyc, Opthalmologyc, Paediatricsc, Pain medicinec, Pathologyc, Personalised medicinec, Physiologyc, Psychiatryc, Public health and epidemiologyc, Reproductive healthc, Respiratory medicinec, Surgeryc, Systems medicinec, Toxicologyc, Translational medicinec, Trauma medicinec, Tropical medicinec, Urology and nephrologyc, Veterinary medicinec

Medicines research and developmentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3376

has super-classes
Biomedical sciencec
has sub-classes
Biotherapeuticsc, Drug developmentc, Drug discoveryc, Drug metabolismc, Preclinical and clinical studiesc, Quality affairsc, Regulatory affairsc, Safety sciencesc

medlinec back to ToC or Class ToC

IRI: http://edamontology.org/format_2194

has super-classes
Article formatc
Textual formatc

Medline Display Formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1735

Bibliographic reference information including citation information is included
has super-classes
Textual formatc
Bibliographic reference formatc

Medline UIc back to ToC or Class ToC

IRI: http://edamontology.org/data_1189

The use of Medline UI has been replaced by the PubMed unique identifier.
has super-classes
Article IDc
Accessionc

megac back to ToC or Class ToC

IRI: http://edamontology.org/format_1991

has super-classes
mega variantc

mega variantc back to ToC or Class ToC

IRI: http://edamontology.org/format_2923

has super-classes
Textual formatc
Sequence record format (text)c
Alignment format (text)c
has sub-classes
megac, meganonc

mega-seqc back to ToC or Class ToC

IRI: http://edamontology.org/format_1946

has super-classes
Textual formatc
Sequence record format (text)c

meganonc back to ToC or Class ToC

IRI: http://edamontology.org/format_1992

has super-classes
mega variantc

meganon sequence formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1971

has super-classes
deprecated classc

Membrane and lipoproteinsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0820

has super-classes
Proteinsc

MEME background frequencies filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1345

has super-classes
deprecated classc

MEME background Markov modelc back to ToC or Class ToC

IRI: http://edamontology.org/format_1369

has super-classes
Hidden Markov model formatc
Textual formatc

MEME Dirichlet priorc back to ToC or Class ToC

IRI: http://edamontology.org/format_1350

has super-classes
Dirichlet distribution formatc
Textual formatc

MEME motif alphabetc back to ToC or Class ToC

IRI: http://edamontology.org/data_1344

has super-classes
deprecated classc

MEME motifs directive filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1346

has super-classes
deprecated classc

meme-motifc back to ToC or Class ToC

IRI: http://edamontology.org/format_1360

has super-classes
Sequence motif formatc
Textual formatc

MeSHc back to ToC or Class ToC

IRI: http://edamontology.org/data_1717

has super-classes
deprecated classc

MeSH concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1177

has super-classes
Ontology concept IDc
Accessionc

MeSH vocabularyc back to ToC or Class ToC

IRI: http://edamontology.org/data_0831

has super-classes
deprecated classc

Metabolic diseasec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3323

has super-classes
deprecated classc

Metabolic engineeringc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3939

has super-classes
Biotechnologyc

Metabolic labelingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3715

This includes N-15 metabolic labeling (labeling all proteins and (possibly) all amino acids using N-15 enriched grown medium or feed) and C-13 metabolic labeling (labeling all proteins and (possibly) all amino acids using C-13 enriched grown medium or feed).
has super-classes
Labeled quantificationc

Metabolic network modellingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3660

The terms and synyonyms here reflect that for practical intents and purposes, "pathway" and "network" can be treated the same.
has super-classes
Network analysisc
Pathway analysisc
has topicop some Systems biologyc

Metabolic pathway predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3929

has super-classes
Prediction and recognitionc
Pathway analysisc

Metabolic pathway reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1656

This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.
has super-classes
deprecated classc

Metabolic pathwaysc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0753

has super-classes
deprecated classc

Metabolitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0079

has super-classes
deprecated classc

Metabolomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3172

has super-classes
Omicsc

MetaCyc entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1648

has super-classes
deprecated classc

Metadata retrievalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0304

This includes documentation, general information and other metadata on entities such as databases, database entries and tools.
has super-classes
deprecated classc

Metagenomic sequencingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3837

has super-classes
Sequencingc

Metagenomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3174

has super-classes
Ecologyc
Genomicsc

Metal-binding site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3898

has super-classes
Binding site predictionc

Metal-bound cysteine detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1831

has super-classes
Residue interaction calculationc
Protein cysteine and disulfide bond assignmentc

Metatranscriptomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3941

Metatranscriptomics methods can be used for whole gene expression profiling of complex microbial communities.
has super-classes
Gene expressionc
Transcriptomicsc

Methylated DNA immunoprecipitationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3674

has super-classes
Immunoprecipitation experimentc

Methylation analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3204

has super-classes
Nucleic acid sequence analysisc
has sub-classes
Bisulfite mappingc, DMR identificationc, Gene methylation analysisc, Methylation callingc, Whole genome methylation analysisc

Methylation callingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3205

has super-classes
deprecated classc

Methylation callingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3919

has super-classes
Methylation analysisc

mfc back to ToC or Class ToC

IRI: http://edamontology.org/format_1198

The general MF query format consists of a series of valid atomic symbols, with an optional number or range.
has super-classes
Chemical formula formatc
Textual formatc

mFLJ/mKIAA numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_2393

has super-classes
Accessionc
Gene IDc

MGD gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1612

has super-classes
deprecated classc

MGEDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1725

has super-classes
deprecated classc

MGED concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1185

has super-classes
Ontology concept IDc
Accessionc

MGFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3651

Files includes *m*/*z*, intensity pairs separated by headers; headers can contain a bit more information, including search engine instructions.
has super-classes
Mass spectrometry data formatc

MGI accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_3274

has super-classes
Accessionc
Identifier (hybrid)c

MHC Class I epitopes reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1329

has super-classes
deprecated classc

MHC Class II epitopes reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1330

has super-classes
deprecated classc

MHC peptide immunogenicity predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0413

has super-classes
deprecated classc

MHC peptide immunogenicity reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1536

has super-classes
deprecated classc

mhdc back to ToC or Class ToC

IRI: http://edamontology.org/format_3550

has super-classes
Textual formatc
Image formatc

MHTMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3556

has super-classes
HTMLc

Mice or ratsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0213

The resource may be specific to a group of mice / rats or all mice / rats.
has super-classes
deprecated classc

Michaelis Menten plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_2025

has super-classes
Enzyme kinetics datac

Microarray data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2432

has super-classes
deprecated classc

Microarray data standardisation and normalisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0311

has super-classes
deprecated classc

Microarray experimentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3518

This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates.
has super-classes
Laboratory techniquesc

Microarray experiment data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2056

has super-classes
Experiment annotation formatc
has sub-classes
affymetrix-expc

Microarray experiment reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0931

has super-classes
deprecated classc

Microarray hybridisation datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3117

has super-classes
Expression datac
has sub-classes
Processed microarray datac, Raw microarray datac

Microarray imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_2967

has super-classes
deprecated classc

Microarray metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_3115

This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc.
has super-classes
Expression datac
has sub-classes
Oligonucleotide probe annotationc

Microarray probe designc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0309

has super-classes
Primer and probe designc
Designc
has inputop some Nucleic acid sequencec
has topicop some Gene expressionc
has topicop some Probes and primersc
has outputop some Oligonucleotide probe annotationc

Microarray protocol annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_3116

This might describe e.g. the normalisation methods used to process the raw data.
has super-classes
deprecated classc

Microarray raw data analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2500

has super-classes
deprecated classc

Microarray spots imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1714

has super-classes
Expression datac
Raw imagec

Microarraysc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0200

has super-classes
deprecated classc

Microbial collectionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3339

has super-classes
Sample collectionsc

Microbial ecologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3697

has super-classes
Ecologyc
Microbiologyc

Microbiologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3301

has super-classes
Biologyc
has sub-classes
Microbial ecologyc

Microsatellitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2868

has super-classes
deprecated classc

Microscope image visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3552

has super-classes
Visualisationc
has topicop some Imagingc

MINT IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2615

has super-classes
Protein interaction IDc
Accessionc

mirac back to ToC or Class ToC

IRI: http://edamontology.org/format_1629

has super-classes
Sequence trace formatc
Textual formatc

mirGFF3c back to ToC or Class ToC

IRI: http://edamontology.org/format_3864

mirGFF3 is a specialisation of GFF3; produced by small-RNA-Seq analysis workflows, usable and convertible with the miRTop API (https://mirtop.readthedocs.io/en/latest/), and consumable by tools for downstream analysis.
has super-classes
GFF3c
RNA annotation formatc

MIRIAM data type namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1163

has super-classes
Data resource definition namec
is identifier ofop some Database metadatac
has sub-classes
MIRIAM data type primary namec, MIRIAM data type synonymous namec

MIRIAM data type primary namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1165

The primary name of a MIRIAM data type is taken from a controlled vocabulary.
has super-classes
MIRIAM data type namec

MIRIAM data type synonymous namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1166

A synonymous name for a MIRIAM data type taken from a controlled vocabulary.
has super-classes
MIRIAM data type namec

MIRIAM datatypec back to ToC or Class ToC

IRI: http://edamontology.org/data_1664

A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types.
has super-classes
deprecated classc

MIRIAM identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1162

This is the identifier used internally by MIRIAM for a data type.
has super-classes
Accessionc
Data resource definition accessionc
is identifier ofop some Database metadatac

MIRIAM URIc back to ToC or Class ToC

IRI: http://edamontology.org/data_1164

A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term.
has super-classes
URIc
Accessionc
Data resource definition accessionc
is identifier ofop some Database metadatac

miRNA expression analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3792

has super-classes
Expression analysisc

miRNA target predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0463

has super-classes
trans-regulatory element predictionc

Mismatch penalty scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_1402

has super-classes
Alignment score or penaltyc

Misnomerc back to ToC or Class ToC

IRI: http://edamontology.org/data_1880

has super-classes
deprecated classc

Misspellingc back to ToC or Class ToC

IRI: http://edamontology.org/data_1878

has super-classes
deprecated classc

Mitochondriac back to ToC or Class ToC

IRI: http://edamontology.org/topic_0779

has super-classes
deprecated classc

mmCIFc back to ToC or Class ToC

IRI: http://edamontology.org/format_1477

has super-classes
PDB database entry formatc
Textual formatc

MMDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2667

has super-classes
Structure IDc
Accessionc

Mobile genetic element IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2630

has super-classes
Identifier (by type of data)c
has sub-classes
ACLAME IDc

Mobile genetic elementsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1301

has super-classes
deprecated classc

Mobile genetic elementsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0798

has super-classes
Gene structurec

Model organismsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0621

This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism.
has super-classes
Biologyc

ModelDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2669

has super-classes
Accessionc
Biological model accessionc

Modelling and simulationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2426

has super-classes
Operationc
has topicop some Molecular modellingc
has sub-classes
DNA substitution modellingc, Ecological modellingc, Forcefield parameterisationc, Molecular dynamicsc, Nucleic acid folding analysisc, Protein folding analysisc, Protein modellingc, Simulated gene expression data generationc, Splicing analysisc

Mol2c back to ToC or Class ToC

IRI: http://edamontology.org/format_3816

has super-classes
Chemical data formatc
Textual formatc

Molecular biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3047

has super-classes
Biologyc

Molecular chargec back to ToC or Class ToC

IRI: http://edamontology.org/data_0845

has super-classes
Molecular property (general)c

Molecular datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2528

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Molecular dockingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0478

This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on.
has super-classes
Protein function predictionc
Structure analysisc
has outputop some Protein complexc
has outputop some Protein-ligand complexc
has sub-classes
Protein-ligand dockingc, Protein-protein dockingc

Molecular dockingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0177

has super-classes
deprecated classc

Molecular dynamicsc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2476

has super-classes
Prediction and recognitionc
Modelling and simulationc
Structure analysisc
has outputop some Structurec
has topicop some Structure predictionc
has topicop some Molecular dynamicsc

Molecular dynamicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0176

This includes methods such as Molecular Dynamics, Coarse-grained dynamics, metadynamics, Quantum Mechanics, QM/MM, Markov State Models, etc. This includes resources concerning flexibility and motion in protein and other molecular structures.
has super-classes
Structure predictionc
Biomolecular simulationc

Molecular evolutionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3945

has super-classes
Genotype and phenotypec
Evolutionary biologyc
Omicsc

Molecular geneticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3321

has super-classes
Geneticsc
Computational biologyc
has sub-classes
Gene and protein familiesc, Gene expressionc, Gene structurec, Genetic variationc

Molecular interaction analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2948

has super-classes
deprecated classc

Molecular interaction data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2993

has super-classes
deprecated classc

Molecular interaction IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2627

has super-classes
deprecated classc

Molecular interactions, pathways and networksc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0602

has super-classes
Computational biologyc
has sub-classes
Protein interactionsc

Molecular massc back to ToC or Class ToC

IRI: http://edamontology.org/data_0844

has super-classes
Molecular property (general)c

Molecular medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3388

has super-classes
Translational medicinec

Molecular model refinementc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0322

has super-classes
Optimisation and refinementc
Structure analysisc
has sub-classes
Molecular replacementc, Rigid body refinementc

Molecular modellingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2275

has super-classes
Structure predictionc

Molecular propertyc back to ToC or Class ToC

IRI: http://edamontology.org/data_2087

has super-classes
Datac
has sub-classes
Amino acid propertyc, Atomic propertyc, Carbohydrate propertyc, Molecular property (general)c, Nucleic acid propertyc, Peptide propertyc, Protein propertyc

Molecular property (general)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2050

has super-classes
Molecular propertyc
has sub-classes
Chemical formulac, Concentrationc, Molecular chargec, Molecular massc, QSAR descriptorc

Molecular property identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2110

has super-classes
Identifier (by type of data)c
is identifier ofop some Molecular propertyc
has sub-classes
QSAR descriptor namec

Molecular replacementc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3455

The technique solves the phase problem, i.e. retrieve information concern phases of the structure.
has super-classes
Molecular model refinementc

Molecular similarity scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_1496

has super-classes
deprecated classc

Molecular simulation datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3842

Typically formed by two separated but indivisible pieces of information: topology data (static) and trajectory data (dynamic).
has super-classes
Datac
has topicop some Structure analysisc

Molecular surface analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3351

has super-classes
Structure analysisc
has topicop some Protein structural motifs and surfacesc
has topicop some Protein propertiesc
has sub-classes
Accessible surface calculationc, Molecular surface calculationc, Molecular surface comparisonc, Surface renderingc

Molecular surface calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0387

has super-classes
Molecular surface analysisc

Molecular surface comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3666

has super-classes
Structure comparisonc
Molecular surface analysisc

Molecular weights standard fingerprintc back to ToC or Class ToC

IRI: http://edamontology.org/data_1646

has super-classes
deprecated classc

Molecule accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2901

has super-classes
Molecule identifierc
has sub-classes
Carbohydrate accessionc, Compound accessionc, Lipid accessionc, Oligonucleotide IDc, Peptide IDc, Protein accessionc, Transcript IDc

Molecule identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0982

has super-classes
Identifier (by type of data)c
has sub-classes
Compound identifierc, Lipid identifierc, Molecule accessionc, Molecule namec, Nucleic acid identifierc, Peptide identifierc, Protein identifierc

Molecule interaction reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2599

has super-classes
deprecated classc

Molecule namec back to ToC or Class ToC

IRI: http://edamontology.org/data_0984

has super-classes
Molecule identifierc
Namec
has sub-classes
Chromosome namec, Compound namec, Protein namec

Molecule reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2529

has super-classes
deprecated classc

Molecule typec back to ToC or Class ToC

IRI: http://edamontology.org/data_0985

For example, 'Protein', 'DNA', 'RNA' etc.
has super-classes
deprecated classc

Moleculesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2839

has super-classes
deprecated classc

Molfilec back to ToC or Class ToC

IRI: http://edamontology.org/format_3815

has super-classes
Chemical data formatc
Textual formatc

Monosaccharide accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2898

has super-classes
Monosaccharide identifierc
has sub-classes
MonosaccharideDB IDc

Monosaccharide identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0996

has super-classes
Compound identifierc
has sub-classes
Monosaccharide accessionc

MonosaccharideDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2746

has super-classes
Accessionc
Monosaccharide accessionc

Morphology parameterc back to ToC or Class ToC

IRI: http://edamontology.org/data_3723

has super-classes
Experimental measurementc

Motif database searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0341

has super-classes
deprecated classc

Mouse clinicc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3338

has super-classes
Sample collectionsc

MPSS data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0529

has super-classes
deprecated classc

MPSS experimental datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0934

has super-classes
deprecated classc

MRIc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3444

has super-classes
Imagingc

MRI imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_3442

has super-classes
Raw imagec
has topicop some Medical imagingc

MRM/SRMc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3636

has super-classes
Protein quantificationc

MSAMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3849

has super-classes
Alignment formatc
Binary formatc

MSDchem ligand dictionary entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1704

has super-classes
deprecated classc

MSFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3702

This format corresponds to an SQLite database, and you can look into the files with e.g. SQLiteStudio3. There are also some readers (http://doi.org/10.1021/pr2005154) and converters (http://doi.org/10.1016/j.jprot.2015.06.015) for this format available, which re-engineered the database schema, but there is no official DB schema specification of Thermo Scientific for the format.
has super-classes
Mass spectrometry data formatc

msf alignment formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1993

has super-classes
deprecated classc

mshc back to ToC or Class ToC

IRI: http://edamontology.org/format_3911

has super-classes
Binary formatc
Raw sequence formatc
is format ofop some Sequence checksumc

mspcrunchc back to ToC or Class ToC

IRI: http://edamontology.org/format_1334

has super-classes
Database hits (sequence) formatc
Textual formatc

MTXc back to ToC or Class ToC

IRI: http://edamontology.org/format_3916

has super-classes
Gene expression report formatc
Textual formatc
Matrix formatc
is format ofop some Gene expression matrixc
is format ofop some Sequence tag profilec

Multilocus sequence typingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3840

has super-classes
Genotypingc

Multiple nucleic acid tertiary structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1492

has super-classes
deprecated classc

Multiple nucleotide sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1389

has super-classes
deprecated classc

Multiple protein sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1390

has super-classes
deprecated classc

Multiple protein tertiary structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1484

has super-classes
deprecated classc

Multiple protein tertiary structure alignment (all atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1489

has super-classes
deprecated classc

Multiple protein tertiary structure alignment (C-alpha atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1490

C-beta atoms from amino acid side-chains may be included.
has super-classes
deprecated classc

Multiple sample visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3744

has super-classes
Visualisationc

Multiple sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0492

This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment.
has super-classes
Sequence alignmentc

Multiple structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0504

This includes methods that use an existing alignment.
has super-classes
Structure alignmentc

Musculoskeletal medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3416

has super-classes
Medicinec

Mutation annotation (basic)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2212

has super-classes
deprecated classc

Mutation annotation (functional)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2215

has super-classes
deprecated classc

Mutation annotation (prevalence)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2213

has super-classes
deprecated classc

Mutation annotation (prognostic)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2214

has super-classes
deprecated classc

Mutation IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2209

has super-classes
Accessionc
Mutation identifierc

Mutation identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2538

has super-classes
Identifier (by type of data)c
has sub-classes
Mutation IDc

Mutation typec back to ToC or Class ToC

IRI: http://edamontology.org/data_2132

has super-classes
deprecated classc

myGridc back to ToC or Class ToC

IRI: http://edamontology.org/data_1726

The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.
has super-classes
deprecated classc

myGrid concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1186

The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services.
has super-classes
Ontology concept IDc
Accessionc

mzDatac back to ToC or Class ToC

IRI: http://edamontology.org/format_3834

has super-classes
XMLc
Mass spectrometry data formatc

mzIdentMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3247

has super-classes
XMLc
Mass spectrometry data formatc

mzMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3244

mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center.
has super-classes
XMLc
Mass spectrometry data formatc

mzQuantMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3248

has super-classes
XMLc
Mass spectrometry data formatc

mzTabc back to ToC or Class ToC

IRI: http://edamontology.org/format_3681

has super-classes
Textual formatc
Mass spectrometry data formatc

mzXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3654

has super-classes
Mass spectrometry data formatc

N-Quadsc back to ToC or Class ToC

IRI: http://edamontology.org/format_3956

N-Quads should not be confused with N-Triples which does not contain graph information.
has super-classes
Textual formatc
RDF formatc

N-Triplesc back to ToC or Class ToC

IRI: http://edamontology.org/format_3256

N-Triples should not be confused with Notation 3 which is a superset of Turtle.
has super-classes
Textual formatc
RDF formatc

NACCESS log filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1681

has super-classes
deprecated classc

Namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2099

has super-classes
Identifierc
has sub-classes
Atom namec, Biological model namec, CABRI catalogue namec, Cell type namec, Codon usage table namec, Comparison matrix namec, ConsensusPathDB entity namec, Data resource definition namec, Database field namec, Database namec, Directory namec, Disease namec, EMBOSS Uniform Feature Objectc, EMBOSS Uniform Sequence Addressc, File format namec, File namec, Gene namec, Genetic code namec, Logical operatorc, Molecule namec, ORF namec, Ontology concept namec, Ontology namec, Operating system namec, Organism namec, Phenotype namec, Protein family namec, Protein fold namec, QSAR descriptor namec, RFAM namec, Reference map name (SWISS-2DPAGE)c, Sequence feature labelc, Sequence namec, Sequencing metadata namec, Toxin namec, WormBase namec

Named-entity and concept recognitionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3280

has super-classes
Information extractionc

Natural language processingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0218

has super-classes
Literature and languagec
Computer sciencec

Natural product identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3803

has super-classes
Spectral analysisc

nbrf/pirc back to ToC or Class ToC

IRI: http://edamontology.org/format_1948

has super-classes
Textual formatc

Nc statisticc back to ToC or Class ToC

IRI: http://edamontology.org/data_1601

has super-classes
deprecated classc

NCBI formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1972

There are several variants of this.
has super-classes
FASTA-like (text)c

NCBI gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1782

has super-classes
deprecated classc

NCBI genetic code IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3022

has super-classes
Accessionc
Genetic code identifierc

NCBI genome accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2787

has super-classes
Accessionc
Genome accessionc

NCBI Genome Project IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2786

has super-classes
Accessionc
Genome accessionc

NCBI locus tagc back to ToC or Class ToC

IRI: http://edamontology.org/data_1900

has super-classes
Locus IDc
Accessionc

NCBI taxonc back to ToC or Class ToC

IRI: http://edamontology.org/data_1875

has super-classes
Taxonc

NCBI taxonomy IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1179

has super-classes
Ontology concept IDc
Accessionc
Organism accessionc

NCBI taxonomy vocabularyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1719

has super-classes
deprecated classc

NCBI versionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2315

Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number.
has super-classes
Accessionc
Sequence accession (hybrid)c

NCI-Nature pathway entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2341

has super-classes
deprecated classc

netCDFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3650

has super-classes
Binary formatc
Mass spectrometry data formatc
Trajectory format (binary)c

Network analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3927

has super-classes
Analysisc
has topicop some Systems biologyc
has topicop some Molecular interactions, pathways and networksc
has sub-classes
Gene regulatory network analysisc, Gene regulatory network predictionc, Metabolic network modellingc, Network visualisationc, Protein interaction network analysisc, Protein interaction network predictionc, Weighted correlation network analysisc

Network simulationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3562

Notions of pathway and network were mixed up, EDAM 1.24 disentangles them.
has super-classes
deprecated classc

Network visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3925

has super-classes
Visualisationc
Network analysisc
has inputop some Pathway or networkc

Neurite measurementc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3450

has super-classes
Image analysisc
has topicop some Cell biologyc

Neurobiologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3304

has super-classes
Biomedical sciencec

Neurologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3334

has super-classes
Medicinec

NeuroMorpho IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2657

has super-classes
Accessionc
Cell type accessionc

NeuronDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2656

has super-classes
Accessionc
Cell type accessionc

Neutron diffractionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3448

has super-classes
Structural biologyc
Imagingc

newickc back to ToC or Class ToC

IRI: http://edamontology.org/format_1910

has super-classes
Textual formatc
Phylogenetic tree format (text)c

NeXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3160

has super-classes
XMLc
Phylogenetic tree format (XML)c

nexus alignment formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1994

has super-classes
deprecated classc

Nexus formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1912

has super-classes
Textual formatc
Phylogenetic tree format (text)c

nexus-seqc back to ToC or Class ToC

IRI: http://edamontology.org/format_1949

has super-classes
Textual formatc
Sequence record format (text)c
Alignment format (text)c

nexusnonc back to ToC or Class ToC

IRI: http://edamontology.org/format_1973

has super-classes
Textual formatc
Sequence record format (text)c
Alignment format (text)c

nexusnon alignment formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1995

has super-classes
deprecated classc

NGS experimentc back to ToC or Class ToC

IRI: http://edamontology.org/data_3165

has super-classes
deprecated classc

niic back to ToC or Class ToC

IRI: http://edamontology.org/format_3549

has super-classes
Binary formatc
Image formatc

NLP annotation formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3862

has super-classes
NLP formatc
has sub-classes
NLP corpus formatc

NLP corpus formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3863

has super-classes
NLP annotation formatc

NLP formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3841

has super-classes
Format (by type of data)c
has sub-classes
NLP annotation formatc

NMRc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0593

has super-classes
Structural biologyc
Imagingc

NMR data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3824

has super-classes
Format (by type of data)c
is format ofop some NMR spectrumc
has sub-classes
NMReDATAc, nmrMLc

NMR spectrumc back to ToC or Class ToC

IRI: http://edamontology.org/data_3488

has super-classes
Spectrumc
has topicop some Structural biologyc

NMReDATAc back to ToC or Class ToC

IRI: http://edamontology.org/format_3906

NMReData is a text based data standard for processed NMR data. It is relying on SDF molecule data and allows to store assignments of NMR peaks to molecule features. The NMR-extracted data (or “NMReDATA”) includes: Chemical shift,scalar coupling, 2D correlation, assignment, etc. Find more in the paper at D. Jeannerat, Magn. Reson. in Chem., 2017, 55, 7-14.
has super-classes
Textual formatc
NMR data formatc

nmrMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3825

has super-classes
XMLc
NMR data formatc

Nomenclaturec back to ToC or Class ToC

IRI: http://edamontology.org/topic_2811

has super-classes
deprecated classc

Non-coding RNAc back to ToC or Class ToC

IRI: http://edamontology.org/data_3137

has super-classes
deprecated classc

Northern blot experimentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3522

has super-classes
deprecated classc

Northern blot imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_2586

has super-classes
Raw imagec

Northern blot reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2866

has super-classes
deprecated classc

Notation3c back to ToC or Class ToC

IRI: http://edamontology.org/format_3257

has super-classes
Textual formatc
RDF formatc

nrrdc back to ToC or Class ToC

IRI: http://edamontology.org/format_3551

has super-classes
Textual formatc
Image formatc

Nucleic acid analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2501

has super-classes
deprecated classc

Nucleic acid classificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2986

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Nucleic acid classificationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0722

has super-classes
deprecated classc

Nucleic acid comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2998

has super-classes
Comparisonc
has sub-classes
Codon usage table comparisonc, Differential gene expression analysisc, Nucleic acid structure comparisonc

Nucleic acid curvature calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0461

This includes properties such as.
has super-classes
Nucleic acid property calculationc
has outputop some Nucleic acid propertyc

Nucleic acid datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2525

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Nucleic acid density plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_2167

has super-classes
Sequence composition reportc
Plotc

Nucleic acid density plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2284

has super-classes
Sequence composition calculationc
Sequence visualisationc

Nucleic acid designc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3095

has super-classes
Designc
Nucleic acid sequence analysisc
has sub-classes
DNA vaccine designc, In vitro selectionc, Primer and probe designc, RNA inverse foldingc

Nucleic acid designc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2953

has super-classes
deprecated classc

Nucleic acid enthalpyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1584

has super-classes
Nucleic acid thermodynamic datac

Nucleic acid entropyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1585

has super-classes
Nucleic acid thermodynamic datac

Nucleic acid feature detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0415

This is placeholder but does not comprehensively include all child concepts - please inspect other concepts under "Nucleic acid sequence analysis" for example "Gene prediction", for other feature detection operations.
has super-classes
Prediction and recognitionc
Nucleic acid sequence analysisc
has outputop some Nucleic acid featuresc
has topicop some Sequence sites, features and motifsc
has sub-classes
CpG island and isochore detectionc, Differential binding analysisc, Nucleosome position predictionc, Peak callingc, PolyA signal detectionc, Quadruplex formation site detectionc, RNA secondary structure predictionc, Repeat sequence detectionc, Restriction site recognitionc, Transposon predictionc, Vector sequence detectionc

Nucleic acid feature detectionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3073

has super-classes
deprecated classc

Nucleic acid feature identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1018

has super-classes
deprecated classc

Nucleic acid featuresc back to ToC or Class ToC

IRI: http://edamontology.org/data_1276

This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features.
has super-classes
Sequence featuresc
has sub-classes
Gene transcript reportc

Nucleic acid features (codon)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2116

has super-classes
deprecated classc

Nucleic acid features (d-loop)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3132

A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule.
has super-classes
deprecated classc

Nucleic acid features (difference and change)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3122

has super-classes
deprecated classc

Nucleic acid features (immunoglobulin gene structure)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3140

has super-classes
deprecated classc

Nucleic acid features (microRNA)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1310

has super-classes
deprecated classc

Nucleic acid features (primers) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2061

has super-classes
Format (by type of data)c
has sub-classes
Primer3 primerc

Nucleic acid features (quadruplexes)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1303

has super-classes
deprecated classc

Nucleic acid features (restriction sites) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2158

has super-classes
Format (by type of data)c
has sub-classes
REBASE restriction sitesc, restover formatc, restrict formatc

Nucleic acid features (siRNA)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2169

has super-classes
deprecated classc

Nucleic acid features (stem loop)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3133

A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs.
has super-classes
deprecated classc

Nucleic acid foldingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0112

has super-classes
deprecated classc

Nucleic acid folding analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0279

has super-classes
Nucleic acid structure predictionc
Modelling and simulationc
Nucleic acid structure analysisc
has outputop some Nucleic acid folding reportc

Nucleic acid folding energy calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1769

has super-classes
deprecated classc

Nucleic acid folding family identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1768

has super-classes
deprecated classc

Nucleic acid folding prediction (alignment-based)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3471

has super-classes
deprecated classc

Nucleic acid folding reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1596

has super-classes
Nucleic acid reportc

Nucleic acid identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2119

has super-classes
Molecule identifierc
is identifier ofop some Nucleic acid reportc
has sub-classes
Chromosome namec, Oligonucleotide IDc, Plasmid identifierc, Transcript IDc

Nucleic acid melting curvec back to ToC or Class ToC

IRI: http://edamontology.org/data_2958

has super-classes
deprecated classc

Nucleic acid melting curve plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0458

has super-classes
Nucleic acid melting profile plottingc

Nucleic acid melting profilec back to ToC or Class ToC

IRI: http://edamontology.org/data_1583

A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence.
has super-classes
Nucleic acid thermodynamic datac

Nucleic acid melting profile plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0456

A melting profile is used to visualise and analyse partly melted DNA conformations.
has super-classes
Nucleic acid property calculationc
Visualisationc
has outputop some Nucleic acid melting profilec
has sub-classes
Nucleic acid melting curve plottingc, Nucleic acid probability profile plottingc, Nucleic acid stitch profile plottingc, Nucleic acid temperature profile plottingc

Nucleic acid melting temperaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1586

has super-classes
deprecated classc

Nucleic acid melting temperaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_2139

has super-classes
Nucleic acid thermodynamic datac

Nucleic acid probability profilec back to ToC or Class ToC

IRI: http://edamontology.org/data_2959

has super-classes
deprecated classc

Nucleic acid probability profile plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0459

has super-classes
Nucleic acid melting profile plottingc

Nucleic acid propertyc back to ToC or Class ToC

IRI: http://edamontology.org/data_0912

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Molecular propertyc
has sub-classes
DNA base structural datac, Nucleic acid thermodynamic datac

Nucleic acid property calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0262

has super-classes
Calculationc
has outputop some Nucleic acid propertyc
has sub-classes
Nucleic acid curvature calculationc, Nucleic acid melting profile plottingc, Nucleic acid thermodynamic property calculationc, Restriction digestc

Nucleic acid property processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0261

has super-classes
deprecated classc

Nucleic acid repeatsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3126

This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit.
has super-classes
deprecated classc

Nucleic acid reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2084

has super-classes
Reportc
has sub-classes
Chromosome reportc, Gene family reportc, Gene reportc, Genetic linkage reportc, Nucleic acid folding reportc, Nucleic acid structure reportc

Nucleic acid restrictionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0100

has super-classes
deprecated classc

Nucleic acid sequencec back to ToC or Class ToC

IRI: http://edamontology.org/data_2977

has super-classes
Sequencec
has sub-classes
DNA sequencec, Nucleic acid sequence recordc, RNA sequencec

Nucleic acid sequence (raw)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2975

has super-classes
deprecated classc

Nucleic acid sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1383

has super-classes
Sequence alignmentc

Nucleic acid sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0740

has super-classes
deprecated classc

Nucleic acid sequence alignment analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2507

has super-classes
deprecated classc

Nucleic acid sequence analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2478

has super-classes
Sequence analysisc
has topicop some Nucleic acidsc
has inputop some Nucleic acid sequencec
has sub-classes
Chimera detectionc, Codon usage analysisc, DNA barcodingc, DNA profilingc, DNA testingc, Gene predictionc, Genome analysisc, Linkage analysisc, Methylation analysisc, Nucleic acid designc, Nucleic acid feature detectionc, Selection detectionc, Sequence assemblyc, Sequence read processingc, Sequencing quality controlc, Species frequency estimationc, Variant callingc, Virtual PCRc

Nucleic acid sequence analysisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0640

has super-classes
deprecated classc

Nucleic acid sequence comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2508

has super-classes
deprecated classc

Nucleic acid sequence composition (report)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3086

has super-classes
deprecated classc

Nucleic acid sequence feature detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3430

has super-classes
deprecated classc

Nucleic acid sequence recordc back to ToC or Class ToC

IRI: http://edamontology.org/data_2887

has super-classes
Sequence recordc
Nucleic acid sequencec

Nucleic acid sequence record (full)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2889

has super-classes
deprecated classc

Nucleic acid sequence record (lite)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2046

has super-classes
deprecated classc

Nucleic acid sequence visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2515

Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
has super-classes
deprecated classc

Nucleic acid sequencesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3042

has super-classes
deprecated classc

Nucleic acid signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_3492

has super-classes
Sequence signature reportc

Nucleic acid sites and featuresc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0747

has super-classes
deprecated classc

Nucleic acid sites, features and motifsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3511

Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs.
has super-classes
Nucleic acidsc
Sequence sites, features and motifsc
has sub-classes
DNA binding sitesc

Nucleic acid stitch profilec back to ToC or Class ToC

IRI: http://edamontology.org/data_1587

has super-classes
deprecated classc

Nucleic acid stitch profile plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0457

A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range.
has super-classes
Nucleic acid melting profile plottingc

Nucleic acid structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_1459

has super-classes
Structurec
has topicop some Nucleic acid structure analysisc
has sub-classes
DNA structurec, RNA structurec

Nucleic acid structurec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3039

has super-classes
deprecated classc

Nucleic acid structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1482

has super-classes
Structure alignmentc
has sub-classes
DNA structure alignmentc, RNA structure alignmentc

Nucleic acid structure analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2481

has super-classes
Structure analysisc
has inputop some Nucleic acid structurec
has topicop some Nucleic acid structure analysisc
has sub-classes
Essential dynamicsc, Nucleic acid folding analysisc, Nucleic acid structure comparisonc, Nucleic acid structure predictionc, RNA secondary structure analysisc

Nucleic acid structure analysisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0097

Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc.
has super-classes
Nucleic acidsc
Structure analysisc

Nucleic acid structure comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2518

has super-classes
Nucleic acid structure analysisc
Structure comparisonc
Nucleic acid comparisonc

Nucleic acid structure comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2280

Use this concept for methods that are exclusively for nucleic acid structures.
has super-classes
deprecated classc

Nucleic acid structure datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2086

has super-classes
deprecated classc

Nucleic acid structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0475

Methods might identify thermodynamically stable or evolutionarily conserved structures.
has super-classes
Prediction and recognitionc
Nucleic acid structure analysisc
has outputop some Nucleic acid structurec
has sub-classes
DNA structure predictionc, Nucleic acid folding analysisc, RNA secondary structure predictionc, RNA structure predictionc

Nucleic acid structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0173

has super-classes
deprecated classc

Nucleic acid structure reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3128

has super-classes
Nucleic acid reportc
Structure reportc

Nucleic acid temperature profilec back to ToC or Class ToC

IRI: http://edamontology.org/data_2960

has super-classes
deprecated classc

Nucleic acid temperature profile plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0460

has super-classes
Nucleic acid melting profile plottingc

Nucleic acid thermodynamic datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2985

has super-classes
Nucleic acid propertyc
has sub-classes
Nucleic acid enthalpyc, Nucleic acid entropyc, Nucleic acid melting profilec, Nucleic acid melting temperaturec

Nucleic acid thermodynamic property calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0455

has super-classes
Nucleic acid property calculationc
has outputop some Nucleic acid thermodynamic datac

Nucleic acid thermodynamicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0094

has super-classes
deprecated classc

Nucleic acidsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0077

has super-classes
Computational biologyc
has sub-classes
DNAc, Nucleic acid sites, features and motifsc, Nucleic acid structure analysisc, RNAc

Nucleic acids-binding site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0420

This includes methods that predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).
has super-classes
Binding site predictionc
has sub-classes
DNA binding site predictionc, RNA binding site predictionc

Nucleosome exclusion sequencesc back to ToC or Class ToC

IRI: http://edamontology.org/data_1306

has super-classes
deprecated classc

Nucleosome formation potential predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0453

has super-classes
deprecated classc

Nucleosome position predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0432

has super-classes
Nucleic acid feature detectionc

nucleotidec back to ToC or Class ToC

IRI: http://edamontology.org/format_1207

Non-sequence characters may be used for example for gaps.
has super-classes
Textual formatc
Raw sequence formatc
has sub-classes
completely unambiguous pure nucleotidec, dnac, pure nucleotidec, rnac, unambiguous pure nucleotidec

Nucleotide base annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0911

has super-classes
deprecated classc

Nucleotide codec back to ToC or Class ToC

IRI: http://edamontology.org/data_1007

has super-classes
Compound namec
Nucleotide identifierc

Nucleotide comparison matrix (floats)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1451

has super-classes
deprecated classc

Nucleotide comparison matrix (integers)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1450

has super-classes
deprecated classc

Nucleotide identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0995

has super-classes
Compound identifierc
has sub-classes
Nucleotide codec

Number of iterationsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1693

has super-classes
deprecated classc

Number of output entitiesc back to ToC or Class ToC

IRI: http://edamontology.org/data_1694

has super-classes
deprecated classc

Nutritional sciencec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3390

has super-classes
Biomedical sciencec

OBOc back to ToC or Class ToC

IRI: http://edamontology.org/format_2549

has super-classes
OBO formatc
Textual formatc

OBO file format namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2254

has super-classes
File format namec

OBO formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2196

has super-classes
Ontology formatc
has sub-classes
OBOc, OBO-XMLc

OBO-XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_2550

has super-classes
OBO formatc
XMLc

Obsolete concept (EDAM)c back to ToC or Class ToC

IRI: http://www.geneontology.org/formats/oboInOwl#ObsoleteClass

Needed for conversion to the OBO format.
has super-classes
deprecated classc

Oligonucleotide IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2718

has super-classes
Nucleic acid identifierc
Molecule accessionc
has sub-classes
DiProDB IDc, dbProbe IDc

Oligonucleotide probe annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2717

has super-classes
Microarray metadatac
has topicop some Probes and primersc

Oligonucleotide probe datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0932

has super-classes
deprecated classc

Oligonucleotide probe sets annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2966

has super-classes
deprecated classc

OME-TIFFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3727

OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community.
has super-classes
Binary formatc
Image formatc

Omicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3391

has super-classes
Topicc
has sub-classes
Fluxomicsc, Genomicsc, Metabolomicsc, Molecular evolutionc, Phenomicsc, Proteomicsc

OMIM entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1623

has super-classes
deprecated classc

OMIM IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1153

has super-classes
Genotype and phenotype annotation IDc
Accessionc

Oncologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2640

has super-classes
Medicinec

Online coursec back to ToC or Class ToC

IRI: http://edamontology.org/data_3670

has super-classes
Training materialc

Ontologies, nomenclature and classificationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2829

has super-classes
deprecated classc

Ontologyc back to ToC or Class ToC

IRI: http://edamontology.org/data_0582

has super-classes
Ontology datac
has topicop some Ontology and terminologyc

Ontology and terminologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0089

has super-classes
Informaticsc

Ontology comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3352

has super-classes
Comparisonc

Ontology comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3353

has super-classes
deprecated classc

Ontology conceptc back to ToC or Class ToC

IRI: http://edamontology.org/data_2858

This includes any fields from the concept definition such as concept name, definition, comments and so on.
has super-classes
Ontology datac

Ontology concept commentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1732

has super-classes
deprecated classc

Ontology concept datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0967

has super-classes
Ontology datac
has sub-classes
Ontology concept definitionc, Ontology termc

Ontology concept definitionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1731

has super-classes
Ontology concept datac

Ontology concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1087

has super-classes
Ontology concept identifierc
has sub-classes
BRENDA ontology concept IDc, BioPax concept IDc, Cell type ontology IDc, ChEBI concept IDc, EMAP concept IDc, FMA concept IDc, GO concept IDc, HGNC concept IDc, MGED concept IDc, MeSH concept IDc, NCBI taxonomy IDc, Plant Ontology concept IDc, UMLS concept IDc, myGrid concept IDc

Ontology concept identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_3025

has super-classes
Identifier (by type of data)c
is identifier ofop some Ontology conceptc
has sub-classes
Ontology concept IDc, Ontology concept namec

Ontology concept namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2339

has super-classes
Namec
Ontology concept identifierc

Ontology concept referencec back to ToC or Class ToC

IRI: http://edamontology.org/data_1733

has super-classes
deprecated classc

Ontology datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2353

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Datac
has topicop some Ontology and terminologyc
has sub-classes
Ontologyc, Ontology conceptc, Ontology concept datac

Ontology formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2195

has super-classes
Format (by type of data)c
is format ofop some Ontologyc
has sub-classes
KRSS2 Syntaxc, OBO formatc, OWL formatc, RDF formatc

Ontology identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2338

has super-classes
Identifier (by type of data)c
is identifier ofop some Ontologyc
has sub-classes
Ontology namec

Ontology mappingc back to ToC or Class ToC

IRI: http://edamontology.org/data_3509

has super-classes
Data referencec

Ontology metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_2223

has super-classes
Resource metadatac
has topicop some Ontology and terminologyc

Ontology namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1051

has super-classes
Namec
Ontology identifierc
is identifier ofop some Ontologyc

Ontology relation typec back to ToC or Class ToC

IRI: http://edamontology.org/data_1730

has super-classes
deprecated classc

Ontology termc back to ToC or Class ToC

IRI: http://edamontology.org/data_0966

has super-classes
Ontology concept datac

Ontology visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3559

has super-classes
Visualisationc

Open Annotation formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3784

has super-classes
RDF formatc
JSON-LDc
Annotated text formatc

Operating system namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2131

has super-classes
Namec

Operationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0004

Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.
has sub-classes
Alignmentc, Analysisc, Annotationc, Calculationc, Classificationc, Clusteringc, Comparisonc, Conversionc, Correlationc, Data handlingc, Designc, Generationc, Indexingc, Mappingc, Modelling and simulationc, Optimisation and refinementc, Prediction and recognitionc, Quantificationc, Service managementc, Validationc, Visualisationc
is in domain of
has inputop, has outputop, is function ofop
is in range of
has functionop, is input ofop, is output ofop
is disjoint with
Datac, Formatc, Topicc, deprecated classc

Operation (typed)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2420

has super-classes
deprecated classc

Operonc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1311

has super-classes
deprecated classc

Operon drawingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0579

has super-classes
Map drawingc
has topicop some Gene structurec

Operon predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0435

has super-classes
Gene predictionc

Opthalmologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3417

has super-classes
Medicinec

Optimisation and refinementc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2425

has super-classes
Operationc
has sub-classes
Molecular model refinementc, Sequence alignment refinementc

Ordered locus namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2009

has super-classes
deprecated classc

Ordination plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_3743

has super-classes
Protein propertyc
Plotc

ORF IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2794

has super-classes
Locus IDc
Accessionc
ORF identifierc

ORF identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2795

has super-classes
Identifier (by type of data)c
has sub-classes
ORF IDc, ORF namec

ORF namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1807

has super-classes
Namec
ORF identifierc

Organellesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0616

has super-classes
deprecated classc

Organism accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2908

has super-classes
Organism identifierc
has sub-classes
BRENDA organism IDc, NCBI taxonomy IDc, Strain accessionc, Virus IDc, iHOP organism IDc

Organism identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1869

has super-classes
Identifier (by type of data)c
is identifier ofop some Organism reportc
has sub-classes
Organism accessionc, Organism namec, Strain identifierc, Virus identifierc

Organism namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2909

has super-classes
Organism identifierc
Namec
has sub-classes
Genbank common namec, KEGG organism codec, Strain namec, Taxonc, Taxonomic classificationc

Organism reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2530

has super-classes
Reportc
has sub-classes
Cell line reportc, Genome reportc

Orpha numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_2800

has super-classes
Disease IDc
Accessionc
is identifier ofop some Disease reportc

OrthoXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3850

has super-classes
Gene annotation formatc
XMLc
Sequence record format (XML)c

OSCAR formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1741

OSCAR (Open-Source Chemistry Analysis Routines) software performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts, and chemical data from a document.
has super-classes
Textual formatc
XMLc
Annotated text formatc

Over-representation datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3753

has super-classes
Datac
has sub-classes
GO-term enrichment datac, Pathway overrepresentation datac

OWL formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2197

has super-classes
Ontology formatc
RDF formatc
has sub-classes
Manchester OWL Syntaxc, OWL Functional Syntaxc, OWL/XMLc

OWL Functional Syntaxc back to ToC or Class ToC

IRI: http://edamontology.org/format_3252

has super-classes
OWL formatc
Textual formatc

OWL/XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3262

has super-classes
OWL formatc
XMLc

P-valuec back to ToC or Class ToC

IRI: http://edamontology.org/data_1669

A z-value might be specified as a threshold for reporting hits from database searches.
has super-classes
Statistical estimate scorec

Paediatricsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3418

has super-classes
Medicinec

Pain medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3401

has super-classes
Medicinec

pairc back to ToC or Class ToC

IRI: http://edamontology.org/format_1996

has super-classes
Alignment format (text)c

Pair sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1381

has super-classes
Sequence alignmentc

Pairwise protein tertiary structure alignment (all atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1487

has super-classes
deprecated classc

Pairwise protein tertiary structure alignment (C-alpha atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1488

C-beta atoms from amino acid side-chains may be included.
has super-classes
deprecated classc

Pairwise sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0491

Methods might perform one-to-one, one-to-many or many-to-many comparisons.
has super-classes
Sequence alignmentc
has outputop some Pair sequence alignmentc

Pairwise sequence alignment generation (global)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0494

Global alignment methods identify similarity across the entire length of the sequences.
has super-classes
deprecated classc

Pairwise sequence alignment generation (local)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0493

Local alignment methods identify regions of local similarity.
has super-classes
deprecated classc

Pairwise structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0503

has super-classes
Structure alignmentc

Pairwise structure alignment generation (global)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0508

Global alignment methods identify similarity across the entire structures.
has super-classes
deprecated classc

Pairwise structure alignment generation (local)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0507

Local alignment methods identify regions of local similarity, common substructures etc.
has super-classes
deprecated classc

Paleogenomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3943

has super-classes
Genomicsc

Panther Families and HMMs entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1575

has super-classes
deprecated classc

Panther Pathways entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1655

has super-classes
deprecated classc

Parameterc back to ToC or Class ToC

IRI: http://edamontology.org/data_2527

has super-classes
deprecated classc

Parasitologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3302

has super-classes
Biomedical sciencec

Parsingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1812

has super-classes
Data handlingc
has inputop some Identifierc

Passwordc back to ToC or Class ToC

IRI: http://edamontology.org/data_1690

has super-classes
User IDc

Pathogenicity reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3718

has super-classes
Biosafety reportc

Pathogensc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0783

The resource may be specific to a pathogen, a group of pathogens or all pathogens.
has super-classes
deprecated classc

Pathologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0634

has super-classes
Medicinec
has sub-classes
Infectious diseasec, Rare diseasesc

Pathway analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3928

has super-classes
Analysisc
has topicop some Molecular interactions, pathways and networksc
has topicop some Systems biologyc
has sub-classes
Expression profile pathway mappingc, Metabolic network modellingc, Metabolic pathway predictionc, Pathway visualisationc

Pathway ID (aMAZE)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1156

has super-classes
deprecated classc

Pathway ID (BioCyc)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1157

has super-classes
Accessionc
BioCyc IDc
Pathway or network accessionc

Pathway ID (BioSystems)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2837

has super-classes
Accessionc
Pathway or network accessionc

Pathway ID (ConsensusPathDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2345

has super-classes
Accessionc
Pathway or network accessionc
ConsensusPathDB identifierc

Pathway ID (CPDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1160

This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined.
has super-classes
Accessionc
Pathway or network accessionc

Pathway ID (DQCS)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2670

has super-classes
Accessionc
Pathway or network accessionc

Pathway ID (INOH)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1158

has super-classes
Accessionc
Pathway or network accessionc

Pathway ID (KEGG)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2343

has super-classes
KEGG object identifierc
Accessionc
Pathway or network accessionc

Pathway ID (NCI-Nature)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2344

has super-classes
Accessionc
Pathway or network accessionc

Pathway ID (Panther)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1161

has super-classes
Accessionc
Pathway or network accessionc

Pathway ID (PATIKA)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1159

has super-classes
Accessionc
Pathway or network accessionc

Pathway ID (PharmGKB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2650

has super-classes
Accessionc
Pathway or network accessionc
PharmGKB IDc

Pathway ID (reactome)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1155

has super-classes
Accessionc
Pathway or network accessionc

Pathway ID (SMPDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2659

has super-classes
Accessionc
Pathway or network accessionc

Pathway ID (Unipathway)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2645

has super-classes
Accessionc
Pathway or network accessionc

Pathway ID (WikiPathways)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3952

has super-classes
Accessionc
Identifier (hybrid)c
Pathway or network accessionc

Pathway or networkc back to ToC or Class ToC

IRI: http://edamontology.org/data_2600

has super-classes
Datac
has topicop some Molecular interactions, pathways and networksc

Pathway or network accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2365

has super-classes
Pathway or network identifierc
has sub-classes
Pathway ID (BioCyc)c, Pathway ID (BioSystems)c, Pathway ID (CPDB)c, Pathway ID (ConsensusPathDB)c, Pathway ID (DQCS)c, Pathway ID (INOH)c, Pathway ID (KEGG)c, Pathway ID (NCI-Nature)c, Pathway ID (PATIKA)c, Pathway ID (Panther)c, Pathway ID (PharmGKB)c, Pathway ID (SMPDB)c, Pathway ID (Unipathway)c, Pathway ID (WikiPathways)c, Pathway ID (reactome)c, cPath IDc

Pathway or network analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2497

has super-classes
deprecated classc

Pathway or network annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0946

has super-classes
deprecated classc

Pathway or network comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0277

has super-classes
deprecated classc

Pathway or network datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2983

has super-classes
deprecated classc

Pathway or network identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1082

has super-classes
Identifier (by type of data)c
is identifier ofop some Pathway or networkc
has sub-classes
Pathway or network accessionc, Pathway or network namec

Pathway or network namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2342

has super-classes
Pathway or network identifierc

Pathway or network predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3439

has super-classes
deprecated classc

Pathway or network processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2438

has super-classes
deprecated classc

Pathway or network reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2984

has super-classes
Reportc
has topicop some Molecular interactions, pathways and networksc

Pathway or network visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3083

has super-classes
deprecated classc

Pathway overrepresentation datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3953

has super-classes
Over-representation datac
has topicop some Function analysisc

Pathway visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3926

has super-classes
Visualisationc
Pathway analysisc
has inputop some Pathway or networkc

PATIKA entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1651

has super-classes
deprecated classc

pbmc back to ToC or Class ToC

IRI: http://edamontology.org/format_3601

has super-classes
Binary formatc
Image formatc

PCAzipc back to ToC or Class ToC

IRI: http://edamontology.org/format_3874

The compression is made projecting the Cartesian snapshots collected along the trajectory into an orthogonal space defined by the most relevant eigenvectors obtained by diagonalization of the covariance matrix (PCA). In the compression/decompression process, part of the original information is lost, depending on the final number of eigenvectors chosen. However, with a reasonable choice of the set of eigenvectors the compression typically reduces the trajectory file to less than one tenth of their original size with very acceptable loss of information. Compression with PCAZip can only be applied to unsolvated structures.
has super-classes
Binary formatc
Trajectory format (binary)c

pcdc back to ToC or Class ToC

IRI: http://edamontology.org/format_3594

PCD was developed by Kodak. A PCD file contains five different resolution (ranging from low to high) of a slide or film negative. Due to it PCD is often used by many photographers and graphics professionals for high-end printed applications.
has super-classes
Binary formatc
Image formatc

Pcons report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1551

Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality.
has super-classes
Protein structure report (quality evaluation) formatc
Textual formatc

PCR experimentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3519

has super-classes
Laboratory techniquesc

PCR experiment reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0923

has super-classes
deprecated classc

PCR primer designc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0308

This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs.
has super-classes
Primer and probe designc
has topicop some Probes and primersc
has outputop some PCR primersc
has inputop some Nucleic acid sequencec

PCR primer design (based on gene structure)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0521

has super-classes
deprecated classc

PCR primer design (for conserved primers)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0520

has super-classes
deprecated classc

PCR primer design (for gene transcription profiling)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0519

has super-classes
deprecated classc

PCR primer design (for genotyping polymorphisms)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0518

has super-classes
deprecated classc

PCR primer design (for large scale sequencing)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0517

has super-classes
deprecated classc

PCR primer design (for methylation PCRs)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0522

has super-classes
deprecated classc

PCR primersc back to ToC or Class ToC

IRI: http://edamontology.org/data_1240

has super-classes
Sequence set (nucleic acid)c

pcxc back to ToC or Class ToC

IRI: http://edamontology.org/format_3595

has super-classes
Binary formatc
Image formatc

PDBc back to ToC or Class ToC

IRI: http://edamontology.org/format_1476

has super-classes
PDB database entry formatc
Textual formatc

PDB atom namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1748

has super-classes
Atom namec

PDB atom record formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1747

has super-classes
deprecated classc

PDB database entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1475

has super-classes
Tertiary structure formatc
is format ofop some Trajectory datac
is format ofop some Structurec
has sub-classes
PDBc, PDBMLc, mmCIFc, pdbatomc, pdbatomnucc, pdbseqresc, pdbseqresnucc

PDB file sequence retrievalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1845

has super-classes
deprecated classc

PDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1127

A PDB identification code which consists of 4 characters, the first of which is a digit in the range 0 - 9; the remaining 3 are alpha-numeric, and letters are upper case only. (source: https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1996.pdf)
has super-classes
Structure IDc
Accessionc

PDB insertion codec back to ToC or Class ToC

IRI: http://edamontology.org/data_1856

has super-classes
Sequence positionc

PDB model numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1759

has super-classes
Structure identifierc

PDB residue namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1758

has super-classes
Amino acid name (three letter)c

PDB residue numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1742

has super-classes
Sequence positionc

pdbatomc back to ToC or Class ToC

IRI: http://edamontology.org/format_1950

pdb format in EMBOSS.
has super-classes
PDB database entry formatc
Textual formatc
Sequence record format (text)c

pdbatomnucc back to ToC or Class ToC

IRI: http://edamontology.org/format_1951

pdbnuc format in EMBOSS.
has super-classes
PDB database entry formatc
Textual formatc
Sequence record format (text)c

PDBMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_1478

has super-classes
PDB database entry formatc
XMLc

pdbseqresc back to ToC or Class ToC

IRI: http://edamontology.org/format_1953

pdbseq format in EMBOSS.
has super-classes
PDB database entry formatc
Textual formatc
Sequence record format (text)c

pdbseqresnucc back to ToC or Class ToC

IRI: http://edamontology.org/format_1952

pdbnucseq format in EMBOSS.
has super-classes
PDB database entry formatc
Textual formatc
Sequence record format (text)c

PDFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3508

has super-classes
Binary formatc
Document formatc

Peak callingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3222

Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). "Peak-pair calling" is similar to "Peak calling" in the context of ChIP-exo.
has super-classes
Nucleic acid feature detectionc

Peak detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3215

has super-classes
Spectral analysisc
has inputop some Mass spectrumc

Pearson formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1954

has super-classes
FASTA-like (text)c

PEDc back to ToC or Class ToC

IRI: http://edamontology.org/format_3286

has super-classes
PED/MAPc

PED/MAPc back to ToC or Class ToC

IRI: http://edamontology.org/format_3288

has super-classes
Textual formatc
Individual genetic data formatc
has sub-classes
MAPc, PEDc

Peptide annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0895

has super-classes
deprecated classc

Peptide database searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3646

has super-classes
Database searchc
Peptide identificationc
has sub-classes
Blind peptide database searchc, Target-Decoyc

Peptide hydrophobic momentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1520

Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
has super-classes
Protein hydropathy datac

Peptide IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2906

has super-classes
Peptide identifierc
Molecule accessionc
has sub-classes
PeptideAtlas IDc

Peptide identificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0945

has super-classes
Protein propertyc
Peptide propertyc
has topicop some Proteomicsc

Peptide identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3631

has super-classes
Spectral analysisc
has inputop some Mass spectrumc
has sub-classes
PTM identificationc, Peptide database searchc, Spectral library searchc, Tag-based peptide identificationc, de Novo sequencingc

Peptide identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0988

has super-classes
Molecule identifierc
has sub-classes
Peptide IDc, Polypeptide chain IDc

Peptide immunogenicity datac back to ToC or Class ToC

IRI: http://edamontology.org/data_1534

This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
has super-classes
Protein propertyc
has sub-classes
Hopp and Woods plotc

Peptide immunogenicity predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0252

This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
has super-classes
Protein property calculationc
Protein function predictionc
has topicop some Immunologyc
has outputop some Peptide immunogenicity datac

Peptide mass fingerprintc back to ToC or Class ToC

IRI: http://edamontology.org/data_0944

A molecular weight standard fingerprint is standard protonated molecular masses e.g. from trypsin (modified porcine trypsin, Promega) and keratin peptides.
has super-classes
Mass spectrometry datac
Peptide propertyc
has topicop some Proteomicsc

Peptide molecular weight hitsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1262

has super-classes
Sequence set (protein)c

Peptide molecular weightsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1519

The report might include associated data such as frequency of peptide fragment molecular weights.
has super-classes
Protein propertyc

Peptide propertyc back to ToC or Class ToC

IRI: http://edamontology.org/data_2979

has super-classes
Molecular propertyc
has sub-classes
Peptide identificationc, Peptide mass fingerprintc

PeptideAtlas IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2626

has super-classes
Accessionc
Peptide IDc

Peptides and amino acidsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0613

has super-classes
deprecated classc

pepXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3655

has super-classes
XMLc
Mass spectrometry data formatc

Person identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2118

has super-classes
Identifier (by type of data)c
has sub-classes
Author IDc, Person namec, User IDc

Person namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1692

has super-classes
Person identifierc

Personalised medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3577

has super-classes
Medicinec

Pfam accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1138

has super-classes
Accessionc
Protein family accessionc

Pfam clan IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2758

has super-classes
Accessionc
Protein family accessionc

Pfam domain namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2757

has super-classes
Protein family namec

Pfam entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1576

has super-classes
deprecated classc

pgmc back to ToC or Class ToC

IRI: http://edamontology.org/format_3602

It is designed to be extremely easy to learn and write programs for.
has super-classes
Binary formatc
Image formatc

pgSnpc back to ToC or Class ToC

IRI: http://edamontology.org/format_3012

has super-classes
Textual formatc
Sequence annotation track formatc

Pharmacogenomic test reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1621

The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity.
has super-classes
Genotype/phenotype reportc

Pharmacogenomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0208

has super-classes
Pharmacologyc
Genomicsc

Pharmacologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0202

has super-classes
Biomedical sciencec
has sub-classes
Pharmacogenomicsc

Pharmacovigilancec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3378

Pharmacovigilence concerns safety once a drug has gone to market.
has super-classes
Safety sciencesc

PharmGKB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2649

has super-classes
Accessionc
Identifier (hybrid)c
has sub-classes
Disease ID (PharmGKB)c, Drug ID (PharmGKB)c, Pathway ID (PharmGKB)c

Phasingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3454

has super-classes
Diffraction data analysisc

PHDc back to ToC or Class ToC

IRI: http://edamontology.org/format_1633

has super-classes
Sequence trace formatc
Textual formatc

Phenomenon identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0981

has super-classes
deprecated classc

Phenomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3298

has super-classes
Genotype and phenotypec
Evolutionary biologyc
Omicsc

Phenotype namec back to ToC or Class ToC

IRI: http://edamontology.org/data_3275

has super-classes
Namec

Phosphorylation sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0751

has super-classes
deprecated classc

Phylip character frequencies formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1432

has super-classes
Phylogenetic continuous quantitative character formatc
Textual formatc

Phylip cliques formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1434

has super-classes
Phylogenetic tree report (cliques) formatc
Textual formatc

Phylip continuous quantitative charactersc back to ToC or Class ToC

IRI: http://edamontology.org/format_1430

has super-classes
Phylogenetic continuous quantitative character formatc
Textual formatc

Phylip discrete states formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1433

has super-classes
Phylogenetic discrete states formatc
Textual formatc

Phylip distance matrixc back to ToC or Class ToC

IRI: http://edamontology.org/format_1423

Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float).
has super-classes
Sequence distance matrix formatc
Textual formatc

PHYLIP formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1997

has super-classes
Phylip format variantc

Phylip format variantc back to ToC or Class ToC

IRI: http://edamontology.org/format_2924

has super-classes
Textual formatc
Sequence record format (text)c
Alignment format (text)c
has sub-classes
PHYLIP formatc, PHYLIP sequentialc, Relaxed PHYLIP Interleavedc, Relaxed PHYLIP Sequentialc

phylip property valuesc back to ToC or Class ToC

IRI: http://edamontology.org/format_2243

has super-classes
deprecated classc

phylip sequence formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1955

has super-classes
deprecated classc

PHYLIP sequentialc back to ToC or Class ToC

IRI: http://edamontology.org/format_1998

has super-classes
Phylip format variantc

Phylip tree distance formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1445

has super-classes
Phylogenetic tree report (tree distances) formatc
Textual formatc

Phylip tree formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1435

has super-classes
Textual formatc
Phylogenetic tree format (text)c

Phylip tree rawc back to ToC or Class ToC

IRI: http://edamontology.org/format_1425

has super-classes
Textual formatc
Phylogenetic tree format (text)c

phylipnon sequence formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1956

has super-classes
deprecated classc

Phylogenetic analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0324

Phylgenetic modelling is the modelling of trait evolution and prediction of trait values using phylogeny as a basis.
has super-classes
Analysisc
has topicop some Phylogenyc
has sub-classes
Allele frequency distribution analysisc, Ancestral reconstructionc, Phylogenetic tree bootstrappingc, Phylogenetic tree comparisonc, Phylogenetic tree constructionc, Phylogenetic tree editingc, Phylogenetic tree topology analysisc, Phylogenetic tree visualisationc, Tree datingc

Phylogenetic character cliquesc back to ToC or Class ToC

IRI: http://edamontology.org/data_1428

has super-classes
Phylogenetic datac

Phylogenetic character contrastsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1444

has super-classes
Phylogenetic datac

Phylogenetic character datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0871

As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments
has super-classes
Phylogenetic datac
has sub-classes
Phylogenetic continuous quantitative datac, Phylogenetic discrete datac

Phylogenetic character data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2036

has super-classes
Format (by type of data)c
is format ofop some Phylogenetic character datac
has sub-classes
Phylogenetic continuous quantitative character formatc, Phylogenetic discrete states formatc, Phylogenetic tree report (cliques) formatc, Phylogenetic tree report (invariants) formatc

Phylogenetic character weightsc back to ToC or Class ToC

IRI: http://edamontology.org/data_2994

has super-classes
Phylogenetic datac

Phylogenetic consensus treec back to ToC or Class ToC

IRI: http://edamontology.org/data_2247

has super-classes
deprecated classc

Phylogenetic continuous quantitative character formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2037

has super-classes
Phylogenetic character data formatc
is format ofop some Phylogenetic continuous quantitative datac
has sub-classes
Phylip character frequencies formatc, Phylip continuous quantitative charactersc

Phylogenetic continuous quantitative datac back to ToC or Class ToC

IRI: http://edamontology.org/data_1426

has super-classes
Phylogenetic character datac
has sub-classes
Phylogenetic gene frequencies datac

Phylogenetic datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2523

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Datac
has sub-classes
Phylogenetic character cliquesc, Phylogenetic character contrastsc, Phylogenetic character datac, Phylogenetic character weightsc, Phylogenetic invariantsc, Phylogenetic treec, Phylogenetic tree distancesc

Phylogenetic discrete datac back to ToC or Class ToC

IRI: http://edamontology.org/data_1427

has super-classes
Phylogenetic character datac

Phylogenetic discrete states formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2038

has super-classes
Phylogenetic character data formatc
is format ofop some Phylogenetic discrete datac
has sub-classes
Phylip discrete states formatc

Phylogenetic distance matrix identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1067

has super-classes
deprecated classc

Phylogenetic footprintingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0327

Phylogenetic shadowing is a type of footprinting where many closely related species are used. A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation.
has super-classes
Phylogenetic tree constructionc
has topicop some Phylogenomicsc

Phylogenetic gene frequencies datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2873

has super-classes
Phylogenetic continuous quantitative datac

Phylogenetic invariantsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1429

has super-classes
Phylogenetic datac
has topicop some Genetic variationc

Phylogenetic property valuesc back to ToC or Class ToC

IRI: http://edamontology.org/data_2242

has super-classes
deprecated classc

Phylogenetic property values formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1431

has super-classes
deprecated classc

Phylogenetic reconstructionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3478

Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one.
has super-classes
Phylogenetic tree constructionc
has topicop some Phylogenyc

Phylogenetic reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1438

This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis.
has super-classes
deprecated classc

Phylogenetic sub/super tree constructionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0556

has super-classes
Phylogenetic tree comparisonc

Phylogenetic treec back to ToC or Class ToC

IRI: http://edamontology.org/data_0872

A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'.
has super-classes
Phylogenetic datac
has topicop some Phylogenyc
has sub-classes
Gene treec, Species treec

Phylogenetic tree annotationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0558

has super-classes
Annotationc

Phylogenetic tree bootstrappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0552

has super-classes
Phylogenetic analysisc
Validationc

Phylogenetic tree comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0325

For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc.
has super-classes
Phylogenetic analysisc
Comparisonc
has sub-classes
Consensus tree constructionc, Phylogenetic sub/super tree constructionc, Phylogenetic tree distances calculationc, Phylogenetic tree reconciliationc

Phylogenetic tree constructionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0323

Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated.
has super-classes
Phylogenetic analysisc
Generationc
has outputop some Phylogenetic treec
has topicop some Sequence analysisc
has sub-classes
Consensus tree constructionc, Gene tree constructionc, Phylogenetic footprintingc, Phylogenetic reconstructionc, Phylogenetic tree construction (data centric)c, Phylogenetic tree construction (method centric)c, Species tree constructionc

Phylogenetic tree construction (AI methods)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0549

has super-classes
Phylogenetic tree construction (method centric)c

Phylogenetic tree construction (data centric)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0538

Subconcepts of this concept reflect different types of data used to generate a tree, and provide an alternate axis for curation.
has super-classes
Phylogenetic tree constructionc
has sub-classes
Phylogenetic tree construction (from continuous quantitative characters)c, Phylogenetic tree construction (from gene frequencies)c, Phylogenetic tree construction (from molecular sequences)c, Phylogenetic tree construction (from polymorphism data)c

Phylogenetic tree construction (from continuous quantitative characters)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0541

has super-classes
Phylogenetic tree construction (data centric)c
has inputop some Phylogenetic continuous quantitative datac

Phylogenetic tree construction (from gene frequencies)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0542

has super-classes
Phylogenetic tree construction (data centric)c
has topicop some Gene expressionc
has inputop some Phylogenetic gene frequencies datac

Phylogenetic tree construction (from molecular sequences)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0540

Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions.
has super-classes
Phylogenetic tree construction (data centric)c
Sequence analysisc

Phylogenetic tree construction (from polymorphism data)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0543

has super-classes
Phylogenetic tree construction (data centric)c
has topicop some Genetic variationc

Phylogenetic tree construction (maximum likelihood and Bayesian methods)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0547

Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm.
has super-classes
Phylogenetic tree construction (method centric)c

Phylogenetic tree construction (method centric)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0539

Subconcepts of this concept reflect different computational methods used to generate a tree, and provide an alternate axis for curation.
has super-classes
Phylogenetic tree constructionc
has sub-classes
Phylogenetic tree construction (AI methods)c, Phylogenetic tree construction (maximum likelihood and Bayesian methods)c, Phylogenetic tree construction (minimum distance methods)c, Phylogenetic tree construction (parsimony methods)c, Phylogenetic tree construction (quartet methods)c

Phylogenetic tree construction (minimum distance methods)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0546

This includes neighbor joining (NJ) clustering method.
has super-classes
Phylogenetic tree construction (method centric)c

Phylogenetic tree construction (parsimony methods)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0545

This includes evolutionary parsimony (invariants) methods.
has super-classes
Phylogenetic tree construction (method centric)c

Phylogenetic tree construction (quartet methods)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0548

has super-classes
Phylogenetic tree construction (method centric)c

Phylogenetic tree distancesc back to ToC or Class ToC

IRI: http://edamontology.org/data_1442

has super-classes
Phylogenetic datac

Phylogenetic tree distances calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0557

has super-classes
Phylogenetic tree comparisonc
has outputop some Phylogenetic tree distancesc

Phylogenetic tree editingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0326

has super-classes
Phylogenetic analysisc
Editingc
has outputop some Phylogenetic treec
has inputop some Phylogenetic treec

Phylogenetic tree formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2006

has super-classes
Format (by type of data)c
is format ofop some Phylogenetic treec
has sub-classes
Phylogenetic tree format (XML)c, Phylogenetic tree format (text)c

Phylogenetic tree format (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2556

has super-classes
Phylogenetic tree formatc
has sub-classes
ClustalW dendrogramc, Nexus formatc, Phylip tree formatc, Phylip tree rawc, TreeBASE formatc, TreeCon formatc, TreeFam formatc, newickc

Phylogenetic tree format (XML)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2557

has super-classes
Phylogenetic tree formatc
has sub-classes
NeXMLc, phyloXMLc

Phylogenetic tree IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1068

has super-classes
Identifier (by type of data)c
is identifier ofop some Phylogenetic treec
has sub-classes
Ensembl gene tree IDc, TreeBASE study accession numberc, TreeFam accession numberc

Phylogenetic tree imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1707

See also 'Phylogenetic tree'
has super-classes
Imagec

Phylogenetic tree processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2443

has super-classes
deprecated classc

Phylogenetic tree reconciliationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3947

Methods typically test for topological similarity between trees using for example a congruence index.
has super-classes
Phylogenetic tree comparisonc

Phylogenetic tree report (cliques) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2039

has super-classes
Phylogenetic character data formatc
is format ofop some Phylogenetic character cliquesc
has sub-classes
Phylip cliques formatc

Phylogenetic tree report (invariants) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2040

has super-classes
Phylogenetic character data formatc
is format ofop some Phylogenetic invariantsc

Phylogenetic tree report (tree distances) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2049

has super-classes
Format (by type of data)c
is format ofop some Phylogenetic tree distancesc
has sub-classes
Phylip tree distance formatc

Phylogenetic tree report (tree evaluation)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1441

has super-classes
deprecated classc

Phylogenetic tree report (tree shape)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1440

has super-classes
deprecated classc

Phylogenetic tree report (tree stratigraphic)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1443

has super-classes
deprecated classc

Phylogenetic tree topology analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0551

has super-classes
Phylogenetic analysisc

Phylogenetic tree typec back to ToC or Class ToC

IRI: http://edamontology.org/data_1122

For example 'nj', 'upgmp' etc.
has super-classes
deprecated classc

Phylogenetic tree visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0567

has super-classes
Phylogenetic analysisc
Visualisationc
has outputop some Phylogenetic treec

Phylogeneticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3293

has super-classes
Sequence analysisc
Phylogenyc

Phylogenomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0194

has super-classes
Sequence analysisc
Genomicsc

Phylogenyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0084

This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc.
has super-classes
Evolutionary biologyc
Computational biologyc
has sub-classes
Cladisticsc, Phylogeneticsc

Phylogeny reconstructionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0191

Currently too specific for the topic sub-ontology (but might be unobsoleted).
has super-classes
deprecated classc

Phylogeny visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2257

has super-classes
deprecated classc

phyloXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3159

has super-classes
XMLc
Phylogenetic tree format (XML)c

Physical mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1280

Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.
has super-classes
Mapc
has sub-classes
Cytogenetic mapc, Radiation hybrid mapc, Sequence mapc

Physical mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2944

has super-classes
DNA mappingc
has outputop some Physical mapc
has topicop some Mappingc
has sub-classes
Bisulfite mappingc, Radiation Hybrid Mappingc, Read mappingc, Sequence tagged site (STS) mappingc

Physicochemical property data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2417

has super-classes
deprecated classc

Physicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3318

has super-classes
Topicc
has sub-classes
Biophysicsc

Physiologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3300

has super-classes
Medicinec

Physiology parameterc back to ToC or Class ToC

IRI: http://edamontology.org/data_3722

has super-classes
Experimental measurementc

Pileupc back to ToC or Class ToC

IRI: http://edamontology.org/format_3015

has super-classes
Textual formatc
Alignment format (pair only)c

pirc back to ToC or Class ToC

IRI: http://edamontology.org/format_1976

has super-classes
deprecated classc

PIR identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1100

has super-classes
Sequence accession (protein)c
Accessionc

PIRSF entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1573

has super-classes
deprecated classc

PIRSF IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1136

has super-classes
Accessionc
Protein family accessionc

pklc back to ToC or Class ToC

IRI: http://edamontology.org/format_3653

Differ from .dta only in subtleties of the header line format and content and support the added feature of being able to.
has super-classes
Mass spectrometry data formatc

plain text format (unformatted)c back to ToC or Class ToC

IRI: http://edamontology.org/format_1964

has super-classes
Textual formatc

Plant biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0780

The resource may be specific to a plant, a group of plants or all plants.
has super-classes
Biologyc

Plant Ontology concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1180

has super-classes
Ontology concept IDc
Accessionc

Plant ontology termc back to ToC or Class ToC

IRI: http://edamontology.org/data_1720

has super-classes
deprecated classc

PlasMapper TextMapc back to ToC or Class ToC

IRI: http://edamontology.org/format_1861

has super-classes
Map formatc
Textual formatc

Plasmid identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2208

has super-classes
Nucleic acid identifierc

Plasmid mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1286

has super-classes
Sequence mapc

Plasmid map drawingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0578

has super-classes
Map drawingc

Plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_2884

has super-classes
Datac
has sub-classes
Base pairing probability matrix dotplotc, Fickett testcode plotc, Histogramc, Hopp and Woods plotc, Nucleic acid density plotc, Ordination plotc, Protein ionisation curvec, Protein titration curvec, Sequence composition plotc, Sequence similarity plotc

Plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3441

has super-classes
deprecated classc

pmcc back to ToC or Class ToC

IRI: http://edamontology.org/format_1739

has super-classes
Article formatc
Textual formatc

PMMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3726

One or more mining models can be contained in a PMML document.
has super-classes
XMLc

PNGc back to ToC or Class ToC

IRI: http://edamontology.org/format_3603

It iis expected to replace the Graphics Interchange Format (GIF).
has super-classes
Binary formatc
Image formatc

POc back to ToC or Class ToC

IRI: http://edamontology.org/format_3330

has super-classes
Alignment format (text)c

PolyA signal detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0428

has super-classes
Nucleic acid feature detectionc

PolyA signal or sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1302

has super-classes
deprecated classc

Polymorphism detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3202

has super-classes
deprecated classc

Polymorphism report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2051

has super-classes
deprecated classc

Polypeptide chain IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1008

This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA
has super-classes
Peptide identifierc
is identifier ofop some Protein chainc

Population geneticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3056

has super-classes
Geneticsc

Population genomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3796

has super-classes
Genomicsc

Position frequency matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_1361

has super-classes
Position-specific scoring matrixc

Position weight matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_1362

Contributions of individual sequences to the matrix might be uneven (weighted).
has super-classes
Position-specific scoring matrixc

Position-specific scoring matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_2854

has super-classes
Sequence profilec
Matrixc
has sub-classes
Fingerprintc, Information content matrixc, Position frequency matrixc, Position weight matrixc

ppmc back to ToC or Class ToC

IRI: http://edamontology.org/format_3596

has super-classes
Binary formatc
Image formatc

pptxc back to ToC or Class ToC

IRI: http://edamontology.org/format_3838

has super-classes
XMLc
Image formatc

Preclinical and clinical studiesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3379

has super-classes
Medicines research and developmentc
Experimental design and studiesc

Prediction and recognitionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2423

has super-classes
Operationc
has sub-classes
Antimicrobial resistance predictionc, Gene regulatory network predictionc, Genetic code predictionc, Metabolic pathway predictionc, Molecular dynamicsc, Nucleic acid feature detectionc, Nucleic acid structure predictionc, Primer and probe designc, Protein architecture recognitionc, Protein disorder predictionc, Protein feature detectionc, Protein function predictionc, Protein identificationc, Protein property calculationc, Protein quaternary structure predictionc, Protein secondary structure predictionc, Protein structure assignmentc, Protein structure predictionc, Sequence feature detectionc, Splicing analysisc, Text miningc, Variant effect predictionc, Virulence predictionc

Prediction and recognition (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3024

has super-classes
deprecated classc

Prediction and recognition (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3023

has super-classes
deprecated classc

PRIDE experiment accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1145

has super-classes
Experiment annotation IDc

PRIDE XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3684

has super-classes
XMLc
Experiment annotation formatc
Mass spectrometry data formatc

Primer and probe designc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2419

has super-classes
Prediction and recognitionc
Nucleic acid designc
has topicop some Probes and primersc
has sub-classes
Microarray probe designc, PCR primer designc

Primer or probe designc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3032

has super-classes
deprecated classc

Primer removalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3237

has super-classes
Sequence cuttingc

Primer3 internal oligo mishybridizing libraryc back to ToC or Class ToC

IRI: http://edamontology.org/data_1242

has super-classes
deprecated classc

Primer3 mispriming library filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1243

has super-classes
deprecated classc

Primer3 primerc back to ToC or Class ToC

IRI: http://edamontology.org/format_1627

has super-classes
Nucleic acid features (primers) formatc
Textual formatc

Primersc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0922

has super-classes
deprecated classc

primersearch primer pairs sequence recordc back to ToC or Class ToC

IRI: http://edamontology.org/data_1244

has super-classes
deprecated classc

Principal component visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2939

The use of Principal Component Analysis (PCA), a multivariate statistical analysis to obtain collective variables on the atomic positional fluctuations, helps to separate the configurational space in two subspaces: an “essential” subspace containing relevant motions, and another one containing irrelevant local fluctuations.
has super-classes
Visualisationc

PRINTS codec back to ToC or Class ToC

IRI: http://edamontology.org/data_1137

has super-classes
Accessionc
Protein family accessionc

PRINTS entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1574

has super-classes
deprecated classc

Probabilistic data generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3480

has super-classes
Generationc
has sub-classes
Probabilistic sequence generationc

Probabilistic sequence generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3481

has super-classes
Sequence generationc
Probabilistic data generationc

proBAMc back to ToC or Class ToC

IRI: http://edamontology.org/format_3826

has super-classes
Sequence trace formatc
Binary formatc
Alignment format (pair only)c

proBEDc back to ToC or Class ToC

IRI: http://edamontology.org/format_3827

has super-classes
Textual formatc
Sequence annotation track formatc

Probes and primersc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0632

This includes the design of primers for PCR and DNA amplification or the design of molecular probes.
has super-classes
Sequence analysisc

Processed microarray datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3111

Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip.
has super-classes
Microarray hybridisation datac
has topicop some Gene expressionc

ProDom accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1142

ProDom is a protein domain family database.
has super-classes
Accessionc
Protein family accessionc

ProDom entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1580

has super-classes
deprecated classc

Profile HMMc back to ToC or Class ToC

IRI: http://edamontology.org/data_3949

has super-classes
Sequence profilec
Hidden Markov modelc

Profile-profile alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_0868

has super-classes
deprecated classc

Profile-profile alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0298

has super-classes
deprecated classc

Profile-profile alignment (pairwise)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0511

Methods might perform one-to-one, one-to-many or many-to-many comparisons.
has super-classes
deprecated classc

Prokaryotes and Archaeac back to ToC or Class ToC

IRI: http://edamontology.org/topic_1811

The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes.
has super-classes
deprecated classc

Proline mutation value calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1842

has super-classes
deprecated classc

Promoter IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2727

has super-classes
Identifier (by type of data)c
has sub-classes
ABS IDc, EPD IDc

Promoter predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0440

Methods might recognize CG content, CpG islands, splice sites, polyA signals etc.
has super-classes
Transcriptional regulatory element predictionc
has sub-classes
Exonic splicing enhancer predictionc, Transcription factor binding site predictionc

Promotersc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0111

has super-classes
deprecated classc

Promotersc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1312

has super-classes
deprecated classc

ProQ report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1552

ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features.
has super-classes
Protein structure report (quality evaluation) formatc
Textual formatc

Prosite accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1117

has super-classes
Sequence motif identifierc

Prosite nucleotide patternc back to ToC or Class ToC

IRI: http://edamontology.org/data_1358

has super-classes
deprecated classc

Prosite protein patternc back to ToC or Class ToC

IRI: http://edamontology.org/data_1359

has super-classes
deprecated classc

prosite-patternc back to ToC or Class ToC

IRI: http://edamontology.org/format_1356

has super-classes
Sequence motif formatc
Textual formatc

prosite-profilec back to ToC or Class ToC

IRI: http://edamontology.org/format_1366

has super-classes
Sequence profile formatc
Textual formatc

proteinc back to ToC or Class ToC

IRI: http://edamontology.org/format_1208

Non-sequence characters may be used for gaps and translation stop.
has super-classes
Textual formatc
Raw sequence formatc
has sub-classes
completely unambiguous pure proteinc, pure proteinc, unambiguous pure proteinc

Protein accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2907

has super-classes
Protein identifierc
Molecule accessionc
has sub-classes
Ensembl protein IDc, Enzyme IDc, HPA antibody idc, IMGT/HLA IDc, LGICdb identifierc, Protein ID (CORUM)c, Protein ID (ConoServer)c, Protein ID (CuticleDB)c, Protein ID (DisProt)c, Protein ID (EMBL/GenBank/DDBJ)c, Protein ID (EcID)c, Protein ID (LGICdb)c, Protein ID (PeroxiBase)c, Protein ID (TopDB)c, Signaling Gateway protein IDc, TCIDc, Target ID (TTD)c, Transcription factor accessionc, WormBase wormpep IDc, iHOP symbolc

Protein active site signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1378

A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available.
has super-classes
deprecated classc

Protein active sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3533

has super-classes
deprecated classc

Protein alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_3154

has super-classes
deprecated classc

Protein aliphatic indexc back to ToC or Class ToC

IRI: http://edamontology.org/data_1521

The aliphatic index is the relative protein volume occupied by aliphatic side chains.
has super-classes
Protein hydropathy datac

Protein aliphatic index calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0406

has super-classes
Protein hydropathy calculationc
has outputop some Protein aliphatic indexc

Protein analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2502

has super-classes
deprecated classc

Protein and peptide identificationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0767

has super-classes
deprecated classc

Protein architecture analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0247

has super-classes
Protein structure analysisc
has sub-classes
Protein architecture comparisonc, Protein architecture recognitionc

Protein architecture comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2474

has super-classes
Protein architecture analysisc
Protein comparisonc

Protein architecture recognitionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2475

Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces.
has super-classes
Protein architecture analysisc
Prediction and recognitionc
Structure classificationc

Protein architecture reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0902

has super-classes
deprecated classc

Protein atomc back to ToC or Class ToC

IRI: http://edamontology.org/data_1755

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
Protein structurec

Protein atom surface calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2460

Waters are not considered.
has super-classes
deprecated classc

Protein atom surface calculation (accessible molecular)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1818

Waters are not considered.
has super-classes
deprecated classc

Protein atom surface calculation (accessible)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1817

Waters are not considered.
has super-classes
deprecated classc

Protein binding site prediction (from sequence)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0419

has super-classes
deprecated classc

Protein binding site prediction (from structure)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0388

has super-classes
deprecated classc

Protein binding site signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1379

A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification.
has super-classes
deprecated classc

Protein binding sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3534

has super-classes
Protein sites, features and motifsc

Protein chainc back to ToC or Class ToC

IRI: http://edamontology.org/data_1467

has super-classes
Protein structurec

Protein chain (all atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1471

has super-classes
deprecated classc

Protein chain (C-alpha atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1472

C-beta atoms from amino acid side-chains may be included.
has super-classes
deprecated classc

Protein charge plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_1523

has super-classes
Protein propertyc

Protein chemical modificationsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3537

has super-classes
deprecated classc

Protein classificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2980

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Protein classificationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0595

has super-classes
deprecated classc

Protein cleavage site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0422

has super-classes
Protein feature detectionc
has topicop some Proteomicsc

Protein cleavage sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3536

has super-classes
deprecated classc

Protein cleavage sites and proteolysisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0141

has super-classes
deprecated classc

Protein comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2997

has super-classes
Comparisonc
has sub-classes
Differential protein expression analysisc, Fold recognitionc, Protein architecture comparisonc, Protein function comparisonc, Protein property comparisonc, Protein secondary structure comparisonc, Protein structure comparisonc

Protein complexc back to ToC or Class ToC

IRI: http://edamontology.org/data_2877

has super-classes
Protein structurec

Protein conserved site signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1377

A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification.
has super-classes
deprecated classc

Protein contact mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1547

has super-classes
Protein interaction datac

Protein crystallizabilityc back to ToC or Class ToC

IRI: http://edamontology.org/data_1525

has super-classes
Protein hydropathy datac

Protein crystallizability predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0410

has super-classes
Protein hydropathy calculationc
has outputop some Protein crystallizabilityc

Protein cysteine and disulfide bond assignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1850

has super-classes
Protein structure assignmentc
has topicop some Protein folding, stability and designc
has sub-classes
Cysteine bridge detectionc, Free cysteine detectionc, Metal-bound cysteine detectionc

Protein datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2524

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Protein databasesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2225

has super-classes
deprecated classc

Protein designc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0150

has super-classes
deprecated classc

Protein dipole momentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1545

has super-classes
Protein propertyc

Protein dipole moment calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0386

has super-classes
Protein property calculationc
has outputop some Protein dipole momentc

Protein disorder predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3904

has super-classes
Prediction and recognitionc
Protein feature detectionc
has topicop some Microbiologyc

Protein disordered structurec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3538

has super-classes
Protein structure analysisc

Protein distance matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_1546

has super-classes
Protein interaction datac
Distance matrixc

Protein distance matrix calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0391

has super-classes
Residue distance calculationc
has outputop some Protein distance matrixc
has sub-classes
Contact map calculationc

Protein domainc back to ToC or Class ToC

IRI: http://edamontology.org/data_1468

has super-classes
Protein structurec
has topicop some Protein folds and structural domainsc

Protein domain (all atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1473

has super-classes
deprecated classc

Protein domain (C-alpha atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1474

C-beta atoms from amino acid side-chains may be included.
has super-classes
deprecated classc

Protein domain classificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0900

has super-classes
deprecated classc

Protein domain classification formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3097

has super-classes
Format (by type of data)c
is format ofop some Protein family reportc
has sub-classes
CATH domain report formatc, InterProScan XMLc, Raw CATH domain classification formatc, Raw SCOP domain classification formatc

Protein domain classification nodec back to ToC or Class ToC

IRI: http://edamontology.org/data_3101

has super-classes
deprecated classc

Protein domain IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1038

This is typically a character or string concatenated with a PDB identifier and a chain identifier.
has super-classes
Identifier (by type of data)c
is identifier ofop some Protein domainc
has sub-classes
CATH identifierc, CDD IDc, SCOP domain identifierc

Protein domain recognitionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0246

has super-classes
Protein structure analysisc
Protein feature detectionc
has topicop some Protein folds and structural domainsc
has sub-classes
Protein peelingc

Protein domain signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1373

Protein domain signatures identify structural or functional domains or other units with defined boundaries.
has super-classes
deprecated classc

Protein domainsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3539

has super-classes
deprecated classc

Protein expressionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0108

has super-classes
Proteinsc
has sub-classes
Protein modificationsc, Protein targeting and localisationc, Protein variantsc

Protein extinction coefficientc back to ToC or Class ToC

IRI: http://edamontology.org/data_1531

has super-classes
Protein propertyc

Protein extinction coefficient calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0399

has super-classes
Protein property calculationc
has outputop some Protein extinction coefficientc

Protein familiesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0724

has super-classes
deprecated classc

Protein family accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2910

has super-classes
Protein family identifierc
has sub-classes
Gene3D IDc, HAMAP IDc, InterPro accessionc, PIRSF IDc, PRINTS codec, Pfam accession numberc, Pfam clan IDc, ProDom accession numberc, Protein family ID (GeneFarm)c, Protein family ID (PANTHER)c, SMART accession numberc, Superfamily hidden Markov model numberc, TCDB IDc, TIGRFam IDc

Protein family ID (GeneFarm)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2731

has super-classes
Accessionc
Protein family accessionc

Protein family ID (PANTHER)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2783

has super-classes
Accessionc
Protein family accessionc

Protein family identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1075

has super-classes
Identifier (by type of data)c
is identifier ofop some Protein family reportc
has sub-classes
Protein family accessionc, Protein family namec

Protein family namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1131

has super-classes
Protein family identifierc
Namec
has sub-classes
InterPro entry namec, Pfam domain namec, SMART domain namec

Protein family reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0907

has super-classes
Protein reportc
has topicop some Gene and protein familiesc

Protein family report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2052

has super-classes
Format (by type of data)c
is format ofop some Protein family reportc

Protein family signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1372

Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures.
has super-classes
deprecated classc

Protein feature detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3092

Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group.
has super-classes
Prediction and recognitionc
Protein sequence analysisc
has outputop some Protein featuresc
has topicop some Sequence sites, features and motifsc
has topicop some Proteinsc
has sub-classes
Binding site predictionc, Disulfide bond predictionc, Epitope mappingc, Fold recognitionc, PTM site predictionc, Protein cleavage site predictionc, Protein disorder predictionc, Protein domain recognitionc, Protein secondary structure predictionc, Protein signal peptide detectionc, Structural motif discoveryc

Protein feature detectionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3074

has super-classes
deprecated classc

Protein feature identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1019

has super-classes
deprecated classc

Protein feature prediction (from sequence)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0414

Methods typically involve scanning for known motifs, patterns and regular expressions.
has super-classes
deprecated classc

Protein feature prediction (from structure)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3090

has super-classes
deprecated classc

Protein featuresc back to ToC or Class ToC

IRI: http://edamontology.org/data_1277

This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features.
has super-classes
Protein reportc
Sequence featuresc

Protein features (domains) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2542

has super-classes
deprecated classc

Protein features (epitopes)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1327

Epitope mapping is commonly done during vaccine design.
has super-classes
deprecated classc

Protein features (mutation)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0904

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
deprecated classc

Protein features (PEST sites)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1331

'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically.
has super-classes
deprecated classc

Protein features (post-translation modifications)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1324

has super-classes
deprecated classc

Protein features (sites)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1321

Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids.
has super-classes
deprecated classc

Protein features report (active sites)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1325

has super-classes
deprecated classc

Protein features report (binding sites)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1326

has super-classes
deprecated classc

Protein features report (chemical modifications)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2191

has super-classes
deprecated classc

Protein features report (cleavage sites)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1323

has super-classes
deprecated classc

Protein features report (disordered structure)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2722

has super-classes
deprecated classc

Protein features report (domains)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0901

has super-classes
deprecated classc

Protein features report (key folding sites)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2989

has super-classes
deprecated classc

Protein features report (nucleic acid binding sites)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1328

has super-classes
deprecated classc

Protein features report (repeats)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3129

has super-classes
deprecated classc

Protein features report (secondary structure)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0876

has super-classes
deprecated classc

Protein features report (signal peptides)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1322

has super-classes
deprecated classc

Protein features report (super-secondary)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0877

Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
has super-classes
deprecated classc

Protein flexibility or motion reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1541

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
deprecated classc

Protein fold namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1867

has super-classes
Namec

Protein fold recognitionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0180

has super-classes
deprecated classc

Protein fold recognition reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1564

Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
has super-classes
deprecated classc

Protein folding analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2415

has super-classes
Protein structure analysisc
Modelling and simulationc
has outputop some Protein structure reportc
has topicop some Protein folding, stability and designc

Protein folding pathway predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0329

has super-classes
deprecated classc

Protein folding reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0903

has super-classes
deprecated classc

Protein folding simulationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0328

has super-classes
deprecated classc

Protein folding site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0421

has super-classes
deprecated classc

Protein folding, stability and designc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0130

has super-classes
Protein structure analysisc

Protein folds and structural domainsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0736

This includes topological domains such as cytoplasmic regions in a protein.
has super-classes
Protein structure analysisc

Protein fragment weight comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2929

has super-classes
Protein molecular weight calculationc
Protein property comparisonc

Protein function analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2414

has super-classes
deprecated classc

Protein function comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1778

has super-classes
Protein function predictionc
Protein comparisonc
has topicop some Function analysisc

Protein function predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1777

For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead.
has super-classes
Prediction and recognitionc
Analysisc
has topicop some Function analysisc
has sub-classes
Binding site predictionc, Molecular dockingc, Peptide immunogenicity predictionc, Protein function comparisonc, Protein signal peptide detectionc, Protein-nucleic acid interaction analysisc, Protein-protein interaction analysisc, Subcellular localisation predictionc

Protein function predictionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2276

has super-classes
deprecated classc

Protein function prediction (from sequence)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3084

For functional properties that are positional, use 'Protein site detection' instead.
has super-classes
deprecated classc

Protein geometry calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0249

has super-classes
Protein property calculationc
has outputop some Protein geometry datac
has sub-classes
Ramachandran plot calculationc

Protein geometry datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2991

has super-classes
Protein propertyc
has sub-classes
Ramachandran plotc

Protein geometry validationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1844

has super-classes
Protein structure validationc

Protein globularityc back to ToC or Class ToC

IRI: http://edamontology.org/data_1526

has super-classes
Protein hydropathy datac

Protein globularity predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0408

has super-classes
Protein hydropathy calculationc
has outputop some Protein globularityc

Protein hydrogen bondsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1549

has super-classes
Protein interaction datac

Protein hydrogen exchange ratec back to ToC or Class ToC

IRI: http://edamontology.org/data_1530

has super-classes
Protein propertyc

Protein hydrogen exchange rate calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0404

has super-classes
Protein pKa calculationc
has outputop some Protein hydrogen exchange ratec

Protein hydropathyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0137

has super-classes
deprecated classc

Protein hydropathy calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2574

has super-classes
Protein property calculationc
has outputop some Protein hydropathy datac
has topicop some Protein propertiesc
has sub-classes
Protein aliphatic index calculationc, Protein crystallizability predictionc, Protein globularity predictionc, Protein hydrophobic moment plottingc, Protein hydrophobic region calculationc, Protein solubility predictionc

Protein hydropathy calculation (from sequence)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0401

has super-classes
deprecated classc

Protein hydropathy calculation (from structure)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0383

has super-classes
deprecated classc

Protein hydropathy cluster calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0385

has super-classes
deprecated classc

Protein hydropathy datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2970

has super-classes
Protein propertyc
has sub-classes
Peptide hydrophobic momentc, Protein aliphatic indexc, Protein crystallizabilityc, Protein globularityc, Protein sequence hydropathy plotc, Protein solubilityc

Protein hydrophobic moment plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0407

Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
has super-classes
Sequence visualisationc
Protein hydropathy calculationc
has outputop some Peptide hydrophobic momentc

Protein hydrophobic region calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0405

has super-classes
Protein hydropathy calculationc

Protein ID (ConoServer)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2804

has super-classes
Accessionc
Protein accessionc

Protein ID (CORUM)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2713

has super-classes
Accessionc
Protein accessionc

Protein ID (CuticleDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2715

has super-classes
Accessionc
Protein accessionc

Protein ID (DisProt)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2723

has super-classes
Accessionc
Protein accessionc

Protein ID (EcID)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2802

has super-classes
Accessionc
Protein accessionc

Protein ID (EMBL/GenBank/DDBJ)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3029

This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein.
has super-classes
Accessionc
Protein accessionc

Protein ID (LGICdb)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2797

has super-classes
Accessionc
Protein accessionc

Protein ID (PeroxiBase)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2792

has super-classes
Accessionc
Protein accessionc

Protein ID (TopDB)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2789

has super-classes
Accessionc
Protein accessionc

Protein identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3767

has super-classes
Prediction and recognitionc
Spectral analysisc
has inputop some Mass spectrumc

Protein identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0989

has super-classes
Molecule identifierc
is identifier ofop some Protein reportc
has sub-classes
Enzyme identifierc, Protein accessionc, Protein namec, Transcription factor identifierc

Protein imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_3153

has super-classes
Imagec
has sub-classes
Protein secondary structure imagec, Protein structure imagec

Protein interaction datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0906

has super-classes
Protein propertyc
has topicop some Protein interactionsc
has sub-classes
Protein contact mapc, Protein distance matrixc, Protein hydrogen bondsc, Protein residue 3D clusterc, Protein-ligand interaction reportc

Protein interaction data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2405

has super-classes
deprecated classc

Protein interaction experimentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3957

This used to have the ID http://edamontology.org/topic_3557 but the numerical part (owing to an error) duplicated http://edamontology.org/operation_3557 ('Imputation'). ID of this concept set to http://edamontology.org/topic_3957 in EDAM 1.24.
has super-classes
Laboratory techniquesc

Protein interaction formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2054

has super-classes
Format (by type of data)c
is format ofop some Protein interaction datac
has sub-classes
PSI MI TAB (MITAB)c, PSI MI XML (MIF)c, STRING entry format (XML)c

Protein interaction IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1074

has super-classes
Identifier (by type of data)c
is identifier ofop some Protein interaction datac
has sub-classes
BIND accession numberc, BioGRID interaction IDc, DIP IDc, IntAct accession numberc, MINT IDc, MatrixDB interaction IDc, STRING IDc, iRefIndex IDc

Protein interaction network analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0276

has super-classes
Protein-protein interaction analysisc
Network analysisc
has topicop some Protein interactionsc
has outputop some Pathway or network reportc

Protein interaction network predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3094

has super-classes
Protein-protein interaction analysisc
Network analysisc

Protein interaction network processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2445

has super-classes
deprecated classc

Protein interaction network visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0572

has super-classes
deprecated classc

Protein interaction networksc back to ToC or Class ToC

IRI: http://edamontology.org/data_1663

has super-classes
deprecated classc

Protein interaction networksc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3044

has super-classes
deprecated classc

Protein interaction predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2492

has super-classes
Protein-protein interaction analysisc
has outputop some Protein interaction datac
has topicop some Protein interactionsc

Protein interaction raw datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0905

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
Experimental measurementc

Protein interaction raw data analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0273

has super-classes
deprecated classc

Protein interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0128

This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques.
has super-classes
Proteinsc
Molecular interactions, pathways and networksc

Protein ionisation curvec back to ToC or Class ToC

IRI: http://edamontology.org/data_2165

has super-classes
Protein propertyc
Plotc

Protein isoelectric pointc back to ToC or Class ToC

IRI: http://edamontology.org/data_1528

has super-classes
Protein propertyc

Protein isoelectric point calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0403

has super-classes
Protein pKa calculationc
has outputop some Protein isoelectric pointc

Protein key folding sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3540

has super-classes
deprecated classc

Protein membrane regionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1456

has super-classes
deprecated classc

Protein microarraysc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0135

has super-classes
deprecated classc

Protein modellingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0477

The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimisation etc.
has super-classes
Protein structure predictionc
Modelling and simulationc
has topicop some Molecular modellingc
has sub-classes
Backbone modellingc, Loop modellingc, Side chain modellingc

Protein modification IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2618

has super-classes
Identifier (by type of data)c
has sub-classes
RESID IDc, Unimod IDc

Protein modificationsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0601

EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000)
has super-classes
Protein expressionc

Protein molecular weight calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0398

has super-classes
Protein property calculationc
has outputop some Peptide molecular weightsc
has topicop some Proteomicsc
has sub-classes
Protein fragment weight comparisonc

Protein namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1009

has super-classes
Molecule namec
Protein identifierc
has sub-classes
Enzyme namec, Kinase namec, Protein name (UniProt)c, Transcription factor namec

Protein name (UniProt)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2764

has super-classes
Protein namec

Protein non-canonical interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1550

has super-classes
deprecated classc

Protein non-covalent interactions reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1540

has super-classes
deprecated classc

Protein optical densityc back to ToC or Class ToC

IRI: http://edamontology.org/data_1532

has super-classes
Protein propertyc

Protein peelingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0390

has super-classes
Protein domain recognitionc

Protein pKa calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0400

has super-classes
Protein property calculationc
has outputop some Protein propertyc
has topicop some Protein propertiesc
has sub-classes
Protein hydrogen exchange rate calculationc, Protein isoelectric point calculationc, Protein titration curve plottingc

Protein pKa valuec back to ToC or Class ToC

IRI: http://edamontology.org/data_1529

has super-classes
Protein propertyc

Protein post-translational modification signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1380

A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible.
has super-classes
deprecated classc

Protein post-translational modificationsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3541

has super-classes
deprecated classc

Protein propertiesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0123

has super-classes
Proteinsc

Protein propertyc back to ToC or Class ToC

IRI: http://edamontology.org/data_0897

This is a broad data type and is used a placeholder for other, more specific types. Data may be based on analysis of nucleic acid sequence or structural data, for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure).
has super-classes
Molecular propertyc
has sub-classes
Enzyme kinetics datac, Ordination plotc, Peptide identificationc, Peptide immunogenicity datac, Peptide molecular weightsc, Protein charge plotc, Protein dipole momentc, Protein extinction coefficientc, Protein geometry datac, Protein hydrogen exchange ratec, Protein hydropathy datac, Protein interaction datac, Protein ionisation curvec, Protein isoelectric pointc, Protein optical densityc, Protein pKa valuec, Protein secondary structurec, Protein solvent accessibilityc, Protein titration curvec, Rate of associationc

Protein property calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0250

This includes methods to render and visualise the properties of a protein sequence, and a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc.
has super-classes
Prediction and recognitionc
Calculationc
has sub-classes
3D-1D scoring matrix generationc, Enzyme kinetics calculationc, Peptide immunogenicity predictionc, Protein dipole moment calculationc, Protein extinction coefficient calculationc, Protein geometry calculationc, Protein hydropathy calculationc, Protein molecular weight calculationc, Protein pKa calculationc, Residue contact predictionc, Residue interaction calculationc, Simulation analysisc, Spectrum calculationc

Protein property calculation (from sequence)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3088

has super-classes
deprecated classc

Protein property calculation (from structure)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0243

has super-classes
deprecated classc

Protein property comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2930

has super-classes
Protein comparisonc
has outputop some Protein propertyc
has sub-classes
Protein fragment weight comparisonc

Protein quantificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3630

has super-classes
Spectral analysisc
Quantificationc
has inputop some Mass spectrumc
has sub-classes
Label-free quantificationc, Labeled quantificationc, MRM/SRMc

Protein quaternary structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3350

has super-classes
Prediction and recognitionc

Protein region signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1374

A protein region signature defines a region which cannot be described as a protein family or domain signature.
has super-classes
deprecated classc

Protein repeat signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1375

A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain.
has super-classes
deprecated classc

Protein reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0896

has super-classes
Reportc
has sub-classes
Protein family reportc, Protein featuresc, Protein structure reportc

Protein report (enzyme) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2063

has super-classes
deprecated classc

Protein report (function)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1776

For properties that can be mapped to a sequence, use 'Sequence report' instead.
has super-classes
deprecated classc

Protein report (membrane protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2401

has super-classes
deprecated classc

Protein report (transcription factor)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2147

This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites.
has super-classes
deprecated classc

Protein report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2062

has super-classes
Format (by type of data)c
is format ofop some Protein reportc
has sub-classes
BcFormsc

Protein residuec back to ToC or Class ToC

IRI: http://edamontology.org/data_1756

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
Protein structurec

Protein residue 3D clusterc back to ToC or Class ToC

IRI: http://edamontology.org/data_1548

has super-classes
Protein interaction datac

Protein residue interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0144

has super-classes
deprecated classc

Protein residue surface calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2461

has super-classes
deprecated classc

Protein residue surface calculation (accessible molecular)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1821

Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
has super-classes
deprecated classc

Protein residue surface calculation (accessible)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1819

Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
has super-classes
deprecated classc

Protein residue surface calculation (vacuum accessible)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1820

Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
has super-classes
deprecated classc

Protein residue surface calculation (vacuum molecular)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1822

Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
has super-classes
deprecated classc

Protein secondary database searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0340

has super-classes
deprecated classc

Protein secondary structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_2956

has super-classes
Protein propertyc

Protein secondary structurec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0694

This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data.
has super-classes
deprecated classc

Protein secondary structurec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3542

Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
has super-classes
Protein structure analysisc

Protein secondary structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_0878

has super-classes
Secondary structure alignmentc

Protein secondary structure alignment generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0501

has super-classes
deprecated classc

Protein secondary structure analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2416

has super-classes
Protein structure analysisc
has outputop some Protein secondary structurec
has topicop some Protein structure analysisc
has sub-classes
Protein secondary structure comparisonc, Protein secondary structure predictionc

Protein secondary structure assignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0319

has super-classes
Protein structure assignmentc
has topicop some Protein structure analysisc
has topicop some Structural biologyc

Protein secondary structure assignment (from CD data)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0535

has super-classes
deprecated classc

Protein secondary structure assignment (from coordinate data)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0534

has super-classes
deprecated classc

Protein secondary structure comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2488

has super-classes
Protein secondary structure analysisc
Protein comparisonc

Protein secondary structure formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2077

has super-classes
Format (by type of data)c
has sub-classes
dsspc, hsspc

Protein secondary structure imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1709

has super-classes
Protein imagec
has sub-classes
Helical netc, Helical wheelc

Protein secondary structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0267

Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc.
has super-classes
Protein secondary structure analysisc
Prediction and recognitionc
Protein sequence analysisc
Protein feature detectionc
has sub-classes
Protein secondary structure prediction (coils)c, Protein secondary structure prediction (helices)c, Protein secondary structure prediction (turns)c, Protein super-secondary structure predictionc, Transmembrane protein predictionc

Protein secondary structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0178

has super-classes
deprecated classc

Protein secondary structure prediction (coils)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0470

has super-classes
Protein secondary structure predictionc

Protein secondary structure prediction (helices)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0468

has super-classes
Protein secondary structure predictionc

Protein secondary structure prediction (integrated)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0467

has super-classes
deprecated classc

Protein secondary structure prediction (turns)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0469

has super-classes
Protein secondary structure predictionc

Protein secondary structure processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2444

has super-classes
deprecated classc

Protein secondary structure visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0569

has super-classes
deprecated classc

Protein sequencec back to ToC or Class ToC

IRI: http://edamontology.org/data_2976

has super-classes
Sequencec
has sub-classes
Protein sequence recordc

Protein sequence (raw)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2974

has super-classes
deprecated classc

Protein sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1384

has super-classes
Sequence alignmentc

Protein sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0741

A sequence profile typically represents a sequence alignment.
has super-classes
deprecated classc

Protein sequence alignment analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2506

has super-classes
deprecated classc

Protein sequence analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2479

has super-classes
Sequence analysisc
has topicop some Proteinsc
has inputop some Protein sequencec
has sub-classes
Fold recognitionc, Protein feature detectionc, Protein secondary structure predictionc, Protein structure predictionc, Residue contact predictionc

Protein sequence analysisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0639

has super-classes
deprecated classc

Protein sequence cleavagec back to ToC or Class ToC

IRI: http://edamontology.org/operation_0366

has super-classes
Sequence generationc
has outputop some Proteolytic digestc
has topicop some Proteomicsc

Protein sequence comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2509

has super-classes
deprecated classc

Protein sequence compositionc back to ToC or Class ToC

IRI: http://edamontology.org/data_3085

has super-classes
deprecated classc

Protein sequence feature detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3087

has super-classes
deprecated classc

Protein sequence hydropathy plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_1522

Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation.
has super-classes
Protein hydropathy datac

Protein sequence properties plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_2164

has super-classes
deprecated classc

Protein sequence recordc back to ToC or Class ToC

IRI: http://edamontology.org/data_2886

has super-classes
Sequence recordc
Protein sequencec

Protein sequence record (full)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2888

has super-classes
deprecated classc

Protein sequence record (lite)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2047

has super-classes
deprecated classc

Protein sequence repeatsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3543

has super-classes
deprecated classc

Protein sequence visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2516

Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here.
has super-classes
deprecated classc

Protein sequence-structure scoring matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_0892

has super-classes
Matrixc
has sub-classes
3D-1D scoring matrixc

Protein sequencesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3043

has super-classes
deprecated classc

Protein signal peptide detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0418

Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.
has super-classes
Protein function predictionc
Protein feature detectionc
has topicop some Protein targeting and localisationc

Protein signal peptide detection (bacteria)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0412

has super-classes
deprecated classc

Protein signal peptide detection (eukaryotes)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0411

has super-classes
deprecated classc

Protein signal peptidesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3544

has super-classes
deprecated classc

Protein signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1355

has super-classes
Sequence signature reportc

Protein signature typec back to ToC or Class ToC

IRI: http://edamontology.org/data_2357

has super-classes
deprecated classc

Protein site signaturec back to ToC or Class ToC

IRI: http://edamontology.org/data_1376

A protein site signature is a classifier for a specific site in a protein.
has super-classes
deprecated classc

Protein sites and featuresc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0748

has super-classes
deprecated classc

Protein sites, features and motifsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3510

A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle.
has super-classes
Proteinsc
Sequence sites, features and motifsc
has sub-classes
Protein binding sitesc

Protein SNP mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0330

has super-classes
deprecated classc

Protein solubilityc back to ToC or Class ToC

IRI: http://edamontology.org/data_1524

has super-classes
Protein hydropathy datac

Protein solubility predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0409

has super-classes
Protein hydropathy calculationc
has outputop some Protein solubilityc

Protein solvent accessibilityc back to ToC or Class ToC

IRI: http://edamontology.org/data_1542

This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc.
has super-classes
Protein propertyc

Protein structural motifc back to ToC or Class ToC

IRI: http://edamontology.org/data_2878

has super-classes
Protein structurec

Protein structural motifs and surfacesc back to ToC or Class ToC

IRI: http://edamontology.org/data_0899

has super-classes
deprecated classc

Protein structural motifs and surfacesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0166

This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc.
has super-classes
Protein structure analysisc

Protein structural quality reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1539

Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc.
has super-classes
Protein structure reportc

Protein structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_1460

has super-classes
Structurec
has topicop some Protein structure analysisc
has sub-classes
C-alpha tracec, Protein atomc, Protein chainc, Protein complexc, Protein domainc, Protein residuec, Protein structural motifc, Protein-ligand complexc

Protein structure (all atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1469

has super-classes
deprecated classc

Protein structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1481

has super-classes
Structure alignmentc

Protein structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2826

has super-classes
deprecated classc

Protein structure analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2406

has super-classes
Structure analysisc
has inputop some Protein structurec
has topicop some Protein structure analysisc
has sub-classes
Fold recognitionc, Protein architecture analysisc, Protein domain recognitionc, Protein folding analysisc, Protein secondary structure analysisc, Protein structure assignmentc, Protein structure comparisonc, Protein structure predictionc, Protein structure validationc, Structural motif discoveryc

Protein structure analysisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2814

has super-classes
Proteinsc
Structure analysisc
has sub-classes
Protein disordered structurec, Protein folding, stability and designc, Protein folds and structural domainsc, Protein secondary structurec, Protein structural motifs and surfacesc

Protein structure assignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0320

has super-classes
Protein structure analysisc
Prediction and recognitionc
has topicop some Structural biologyc
has outputop some Protein structurec
has sub-classes
Protein cysteine and disulfide bond assignmentc, Protein secondary structure assignmentc

Protein structure assignment (from NMR data)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0537

has super-classes
deprecated classc

Protein structure assignment (from X-ray crystallographic data)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0536

has super-classes
deprecated classc

Protein structure comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2487

Methods might identify structural neighbors, find structural similarities or define a structural core.
has super-classes
Protein structure analysisc
Structure comparisonc
Protein comparisonc
has inputop some Protein structurec

Protein structure comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0143

Use this concept for methods that are exclusively for protein structure.
has super-classes
deprecated classc

Protein structure imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_2992

has super-classes
Structure imagec
Protein imagec

Protein structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0474

has super-classes
Protein structure analysisc
Prediction and recognitionc
Protein sequence analysisc
has outputop some Protein structurec
has sub-classes
Ab initio structure predictionc, Protein modellingc

Protein structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0172

has super-classes
deprecated classc

Protein structure raw datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2537

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
Experimental measurementc
has sub-classes
CD spectrac, Electron density mapc, Raw NMR datac

Protein structure reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1537

has super-classes
Protein reportc
Structure reportc
has sub-classes
Protein structural quality reportc

Protein structure report (quality evaluation) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2065

has super-classes
Format (by type of data)c
is format ofop some Protein structural quality reportc
has sub-classes
Pcons report formatc, ProQ report formatc

Protein structure validationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0321

The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc.
has super-classes
Protein structure analysisc
Validationc
has outputop some Protein structural quality reportc
has topicop some Molecular modellingc
has sub-classes
Maximum occurence analysisc, Protein geometry validationc, Residue bump detectionc, Residue packing validationc

Protein subcellular localisationc back to ToC or Class ToC

IRI: http://edamontology.org/data_1533

has super-classes
deprecated classc

Protein super-secondary structurec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3531

has super-classes
deprecated classc

Protein super-secondary structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0268

Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
has super-classes
Protein secondary structure predictionc
has outputop some Protein featuresc

Protein surface calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2462

has super-classes
deprecated classc

Protein surface calculation (accessible molecular)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1823

has super-classes
deprecated classc

Protein surface calculation (accessible)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1824

has super-classes
deprecated classc

Protein surface reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1543

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
deprecated classc

Protein targeting and localisationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0140

has super-classes
Protein expressionc

Protein tertiary structurec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0698

has super-classes
deprecated classc

Protein tertiary structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0179

has super-classes
deprecated classc

Protein threadingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0302

Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
has super-classes
Fold recognitionc
has inputop some Protein structurec
has outputop some Sequence-structure alignmentc

Protein titration curvec back to ToC or Class ToC

IRI: http://edamontology.org/data_1527

has super-classes
Protein propertyc
Plotc

Protein titration curve plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0402

has super-classes
Visualisationc
Protein pKa calculationc
has outputop some Protein titration curvec

Protein topological domainsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3118

has super-classes
deprecated classc

Protein topologyc back to ToC or Class ToC

IRI: http://edamontology.org/data_0875

The location and size of the secondary structure elements and intervening loop regions is usually indicated.
has super-classes
deprecated classc

Protein variantsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3120

has super-classes
Protein expressionc

Protein-drug interaction reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2402

has super-classes
deprecated classc

Protein-drug interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3515

has super-classes
deprecated classc

Protein-ligand complexc back to ToC or Class ToC

IRI: http://edamontology.org/data_1461

This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead.
has super-classes
Protein structurec

Protein-ligand dockingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0482

Virtual screening is used in drug discovery to search libraries of small molecules in order to identify those molecules which are most likely to bind to a drug target (typically a protein receptor or enzyme).
has super-classes
Molecular dockingc
has topicop some Protein interactionsc
has outputop some Protein-ligand complexc
has sub-classes
Virtual screeningc

Protein-ligand interaction reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1566

has super-classes
Protein interaction datac

Protein-ligand interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0148

has super-classes
deprecated classc

Protein-ligand interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3514

has super-classes
deprecated classc

Protein-metal contact calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1834

has super-classes
Residue interaction calculationc

Protein-motif interactionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2378

has super-classes
deprecated classc

Protein-nucleic acid binding sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3535

has super-classes
deprecated classc

Protein-nucleic acid interaction analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0389

has super-classes
Protein function predictionc
has topicop some Protein interactionsc
has sub-classes
DNA-binding protein predictionc, RNA-binding protein predictionc

Protein-nucleic acid interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0149

has super-classes
deprecated classc

Protein-nucleic acid interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3525

has super-classes
deprecated classc

Protein-nucleic acid interactions reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1567

has super-classes
deprecated classc

Protein-protein binding site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2464

has super-classes
Binding site predictionc
has outputop some Protein interaction datac
has topicop some Protein interactionsc

Protein-protein dockingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3899

has super-classes
Molecular dockingc
has topicop some Protein interactionsc
has outputop some Protein-ligand complexc

Protein-protein interaction analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2949

has super-classes
Protein function predictionc
has topicop some Protein interactionsc
has outputop some Protein interaction datac
has sub-classes
Protein interaction network analysisc, Protein interaction network predictionc, Protein interaction predictionc

Protein-protein interaction prediction (from protein sequence)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0274

has super-classes
deprecated classc

Protein-protein interaction prediction (from protein structure)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0275

has super-classes
deprecated classc

Protein-protein interaction reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1565

has super-classes
deprecated classc

Protein-protein interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0147

has super-classes
deprecated classc

Protein-protein interactionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3526

has super-classes
deprecated classc

Proteinsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0078

has super-classes
Computational biologyc
has sub-classes
Enzymesc, Gene and protein familiesc, Membrane and lipoproteinsc, Protein expressionc, Protein interactionsc, Protein propertiesc, Protein sites, features and motifsc, Protein structure analysisc, Transcription factors and regulatory sitesc

Proteogenomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3922

has super-classes
Genomicsc

Proteolytic digestc back to ToC or Class ToC

IRI: http://edamontology.org/data_1238

has super-classes
Sequence set (protein)c
has topicop some Proteomicsc

Proteomec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0644

has super-classes
deprecated classc

ProteomeXchange IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3759

has super-classes
Experiment annotation IDc

Proteomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0121

Includes metaproteomics: proteomics analysis of an environmental sample.
has super-classes
Omicsc

Proteomics experimentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3520

This includes two-dimensional gel electrophoresis (2D PAGE) experiments, gels or spots in a gel. Also mass spectrometry - an analytical chemistry technique that measures the mass-to-charge ratio and abundance of ions in the gas phase. Also Northern blot experiments.
has super-classes
Laboratory techniquesc

Proteomics experiment reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3426

has super-classes
deprecated classc

Protocolc back to ToC or Class ToC

IRI: http://edamontology.org/data_2531

has super-classes
Reportc

protXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3747

No human-consumable information about this format is available (see http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML).
has super-classes
XMLc
Mass spectrometry data formatc

Proximity map plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2937

has super-classes
Expression data visualisationc

PSc back to ToC or Class ToC

IRI: http://edamontology.org/format_3696

has super-classes
Textual formatc
has sub-classes
EPSc

psdc back to ToC or Class ToC

IRI: http://edamontology.org/format_3597

has super-classes
Binary formatc
Image formatc

PSDMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3851

has super-classes
Sequence feature annotation formatc
XMLc

PseudoCAP gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2328

has super-classes
deprecated classc

PSFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3882

The high similarity in the functional form of the two potential energy functions used by AMBER and CHARMM force-fields gives rise to the possible use of one force-field within the other MD engine. Therefore, the conversion of PSF files to AMBER Prmtop format is possible with the use of AMBER chamber (CHARMM - AMBER) program.
has super-classes
Tertiary structure formatc
Textual formatc
Topology formatc

PSI MI TAB (MITAB)c back to ToC or Class ToC

IRI: http://edamontology.org/format_3242

has super-classes
Protein interaction formatc
Textual formatc

PSI MI XML (MIF)c back to ToC or Class ToC

IRI: http://edamontology.org/format_3158

has super-classes
Protein interaction formatc
XMLc
has sub-classes
PSI-PARc

PSI-PARc back to ToC or Class ToC

IRI: http://edamontology.org/format_3243

has super-classes
PSI MI XML (MIF)c

Psiblast checkpoint filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1236

A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'.
has super-classes
deprecated classc

PSLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3007

has super-classes
Textual formatc
Sequence annotation track formatc
Alignment format (pair only)c

Psychiatryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3419

has super-classes
Medicinec

PTM identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3645

has super-classes
Peptide identificationc
has sub-classes
PTM localisationc

PTM localisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3755

has super-classes
PTM identificationc

PTM site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0417

Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc.
has super-classes
Protein feature detectionc
has topicop some Protein modificationsc

PubAnnotation formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3781

has super-classes
JSONc
Annotated text formatc

PubChem bioassay IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2638

has super-classes
Identifier (by type of data)c
PubChem IDc

PubChem CIDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1172

has super-classes
PubChem IDc
Compound accessionc

PubChem entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1701

has super-classes
deprecated classc

PubChem IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2639

has super-classes
Accessionc
Identifier (hybrid)c
has sub-classes
PubChem CIDc, PubChem bioassay IDc

Public health and epidemiologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3305

has super-classes
Medicinec

PubMed citationc back to ToC or Class ToC

IRI: http://edamontology.org/format_1734

has super-classes
Textual formatc
Bibliographic reference formatc

PubMed IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1187

has super-classes
Article IDc
Accessionc

PubMed XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3848

has super-classes
XMLc
Bibliographic reference formatc

PubTator formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3783

has super-classes
Textual formatc
Annotated text formatc

purec back to ToC or Class ToC

IRI: http://edamontology.org/format_2094

has super-classes
Textual formatc
Raw sequence formatc
has sub-classes
completely unambiguous purec, pure nucleotidec, pure proteinc, unambiguous purec

pure dnac back to ToC or Class ToC

IRI: http://edamontology.org/format_1215

has super-classes
pure nucleotidec
dnac

Pure mathematicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3570

has super-classes
Mathematicsc

pure nucleotidec back to ToC or Class ToC

IRI: http://edamontology.org/format_1210

has super-classes
nucleotidec
purec
has sub-classes
pure dnac, pure rnac

pure proteinc back to ToC or Class ToC

IRI: http://edamontology.org/format_1219

has super-classes
proteinc
purec

pure rnac back to ToC or Class ToC

IRI: http://edamontology.org/format_1217

has super-classes
pure nucleotidec
rnac

Q-valuec back to ToC or Class ToC

IRI: http://edamontology.org/data_3932

Q-values are widely used in high-throughput data analysis (e.g. detection of differentially expressed genes from transcriptome data).
has super-classes
Statistical estimate scorec

qcMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3683

The focus of qcML is towards mass spectrometry based proteomics, but the format is suitable for metabolomics and sequencing as well.
has super-classes
XMLc
Experiment annotation formatc
Mass spectrometry data formatc

QSAR descriptorc back to ToC or Class ToC

IRI: http://edamontology.org/data_0847

QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties.
has super-classes
Molecular property (general)c
has sub-classes
QSAR descriptor (constitutional)c, QSAR descriptor (electronic)c, QSAR descriptor (geometrical)c, QSAR descriptor (molecular)c, QSAR descriptor (topological)c

QSAR descriptor (constitutional)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1201

has super-classes
QSAR descriptorc

QSAR descriptor (electronic)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1202

has super-classes
QSAR descriptorc

QSAR descriptor (geometrical)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1203

has super-classes
QSAR descriptorc

QSAR descriptor (molecular)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1205

has super-classes
QSAR descriptorc

QSAR descriptor (topological)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1204

has super-classes
QSAR descriptorc

QSAR descriptor namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1061

has super-classes
Namec
Molecular property identifierc
is identifier ofop some QSAR descriptorc

QTL mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1860

has super-classes
Genetic mapc

Quadruplex formation site detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0429

Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets.
has super-classes
Nucleic acid feature detectionc
has outputop some Nucleic acid structure reportc

qualc back to ToC or Class ToC

IRI: http://edamontology.org/format_3607

Phred quality scores are defined as a property which is logarithmically related to the base-calling error probabilities.
has super-classes
FASTQ-like format (text)c
Textual formatc
Sequence quality report format (text)c
has sub-classes
qual454c, qualilluminac, qualsolexac, qualsolidc

qual454c back to ToC or Class ToC

IRI: http://edamontology.org/format_3611

has super-classes
qualc

qualilluminac back to ToC or Class ToC

IRI: http://edamontology.org/format_3609

Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 "B", is used also at the end of reads as a Read Segment Quality Control Indicator.
has super-classes
FASTQ-illuminac
qualc

Quality affairsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3393

has super-classes
Medicines research and developmentc

Quality control reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3914

has super-classes
Reportc

qualsolexac back to ToC or Class ToC

IRI: http://edamontology.org/format_3608

Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)
has super-classes
FASTQ-solexac
qualc

qualsolidc back to ToC or Class ToC

IRI: http://edamontology.org/format_3610

For SOLiD data, the sequence is in color space, except the first position. The quality values are those of the Sanger format.
has super-classes
qualc

Quantificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3799

has super-classes
Operationc
has sub-classes
Protein quantificationc, RNA-Seq quantificationc

Quantitative geneticsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3055

has super-classes
Genotype and phenotypec

Quantitative trait locusc back to ToC or Class ToC

IRI: http://edamontology.org/data_1906

A QTL sometimes but does not necessarily correspond to a gene.
has super-classes
deprecated classc

Query and retrievalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0224

has super-classes
Data handlingc
has topicop some Biological databasesc
has outputop some Datac
has sub-classes
Data retrievalc, Database searchc

Query languagec back to ToC or Class ToC

IRI: http://edamontology.org/format_3787

has super-classes
Format (by type of data)c
is format ofop some Query scriptc

Query scriptc back to ToC or Class ToC

IRI: http://edamontology.org/data_3786

has super-classes
Datac

quicktandemc back to ToC or Class ToC

IRI: http://edamontology.org/format_1295

has super-classes
Sequence features (repeats) formatc
Textual formatc

R file formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3554

has super-classes
Textual formatc

Radiation hybrid mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_2870

The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map.
has super-classes
Physical mapc

Radiation Hybrid Mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0485

has super-classes
Physical mappingc
has outputop some Radiation hybrid mapc

Ramachandran plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_1544

has super-classes
Protein geometry datac

Ramachandran plot calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0396

has super-classes
Protein geometry calculationc
has outputop some Ramachandran plotc

Ramachandran plot validationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0397

has super-classes
deprecated classc

Random sequence generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0364

has super-classes
Sequence generationc

Rare diseasesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3325

has super-classes
Pathologyc

Rarefactionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3797

has super-classes
Calculationc

rastc back to ToC or Class ToC

IRI: http://edamontology.org/format_3605

The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.
has super-classes
Binary formatc
Image formatc

Rate of associationc back to ToC or Class ToC

IRI: http://edamontology.org/data_3451

has super-classes
Protein propertyc

rawc back to ToC or Class ToC

IRI: http://edamontology.org/format_1957

has super-classes
Textual formatc
Raw sequence formatc

Raw CATH domain classificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2236

These are the parsable data files provided by CATH.
has super-classes
deprecated classc

Raw CATH domain classification formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3099

These are the parsable data files provided by CATH.
has super-classes
Protein domain classification formatc

Raw imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_3424

has super-classes
Imagec
has sub-classes
2D PAGE imagec, EM Micrographc, EM Moviec, MRI imagec, Microarray spots imagec, Northern blot imagec

Raw microarray datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3110

Such data as found in Affymetrix CEL or GPR files.
has super-classes
Experimental measurementc
Microarray hybridisation datac

Raw microarray data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3828

has super-classes
Format (by type of data)c
is format ofop some Raw microarray datac
has sub-classes
GPRc

Raw NMR datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0938

has super-classes
Protein structure raw datac

Raw SCOP domain classificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2235

These are the parsable data files provided by SCOP.
has super-classes
deprecated classc

Raw SCOP domain classification formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3098

These are the parsable data files provided by SCOP.
has super-classes
Protein domain classification formatc

Raw sequencec back to ToC or Class ToC

IRI: http://edamontology.org/data_0848

Non-sequence characters may be used for example for gaps and translation stop.
has super-classes
deprecated classc

Raw sequence formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2571

has super-classes
Format (by type of data)c
is format ofop some Sequencec
has sub-classes
.nibc, 2bitc, BioJSON (BioXSD)c, BioXSD (XML)c, BioYAMLc, BpFormsc, ambiguousc, completely unambiguousc, mshc, nucleotidec, proteinc, purec, rawc, unambiguous sequencec, unpurec

rccc back to ToC or Class ToC

IRI: http://edamontology.org/format_3580

has super-classes
Gene expression report formatc
Textual formatc

RDF formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2376

has super-classes
Formatc
Ontology formatc
Linked data formatc
has sub-classes
JSON-LDc, N-Quadsc, N-Triplesc, Notation3c, OWL formatc, Open Annotation formatc, RDF/XMLc, Turtlec, UniProtKB RDFc

RDF/XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3261

RDF/XML is a serialisation syntax for OWL DL, but not for OWL Full.
has super-classes
XMLc
RDF formatc

Reaction datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2978

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Datac
has sub-classes
Enzyme kinetics datac

Reaction IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2108

has super-classes
Identifier (by type of data)c
is identifier ofop some Reaction datac
has sub-classes
Reaction ID (BioCyc)c, Reaction ID (KEGG)c, Reaction ID (MACie)c, Reaction ID (Rhea)c, Reaction ID (SABIO-RK)c

Reaction ID (BioCyc)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2106

has super-classes
Accessionc
BioCyc IDc
Reaction IDc

Reaction ID (KEGG)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2608

has super-classes
KEGG object identifierc
Reaction IDc

Reaction ID (MACie)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2641

has super-classes
Accessionc
Reaction IDc

Reaction ID (Rhea)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2644

has super-classes
Accessionc
Reaction IDc

Reaction ID (SABIO-RK)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2309

has super-classes
Accessionc
Reaction IDc
has sub-classes
Reaction kinetics ID (SABIO-RK)c

Reaction kinetics ID (SABIO-RK)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2648

has super-classes
Reaction ID (SABIO-RK)c

Reactome entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1652

has super-classes
deprecated classc

Read binningc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3798

Binning methods use one or a combination of compositional features or sequence similarity.
has super-classes
Sequence read processingc

Read depth analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3230

has super-classes
Sequence read processingc

Read mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3198

The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences.
has super-classes
Physical mappingc
Sequence read processingc
has sub-classes
Split read mappingc

Read pre-processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3219

For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on.
has super-classes
Sequencing quality controlc
Sequence read processingc

Read summarisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3793

has super-classes
Sequence read processingc

REBASE enzyme numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_2325

has super-classes
Accessionc
Enzyme IDc

REBASE proto enzyme report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1515

has super-classes
deprecated classc

REBASE restriction sitesc back to ToC or Class ToC

IRI: http://edamontology.org/format_1320

has super-classes
Nucleic acid features (restriction sites) formatc
Textual formatc

REBASE withrefm enzyme report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1516

has super-classes
deprecated classc

Recombination detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0451

Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on.
has super-classes
DNA testingc

REDIdb IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2781

has super-classes
Sequence accession (nucleic acid)c
Accessionc

Reference identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3703

has super-classes
Genetic variation analysisc

Reference map name (SWISS-2DPAGE)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2791

has super-classes
Namec
Gel IDc

Reference sample reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3567

has super-classes
Reportc

RefSeq accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1098

has super-classes
Accessionc
Sequence accession (hybrid)c
has sub-classes
Clone ID (RefSeq)c, Gene ID (NCBI)c, RefSeq accession (protein)c

RefSeq accession (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2385

has super-classes
RefSeq accessionc

refseqpc back to ToC or Class ToC

IRI: http://edamontology.org/format_1958

Currently identical to genpept format
has super-classes
Textual formatc
Sequence record format (text)c

Regenerative medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3395

has super-classes
Biomedical sciencec

Regression analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3659

has super-classes
Statistical calculationc

Regular expressionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1352

has super-classes
Datac

Regulatory affairsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3394

has super-classes
Medicines research and developmentc

Regulatory RNAc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3060

has super-classes
deprecated classc

Relation extractionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3625

has super-classes
Text miningc

Relax-NG schemac back to ToC or Class ToC

IRI: http://edamontology.org/data_2251

has super-classes
deprecated classc

Relaxed PHYLIP Interleavedc back to ToC or Class ToC

IRI: http://edamontology.org/format_3819

It differs from Phylip Format (format_1997) on length of the ID sequence. There no length restrictions on the ID, but whitespaces aren't allowed in the sequence ID/Name because one space separates the longest ID and the beginning of the sequence. Sequences IDs must be padded to the longest ID length.
has super-classes
Phylip format variantc

Relaxed PHYLIP Sequentialc back to ToC or Class ToC

IRI: http://edamontology.org/format_3820

It differs from Phylip sequential format (format_1997) on length of the ID sequence. There no length restrictions on the ID, but whitespaces aren't allowed in the sequence ID/Name because one space separates the longest ID and the beginning of the sequence. Sequences IDs must be padded to the longest ID length.
has super-classes
Phylip format variantc

Rendering parameterc back to ToC or Class ToC

IRI: http://edamontology.org/data_2152

has super-classes
deprecated classc

Repeat sequence analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0237

Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length.
has super-classes
Sequence analysisc
has topicop some Sequence composition, complexity and repeatsc
has sub-classes
Repeat sequence detectionc, Repeat sequence organisation analysisc

Repeat sequence detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0379

has super-classes
Repeat sequence analysisc
Nucleic acid feature detectionc

Repeat sequence organisation analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0380

has super-classes
Sequence composition calculationc
Repeat sequence analysisc

Repeat sequencesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0641

has super-classes
deprecated classc

Reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2048

You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing.
has super-classes
Datac
has sub-classes
Biosafety reportc, Clinical trial reportc, Data index reportc, Electronic health recordc, Genotype/phenotype reportc, Image metadatac, Isolation reportc, Nucleic acid reportc, Organism reportc, Pathway or network reportc, Protein reportc, Protocolc, Quality control reportc, Reference sample reportc, Resource metadatac, Sequence alignment reportc, Sequence reportc, Sequence signature reportc, Structure alignment reportc, Structure reportc, Text mining reportc
is disjoint with
Identifierc

Representative sequence identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2233

has super-classes
Sequence comparisonc

Reproductive healthc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3420

has super-classes
Medicinec

RESID IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2619

has super-classes
Accessionc
Protein modification IDc

Residue bump detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1836

has super-classes
Protein structure validationc

Residue cluster calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0393

This includes for example clusters of hydrophobic or charged residues, or clusters of contacting residues which have a key structural or functional role.
has super-classes
Residue distance calculationc
has outputop some Protein residue 3D clusterc

Residue contact calculation (residue-ligand)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1838

has super-classes
deprecated classc

Residue contact calculation (residue-negative ion)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1835

has super-classes
deprecated classc

Residue contact calculation (residue-nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1832

has super-classes
deprecated classc

Residue contact calculation (residue-residue)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2490

has super-classes
deprecated classc

Residue contact predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0272

Methods usually involve multiple sequence alignment analysis.
has super-classes
Protein property calculationc
Protein sequence analysisc
has topicop some Protein folding, stability and designc

Residue distance calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2950

This includes identifying HET groups, which usually correspond to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. It can also include calculation of symmetry contacts, i.e. a contact between two atoms in different asymmetric unit.
has super-classes
Residue interaction calculationc
has sub-classes
Protein distance matrix calculationc, Residue cluster calculationc

Residue interaction calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0248

has super-classes
Protein property calculationc
has topicop some Protein folding, stability and designc
has sub-classes
Hydrogen bond calculationc, Metal-bound cysteine detectionc, Protein-metal contact calculationc, Residue distance calculationc, Salt bridge calculationc

Residue non-canonical interaction detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0395

has super-classes
deprecated classc

Residue packing validationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1843

has super-classes
Protein structure validationc

Residue symmetry contact calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1837

A symmetry contact is a contact between two atoms in different asymmetric unit.
has super-classes
deprecated classc

Residue validationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1913

has super-classes
deprecated classc

Resource metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_2337

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Reportc
has sub-classes
Database entry metadatac, Database metadatac, Ontology metadatac, Sample annotationc, System metadatac, Tool metadatac, User metadatac, Workflow metadatac

Resource typec back to ToC or Class ToC

IRI: http://edamontology.org/data_0005

has super-classes
deprecated classc

Respiratory medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3322

has super-classes
Medicinec

restover formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1319

has super-classes
Nucleic acid features (restriction sites) formatc
Textual formatc

restrict formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1318

has super-classes
Nucleic acid features (restriction sites) formatc
Textual formatc

Restriction digestc back to ToC or Class ToC

IRI: http://edamontology.org/data_1239

has super-classes
Sequence set (nucleic acid)c

Restriction digestc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0365

has super-classes
Sequence generationc
Nucleic acid property calculationc
has outputop some Restriction digestc

Restriction enzyme namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1013

has super-classes
Enzyme namec

Restriction enzyme reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1517

This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc.
has super-classes
deprecated classc

Restriction mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1289

has super-classes
Sequence mapc
Sequence imagec

Restriction map drawingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0575

has super-classes
Map drawingc
has outputop some Restriction mapc

Restriction site creationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0370

has super-classes
Sequence editingc

Restriction site recognitionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0431

has super-classes
Nucleic acid feature detectionc
has topicop some Sequence sites, features and motifsc

Restriction sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1305

has super-classes
deprecated classc

Results sort orderc back to ToC or Class ToC

IRI: http://edamontology.org/data_2134

Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on.
has super-classes
deprecated classc

Retention time predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3633

has super-classes
Calculationc

Reverse complementc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0363

has super-classes
Sequence generationc

RFAM accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2356

has super-classes
Accessionc
RNA family identifierc

RFAM namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2606

has super-classes
Namec
RNA family identifierc

RFLPc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2869

has super-classes
deprecated classc

rgbc back to ToC or Class ToC

IRI: http://edamontology.org/format_3600

has super-classes
Binary formatc
Image formatc

RGD gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1613

has super-classes
deprecated classc

RGD IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2620

has super-classes
Accessionc
Identifier (hybrid)c

RH scoresc back to ToC or Class ToC

IRI: http://edamontology.org/data_0926

Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping.
has super-classes
Experimental measurementc

Ribosomesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0617

has super-classes
deprecated classc

Ricec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0787

has super-classes
deprecated classc

Rigid body refinementc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3456

Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data.
has super-classes
Molecular model refinementc

rnac back to ToC or Class ToC

IRI: http://edamontology.org/format_1213

has super-classes
nucleotidec
has sub-classes
completely unambiguous pure rna sequencec, pure rnac, unambiguous pure rna sequencec

RNAc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0099

has super-classes
Nucleic acidsc
has sub-classes
Functional, regulatory and non-coding RNAc, Gene transcriptsc, RNA splicingc

RNA annotation formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3865

has super-classes
Format (by type of data)c
has sub-classes
mirGFF3c

RNA binding site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3902

has super-classes
Nucleic acids-binding site predictionc

RNA central IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3856

There are canonical and taxon-specific forms of RNAcentral ID. Canonical form e.g. urs_9or10digits identifies an RNA sequence (within the RNA central database) which may appear in multiple sequences. Taxon-specific form identifies a sequence in the specific taxon (e.g. urs_9or10digits_taxonID).
has super-classes
Sequence accession (nucleic acid)c
Accessionc

RNA family identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2355

has super-classes
Identifier (by type of data)c
is identifier ofop some RNA family reportc
has sub-classes
RFAM accessionc, RFAM namec

RNA family reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2354

has super-classes
Gene family reportc

RNA features reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2883

has super-classes
deprecated classc

RNA immunoprecipitationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3794

has super-classes
Immunoprecipitation experimentc

RNA inverse foldingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0483

has super-classes
Nucleic acid designc
has outputop some Sequence set (nucleic acid)c

RNA secondary structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_0880

This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc.
has super-classes
RNA structurec
has topicop some Nucleic acid structure analysisc

RNA secondary structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_0881

has super-classes
Secondary structure alignmentc

RNA secondary structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0502

has super-classes
RNA secondary structure analysisc
Generationc
has outputop some RNA secondary structure alignmentc
has inputop some RNA secondary structurec

RNA secondary structure analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2439

has super-classes
Nucleic acid structure analysisc
has topicop some Nucleic acid structure analysisc
has sub-classes
RNA secondary structure alignmentc, RNA secondary structure predictionc, RNA structure covariance model generationc

RNA secondary structure formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2076

has super-classes
Format (by type of data)c
is format ofop some RNA secondary structurec
has sub-classes
CTc, Dot-bracket formatc, RNAMLc, SSc

RNA secondary structure imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1708

has super-classes
Imagec

RNA secondary structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0278

Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding).
has super-classes
Nucleic acid feature detectionc
Nucleic acid structure predictionc
RNA secondary structure analysisc
has outputop some RNA secondary structurec

RNA secondary structure prediction (shape-based)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3470

has super-classes
deprecated classc

RNA secondary structure visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0568

has super-classes
deprecated classc

RNA sequencec back to ToC or Class ToC

IRI: http://edamontology.org/data_3495

has super-classes
Nucleic acid sequencec

RNA sequence (raw)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3496

has super-classes
deprecated classc

RNA splicingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3320

This includes the study of splice sites, splicing patterns, alternative splicing events and variants, isoforms, etc..
has super-classes
RNAc
Gene expressionc

RNA structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_1465

has super-classes
Nucleic acid structurec
has topicop some Nucleic acid structure analysisc
has sub-classes
RNA secondary structurec, tRNA structurec

RNA structurec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0697

has super-classes
deprecated classc

RNA structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1493

has super-classes
Nucleic acid structure alignmentc

RNA structure covariance model generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3469

has super-classes
RNA secondary structure analysisc
Generationc
has topicop some Nucleic acid structure analysisc

RNA structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2441

has super-classes
Nucleic acid structure predictionc
has outputop some RNA structurec

RNA-binding protein predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3901

has super-classes
Protein-nucleic acid interaction analysisc
has topicop some Protein interactionsc
has outputop some Protein interaction datac

RNA-Seqc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3170

This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs.
has super-classes
Sequencingc

RNA-Seq alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3178

has super-classes
deprecated classc

RNA-Seq analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3680

has super-classes
Expression analysisc
Sequence read processingc
has sub-classes
RNA-seq read count analysisc, RNA-seq time series data analysisc

RNA-Seq quantificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3800

has super-classes
Quantificationc

RNA-seq read count analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3563

has super-classes
RNA-Seq analysisc

RNA-seq time series data analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3565

has super-classes
RNA-Seq analysisc

RNAi experimentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3523

has super-classes
Laboratory techniquesc

RNAi reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3427

has super-classes
deprecated classc

RNAMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3311

has super-classes
Alignment formatc
RNA secondary structure formatc
XMLc

RNAVirusDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2784

Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.
has super-classes
Accessionc
Virus IDc

Root-mean-square deviationc back to ToC or Class ToC

IRI: http://edamontology.org/data_1497

has super-classes
Structure similarity scorec

Rotamer likelihood predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1841

Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.
has super-classes
deprecated classc

rRNAc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0660

has super-classes
deprecated classc

RSFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3485

RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual).
has super-classes
GCG format variantc

RSTc back to ToC or Class ToC

IRI: http://edamontology.org/format_3886

has super-classes
Tertiary structure formatc
Textual formatc
Trajectory format (text)c

Run numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_3735

has super-classes
Sequencing metadata namec

S/MAR predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0444

MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation.
has super-classes
Transcriptional regulatory element predictionc

Safety sciencesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3377

has super-classes
Medicines research and developmentc
has sub-classes
Pharmacovigilancec, Toxicologyc

SAGE data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0528

has super-classes
deprecated classc

SAGE experimental datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0933

has super-classes
deprecated classc

Salt bridge calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1839

Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance.
has super-classes
Residue interaction calculationc

SAMc back to ToC or Class ToC

IRI: http://edamontology.org/format_2573

The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project.
has super-classes
Sequence trace formatc
Textual formatc
Alignment format (pair only)c

Sample annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_3113

This might include compound and dose in a dose response experiment.
has super-classes
Resource metadatac

Sample collectionsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3277

has super-classes
Biomedical sciencec
has sub-classes
Biobankc, Cell culture collectionc, Clone libraryc, Microbial collectionc, Mouse clinicc

Sample comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3731

has super-classes
Comparisonc

SAMPLE file formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3813

has super-classes
Textual formatc

Sample IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3273

has super-classes
Identifier (by type of data)c
is identifier ofop some Sample annotationc

Sanger inverted repeatsc back to ToC or Class ToC

IRI: http://edamontology.org/format_1296

has super-classes
Sequence features (repeats) formatc
Textual formatc

SBGN-MLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3692

has super-classes
Biological pathway or network formatc
XMLc

SBMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_2585

has super-classes
Biological pathway or network formatc
XMLc

SBOLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3725

SBOL introduces a standardised format for the electronic exchange of information on the structural and functional aspects of biological designs.
has super-classes
XMLc

SBRMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3155

has super-classes
XMLc
Biological pathway or network report formatc

SBS data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0530

has super-classes
deprecated classc

SBS experimental datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0935

has super-classes
deprecated classc

SBtabc back to ToC or Class ToC

IRI: http://edamontology.org/format_3688

has super-classes
Biological pathway or network formatc
Textual formatc

Scaffold gap completionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3217

Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced.
has super-classes
Scaffoldingc

Scaffoldingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3216

Scaffold may be positioned along a chromosome physical map to create a "golden path".
has super-classes
Sequence assemblyc
Generationc
has topicop some Nucleic acidsc
has sub-classes
Scaffold gap completionc

Scatter plot plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2940

has super-classes
Visualisationc

Scent annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0964

has super-classes
deprecated classc

Scentsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0618

has super-classes
deprecated classc

SCFc back to ToC or Class ToC

IRI: http://edamontology.org/format_1632

has super-classes
Sequence trace formatc
Binary formatc

Schemac back to ToC or Class ToC

IRI: http://edamontology.org/data_2248

has super-classes
deprecated classc

SCOP classc back to ToC or Class ToC

IRI: http://edamontology.org/data_3141

has super-classes
deprecated classc

SCOP concise classification string (sccs)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1041

An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs.
has super-classes
SCOP domain identifierc

SCOP domain identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1039

has super-classes
Protein domain IDc
Accessionc
has sub-classes
SCOP concise classification string (sccs)c, SCOP sunidc

SCOP familyc back to ToC or Class ToC

IRI: http://edamontology.org/data_3144

has super-classes
deprecated classc

SCOP foldc back to ToC or Class ToC

IRI: http://edamontology.org/data_3142

has super-classes
deprecated classc

SCOP nodec back to ToC or Class ToC

IRI: http://edamontology.org/data_1554

has super-classes
deprecated classc

SCOP proteinc back to ToC or Class ToC

IRI: http://edamontology.org/data_3145

has super-classes
deprecated classc

SCOP speciesc back to ToC or Class ToC

IRI: http://edamontology.org/data_3146

has super-classes
deprecated classc

SCOP sunidc back to ToC or Class ToC

IRI: http://edamontology.org/data_1042

A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level.
has super-classes
SCOP domain identifierc

SCOP superfamilyc back to ToC or Class ToC

IRI: http://edamontology.org/data_3143

has super-classes
deprecated classc

Scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_1772

has super-classes
Datac
has sub-classes
Alignment score or penaltyc, Localisation scorec, Sequence similarity scorec, Statistical estimate scorec, Structure similarity scorec

Score end gaps controlc back to ToC or Class ToC

IRI: http://edamontology.org/data_1395

has super-classes
deprecated classc

scores formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1999

has super-classes
Textual formatc
Alignment format (text)c

SDFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3814

has super-classes
Chemical data formatc
Textual formatc

Search parameterc back to ToC or Class ToC

IRI: http://edamontology.org/data_2079

has super-classes
deprecated classc

SECIS element predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0437

SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines.
has super-classes
Gene predictionc
has outputop some Gene reportc

Secondary structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_2081

has super-classes
deprecated classc

Secondary structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_2366

has super-classes
Alignmentc
has sub-classes
Protein secondary structure alignmentc, RNA secondary structure alignmentc

Secondary structure alignment generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0500

has super-classes
deprecated classc

Secondary structure alignment metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_2598

has super-classes
deprecated classc

Secondary structure alignment metadata (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0879

has super-classes
deprecated classc

Secondary structure alignment metadata (RNA)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0882

has super-classes
deprecated classc

Secondary structure comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2931

has super-classes
deprecated classc

Secondary structure datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2973

has super-classes
deprecated classc

Secondary structure imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_2880

has super-classes
deprecated classc

Secondary structure processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2482

has super-classes
deprecated classc

Secondary structure reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2881

has super-classes
deprecated classc

SED-MLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3685

has super-classes
XMLc
Experiment annotation formatc

Selection detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3950

has super-classes
Nucleic acid sequence analysisc

selexc back to ToC or Class ToC

IRI: http://edamontology.org/format_2000

has super-classes
Textual formatc
Sequence record format (text)c
Alignment format (text)c

selex sequence formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1959

has super-classes
deprecated classc

Sequencec back to ToC or Class ToC

IRI: http://edamontology.org/data_2044

This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles.
has super-classes
Datac
has topicop some Sequence analysisc
has sub-classes
Nucleic acid sequencec, Protein sequencec, Sequence recordc

Sequence accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1093

has super-classes
Sequence identifierc
has sub-classes
Sequence accession (hybrid)c, Sequence accession (nucleic acid)c, Sequence accession (protein)c

Sequence accession (hybrid)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2362

has super-classes
Sequence accessionc
is identifier ofop some Sequence recordc
has sub-classes
GI numberc, NCBI versionc, RefSeq accessionc

Sequence accession (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1097

has super-classes
Sequence accessionc
is identifier ofop some Nucleic acid sequencec
has sub-classes
ASTD IDc, EMBL/GenBank/DDBJ IDc, REDIdb IDc, RNA central IDc, UNITE accessionc, UTR accessionc, UniSTS accessionc

Sequence accession (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1096

has super-classes
Sequence accessionc
is identifier ofop some Protein sequencec
has sub-classes
Gramene identifierc, IPI protein IDc, PIR identifierc, TAIR accession (protein)c, UniParc accessionc, UniProt accessionc

Sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_0863

has super-classes
Alignmentc
has topicop some Sequence analysisc
has sub-classes
Hybrid sequence alignmentc, Nucleic acid sequence alignmentc, Pair sequence alignmentc, Protein sequence alignmentc

Sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0292

See also "Read mapping"
has super-classes
Sequence analysisc
Sequence comparisonc
Alignmentc
has outputop some Sequence alignmentc
has sub-classes
Genome alignmentc, Global alignmentc, Local alignmentc, Multiple sequence alignmentc, Pairwise sequence alignmentc, Sequence profile alignmentc, Structure-based sequence alignmentc, Tree-based sequence alignmentc

Sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0182

This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on.
has super-classes
deprecated classc

Sequence alignment (multiple)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1382

has super-classes
deprecated classc

Sequence alignment (nucleic acid pair)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1386

has super-classes
deprecated classc

Sequence alignment (protein pair)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1387

has super-classes
deprecated classc

Sequence alignment (words)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0861

has super-classes
deprecated classc

Sequence alignment analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0258

has super-classes
Sequence analysisc
has inputop some Sequence alignmentc
has sub-classes
Sequence alignment analysis (conservation)c, Sequence alignment analysis (site correlation)c, Sequence alignment comparisonc, Sequence alignment refinementc, Sequence alignment validationc, Sequence profile generationc

Sequence alignment analysis (conservation)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0448

Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc.
has super-classes
Sequence alignment analysisc

Sequence alignment analysis (site correlation)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0449

This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures.
has super-classes
Sequence alignment analysisc
Correlationc

Sequence alignment comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0259

See also 'Sequence profile alignment'.
has super-classes
Sequence alignment analysisc
Comparisonc

Sequence alignment conversionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0260

has super-classes
Sequence alignment editingc
Conversionc

Sequence alignment editingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3081

has super-classes
Editingc
has sub-classes
Sequence alignment conversionc

Sequence alignment file processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2122

has super-classes
deprecated classc

Sequence alignment formattingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0562

has super-classes
deprecated classc

Sequence alignment generation (multiple profile)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0512

has super-classes
deprecated classc

Sequence alignment IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1066

has super-classes
Identifier (by type of data)c
Accessionc
is identifier ofop some Sequence alignmentc

Sequence alignment imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1711

has super-classes
Imagec

Sequence alignment metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_0866

has super-classes
deprecated classc

Sequence alignment metadata (quality report)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1414

has super-classes
deprecated classc

Sequence alignment parameterc back to ToC or Class ToC

IRI: http://edamontology.org/data_0864

has super-classes
deprecated classc

Sequence alignment processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2463

has super-classes
deprecated classc

Sequence alignment refinementc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2089

has super-classes
Sequence alignment analysisc
Optimisation and refinementc

Sequence alignment reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0867

Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score.
has super-classes
Reportc
has sub-classes
Dotplotc, Sequence assembly reportc, Sequence similarity plotc

Sequence alignment report (site conservation)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1415

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.
has super-classes
deprecated classc

Sequence alignment report (site correlation)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1416

has super-classes
deprecated classc

Sequence alignment typec back to ToC or Class ToC

IRI: http://edamontology.org/data_1120

Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on.
has super-classes
deprecated classc

Sequence alignment validationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0447

Evaluation might be purely sequence-based or use structural information.
has super-classes
Sequence alignment analysisc
Validationc

Sequence alignment visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0565

has super-classes
deprecated classc

Sequence ambiguity calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0235

has super-classes
Sequence composition calculationc
has outputop some Sequence ambiguity reportc
has topicop some Sequence composition, complexity and repeatsc

Sequence ambiguity reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1260

has super-classes
Sequence propertyc

Sequence analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2403

has super-classes
Analysisc
has topicop some Sequence analysisc
has sub-classes
Antimicrobial resistance predictionc, Nucleic acid sequence analysisc, Phylogenetic tree construction (from molecular sequences)c, Protein sequence analysisc, Repeat sequence analysisc, Sequence alignmentc, Sequence alignment analysisc, Sequence classificationc, Sequence comparisonc, Sequence composition calculationc, Sequence database searchc, Sequence editingc, Sequence feature comparisonc, Sequence feature detectionc, Sequence file editingc, Sequence generationc, Sequence motif analysisc, Sequence visualisationc, Virulence predictionc

Sequence analysisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0080

has super-classes
Computational biologyc
has sub-classes
Cladisticsc, Mappingc, Phylogeneticsc, Phylogenomicsc, Probes and primersc, Sequence assemblyc, Sequence composition, complexity and repeatsc

Sequence annotationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0361

has super-classes
Annotationc
has inputop some Sequence recordc
has outputop some Sequence recordc
has sub-classes
Gene functional annotationc, Genome annotationc, SNP annotationc

Sequence annotationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0221

has super-classes
deprecated classc

Sequence annotation track formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2919

has super-classes
Sequence feature annotation formatc
is format ofop some Annotation trackc
has sub-classes
BEDc, BTrackc, GENc, GTrackc, MAFc, PSLc, WIGc, bedgraphc, bigBedc, bigWigc, customtrackc, genePredc, pgSnpc, proBEDc

Sequence assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/data_0925

Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included.
has super-classes
Sequence set (nucleic acid)c

Sequence assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0310

For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.
has super-classes
Nucleic acid sequence analysisc
has topicop some Sequence assemblyc
has outputop some Sequence assemblyc
has sub-classes
Cross-assemblyc, De-novo assemblyc, EST assemblyc, Exome assemblyc, Genome assemblyc, Localised reassemblyc, Mapping assemblyc, Scaffoldingc, Transcriptome assemblyc

Sequence assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0196

Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialised case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'.
has super-classes
Sequence analysisc

Sequence assembly componentc back to ToC or Class ToC

IRI: http://edamontology.org/data_1852

has super-classes
deprecated classc

Sequence assembly formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2055

has super-classes
Format (by type of data)c
is format ofop some Sequence assemblyc
has sub-classes
ACEc, AGPc, Sequence assembly format (text)c

Sequence assembly format (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2561

has super-classes
Sequence assembly formatc
has sub-classes
CAFc, ELAND formatc, EXPc, FASTGc, afgc

Sequence assembly IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3266

has super-classes
Sequence set IDc

Sequence assembly reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3181

This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc.
has super-classes
Sequence alignment reportc

Sequence assembly validationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3180

has super-classes
Validationc
Sequencing quality controlc
has outputop some Sequence assembly reportc
has topicop some Sequence assemblyc
has inputop some Sequence assemblyc

Sequence assembly visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3184

has super-classes
Sequence visualisationc

Sequence attributec back to ToC or Class ToC

IRI: http://edamontology.org/data_2534

has super-classes
Datac
has sub-classes
Sequence checksumc, Sequence lengthc, Sequence positionc, Sequence rangec, Sequence versionc

Sequence checksumc back to ToC or Class ToC

IRI: http://edamontology.org/data_2190

has super-classes
Sequence attributec

Sequence checksum generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3348

has super-classes
Generationc
has inputop some Sequencec
has topicop some Data acquisitionc

Sequence classificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2995

has super-classes
Sequence analysisc
Classificationc
has sub-classes
Taxonomic classificationc, Variant classificationc

Sequence classificationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0594

Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences.
has super-classes
deprecated classc

Sequence clusterc back to ToC or Class ToC

IRI: http://edamontology.org/data_1235

The cluster might include sequences identifiers, short descriptions, alignment and summary information.
has super-classes
Sequence setc
has topicop some Gene and protein familiesc
has sub-classes
Sequence cluster (nucleic acid)c, Sequence cluster (protein)c

Sequence cluster (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1246

The sequences are typically related, for example a family of sequences.
has super-classes
Sequence set (nucleic acid)c
Sequence clusterc

Sequence cluster (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1245

The sequences are typically related, for example a family of sequences.
has super-classes
Sequence set (protein)c
Sequence clusterc

Sequence cluster formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2170

has super-classes
Format (by type of data)c
is format ofop some Sequence clusterc
has sub-classes
Sequence cluster format (nucleic acid)c, Sequence cluster format (protein)c

Sequence cluster format (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2172

has super-classes
Sequence cluster formatc
has sub-classes
affymetrixc

Sequence cluster format (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2171

has super-classes
Sequence cluster formatc

Sequence cluster IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1112

has super-classes
Sequence set IDc
is identifier ofop some Sequence clusterc
has sub-classes
Sequence cluster ID (COG)c, Sequence cluster ID (CluSTr)c, Sequence cluster ID (SYSTERS)c, Sequence cluster ID (UniGene)c, Sequence cluster ID (UniRef)c

Sequence cluster ID (CluSTr)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2612

has super-classes
Sequence cluster IDc
Accessionc

Sequence cluster ID (COG)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1113

has super-classes
Sequence cluster IDc
Accessionc

Sequence cluster ID (SYSTERS)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2220

has super-classes
Sequence cluster IDc
Accessionc

Sequence cluster ID (UniGene)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1104

has super-classes
Sequence cluster IDc
Accessionc

Sequence cluster ID (UniRef)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2346

has super-classes
Sequence cluster IDc
Accessionc
has sub-classes
Sequence cluster ID (UniRef100)c, Sequence cluster ID (UniRef50)c, Sequence cluster ID (UniRef90)c

Sequence cluster ID (UniRef100)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2347

has super-classes
Sequence cluster ID (UniRef)c

Sequence cluster ID (UniRef50)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2349

has super-classes
Sequence cluster ID (UniRef)c

Sequence cluster ID (UniRef90)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2348

has super-classes
Sequence cluster ID (UniRef)c

Sequence cluster processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2452

has super-classes
deprecated classc

Sequence cluster visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0566

has super-classes
Visualisationc
has inputop some Sequence clusterc

Sequence clusteringc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0291

The clusters may be output or used internally for some other purpose.
has super-classes
Sequence comparisonc
Generationc
Clusteringc
has outputop some Sequence clusterc
has sub-classes
Functional clusteringc

Sequence clusteringc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0164

This includes systems that generate, process and analyse sequence clusters.
has super-classes
deprecated classc

Sequence clusters and classificationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3052

This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc.
has super-classes
deprecated classc

Sequence comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2451

has super-classes
Sequence analysisc
Comparisonc
has outputop some Sequence reportc
has inputop some Sequencec
has sub-classes
Genome comparisonc, Representative sequence identificationc, Sequence alignmentc, Sequence clusteringc, Sequence distance matrix generationc, Sequence motif comparisonc, Sequence redundancy removalc, Sequence similarity searchc, Sequence word comparisonc, Sequencing error detectionc

Sequence comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0159

The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences.
has super-classes
deprecated classc

Sequence complexity calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0234

has super-classes
Sequence composition calculationc
has outputop some Sequence complexity reportc
has topicop some Sequence composition, complexity and repeatsc

Sequence complexity reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1259

has super-classes
Sequence propertyc

Sequence composition calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0236

has super-classes
Sequence analysisc
Calculationc
has outputop some Sequence composition reportc
has topicop some Sequence composition, complexity and repeatsc
has sub-classes
Nucleic acid density plottingc, Repeat sequence organisation analysisc, Sequence ambiguity calculationc, Sequence complexity calculationc, k-mer countingc

Sequence composition calculation (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0377

has super-classes
deprecated classc

Sequence composition calculation (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0378

has super-classes
deprecated classc

Sequence composition plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_2166

has super-classes
Sequence composition reportc
Plotc

Sequence composition reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1261

has super-classes
Sequence propertyc
has sub-classes
Amino acid frequencies tablec, Amino acid word frequencies tablec, Base frequencies tablec, Base position variability plotc, Base word frequencies tablec, Nucleic acid density plotc, Sequence composition plotc

Sequence composition tablec back to ToC or Class ToC

IRI: http://edamontology.org/data_1264

has super-classes
deprecated classc

Sequence composition, complexity and repeatsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0157

This includes repetitive elements within a nucleic acid sequence, e.g. long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a sequence and other types of repeating unit.
has super-classes
Sequence analysisc

Sequence contamination filteringc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3187

has super-classes
Sequencing quality controlc

Sequence conversionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0233

has super-classes
Sequence editingc
Conversionc
has sub-classes
DNA back-translationc, DNA transcriptionc, DNA translationc

Sequence coordinate conversionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3267

has super-classes
Conversionc
has inputop some Sequence coordinatesc
has outputop some Sequence coordinatesc

Sequence coordinatesc back to ToC or Class ToC

IRI: http://edamontology.org/data_2012

This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position.
has super-classes
Datac
Sequence positionc
Sequence rangec
has sub-classes
Cytoband positionc

Sequence cuttingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0369

has super-classes
Sequence editingc
has sub-classes
Primer removalc, Sequence trimmingc

Sequence datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2925

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Sequence data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2503

has super-classes
deprecated classc

Sequence database cross-referencesc back to ToC or Class ToC

IRI: http://edamontology.org/data_1674

has super-classes
deprecated classc

Sequence database hits alignments listc back to ToC or Class ToC

IRI: http://edamontology.org/data_1339

has super-classes
deprecated classc

Sequence database hits evaluation datac back to ToC or Class ToC

IRI: http://edamontology.org/data_1340

has super-classes
deprecated classc

Sequence database hits scores listc back to ToC or Class ToC

IRI: http://edamontology.org/data_1338

has super-classes
deprecated classc

Sequence database namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1057

has super-classes
deprecated classc

Sequence database searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0338

This excludes direct retrieval methods (e.g. the dbfetch program).
has super-classes
Sequence analysisc
Database searchc
has outputop some Sequence search resultsc
has sub-classes
Sequence database search (by property)c, Sequence similarity searchc

Sequence database searchc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0163

The query is a sequence-based entity such as another sequence, a motif or profile.
has super-classes
deprecated classc

Sequence database search (by amino acid composition)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0348

has super-classes
deprecated classc

Sequence database search (by isoelectric point)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0356

has super-classes
deprecated classc

Sequence database search (by molecular weight)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0355

has super-classes
deprecated classc

Sequence database search (by motif or pattern)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0347

has super-classes
deprecated classc

Sequence database search (by property)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0349

has super-classes
Sequence database searchc

Sequence database search (by sequence for primer sequences)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0354

STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers.
has super-classes
deprecated classc

Sequence database search (by sequence using global alignment-based methods)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0353

This includes tools based on the Needleman and Wunsch algorithm.
has super-classes
deprecated classc

Sequence database search (by sequence using local alignment-based methods)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0352

This includes tools based on the Smith-Waterman algorithm or FASTA.
has super-classes
deprecated classc

Sequence database search (by sequence using profile-based methods)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0351

This includes tools based on PSI-BLAST.
has super-classes
deprecated classc

Sequence database search (by sequence using word-based methods)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0350

Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps.
has super-classes
deprecated classc

Sequence databasesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3041

has super-classes
deprecated classc

Sequence distance matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_0870

Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix.
has super-classes
Distance matrixc

Sequence distance matrix formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2067

has super-classes
Format (by type of data)c
is format ofop some Sequence distance matrixc
has sub-classes
Phylip distance matrixc

Sequence distance matrix generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0289

has super-classes
Sequence comparisonc
Generationc
has outputop some Sequence distance matrixc
has topicop some Phylogenyc

Sequence editingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0231

has super-classes
Sequence analysisc
Editingc
has sub-classes
Restriction site creationc, Sequence conversionc, Sequence cuttingc, Sequence file editingc, Sequence maskingc, Sequence mergingc, Sequence mutation and randomisationc

Sequence editingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0156

has super-classes
deprecated classc

Sequence editing (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2511

has super-classes
deprecated classc

Sequence editing (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2512

has super-classes
deprecated classc

Sequence feature analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2408

has super-classes
deprecated classc

Sequence feature annotation formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1920

has super-classes
Format (by type of data)c
is format ofop some Sequence featuresc
has sub-classes
BTrackc, BioJSON (BioXSD)c, BioJSON (Jalview)c, BioXSD (XML)c, BioYAMLc, GSuitec, PSDMLc, Sequence annotation track formatc, Sequence feature table formatc, UniParc XMLc, UniRef XMLc, debug-featc

Sequence feature comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0256

has super-classes
Sequence analysisc
Comparisonc
has topicop some Sequence sites, features and motifsc
has inputop some Feature tablec
has inputop some Sequence recordc
has sub-classes
Genome feature comparisonc

Sequence feature detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0253

Look at "Protein feature detection" (http://edamontology.org/operation_3092) and "Nucleic acid feature detection" (http://edamontology.org/operation_0415) in case more specific terms are needed.
has super-classes
Sequence analysisc
Prediction and recognitionc
has topicop some Sequence sites, features and motifsc
has outputop some Sequence featuresc
has sub-classes
Sequence motif discoveryc, Sequence motif recognitionc

Sequence feature detectionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3072

has super-classes
deprecated classc

Sequence feature IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1015

has super-classes
Sequence feature identifierc
has sub-classes
Sequence feature ID (SwissRegulon)c

Sequence feature ID (SwissRegulon)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2736

This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end".
has super-classes
Sequence feature IDc
Accessionc

Sequence feature identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_3034

has super-classes
Identifier (by type of data)c
is identifier ofop some Sequence featuresc
has sub-classes
EMBOSS Uniform Feature Objectc, Sequence feature IDc, Sequence feature labelc

Sequence feature keyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1020

A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence.
has super-classes
Sequence features metadatac

Sequence feature labelc back to ToC or Class ToC

IRI: http://edamontology.org/data_1022

A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature.
has super-classes
Namec
Sequence features metadatac
Sequence feature identifierc

Sequence feature namec back to ToC or Class ToC

IRI: http://edamontology.org/data_3107

has super-classes
deprecated classc

Sequence feature qualifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1021

Feature qualifiers hold information about a feature beyond that provided by the feature key and location.
has super-classes
Sequence features metadatac

Sequence feature sourcec back to ToC or Class ToC

IRI: http://edamontology.org/data_0856

This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human).
has super-classes
Sequence features metadatac

Sequence feature table formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2548

has super-classes
Sequence feature annotation formatc
is format ofop some Sequence featuresc
has sub-classes
BTrackc, Sequence feature table format (XML)c, Sequence feature table format (text)c, uniprotkb-like formatc

Sequence feature table format (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2206

has super-classes
Sequence feature table formatc
has sub-classes
EMBL formatc, GFFc, GTrackc, GenBank formatc, Sequin formatc

Sequence feature table format (XML)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2553

has super-classes
Sequence feature table formatc
has sub-classes
DASGFFc

Sequence feature typec back to ToC or Class ToC

IRI: http://edamontology.org/data_3268

has super-classes
deprecated classc

Sequence featuresc back to ToC or Class ToC

IRI: http://edamontology.org/data_1255

This includes annotation of positional sequence features, organised into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required.
has super-classes
Datac
has sub-classes
Annotation trackc, Feature tablec, Nucleic acid featuresc, Protein featuresc

Sequence features (comparative)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1256

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
has super-classes
deprecated classc

Sequence features (compositionally-biased regions)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3119

has super-classes
deprecated classc

Sequence features (repeats)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1299

The report might include derived data map such as classification, annotation, organisation, periodicity etc.
has super-classes
deprecated classc

Sequence features (repeats) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2155

has super-classes
Format (by type of data)c
has sub-classes
EMBOSS repeatc, Sanger inverted repeatsc, quicktandemc

Sequence features metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_2914

has super-classes
Datac
has sub-classes
Sequence feature keyc, Sequence feature labelc, Sequence feature qualifierc, Sequence feature sourcec

Sequence file editingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2121

has super-classes
Sequence editingc
Sequence analysisc

Sequence formattingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0561

has super-classes
deprecated classc

Sequence generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0230

has super-classes
Sequence analysisc
Generationc
has sub-classes
Base-callingc, Probabilistic sequence generationc, Protein sequence cleavagec, Random sequence generationc, Restriction digestc, Reverse complementc, de Novo sequencingc

Sequence generation (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2513

has super-classes
deprecated classc

Sequence generation (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2514

has super-classes
deprecated classc

Sequence identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1063

has super-classes
Identifier (by type of data)c
is identifier ofop some Sequencec
has sub-classes
EMBOSS Uniform Sequence Addressc, Sequence accessionc, Sequence namec

Sequence identifier (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2289

has super-classes
deprecated classc

Sequence identifier (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2288

has super-classes
deprecated classc

Sequence identityc back to ToC or Class ToC

IRI: http://edamontology.org/data_1412

has super-classes
Sequence similarity scorec

Sequence imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_2969

has super-classes
Sequence reportc
Imagec
has sub-classes
Restriction mapc, Sequence trace imagec

Sequence information reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1253

has super-classes
deprecated classc

Sequence lengthc back to ToC or Class ToC

IRI: http://edamontology.org/data_1249

has super-classes
Sequence attributec

Sequence length rangec back to ToC or Class ToC

IRI: http://edamontology.org/data_1252

has super-classes
deprecated classc

Sequence length specificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0854

has super-classes
deprecated classc

Sequence mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1279

A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment.
has super-classes
Physical mapc
has sub-classes
Gene mapc, Genome mapc, Plasmid mapc, Restriction mapc

Sequence mask characterc back to ToC or Class ToC

IRI: http://edamontology.org/data_0851

has super-classes
deprecated classc

Sequence mask parameterc back to ToC or Class ToC

IRI: http://edamontology.org/data_2023

has super-classes
deprecated classc

Sequence mask typec back to ToC or Class ToC

IRI: http://edamontology.org/data_0852

Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.
has super-classes
deprecated classc

Sequence maskingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0368

For example, SNPs or repeats in a DNA sequence might be masked.
has super-classes
Sequence editingc

Sequence mergingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0232

has super-classes
Sequence editingc

Sequence metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_0855

This is used for such things as a report including the sequence identifier, type and length.
has super-classes
deprecated classc

Sequence motifc back to ToC or Class ToC

IRI: http://edamontology.org/data_1353

has super-classes
Sequence signature datac
has topicop some Sequence sites, features and motifsc
has sub-classes
Sequence motif (nucleic acid)c, Sequence motif (protein)c

Sequence motif (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2070

has super-classes
Sequence motifc

Sequence motif (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2071

has super-classes
Sequence motifc

Sequence motif analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2404

has super-classes
Sequence analysisc
has sub-classes
Sequence motif comparisonc, Sequence motif discoveryc, Sequence motif recognitionc

Sequence motif comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0240

has super-classes
Sequence motif analysisc
Sequence comparisonc
has outputop some Sequence signature matchesc
has topicop some Sequence sites, features and motifsc

Sequence motif datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2981

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Sequence motif discoveryc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0238

Motifs and patterns might be conserved or over-represented (occur with improbable frequency).
has super-classes
Sequence feature detectionc
Sequence motif analysisc
has topicop some Sequence sites, features and motifsc
has outputop some Sequence signature matchesc

Sequence motif formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2068

has super-classes
Format (by type of data)c
is format ofop some Sequence motifc
has sub-classes
EMBOSS sequence patternc, meme-motifc, prosite-patternc

Sequence motif identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1114

has super-classes
Identifier (by type of data)c
is identifier ofop some Sequence motifc
has sub-classes
ELM IDc, Prosite accession numberc, UTRSite IDc

Sequence motif matchesc back to ToC or Class ToC

IRI: http://edamontology.org/data_1298

has super-classes
deprecated classc

Sequence motif matches (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3131

has super-classes
deprecated classc

Sequence motif matches (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3130

has super-classes
deprecated classc

Sequence motif or profilec back to ToC or Class ToC

IRI: http://edamontology.org/topic_0598

This includes comparison, discovery, recognition etc. of sequence motifs.
has super-classes
deprecated classc

Sequence motif recognitionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0239

has super-classes
Sequence feature detectionc
Sequence motif analysisc
has outputop some Sequence signature matchesc
has topicop some Sequence sites, features and motifsc

Sequence motif renderingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0574

has super-classes
deprecated classc

Sequence motifsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0158

has super-classes
deprecated classc

Sequence mutation and randomisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0367

has super-classes
Sequence editingc

Sequence namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2154

has super-classes
Sequence identifierc
Namec
has sub-classes
UniProt IDc

Sequence offsetc back to ToC or Class ToC

IRI: http://edamontology.org/data_2145

has super-classes
deprecated classc

Sequence positionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1016

has super-classes
Sequence attributec
has sub-classes
Codon numberc, PDB insertion codec, PDB residue numberc, Sequence coordinatesc

Sequence position specificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_1014

has super-classes
deprecated classc

Sequence processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2446

has super-classes
deprecated classc

Sequence processing (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2448

has super-classes
deprecated classc

Sequence processing (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2447

has super-classes
deprecated classc

Sequence profilec back to ToC or Class ToC

IRI: http://edamontology.org/data_1354

has super-classes
Sequence signature datac
has topicop some Sequence sites, features and motifsc
has sub-classes
Position-specific scoring matrixc, Profile HMMc

Sequence profile alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0300

A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
has super-classes
Sequence alignmentc
has topicop some Sequence sites, features and motifsc
has inputop some Sequence profilec

Sequence profile datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2788

has super-classes
deprecated classc

Sequence profile datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2982

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Sequence profile database searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0342

has super-classes
deprecated classc

Sequence profile formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2069

has super-classes
Format (by type of data)c
is format ofop some Sequence profilec
has sub-classes
Hidden Markov model formatc, JASPAR formatc, prosite-profilec

Sequence profile generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0296

has super-classes
Sequence alignment analysisc
Generationc
has inputop some Sequence alignmentc
has topicop some Sequence sites, features and motifsc
has outputop some Sequence profilec

Sequence profile IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1115

A sequence profile typically represents a sequence alignment.
has super-classes
Identifier (by type of data)c
is identifier ofop some Sequence profilec
has sub-classes
CDD PSSM-IDc, HMMER hidden Markov model IDc, JASPAR profile IDc

Sequence profile namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2150

has super-classes
deprecated classc

Sequence profile processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2413

has super-classes
deprecated classc

Sequence profile typec back to ToC or Class ToC

IRI: http://edamontology.org/data_2130

has super-classes
deprecated classc

Sequence profiles and HMMsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0188

Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.
has super-classes
deprecated classc

Sequence propertyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1254

has super-classes
Sequence reportc
has sub-classes
Sequence ambiguity reportc, Sequence complexity reportc, Sequence composition reportc

Sequence property (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1258

has super-classes
deprecated classc

Sequence property (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1257

has super-classes
deprecated classc

Sequence quality report format (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_3606

has super-classes
Format (by type of data)c
is format ofop some Reportc
has sub-classes
qualc

Sequence rangec back to ToC or Class ToC

IRI: http://edamontology.org/data_1017

has super-classes
Sequence attributec
has sub-classes
Sequence coordinatesc

Sequence range formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2078

has super-classes
Format (by type of data)c
is format ofop some Sequence rangec
has sub-classes
Cytoband formatc, EMBL feature locationc

Sequence read processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3921

has super-classes
Nucleic acid sequence analysisc
has sub-classes
Demultiplexingc, RNA-Seq analysisc, Read binningc, Read depth analysisc, Read mappingc, Read pre-processingc, Read summarisationc

Sequence recordc back to ToC or Class ToC

IRI: http://edamontology.org/data_0849

has super-classes
Sequencec
has sub-classes
Nucleic acid sequence recordc, Protein sequence recordc

Sequence record formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1919

has super-classes
Format (by type of data)c
is format ofop some Sequence recordc
has sub-classes
BioJSON (BioXSD)c, BioXSD (XML)c, BioYAMLc, EMBL-like formatc, FASTA-likec, GenBank-like formatc, Sequence record format (XML)c, Sequence record format (text)c, Sequence trace formatc, uniprotkb-like formatc

Sequence record format (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2551

has super-classes
Sequence record formatc
has sub-classes
ASN.1 sequence formatc, GCG format variantc, GDEc, GFF2-seqc, GFF3-seqc, Phylip format variantc, Staden experiment formatc, Staden formatc, TreeCon-seqc, acedbc, codatac, debug-seqc, fitch programc, hennig86c, igc, igstrictc, jackkniferc, jackknifernonc, mase formatc, mega variantc, mega-seqc, nexus-seqc, nexusnonc, pdbatomc, pdbatomnucc, pdbseqresc, pdbseqresnucc, refseqpc, selexc, strider formatc

Sequence record format (XML)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2552

has super-classes
Sequence record formatc
has sub-classes
BEASTc, BSMLc, Chado-XMLc, DAS formatc, OrthoXMLc, SeqXMLc, UniProtKB XMLc, dasdnac

Sequence record fullc back to ToC or Class ToC

IRI: http://edamontology.org/data_2201

has super-classes
deprecated classc

Sequence record full formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2202

has super-classes
deprecated classc

Sequence record litec back to ToC or Class ToC

IRI: http://edamontology.org/data_2043

has super-classes
deprecated classc

Sequence record lite formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2203

has super-classes
deprecated classc

Sequence redundancy removalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0290

has super-classes
Sequence comparisonc
has outputop some Sequencec

Sequence reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2955

has super-classes
Reportc
has sub-classes
Sequence imagec, Sequence propertyc

Sequence retrievalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1813

This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.
has super-classes
deprecated classc

Sequence retrieval (by code)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0344

has super-classes
deprecated classc

Sequence retrieval (by keyword)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0345

has super-classes
deprecated classc

Sequence searchc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3346

has super-classes
deprecated classc

Sequence search resultsc back to ToC or Class ToC

IRI: http://edamontology.org/data_0857

The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc.
has super-classes
Database search resultsc

Sequence setc back to ToC or Class ToC

IRI: http://edamontology.org/data_0850

An example is an alignment reference; one or a set of reference molecular sequences, structures, or profiles used for alignment of genomic, transcriptomic, or proteomic experimental data.
has super-classes
Datac
has sub-classes
Sequence clusterc, Sequence set (nucleic acid)c, Sequence set (protein)c

Sequence set (bootstrapped)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2245

Bootstrapping is often performed in phylogenetic analysis.
has super-classes
deprecated classc

Sequence set (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1234

has super-classes
Sequence setc
has sub-classes
PCR primersc, Restriction digestc, Sequence assemblyc, Sequence cluster (nucleic acid)c, Sequence tracec

Sequence set (polymorphic)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2874

has super-classes
deprecated classc

Sequence set (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1233

has super-classes
Sequence setc
has sub-classes
Peptide molecular weight hitsc, Proteolytic digestc, Sequence cluster (protein)c

Sequence set (stream)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2173

This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time.
has super-classes
deprecated classc

Sequence set IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1064

has super-classes
Identifier (by type of data)c
is identifier ofop some Sequence setc
has sub-classes
Sequence assembly IDc, Sequence cluster IDc

Sequence signature datac back to ToC or Class ToC

IRI: http://edamontology.org/data_0860

This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on.
has super-classes
Datac
has topicop some Sequence sites, features and motifsc
has sub-classes
Sequence motifc, Sequence profilec, Sequence signature matchesc

Sequence signature identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1065

has super-classes
deprecated classc

Sequence signature mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_1281

has super-classes
deprecated classc

Sequence signature matchesc back to ToC or Class ToC

IRI: http://edamontology.org/data_0858

This includes reports of hits from a search of a protein secondary or domain database. Data associated with the search or alignment might also be included, e.g. ranked list of best-scoring sequences, a graphical representation of scores etc.
has super-classes
Sequence signature datac
Alignmentc

Sequence signature modelc back to ToC or Class ToC

IRI: http://edamontology.org/data_0859

has super-classes
deprecated classc

Sequence signature reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2762

has super-classes
Reportc
has topicop some Sequence sites, features and motifsc
has sub-classes
Nucleic acid signaturec, Protein signaturec

Sequence similarityc back to ToC or Class ToC

IRI: http://edamontology.org/data_1413

Data Type is float probably.
has super-classes
Sequence similarity scorec
has sub-classes
Bit scorec

Sequence similarity plotc back to ToC or Class ToC

IRI: http://edamontology.org/data_2161

Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.
has super-classes
Sequence alignment reportc
Plotc

Sequence similarity scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_0865

has super-classes
Scorec
has sub-classes
Sequence identityc, Sequence similarityc

Sequence similarity searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0346

has super-classes
Sequence database searchc
Structure database searchc
Sequence comparisonc

Sequence sites, features and motifsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0160

has super-classes
Computational biologyc
has sub-classes
Nucleic acid sites, features and motifsc, Protein sites, features and motifsc

Sequence submissionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1780

has super-classes
deprecated classc

Sequence tag mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0527

Sequence tag mapping assigns experimentally obtained sequence tags to known transcripts or annotate potential virtual sequence tags in a genome.
has super-classes
Annotationc
DNA mappingc

Sequence tag profilec back to ToC or Class ToC

IRI: http://edamontology.org/data_2535

SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from.
has super-classes
Gene expression profilec

Sequence tag profile (with gene assignment)c back to ToC or Class ToC

IRI: http://edamontology.org/data_0936

has super-classes
deprecated classc

Sequence tagged site (STS) mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2871

An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences.
has super-classes
Physical mappingc
has outputop some Sequence mapc

Sequence tagged sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3139

has super-classes
deprecated classc

Sequence tracec back to ToC or Class ToC

IRI: http://edamontology.org/data_0924

This is the raw data produced by a DNA sequencing machine.
has super-classes
Sequence set (nucleic acid)c
Experimental measurementc

Sequence trace formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2057

has super-classes
Sequence record formatc
is format ofop some Sequence tracec
has sub-classes
AB1c, ABIc, BAMc, FASTQ-like formatc, PHDc, SAMc, SCFc, SFFc, SRFc, ZTRc, mirac, proBAMc

Sequence trace imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_2168

has super-classes
Sequence imagec

Sequence trimmingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3192

This includes ennd trimming Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. trimming to a reference sequence, Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. vector trimming Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences.
has super-classes
Sequence cuttingc

Sequence typec back to ToC or Class ToC

IRI: http://edamontology.org/data_1094

Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).
has super-classes
deprecated classc

Sequence variation annotation formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2921

has super-classes
Format (by type of data)c
is format ofop some Sequence variationsc
has sub-classes
BCFc, Ensembl variation file formatc, GVFc, Gemini SQLite formatc, VCFc

Sequence variation IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2294

has super-classes
Identifier (by type of data)c
has sub-classes
COSMIC IDc, GeneSNP IDc, HGMD IDc, dbSNP IDc

Sequence variationsc back to ToC or Class ToC

IRI: http://edamontology.org/data_3498

Variations are stored along with a reference genome.
has super-classes
Datac
has topicop some Genetic variationc

Sequence versionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1771

has super-classes
Sequence attributec

Sequence visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0564

has super-classes
Visualisationc
Sequence analysisc
has inputop some Sequencec
has outputop some Sequence imagec
has sub-classes
Base position variability plottingc, Dot plot plottingc, Genome visualisationc, Nucleic acid density plottingc, Protein hydrophobic moment plottingc, Sequence assembly visualisationc

Sequence widthc back to ToC or Class ToC

IRI: http://edamontology.org/data_2136

has super-classes
deprecated classc

Sequence word comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0288

has super-classes
Sequence comparisonc
has sub-classes
Dot plot plottingc

Sequence-3D profile alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_0891

has super-classes
deprecated classc

Sequence-MEME profile alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/format_1419

has super-classes
Sequence-profile alignment formatc
Textual formatc

Sequence-profile alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_0869

has super-classes
deprecated classc

Sequence-profile alignment (Domainatrix signature)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1417

has super-classes
deprecated classc

Sequence-profile alignment (fingerprint)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1420

has super-classes
deprecated classc

Sequence-profile alignment (HMM)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1418

has super-classes
deprecated classc

Sequence-profile alignment (HMM) formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2015

has super-classes
deprecated classc

Sequence-profile alignment formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2014

has super-classes
Format (by type of data)c
is format ofop some Sequence signature matchesc
has sub-classes
HMMER profile alignment (HMM versus sequences)c, HMMER profile alignment (sequences versus HMMs)c, Sequence-MEME profile alignmentc

Sequence-structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_0893

has super-classes
Alignmentc

Sequence-to-3D-profile alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0301

has super-classes
deprecated classc

Sequencingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3168

has super-classes
Laboratory techniquesc
has sub-classes
ChIP-seqc, Exome sequencingc, Genome resequencingc, Metagenomic sequencingc, RNA-Seqc, Whole genome sequencingc

Sequencing error detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3195

has super-classes
Sequence comparisonc
has topicop some Sequencingc
has sub-classes
Frameshift detectionc

Sequencing metadata namec back to ToC or Class ToC

IRI: http://edamontology.org/data_3732

has super-classes
Namec
has sub-classes
Flow cell identifierc, Lane identifierc, Run numberc

Sequencing quality controlc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3218

Analyse raw sequence data from a sequencing pipeline and identify (and possiby fix) problems.
has super-classes
Validationc
Nucleic acid sequence analysisc
has sub-classes
Read pre-processingc, Sequence assembly validationc, Sequence contamination filteringc, Variant filteringc

Sequencing-based expression profile data analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2498

has super-classes
deprecated classc

Sequencing-based expression profile data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0312

has super-classes
deprecated classc

SEQUEST .out filec back to ToC or Class ToC

IRI: http://edamontology.org/format_3758

has super-classes
Textual formatc
Mass spectrometry data formatc

Sequin formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3701

has super-classes
Sequence feature table format (text)c

SeqXMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3852

has super-classes
XMLc
Sequence record format (XML)c

Server metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_2218

has super-classes
deprecated classc

Service compositionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3762

has super-classes
Service managementc

Service discoveryc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3761

has super-classes
Service managementc

Service invocationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3763

has super-classes
Service managementc

Service managementc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3760

has super-classes
Operationc
has sub-classes
Service compositionc, Service discoveryc, Service invocationc

SFFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3284

has super-classes
Sequence trace formatc
Binary formatc

SGD gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1614

has super-classes
deprecated classc

SGD IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2632

has super-classes
Accessionc
Identifier (hybrid)c
has sub-classes
Gene ID (SGD)c, Locus ID (SGD)c

Side chain modellingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0480

This includes rotamer likelihood prediction: the prediction of rotamer likelihoods for all 20 amino acid types at each position in a protein structure, where output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.
has super-classes
Protein modellingc

sifc back to ToC or Class ToC

IRI: http://edamontology.org/format_3619

has super-classes
Biological pathway or network formatc

Signal or transit peptidec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3135

has super-classes
deprecated classc

Signal transduction pathway reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_1659

has super-classes
deprecated classc

Signaling Gateway protein IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2617

has super-classes
Accessionc
Protein accessionc

Signaling pathwaysc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0754

has super-classes
deprecated classc

SILACc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3638

has super-classes
Labeled quantificationc

Simulated gene expression data generationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3566

has super-classes
Modelling and simulationc

Simulationc back to ToC or Class ToC

IRI: http://edamontology.org/data_3869

has super-classes
Datac
has sub-classes
Forcefield parametersc, Topology datac, Trajectory datac

Simulation analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0244

Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure.
has super-classes
Protein property calculationc
has sub-classes
Essential dynamicsc

Simulation experimentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3524

has super-classes
Laboratory techniquesc

Simulation experiment reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_3428

has super-classes
deprecated classc

Single particle alignment and classificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3458

A micrograph can include particles in multiple different orientations and/or conformations. Particles are compared and organised into sets based on their similarity. Typically iterations of classification and alignment and are performed to optimise the final 3D EM map.
has super-classes
Classificationc
Single particle analysisc

Single particle analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3457

Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM).
has super-classes
Structure analysisc
Image analysisc
has topicop some Structural biologyc
has sub-classes
Single particle alignment and classificationc

siRNA binding specificity predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0465

has super-classes
trans-regulatory element predictionc
has topicop some Functional, regulatory and non-coding RNAc

siRNA duplex predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2008

has super-classes
trans-regulatory element predictionc
has topicop some Functional, regulatory and non-coding RNAc

SISYPHUS IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2793

has super-classes
Structure alignment IDc
Accessionc

Small molecule datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2601

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Small molecule data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2123

has super-classes
deprecated classc

Small molecule reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0962

has super-classes
Structure reportc
has topicop some Small moleculesc
has sub-classes
Drug reportc

Small molecule structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_1463

has super-classes
Structurec
has topicop some Small moleculesc
has sub-classes
Drug structurec, Toxin structurec

Small moleculesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0154

Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included.
has super-classes
Structure analysisc

SMART accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1139

has super-classes
Accessionc
Protein family accessionc

SMART domain assignment report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1563

The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues.
has super-classes
deprecated classc

SMART domain namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2782

has super-classes
Protein family namec

SMART entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1577

has super-classes
deprecated classc

SMART protein schematicc back to ToC or Class ToC

IRI: http://edamontology.org/data_1293

has super-classes
deprecated classc

smartsc back to ToC or Class ToC

IRI: http://edamontology.org/format_1200

has super-classes
SMILESc

SMILESc back to ToC or Class ToC

IRI: http://edamontology.org/format_1196

has super-classes
Chemical formula formatc
Textual formatc
has sub-classes
smartsc

SMILES stringc back to ToC or Class ToC

IRI: http://edamontology.org/data_2301

has super-classes
Chemical formulac

Smith-Waterman formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1335

has super-classes
Database hits (sequence) formatc
Textual formatc

SNPc back to ToC or Class ToC

IRI: http://edamontology.org/data_2092

has super-classes
deprecated classc

SNPc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2277

has super-classes
deprecated classc

SNP annotationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3661

has super-classes
Sequence annotationc

SNP callingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3201

has super-classes
deprecated classc

SNP detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0484

This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc.
has super-classes
Variant callingc

snpeffdbc back to ToC or Class ToC

IRI: http://edamontology.org/format_3624

has super-classes
Binary formatc
Data index formatc

Software engineeringc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3372

has super-classes
Computer sciencec

Sortingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3802

has super-classes
Data handlingc

SPARQLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3790

has super-classes
Textual formatc

Species frequency estimationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3221

has super-classes
Nucleic acid sequence analysisc
has topicop some Metagenomicsc

Species namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1045

has super-classes
Taxonc

Species treec back to ToC or Class ToC

IRI: http://edamontology.org/data_3272

has super-classes
Phylogenetic treec

Species tree constructionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0544

has super-classes
Phylogenetic tree constructionc

Specific protein resourcesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0635

has super-classes
deprecated classc

Spectral analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3214

has super-classes
Analysisc
has topicop some Proteomicsc
has sub-classes
Chromatographic alignmentc, Deisotopingc, Mass spectra calibrationc, Natural product identificationc, Peak detectionc, Peptide identificationc, Protein identificationc, Protein quantificationc, Spectrum calculationc

Spectral countingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3637

has super-classes
Label-free quantificationc

Spectral library searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3801

has super-classes
Peptide identificationc
has inputop some Mass spectrumc

Spectrumc back to ToC or Class ToC

IRI: http://edamontology.org/data_3483

has super-classes
Datac
has sub-classes
NMR spectrumc

Spectrum calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3860

has super-classes
Protein property calculationc
Spectral analysisc
has inputop some Mass spectrumc

Splice site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0433

Methods might require a pre-mRNA or genomic DNA sequence.
has super-classes
Splicing analysisc
has topicop some Gene structurec

Splice sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1307

has super-classes
deprecated classc

Splicing analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2499

has super-classes
Prediction and recognitionc
Modelling and simulationc
Gene predictionc
has topicop some Gene structurec
has sub-classes
Alternative splicing predictionc, Splice site predictionc

Split read mappingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3199

has super-classes
Read mappingc

Splittingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3359

has super-classes
Data handlingc

spMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3250

has super-classes
XMLc
Experiment annotation formatc

Spot IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2373

has super-classes
Identifier (by type of data)c
has sub-classes
Spot ID (HSC-2DPAGE)c, Spot serial numberc

Spot ID (HSC-2DPAGE)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2375

has super-classes
Accessionc
Spot IDc

Spot serial numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_2374

has super-classes
Accessionc
Spot IDc

SPSSc back to ToC or Class ToC

IRI: http://edamontology.org/format_3555

has super-classes
Textual formatc

SQLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3788

has super-classes
Textual formatc

SQLite formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3621

has super-classes
Binary formatc
has sub-classes
Gemini SQLite formatc

SRA formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3698

has super-classes
Binary formatc

SRFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3017

has super-classes
Sequence trace formatc
Binary formatc

srs formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2002

has super-classes
Textual formatc
Alignment format (text)c

srspairc back to ToC or Class ToC

IRI: http://edamontology.org/format_2003

has super-classes
Textual formatc
Alignment format (pair only)c

SSc back to ToC or Class ToC

IRI: http://edamontology.org/format_3310

has super-classes
RNA secondary structure formatc
Textual formatc

Staden experiment formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1928

has super-classes
Textual formatc
Sequence record format (text)c

Staden formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1960

has super-classes
Textual formatc
Sequence record format (text)c

Standardisation and normalisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3435

In the simplest normalisation means adjusting values measured on different scales to a common scale (often between 0.0 and 1.0), but can refer to more sophisticated adjustment whereby entire probability distributions of adjusted values are brought into alignment. Standardisation typically refers to an operation whereby a range of values are standardised to measure how many standard deviations a value is from its mean.
has super-classes
Statistical calculationc

Statistical calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2238

has super-classes
Calculationc
has sub-classes
Imputationc, Regression analysisc, Standardisation and normalisationc, Statistical inferencec, Statistical modellingc

Statistical estimate scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_0951

has super-classes
Scorec
has sub-classes
E-valuec, P-valuec, Q-valuec, Z-valuec

Statistical inferencec back to ToC or Class ToC

IRI: http://edamontology.org/operation_3658

has super-classes
Statistical calculationc

Statistical modellingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3664

has super-classes
Statistical calculationc

Statistics and probabilityc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2269

has super-classes
Mathematicsc

Stock numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_2779

has super-classes
Identifier (by type of data)c
has sub-classes
Stock number (TAIR)c

Stock number (TAIR)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2780

has super-classes
Accessionc
Stock numberc

Stockholm formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1961

has super-classes
Textual formatc
Alignment format (text)c

Strain accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2912

has super-classes
Strain identifierc
Organism accessionc
is identifier ofop some Cell line reportc
has sub-classes
CCAP strain numberc

Strain data formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2210

has super-classes
deprecated classc

Strain identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2379

has super-classes
Organism identifierc
has sub-classes
Strain accessionc, Strain namec

Strain namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1046

has super-classes
Strain identifierc
Organism namec
has sub-classes
Cell line namec

STRIDE log filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1680

has super-classes
deprecated classc

strider formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1962

has super-classes
Textual formatc
Sequence record format (text)c

STRING entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2560

has super-classes
deprecated classc

STRING entry format (HTML)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2303

has super-classes
deprecated classc

STRING entry format (XML)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2304

has super-classes
Protein interaction formatc
XMLc

STRING IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2302

has super-classes
Protein interaction IDc
Accessionc

Structural (3D) profile alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_0890

has super-classes
Alignmentc

Structural (3D) profile IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1071

has super-classes
Identifier (by type of data)c
is identifier ofop some Structural profilec

Structural (3D) profilesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0167

has super-classes
deprecated classc

Structural biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1317

This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.
has super-classes
Biologyc
has sub-classes
Electron microscopyc, NMRc, Neutron diffractionc, Structural genomicsc, X-ray diffractionc

Structural datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2053

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
deprecated classc

Structural data processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2504

has super-classes
deprecated classc

Structural distance matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_2856

has super-classes
Distance matrixc

Structural genomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0122

has super-classes
Genomicsc
Structural biologyc

Structural genomics target selectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0318

Methods will typically navigate a graph of protein families of known structure.
has super-classes
deprecated classc

Structural motif discoveryc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0245

This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc.
has super-classes
Protein structure analysisc
Protein feature detectionc
has topicop some Protein structural motifs and surfacesc

Structural profilec back to ToC or Class ToC

IRI: http://edamontology.org/data_0889

has super-classes
Datac
has topicop some Structure analysisc

Structural profile alignment generation (multiple)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0514

has super-classes
deprecated classc

Structural profile processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2411

has super-classes
deprecated classc

Structural similarity searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0360

has super-classes
Structure database searchc
Structure comparisonc

Structural transformation matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_1494

has super-classes
Matrixc

Structural variation detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3228

Methods might involve analysis of whole-genome array comparative genome hybridisation or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies.
has super-classes
Genetic variation analysisc

Structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_0883

The coordinate data may be predicted or real.
has super-classes
Datac
has topicop some Structure analysisc
has sub-classes
3D EM Mapc, 3D EM Maskc, Carbohydrate structurec, Lipid structurec, Nucleic acid structurec, Protein structurec, Small molecule structurec

Structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/data_0886

A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition.
has super-classes
Alignmentc
has topicop some Structure analysisc
has sub-classes
Nucleic acid structure alignmentc, Protein structure alignmentc, Structure alignment (pair)c

Structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0295

has super-classes
Structure analysisc
Structure comparisonc
Alignmentc
has outputop some Structure alignmentc
has sub-classes
Global structure alignmentc, Local structure alignmentc, Multiple structure alignmentc, Pairwise structure alignmentc

Structure alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0183

This includes the generation, storage, analysis, rendering etc. of structure alignments.
has super-classes
deprecated classc

Structure alignment (multiple)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1480

has super-classes
deprecated classc

Structure alignment (nucleic acid pair)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1491

has super-classes
deprecated classc

Structure alignment (pair)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1479

has super-classes
Structure alignmentc

Structure alignment (protein all atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1485

has super-classes
deprecated classc

Structure alignment (protein C-alpha atoms)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1486

C-beta atoms from amino acid side-chains may be considered.
has super-classes
deprecated classc

Structure alignment (protein pair)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1483

has super-classes
deprecated classc

Structure alignment (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0505

has super-classes
deprecated classc

Structure alignment (RNA)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0506

has super-classes
deprecated classc

Structure alignment IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1072

has super-classes
Identifier (by type of data)c
is identifier ofop some Structure alignmentc
has sub-classes
SISYPHUS IDc

Structure alignment processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2952

has super-classes
deprecated classc

Structure alignment reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0887

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Reportc

Structure analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2480

has super-classes
Analysisc
has topicop some Structure analysisc
has sub-classes
3D profile generationc, Diffraction data analysisc, Molecular dockingc, Molecular dynamicsc, Molecular model refinementc, Molecular surface analysisc, Nucleic acid structure analysisc, Protein structure analysisc, Single particle analysisc, Structure alignmentc, Structure classificationc, Structure comparisonc, Structure visualisationc

Structure analysisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0081

This includes related concepts such as structural properties, alignments and structural motifs.
has super-classes
Computational biologyc
has sub-classes
Carbohydratesc, Lipidsc, Nucleic acid structure analysisc, Protein structure analysisc, Small moleculesc, Structure predictionc

Structure classificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2996

has super-classes
Structure analysisc
Classificationc
has sub-classes
Protein architecture recognitionc

Structure clusteringc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2844

has super-classes
Clusteringc

Structure comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2483

has super-classes
Comparisonc
Structure analysisc
has topicop some Structure analysisc
has sub-classes
Chemical redundancy removalc, Molecular surface comparisonc, Nucleic acid structure comparisonc, Protein structure comparisonc, Structural similarity searchc, Structure alignmentc

Structure comparisonc back to ToC or Class ToC

IRI: http://edamontology.org/topic_1770

This might involve comparison of secondary or tertiary (3D) structural information.
has super-classes
deprecated classc

Structure database searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0339

has super-classes
Database searchc
has topicop some Structure analysisc
has sub-classes
Sequence similarity searchc, Structural similarity searchc

Structure database searchc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2271

The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template.
has super-classes
deprecated classc

Structure database search (by sequence)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0359

has super-classes
deprecated classc

Structure database search resultsc back to ToC or Class ToC

IRI: http://edamontology.org/data_0885

has super-classes
deprecated classc

Structure databasesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3038

has super-classes
deprecated classc

Structure determinationc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2226

has super-classes
deprecated classc

Structure editingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3080

has super-classes
Editingc
has inputop some Structurec

Structure file processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2234

has super-classes
deprecated classc

Structure formattingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1848

has super-classes
deprecated classc

Structure IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1070

has super-classes
Structure identifierc
has sub-classes
MMDB IDc, PDB IDc

Structure identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_3035

has super-classes
Identifier (by type of data)c
is identifier ofop some Structurec
has sub-classes
PDB model numberc, Structure IDc

Structure imagec back to ToC or Class ToC

IRI: http://edamontology.org/data_1710

has super-classes
Imagec
has sub-classes
Chemical structure imagec, Protein structure imagec

Structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0271

has super-classes
deprecated classc

Structure predictionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0082

This includes the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s), for example by threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).
has super-classes
Structure analysisc
has sub-classes
Molecular dynamicsc, Molecular modellingc

Structure processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2465

has super-classes
deprecated classc

Structure processing (nucleic acid)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2519

has super-classes
deprecated classc

Structure processing (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2459

has super-classes
deprecated classc

Structure processing (RNA)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_2440

has super-classes
deprecated classc

Structure reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_2085

has super-classes
Reportc
has sub-classes
Carbohydrate reportc, Lipid reportc, Nucleic acid structure reportc, Protein structure reportc, Small molecule reportc

Structure retrievalc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1814

This includes direct retrieval methods but not those that perform calculations on the sequence or structure.
has super-classes
deprecated classc

Structure retrieval (by code)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0357

has super-classes
deprecated classc

Structure retrieval (by keyword)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0358

has super-classes
deprecated classc

Structure retrieval (water)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_1914

has super-classes
deprecated classc

Structure similarity scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_0888

has super-classes
Scorec
has sub-classes
Root-mean-square deviationc, Tanimoto similarity scorec

Structure visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0570

This includes visualisation of protein secondary structure such as knots, pseudoknots etc. as well as tertiary and quaternary structure.
has super-classes
Visualisationc
Structure analysisc
has outputop some Structure imagec
has inputop some Structurec
has sub-classes
Helical wheel drawingc, Surface renderingc, Topology diagram drawingc, Trajectory visualizationc, Transmembrane protein visualisationc

Structure-based sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0294

has super-classes
Sequence alignmentc

Study topicc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2809

has super-classes
deprecated classc

Subcellular localisation predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2489

The prediction might include subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.
has super-classes
Protein function predictionc
has topicop some Protein targeting and localisationc

Superfamily entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1578

has super-classes
deprecated classc

Superfamily hidden Markov model numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1140

has super-classes
Accessionc
Protein family accessionc

Surface renderingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1816

A dot has three coordinates (x,y,z) and (typically) a color.
has super-classes
Structure visualisationc
Molecular surface analysisc

Surgeryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3421

has super-classes
Medicinec

SVGc back to ToC or Class ToC

IRI: http://edamontology.org/format_3604

The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999.
has super-classes
XMLc
Image formatc

swiss featurec back to ToC or Class ToC

IRI: http://edamontology.org/format_1977

has super-classes
deprecated classc

Swiss-Prot to PDB mappingc back to ToC or Class ToC

IRI: http://edamontology.org/data_1673

has super-classes
deprecated classc

Synonymc back to ToC or Class ToC

IRI: http://edamontology.org/data_1877

has super-classes
deprecated classc

Synthetic biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3895

has super-classes
Biologyc
Biotechnologyc

Synthetic chemistryc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3371

has super-classes
Chemistryc
has sub-classes
Chemical biologyc, Medicinal chemistryc

System metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_3106

has super-classes
Resource metadatac

Systems biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2259

This includes databases of models and methods to construct or analyse a model.
has super-classes
Biologyc

Systems medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3396

has super-classes
Medicinec

T-Coffee formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2004

has super-classes
Textual formatc
Alignment format (text)c

T3DB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2662

has super-classes
Accessionc
Toxin accessionc

tabixc back to ToC or Class ToC

IRI: http://edamontology.org/format_3616

has super-classes
Binary formatc
Image formatc

Tabix index file formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3700

has super-classes
Binary formatc
Data index formatc
is format ofop some Data indexc

Tag-based peptide identificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3643

has super-classes
Peptide identificationc

TAIR accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2387

has super-classes
Accessionc
Identifier (hybrid)c
has sub-classes
TAIR accession (gene)c, TAIR accession (protein)c

TAIR accession (At gene)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2388

has super-classes
TAIR accession (gene)c

TAIR accession (gene)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1037

has super-classes
Gene IDc
TAIR accessionc
has sub-classes
TAIR accession (At gene)c

TAIR accession (protein)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2621

has super-classes
Sequence accession (protein)c
TAIR accessionc

TAIR gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1616

has super-classes
deprecated classc

Tanimoto similarity scorec back to ToC or Class ToC

IRI: http://edamontology.org/data_1498

A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types.
has super-classes
Structure similarity scorec

Target ID (TTD)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2654

has super-classes
Accessionc
Protein accessionc

Target-Decoyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3649

has super-classes
Validationc
Peptide database searchc

Tau angle calculationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_1828

Tau is the backbone angle N-Calpha-C (angle over the C-alpha).
has super-classes
deprecated classc

Taverna workflow formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1665

has super-classes
Workflow formatc
XMLc

Taverna workflow IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1167

has super-classes
Workflow IDc
Accessionc

Taxonc back to ToC or Class ToC

IRI: http://edamontology.org/data_1868

For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary.
has super-classes
Organism namec
has sub-classes
Family namec, Genus namec, Kingdom namec, NCBI taxonc, Species namec, UTRdb taxonc, UniGene taxonc

Taxonomic classificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_1872

Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included.
has super-classes
Organism namec

Taxonomic classificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3460

has super-classes
Sequence classificationc

Taxonomyc back to ToC or Class ToC

IRI: http://edamontology.org/data_3028

This is a broad data type and is used a placeholder for other, more specific types.
has super-classes
Datac
has topicop some Phylogenyc

Taxonomyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0637

has super-classes
Evolutionary biologyc

TCDB IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2614

OBO file for regular expression.
has super-classes
Accessionc
Protein family accessionc

TCIDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2756

has super-classes
Accessionc
Protein accessionc

Term ID listc back to ToC or Class ToC

IRI: http://edamontology.org/data_2765

The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included.
has super-classes
deprecated classc

Terminal gap extension penaltyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1411

has super-classes
Gap extension penaltyc

Terminal gap opening penaltyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1410

has super-classes
Gap opening penaltyc

Terminal gap penaltyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1400

has super-classes
deprecated classc

Tertiary structure formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2033

has super-classes
Format (by type of data)c
has sub-classes
AMBER topc, CHARMM rtfc, GROMACS itpc, GROMACS topc, PDB database entry formatc, PSFc, RSTc, XYZc, mdcrdc, trrc

Tertiary structure recordc back to ToC or Class ToC

IRI: http://edamontology.org/data_0884

has super-classes
deprecated classc

Textc back to ToC or Class ToC

IRI: http://edamontology.org/data_3671

has super-classes
Text datac
has sub-classes
Annotated textc, Articlec

Text annotationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3778

has super-classes
Annotationc
has topicop some Literature and languagec
has inputop some Textc
has outputop some Annotated textc

Text datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2526

This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.
has super-classes
Datac
has topicop some Literature and languagec
has sub-classes
Abstractc, Annotated textc, Articlec, Bibliographyc, Citationc, Textc, Text mining reportc

Text miningc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0306

has super-classes
Prediction and recognitionc
Analysisc
has topicop some Natural language processingc
has inputop some Textc
has outputop some Text mining reportc
has sub-classes
Information extractionc, Information retrievalc, Relation extractionc

Text mining reportc back to ToC or Class ToC

IRI: http://edamontology.org/data_0972

A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles.
has super-classes
Reportc
Text datac

Text mining report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2021

has super-classes
Format (by type of data)c
is format ofop some Text mining reportc
has sub-classes
iHOP formatc

Text processingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2505

has super-classes
deprecated classc

Textual formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2330

Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual).
has super-classes
Formatc
has sub-classes
ACEc, AGPc, AMBER frcmodc, AMBER offc, AMBER topc, ASN.1 sequence formatc, BEDc, BELc, BIOM formatc, BLAST resultsc, BcFormsc, BioNLP Shared Task formatc, BpFormsc, CAFc, CHARMM rtfc, CHPc, CTc, CiteXplore-allc, CiteXplore-corec, ClustalW dendrogramc, ClustalW formatc, Cytoband formatc, Cytoscape input file formatc, DIALIGN formatc, DSVc, Dot-bracket formatc, ELAND formatc, EMBL feature locationc, EMBL-like (text)c, EMBOSS repeatc, EMBOSS sequence patternc, EMBOSS simple formatc, EXPc, Ensembl variation file formatc, FASTA search results formatc, FASTA-like (text)c, FASTGc, FASTQ-like format (text)c, GCGc, GCG format variantc, GCT/Res formatc, GDEc, GENc, GFFc, GMLc, GPRc, GROMACS itpc, GROMACS topc, GSuitec, GTrackc, GenBank-like format (text)c, HET group dictionary entry formatc, HMMER Dirichlet priorc, HMMER emission and transitionc, HMMER formatc, HMMER profile alignment (HMM versus sequences)c, HMMER profile alignment (sequences versus HMMs)c, HMMER-alnc, ISA-TABc, InChIc, InChIKeyc, InterPro hits formatc, JASPAR formatc, JCAMP-DXc, KRSS2 Syntaxc, LAVc, LocARNA PPc, MAFc, MCPDc, MEME Dirichlet priorc, MEME background Markov modelc, MTXc, Manchester OWL Syntaxc, Mascot .dat filec, MaxQuant APL peaklist formatc, Medline Display Formatc, Mol2c, Molfilec, N-Quadsc, N-Triplesc, NMReDATAc, Nexus formatc, Notation3c, OBOc, OSCAR formatc, OWL Functional Syntaxc, PDBc, PED/MAPc, PHDc, PSc, PSFc, PSI MI TAB (MITAB)c, PSLc, Pcons report formatc, Phylip character frequencies formatc, Phylip cliques formatc, Phylip continuous quantitative charactersc, Phylip discrete states formatc, Phylip distance matrixc, Phylip format variantc, Phylip tree distance formatc, Phylip tree formatc, Phylip tree rawc, Pileupc, PlasMapper TextMapc, Primer3 primerc, ProQ report formatc, PubMed citationc, PubTator formatc, R file formatc, REBASE restriction sitesc, RSTc, SAMc, SAMPLE file formatc, SBtabc, SDFc, SEQUEST .out filec, SMILESc, SPARQLc, SPSSc, SQLc, SSc, Sanger inverted repeatsc, Sequence-MEME profile alignmentc, Smith-Waterman formatc, Staden experiment formatc, Staden formatc, Stockholm formatc, T-Coffee formatc, TreeBASE formatc, TreeCon formatc, TreeCon-seqc, TreeFam formatc, Turtlec, UniProt-like (text)c, VCFc, Vienna local RNA secondary structure formatc, WIGc, XQueryc, XYZc, aaindexc, affymetrixc, affymetrix-expc, afgc, ambiguousc, arffc, axtc, bedgraphc, celc, chrominfoc, codatac, completely unambiguousc, customtrackc, dafc, datc, dbGaP formatc, debugc, debug-featc, debug-seqc, dhfc, dsspc, est2genome formatc, findkmc, fitch programc, genePredc, hennig86c, hsspc, igc, igstrictc, jackkniferc, jackknifernonc, latexc, lhfc, markx0 variantc, mase formatc, matchc, mdcrdc, medlinec, mega variantc, mega-seqc, meme-motifc, mfc, mhdc, mirac, mmCIFc, mspcrunchc, mzTabc, nbrf/pirc, newickc, nexus-seqc, nexusnonc, nrrdc, nucleotidec, pdbatomc, pdbatomnucc, pdbseqresc, pdbseqresnucc, pgSnpc, plain text format (unformatted)c, pmcc, proBEDc, prosite-patternc, prosite-profilec, proteinc, purec, qualc, quicktandemc, rawc, rccc, refseqpc, restover formatc, restrict formatc, scores formatc, selexc, srs formatc, srspairc, strider formatc, trrc, unambiguous sequencec, unpurec
is disjoint with
Binary formatc

Theoretical biologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0771

has super-classes
deprecated classc

Thermo RAWc back to ToC or Class ToC

IRI: http://edamontology.org/format_3712

Proprietary format for which documentation is not available.
has super-classes
Binary formatc
Mass spectrometry data formatc

Threadingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0184

has super-classes
deprecated classc

Thresholdc back to ToC or Class ToC

IRI: http://edamontology.org/data_2146

has super-classes
deprecated classc

TIDE TXTc back to ToC or Class ToC

IRI: http://edamontology.org/format_3835

has super-classes
XMLc
Mass spectrometry data formatc

TIFFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3591

The TIFF format is perhaps the most versatile and diverse bitmap format in existence. Its extensible nature and support for numerous data compression schemes allow developers to customize the TIFF format to fit any peculiar data storage needs.
has super-classes
Binary formatc
Image formatc

TIGR gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1619

has super-classes
deprecated classc

TIGR identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1036

has super-classes
Accessionc
Identifier (hybrid)c
Gene IDc

TIGRFam entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1579

has super-classes
deprecated classc

TIGRFam IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1141

has super-classes
Accessionc
Protein family accessionc

TMT-tagc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3641

has super-classes
Labeled quantificationc

TNGc back to ToC or Class ToC

IRI: http://edamontology.org/format_3876

Fully architecture-independent format, regarding both endianness and the ability to mix single/double precision trajectories and I/O libraries. Self-sufficient, it should not require any other files for reading, and all the data should be contained in a single file for easy transport. Temporal compression of data, improving the compression rate of the previous XTC format. Possibility to store meta-data with information about the simulation. Direct access to a particular frame. Efficient parallel I/O.
has super-classes
Binary formatc
Trajectory format (binary)c

Togglec back to ToC or Class ToC

IRI: http://edamontology.org/data_2135

has super-classes
deprecated classc

Tomographyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3452

has super-classes
Imagingc

Toolc back to ToC or Class ToC

IRI: http://edamontology.org/data_0007

has super-classes
deprecated classc

Tool identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_0977

has super-classes
Identifier (by type of data)c
has sub-classes
Tool namec

Tool logc back to ToC or Class ToC

IRI: http://edamontology.org/data_1678

has super-classes
deprecated classc

Tool metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_0958

has super-classes
Resource metadatac

Tool namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1190

has super-classes
Tool identifierc
has sub-classes
Tool name (BLAST)c, Tool name (EMBASSY package)c, Tool name (EMBOSS)c, Tool name (FASTA)c, Tool name (signature)c

Tool name (BLAST)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1192

This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'.
has super-classes
Tool namec

Tool name (EMBASSY package)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1195

has super-classes
Tool namec

Tool name (EMBOSS)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1194

has super-classes
Tool namec

Tool name (FASTA)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1193

This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'.
has super-classes
Tool namec

Tool name (signature)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1191

Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP.
has super-classes
Tool namec

Tool topicc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2807

has super-classes
deprecated classc

Tool version informationc back to ToC or Class ToC

IRI: http://edamontology.org/data_1671

has super-classes
deprecated classc

Topicc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0003

has sub-classes
Biologyc, Biomedical sciencec, Chemistryc, Computational biologyc, Computer sciencec, Experimental design and studiesc, Informaticsc, Laboratory techniquesc, Literature and languagec, Mathematicsc, Medicinec, Omicsc, Physicsc
is in domain of
is topic ofop
is in range of
has topicop
is disjoint with
Datac, Formatc, Operationc, deprecated classc

Topology datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3872

has super-classes
Simulationc

Topology diagram drawingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2486

has super-classes
Structure visualisationc
has outputop some Protein structure imagec

Topology formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3879

Many different file formats exist describing structural molecular topology. Tipically, each MD package or simulation software works with their own implementation (e.g. GROMACS top, CHARMM psf, AMBER prmtop).
has super-classes
Format (by type of data)c
is format ofop some Topology datac
has sub-classes
AMBER topc, CHARMM rtfc, GROMACS itpc, GROMACS topc, PSFc

Toxicologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2840

has super-classes
Medicinec
Safety sciencesc

Toxin accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2897

has super-classes
Toxin identifierc
has sub-classes
ArachnoServer IDc, T3DB IDc

Toxin annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2400

has super-classes
deprecated classc

Toxin identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2576

has super-classes
Compound identifierc
is identifier ofop some Toxin structurec
has sub-classes
Toxin accessionc, Toxin namec

Toxin namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2896

has super-classes
Namec
Toxin identifierc

Toxin structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_2852

has super-classes
Small molecule structurec

Toxins and targetsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2661

has super-classes
deprecated classc

Training materialc back to ToC or Class ToC

IRI: http://edamontology.org/data_3669

has super-classes
Datac
has sub-classes
Online coursec

Trajectory datac back to ToC or Class ToC

IRI: http://edamontology.org/data_3870

has super-classes
Simulationc

Trajectory formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3866

Formats differ on what they are able to store (coordinates, velocities, topologies) and how they are storing it (raw, compressed, textual, binary).
has super-classes
Format (by type of data)c
is format ofop some Trajectory datac
has sub-classes
Trajectory format (binary)c, Trajectory format (text)c

Trajectory format (binary)c back to ToC or Class ToC

IRI: http://edamontology.org/format_3867

has super-classes
Trajectory formatc
has sub-classes
BinPosc, HDFc, HDF5c, PCAzipc, TNGc, XTCc, netCDFc

Trajectory format (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_3868

has super-classes
Trajectory formatc
has sub-classes
RSTc, XYZc, mdcrdc, trrc

Trajectory visualizationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3890

has super-classes
Structure visualisationc
has outputop some Helical wheelc

TraMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3246

has super-classes
XMLc
Mass spectrometry data formatc

trans-regulatory element predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0443

Trans-regulatory elements regulate genes distant from the gene from which they were transcribed.
has super-classes
Transcriptional regulatory element predictionc
has topicop some Functional, regulatory and non-coding RNAc
has sub-classes
miRNA target predictionc, siRNA binding specificity predictionc, siRNA duplex predictionc

Transcript IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2769

has super-classes
Nucleic acid identifierc
Molecule accessionc
is identifier ofop some Nucleic acid featuresc
has sub-classes
Clone IDc, Ensembl transcript IDc, HIT IDc

Transcriptionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0110

has super-classes
deprecated classc

Transcription factor accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2911

has super-classes
Transcription factor identifierc
Protein accessionc
has sub-classes
AraC-XylS IDc, DBD IDc, TRANSFAC accession numberc

Transcription factor binding site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0445

has super-classes
Promoter predictionc

Transcription factor binding sitesc back to ToC or Class ToC

IRI: http://edamontology.org/data_1315

has super-classes
deprecated classc

Transcription factor identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_1077

has super-classes
Identifier (by type of data)c
Protein identifierc
has sub-classes
Transcription factor accessionc, Transcription factor namec

Transcription factor namec back to ToC or Class ToC

IRI: http://edamontology.org/data_2755

has super-classes
Protein namec
Transcription factor identifierc

Transcription factors and regulatory sitesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0749

This includes CpG rich regions (isochores) in a nucleotide sequence.
has super-classes
Proteinsc
Gene expressionc
DNA binding sitesc

Transcription regulatory sequence analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0241

For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors.
has super-classes
deprecated classc

Transcriptional features (report)c back to ToC or Class ToC

IRI: http://edamontology.org/data_3138

This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.
has super-classes
deprecated classc

Transcriptional regulatory element predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0438

This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc.
has super-classes
Gene predictionc
has topicop some Transcription factors and regulatory sitesc
has sub-classes
Promoter predictionc, S/MAR predictionc, cis-regulatory element predictionc, trans-regulatory element predictionc

Transcriptional regulatory element prediction (RNA-cis)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_0442

has super-classes
deprecated classc

Transcriptome assemblyc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3258

has super-classes
Sequence assemblyc
has outputop some Sequence assemblyc
has topicop some Sequence assemblyc

Transcriptome assembly (de novo)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3259

has super-classes
deprecated classc

Transcriptome assembly (mapping)c back to ToC or Class ToC

IRI: http://edamontology.org/operation_3260

has super-classes
deprecated classc

Transcriptomicsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3308

has super-classes
Gene expressionc
Genomicsc
has sub-classes
Metatranscriptomicsc

TRANSFAC accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1143

has super-classes
Accessionc
Transcription factor accessionc

Transition matrixc back to ToC or Class ToC

IRI: http://edamontology.org/data_3354

Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa.
has super-classes
Matrixc

Translation frame specificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2126

has super-classes
deprecated classc

Translation initiation site predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0439

has super-classes
Coding region predictionc
has topicop some Protein expressionc

Translation phase specificationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2336

has super-classes
deprecated classc

Translational medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3342

has super-classes
Medicinec
has sub-classes
Molecular medicinec

Transmembrane protein analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0270

Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods).
has super-classes
Analysisc
has topicop some Membrane and lipoproteinsc
has sub-classes
Transmembrane protein predictionc, Transmembrane protein visualisationc

Transmembrane protein database searchc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0343

has super-classes
deprecated classc

Transmembrane protein predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0269

has super-classes
Protein secondary structure predictionc
Transmembrane protein analysisc

Transmembrane protein predictionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2278

has super-classes
deprecated classc

Transmembrane protein visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2241

has super-classes
Transmembrane protein analysisc
Structure visualisationc
has outputop some Protein structure imagec

Transposon predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0427

has super-classes
Nucleic acid feature detectionc

Trauma medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3414

has super-classes
Medicinec

Tree datingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3942

has super-classes
Phylogenetic analysisc

Tree-based sequence alignmentc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0499

This is supposed to give a more biologically meaningful alignment than standard alignments.
has super-classes
Sequence alignmentc
has topicop some Phylogenyc

TreeBASE formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1436

has super-classes
Textual formatc
Phylogenetic tree format (text)c

TreeBASE study accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1123

has super-classes
Phylogenetic tree IDc
Accessionc

TreeCon formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1911

has super-classes
Textual formatc
Phylogenetic tree format (text)c

treecon sequence formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1965

has super-classes
deprecated classc

TreeCon-seqc back to ToC or Class ToC

IRI: http://edamontology.org/format_2005

has super-classes
Textual formatc
Sequence record format (text)c
Alignment format (text)c

TreeFam accession numberc back to ToC or Class ToC

IRI: http://edamontology.org/data_1124

has super-classes
Phylogenetic tree IDc
Accessionc

TreeFam formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1437

has super-classes
Textual formatc
Phylogenetic tree format (text)c

Treemap visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2942

has super-classes
Expression data visualisationc

TREMBL accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_1101

has super-classes
deprecated classc

Trim endsc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3189

For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.
has super-classes
deprecated classc

Trim to referencec back to ToC or Class ToC

IRI: http://edamontology.org/operation_3191

has super-classes
deprecated classc

Trim vectorc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3190

has super-classes
deprecated classc

tRNAc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0663

has super-classes
deprecated classc

tRNA gene predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0464

has super-classes
Gene predictionc
has topicop some Functional, regulatory and non-coding RNAc

tRNA structurec back to ToC or Class ToC

IRI: http://edamontology.org/data_1466

has super-classes
RNA structurec

Tropical medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3575

has super-classes
Medicinec

trrc back to ToC or Class ToC

IRI: http://edamontology.org/format_3910

has super-classes
Tertiary structure formatc
Textual formatc
Trajectory format (text)c

TSVc back to ToC or Class ToC

IRI: http://edamontology.org/format_3475

has super-classes
DSVc
has sub-classes
MAGE-TABc

Tumor annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2217

has super-classes
deprecated classc

Turtlec back to ToC or Class ToC

IRI: http://edamontology.org/format_3255

The SPARQL Query Language incorporates a very similar syntax.
has super-classes
Textual formatc
RDF formatc

Two-dimensional gel electrophoresisc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0133

has super-classes
deprecated classc

Typec back to ToC or Class ToC

IRI: http://edamontology.org/data_2100

has super-classes
deprecated classc

UMLSc back to ToC or Class ToC

IRI: http://edamontology.org/data_1721

has super-classes
deprecated classc

UMLS concept IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1181

has super-classes
Ontology concept IDc
Accessionc

UMLS vocabularyc back to ToC or Class ToC

IRI: http://edamontology.org/data_0835

has super-classes
deprecated classc

unambiguous purec back to ToC or Class ToC

IRI: http://edamontology.org/format_1206

has super-classes
purec
unambiguous sequencec
has sub-classes
unambiguous pure dnac, unambiguous pure nucleotidec, unambiguous pure proteinc, unambiguous pure rna sequencec

unambiguous pure dnac back to ToC or Class ToC

IRI: http://edamontology.org/format_1214

has super-classes
unambiguous purec
dnac

unambiguous pure nucleotidec back to ToC or Class ToC

IRI: http://edamontology.org/format_1211

has super-classes
unambiguous purec
nucleotidec

unambiguous pure proteinc back to ToC or Class ToC

IRI: http://edamontology.org/format_1218

has super-classes
unambiguous purec
proteinc

unambiguous pure rna sequencec back to ToC or Class ToC

IRI: http://edamontology.org/format_1216

has super-classes
unambiguous purec
rnac

unambiguous sequencec back to ToC or Class ToC

IRI: http://edamontology.org/format_2096

has super-classes
Textual formatc
Raw sequence formatc
has sub-classes
unambiguous purec

Unicellular eukaryotesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2821

The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes.
has super-classes
deprecated classc

UniGene entry formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1228

A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
has super-classes
deprecated classc

UniGene taxonc back to ToC or Class ToC

IRI: http://edamontology.org/data_2594

has super-classes
Taxonc

UNIIc back to ToC or Class ToC

IRI: http://edamontology.org/data_3104

has super-classes
Compound identifierc

Unimod IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_3757

has super-classes
Accessionc
Protein modification IDc

UniParc accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2392

has super-classes
Sequence accession (protein)c
Accessionc

UniParc XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3853

has super-classes
Sequence feature annotation formatc
XMLc

UniProt accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_3021

has super-classes
Sequence accession (protein)c
Accessionc

UniProt accession (extended)c back to ToC or Class ToC

IRI: http://edamontology.org/data_1099

has super-classes
deprecated classc

UniProt formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2188

has super-classes
deprecated classc

UniProt IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2291

has super-classes
Sequence namec
is identifier ofop some Sequence recordc

UniProt keywordc back to ToC or Class ToC

IRI: http://edamontology.org/data_2007

has super-classes
Keywordc

UniProt keywordsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1884

has super-classes
deprecated classc

UniProt-like (text)c back to ToC or Class ToC

IRI: http://edamontology.org/format_2187

has super-classes
Textual formatc
uniprotkb-like formatc
has sub-classes
UniProtKB formatc

UniProtKB formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1963

has super-classes
UniProt-like (text)c

UniProtKB RDFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3771

has super-classes
RDF formatc
uniprotkb-like formatc

UniProtKB XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3770

has super-classes
XMLc
uniprotkb-like formatc
Sequence record format (XML)c

uniprotkb-like formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2547

has super-classes
Sequence record formatc
Sequence feature table formatc
has sub-classes
UniProt-like (text)c, UniProtKB RDFc, UniProtKB XMLc

UniRef XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3854

has super-classes
Sequence feature annotation formatc
XMLc

UniSTS accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2389

has super-classes
Sequence accession (nucleic acid)c
Accessionc

UNITE accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2390

has super-classes
Sequence accession (nucleic acid)c
Accessionc

unpurec back to ToC or Class ToC

IRI: http://edamontology.org/format_2095

has super-classes
Textual formatc
Raw sequence formatc
has sub-classes
consensusc

URIc back to ToC or Class ToC

IRI: http://edamontology.org/data_1047

has super-classes
Identifierc
has sub-classes
MIRIAM URIc, URLc, URNc

URI formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2334

has super-classes
deprecated classc

URLc back to ToC or Class ToC

IRI: http://edamontology.org/data_1052

has super-classes
URIc

URNc back to ToC or Class ToC

IRI: http://edamontology.org/data_1053

has super-classes
URIc
has sub-classes
LSIDc

Urology and nephrologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3422

has super-classes
Medicinec

User IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2101

has super-classes
Person identifierc
has sub-classes
Email addressc, Passwordc, Usernamec

User metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_0960

has super-classes
Resource metadatac

Usernamec back to ToC or Class ToC

IRI: http://edamontology.org/data_1689

has super-classes
User IDc

UTR accessionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2391

has super-classes
Sequence accession (nucleic acid)c
Accessionc

UTRdb taxonc back to ToC or Class ToC

IRI: http://edamontology.org/data_2595

has super-classes
Taxonc

UTRSite IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2761

has super-classes
Sequence motif identifierc

Validationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2428

has super-classes
Operationc
has sub-classes
Format validationc, Phylogenetic tree bootstrappingc, Protein structure validationc, Sequence alignment validationc, Sequence assembly validationc, Sequencing quality controlc, Target-Decoyc

Validation of peptide-spectrum matchesc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3648

has super-classes
deprecated classc

Variant callingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3227

Somatic variant calling is the detection of variations established in somatic cells and hence not inherited as a germ line variant.
has super-classes
Nucleic acid sequence analysisc
Genetic variation analysisc
has sub-classes
Frameshift detectionc, Indel detectionc, SNP detectionc

Variant classificationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3225

Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.)
has super-classes
Sequence classificationc
Genetic variation analysisc

Variant effect predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0331

Protein SNP mapping maps and modesl the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). Methods might predict silent or pathological mutations.
has super-classes
Prediction and recognitionc
has topicop some Protein folding, stability and designc
has topicop some Genetic variationc

Variant filteringc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3675

has super-classes
Sequencing quality controlc

Variant pattern analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3504

Methods often utilise a database of aligned reads.
has super-classes
Genetic variation analysisc

Variant prioritisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3226

Variant prioritisation can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks.
has super-classes
Genetic variation analysisc

VCFc back to ToC or Class ToC

IRI: http://edamontology.org/format_3016

has super-classes
Textual formatc
Sequence variation annotation formatc

VDBc back to ToC or Class ToC

IRI: http://edamontology.org/format_3699

has super-classes
Binary formatc

Vector sequence detectionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0266

has super-classes
Nucleic acid feature detectionc

vectorstrip cloning vector definition filec back to ToC or Class ToC

IRI: http://edamontology.org/data_1241

has super-classes
deprecated classc

Version informationc back to ToC or Class ToC

IRI: http://edamontology.org/data_0953

Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records.
has super-classes
deprecated classc

Vertebratesc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2820

The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates.
has super-classes
deprecated classc

Veterinary medicinec back to ToC or Class ToC

IRI: http://edamontology.org/topic_3397

has super-classes
Medicinec

Vienna local RNA secondary structure formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1458

has super-classes
Dot-bracket formatc
Textual formatc

Vienna RNA calculated energyc back to ToC or Class ToC

IRI: http://edamontology.org/data_1594

has super-classes
deprecated classc

Vienna RNA concentration datac back to ToC or Class ToC

IRI: http://edamontology.org/data_1593

has super-classes
deprecated classc

Vienna RNA parametersc back to ToC or Class ToC

IRI: http://edamontology.org/data_1591

has super-classes
deprecated classc

Vienna RNA structural datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2022

has super-classes
deprecated classc

Vienna RNA structure constraintsc back to ToC or Class ToC

IRI: http://edamontology.org/data_1592

has super-classes
deprecated classc

Virologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0781

has super-classes
Biologyc

Virtual PCRc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0307

has super-classes
Nucleic acid sequence analysisc

Virtual PCRc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0195

has super-classes
deprecated classc

Virtual screeningc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3938

Virtual screening is widely used for lead identification, lead optimization, and scaffold hopping during drug design and discovery. There are two broad categories of virtual screening techniques: ligand-based drug design (e.g. ligand similarity) and structure-based drug design (ligand docking) methods. Ligand similarity methods exploit structural similarities to known active ligands, whereas ligand docking methods use the 3D structure of a target protein to predict the binding modes and affinities of ligands to it.
has super-classes
Protein-ligand dockingc
has topicop some Protein interactionsc
has outputop some Protein-ligand complexc

Virulence predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3461

has super-classes
Sequence analysisc
Prediction and recognitionc
has topicop some Microbiologyc

Virus annotationc back to ToC or Class ToC

IRI: http://edamontology.org/data_2307

has super-classes
deprecated classc

Virus annotation (taxonomy)c back to ToC or Class ToC

IRI: http://edamontology.org/data_2308

has super-classes
deprecated classc

Virus IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2785

has super-classes
Organism accessionc
Virus identifierc
has sub-classes
DPVweb IDc, RNAVirusDB IDc

Virus identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2913

has super-classes
Organism identifierc
has sub-classes
Virus IDc

VisMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3821

has super-classes
Biological pathway or network formatc
XMLc

Visualisationc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0337

This includes methods to render and visualise molecules.
has super-classes
Operationc
has inputop some Imagec
has topicop some Data visualisationc
has outputop some Imagec
has sub-classes
Box-Whisker plot plottingc, Chromatogram visualisationc, Expression data visualisationc, Incident curve plottingc, Map drawingc, Mass spectrum visualisationc, Microscope image visualisationc, Multiple sample visualisationc, Network visualisationc, Nucleic acid melting profile plottingc, Ontology visualisationc, Pathway visualisationc, Phylogenetic tree visualisationc, Principal component visualisationc, Protein titration curve plottingc, Scatter plot plottingc, Sequence cluster visualisationc, Sequence visualisationc, Structure visualisationc

Vmaxc back to ToC or Class ToC

IRI: http://edamontology.org/data_0909

has super-classes
Enzyme kinetics datac

VNTRc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2867

has super-classes
deprecated classc

Volume mapc back to ToC or Class ToC

IRI: http://edamontology.org/data_0940

has super-classes
Experimental measurementc
has topicop some Structural biologyc

Waters RAWc back to ToC or Class ToC

IRI: http://edamontology.org/format_3858

Proprietary format for which documentation is not available, but used by multiple tools.
has super-classes
Binary formatc
Mass spectrometry data formatc

Web portalc back to ToC or Class ToC

IRI: http://edamontology.org/data_2832

has super-classes
deprecated classc

Weighted correlation network analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3766

has super-classes
Network analysisc
has topicop some Molecular interactions, pathways and networksc

Whole gene predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0425

has super-classes
deprecated classc

Whole genome methylation analysisc back to ToC or Class ToC

IRI: http://edamontology.org/operation_3206

has super-classes
Methylation analysisc
Genome analysisc

Whole genome sequencingc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3673

has super-classes
Sequencingc

Whole microarray graph plottingc back to ToC or Class ToC

IRI: http://edamontology.org/operation_2941

has super-classes
deprecated classc

WIFF formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_3710

has super-classes
Binary formatc
Mass spectrometry data formatc

WIGc back to ToC or Class ToC

IRI: http://edamontology.org/format_3005

has super-classes
Textual formatc
Sequence annotation track formatc

Window sizec back to ToC or Class ToC

IRI: http://edamontology.org/data_1251

A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring.
has super-classes
deprecated classc

Window step sizec back to ToC or Class ToC

IRI: http://edamontology.org/data_2141

has super-classes
deprecated classc

Word compositionc back to ToC or Class ToC

IRI: http://edamontology.org/data_2157

has super-classes
deprecated classc

Word sizec back to ToC or Class ToC

IRI: http://edamontology.org/data_1250

Word size is used for example in word-based sequence database search methods.
has super-classes
deprecated classc

Workflowc back to ToC or Class ToC

IRI: http://edamontology.org/data_2972

has super-classes
deprecated classc

Workflow datac back to ToC or Class ToC

IRI: http://edamontology.org/data_2971

has super-classes
deprecated classc

Workflow formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_2032

has super-classes
Format (by type of data)c
has sub-classes
CWLc, KNIME datatable formatc, Taverna workflow formatc

Workflow IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_1083

has super-classes
Identifier (by type of data)c
has sub-classes
Taverna workflow IDc

Workflow metadatac back to ToC or Class ToC

IRI: http://edamontology.org/data_0949

has super-classes
Resource metadatac

Workflowsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0769

has super-classes
Biological databasesc

WormBase classc back to ToC or Class ToC

IRI: http://edamontology.org/data_1092

A WormBase class describes the type of object such as 'sequence' or 'protein'.
has super-classes
WormBase identifierc

WormBase gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1617

has super-classes
deprecated classc

WormBase identifierc back to ToC or Class ToC

IRI: http://edamontology.org/data_2113

has super-classes
Identifier (hybrid)c
has sub-classes
Gene ID (WormBase)c, WormBase classc, WormBase namec, WormBase wormpep IDc

WormBase namec back to ToC or Class ToC

IRI: http://edamontology.org/data_1091

has super-classes
Namec
WormBase identifierc

WormBase wormpep IDc back to ToC or Class ToC

IRI: http://edamontology.org/data_2114

has super-classes
Accessionc
WormBase identifierc
Protein accessionc

Wormsc back to ToC or Class ToC

IRI: http://edamontology.org/topic_0215

has super-classes
deprecated classc

X!Tandem XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3711

has super-classes
XMLc
Mass spectrometry data formatc

X-ray diffractionc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2828

has super-classes
Structural biologyc
Imagingc

xbmc back to ToC or Class ToC

IRI: http://edamontology.org/format_3598

The XBM format was replaced by XPM for X11 in 1989.
has super-classes
Binary formatc
Image formatc

xgmmlc back to ToC or Class ToC

IRI: http://edamontology.org/format_3618

has super-classes
Graph formatc

xlsc back to ToC or Class ToC

IRI: http://edamontology.org/format_3468

has super-classes
XMLc
Document formatc

xlsxc back to ToC or Class ToC

IRI: http://edamontology.org/format_3620

has super-classes
Binary formatc
Document formatc

XMFAc back to ToC or Class ToC

IRI: http://edamontology.org/format_3811

has super-classes
FASTA-like (text)c
Alignment format (text)c

XMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_2332

Data in XML format can be serialised into text, or binary format.
has super-classes
Formatc
has sub-classes
BCMLc, BDMLc, BEASTc, BLAST XML results formatc, BLAST XML v2 results formatc, BSMLc, BioCc, BioXSD (XML)c, CellMLc, Chado-XMLc, CopasiMLc, DAS formatc, DASGFFc, EBI Application Result XMLc, EMBL-like (XML)c, GCDMLc, GPMLc, GelMLc, HSAMLc, InterProScan XMLc, KGMLc, MAGE-MLc, NeXMLc, OBO-XMLc, OSCAR formatc, OWL/XMLc, OrthoXMLc, PDBMLc, PMMLc, PRIDE XMLc, PSDMLc, PSI MI XML (MIF)c, PubMed XMLc, RDF/XMLc, RNAMLc, SBGN-MLc, SBMLc, SBOLc, SBRMLc, SED-MLc, STRING entry format (XML)c, SVGc, SeqXMLc, TIDE TXTc, Taverna workflow formatc, TraMLc, UniParc XMLc, UniProtKB XMLc, UniRef XMLc, VisMLc, X!Tandem XMLc, consensusXMLc, dasdnac, docxc, featureXMLc, iHOP formatc, idXMLc, imzML metadata filec, mzDatac, mzIdentMLc, mzMLc, mzQuantMLc, nmrMLc, pepXMLc, phyloXMLc, pptxc, protXMLc, qcMLc, spMLc, xlsc, xsdc
is disjoint with
Binary formatc

XML Schemac back to ToC or Class ToC

IRI: http://edamontology.org/data_2250

has super-classes
deprecated classc

xpmc back to ToC or Class ToC

IRI: http://edamontology.org/format_3599

Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type.
has super-classes
Binary formatc
Image formatc

XQueryc back to ToC or Class ToC

IRI: http://edamontology.org/format_3789

has super-classes
Textual formatc

xsdc back to ToC or Class ToC

IRI: http://edamontology.org/format_3804

has super-classes
XMLc

XSLT stylesheetc back to ToC or Class ToC

IRI: http://edamontology.org/data_2252

has super-classes
deprecated classc

XTCc back to ToC or Class ToC

IRI: http://edamontology.org/format_3875

XTC uses the External Data Representation (xdr) routines for writing and reading data which were created for the Unix Network File System (NFS). XTC files use a reduced precision (lossy) algorithm which works multiplying the coordinates by a scaling factor (typically 1000), so converting them to pm (GROMACS standard distance unit is nm). This allows an integer rounding of the values. Several other tricks are performed, such as making use of atom proximity information: atoms close in sequence are usually close in space (e.g. water molecules). That makes XTC format the most efficient in terms of disk usage, in most cases reducing by a factor of 2 the size of any other binary trajectory format.
has super-classes
Binary formatc
Trajectory format (binary)c

XYZc back to ToC or Class ToC

IRI: http://edamontology.org/format_3877

XYZ files are structured in this way: First line contains the number of atoms in the file. Second line contains a title, comment, or filename. Remaining lines contain atom information. Each line starts with the element symbol, followed by x, y and z coordinates in angstroms separated by whitespace. Multiple molecules or frames can be contained within one file, so it supports trajectory storage. XYZ files can be directly represented by a molecular viewer, as they contain all the basic information needed to build the 3D model.
has super-classes
Tertiary structure formatc
Textual formatc
Trajectory format (text)c

YAMLc back to ToC or Class ToC

IRI: http://edamontology.org/format_3750

YAML version 1.2 is a superset of JSON; prior versions were "not strictly compatible".
has super-classes
Formatc
has sub-classes
BioYAMLc, CWLc, JSONc

Yeastc back to ToC or Class ToC

IRI: http://edamontology.org/topic_2817

has super-classes
deprecated classc

Z-valuec back to ToC or Class ToC

IRI: http://edamontology.org/data_1668

A z-value might be specified as a threshold for reporting hits from database searches.
has super-classes
Statistical estimate scorec

Zarrc back to ToC or Class ToC

IRI: http://edamontology.org/format_3915

has super-classes
Gene expression report formatc
Binary formatc
Matrix formatc
is format ofop some Gene expression matrixc
is format ofop some Sequence tag profilec

ZFIN gene report formatc back to ToC or Class ToC

IRI: http://edamontology.org/format_1618

has super-classes
deprecated classc

Zinc finger predictionc back to ToC or Class ToC

IRI: http://edamontology.org/operation_0333

has super-classes
deprecated classc

Zoologyc back to ToC or Class ToC

IRI: http://edamontology.org/topic_3500

The study of the animal kingdom.
has super-classes
Biologyc

ZTRc back to ToC or Class ToC

IRI: http://edamontology.org/format_3018

has super-classes
Sequence trace formatc
Binary formatc

Object Properties

has formatop back to ToC or Object Property ToC

IRI: http://edamontology.org/has_format

Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'.
has domain
Datac
has range
Formatc
is inverse of
is format ofop

has functionop back to ToC or Object Property ToC

IRI: http://edamontology.org/has_function

Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts.
has range
Operationc
is inverse of
is function ofop

has identifierop back to ToC or Object Property ToC

IRI: http://edamontology.org/has_identifier

Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'.
has domain
Datac
has range
Identifierc
is inverse of
is identifier ofop

has inputop back to ToC or Object Property ToC

IRI: http://edamontology.org/has_input

Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined.
has domain
Operationc
has range
Datac
is inverse of
is input ofop

has outputop back to ToC or Object Property ToC

IRI: http://edamontology.org/has_output

Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined.
has domain
Operationc
has range
Datac
is inverse of
is output ofop

has topicop back to ToC or Object Property ToC

IRI: http://edamontology.org/has_topic

Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined.
has domain
Datac or Operationc
has range
Topicc
is inverse of
is topic ofop

is format ofop back to ToC or Object Property ToC

IRI: http://edamontology.org/is_format_of

Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined.
has domain
Formatc
has range
Datac
is inverse of
has formatop

is function ofop back to ToC or Object Property ToC

IRI: http://edamontology.org/is_function_of

Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used.
has domain
Operationc
is inverse of
has functionop

is identifier ofop back to ToC or Object Property ToC

IRI: http://edamontology.org/is_identifier_of

Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined.
has domain
Identifierc
has range
Datac
is inverse of
has identifierop

is input ofop back to ToC or Object Property ToC

IRI: http://edamontology.org/is_input_of

Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'.
has domain
Datac
has range
Operationc
is inverse of
has inputop

is output ofop back to ToC or Object Property ToC

IRI: http://edamontology.org/is_output_of

Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'.
has domain
Datac
has range
Operationc
is inverse of
has outputop

is topic ofop back to ToC or Object Property ToC

IRI: http://edamontology.org/is_topic_of

Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'.
has domain
Topicc
has range
Datac or Operationc
is inverse of
has topicop

Annotation Properties

Citationap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/citation

commentap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#comment

comment handleap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/comment_handle

considerap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#consider

contributorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/contributor

Created inap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/created_in

creatorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/creator

dataap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/edam#data

has super-properties
subset propertyap

dateap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/date

deprecation_candidateap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/is_deprecation_candidate

deprecation_commentap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/deprecation_comment

Documentationap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/documentation

edamap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/edam#edam

has super-properties
subset propertyap

eventsap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/edam#events

has super-properties
subset propertyap

Exampleap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/example

Separated by bar ('|'). For more complex data and data formats, it can be a link to a website with examples, instead.

File extensionap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/file_extension

Separated by bar ('|'), without a dot ('.') prefix, preferrably not all capital characters.

formatap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/format

formatsap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/edam#formats

has super-properties
subset propertyap

has alternative idap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasAlternativeId

has sub-properties
hasHumanReadableIdap

has broad synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym

has db x refap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasDbXRef

has db xrefap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasDbXref

has definitionap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasDefinition

has exact synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

has human readable idap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId

has narrow synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym

has related synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym

has subsetap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasSubset

hasHumanReadableIdap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/hasHumanReadableId

has super-properties
has alternative idap

identifiersap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/edam#identifiers

has super-properties
subset propertyap

idspaceap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/idspace

in subsetap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#inSubset

Information standardap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/information_standard

is anti symmetricap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/is_anti_symmetric

is cyclicap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#isCyclic

is metadata tagap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/is_metadata_tag

is reflexiveap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/is_reflexive

is symmetricap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/is_symmetric

isdebtagap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/isdebtag

Media typeap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/media_type

namespaceap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/namespace

next idap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/next_id

notRecommendedForAnnotationap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/notRecommendedForAnnotation

obsoleteap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/edam#obsolete

has super-properties
subset propertyap

Obsolete sinceap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/obsolete_since

Old parentap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/oldParent

Old relatedap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/oldRelated

Ontology usedap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/ontology_used

operationsap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/edam#operations

has super-properties
subset propertyap

Organisationap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/organisation

pageap back to ToC or Annotation Property ToC

IRI: http://xmlns.com/foaf/0.1/page

placeholderap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/edam#placeholder

has super-properties
subset propertyap

refactor_candidateap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/is_refactor_candidate

refactor_commentap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/refactor_comment

Regular expressionap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/regex

remarkap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/remark

replaced byap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#replacedBy

Repositoryap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/repository

saved byap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#savedBy

subset propertyap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#SubsetProperty

has sub-properties
dataap, edamap, eventsap, formatsap, identifiersap, obsoleteap, operationsap, placeholderap, topicsap

thematic_editorap back to ToC or Annotation Property ToC

IRI: http://edamontology.org/thematic_editor

titleap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/title

topicsap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/edam#topics

has super-properties
subset propertyap

transitive overap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/transitive_over

versionap back to ToC or Annotation Property ToC

IRI: http://usefulinc.com/ns/doap#Version

Namespace Declarations back to ToC

default namespace
http://edamontology.org#
10-1007
http://doi.org/10.1007/
10-1016
http://doi.org/10.1016/
10-1021
http://doi.org/10.1021/
10-1074
http://doi.org/10.1074/
10-1101
http://dx.doi.org/10.1101/
10-1186
http://doi.org/10.1186/
10-4018
http://doi.org/10.4018/
10-6084
https://doi.org/10.6084/
10-7490
http://doi.org/10.7490/
1991-october
http://www.bio.net/bionet/mm/bio-soft/1991-October/
2013-bionlp-st-org
http://2013.bionlp-st.org/
420
http://www.clcsupport.com/clcassemblycell/420/
abs
http://arxiv.org/abs/
agp
http://www.ncbi.nlm.nih.gov/assembly/agp/
alignment
https://en.wikipedia.org/wiki/Alignment#
api
http://biopython.org/DIST/docs/api/
application
http://www.iana.org/assignments/media-types/application/
bcforms
https://raw.githubusercontent.com/KarrLab/bcforms/master/bcforms/
binary-file-formats-html
http://khmer.readthedocs.org/en/v2.0/dev/binary-file-formats.html#
bio
http://matra.sourceforge.net/dtdtree/bio/
bioinformatics
http://doi.org/10.1093/bioinformatics/
bioxsd
https://github.com/bioxsd/
bioxsd-org
http://bioxsd.org/
bmp
http://www.fileformat.info/format/bmp/
bpforms
https://raw.githubusercontent.com/KarrLab/bpforms/master/bpforms/
brat-nlplab-org
http://brat.nlplab.org/
capnp
https://raw.githubusercontent.com/marbl/Mash/master/src/mash/capnp/
capnproto-org
https://capnproto.org/
cgi-bin
http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/
chemical-table-file
https://en.wikipedia.org/wiki/Chemical_table_file#
chipseq
http://ccg.vital-it.ch/chipseq/
chromosome
https://en.wikipedia.org/wiki/Chromosome#
common-workflow-language
https://github.com/common-workflow-language/
compbio-soe-ucsc-edu
http://compbio.soe.ucsc.edu/
compbiotoolbox-fmach-it
http://compbiotoolbox.fmach.it/
compomics
https://github.com/compomics/
content
http://bedtools.readthedocs.org/en/latest/content/
core
http://www.openannotation.org/spec/core/
data-shtml
http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#
database
http://doi.org/10.1093/database/
dc
http://purl.org/dc/elements/1.1/
designissues
https://www.w3.org/DesignIssues/
detail-shtml
http://www.nactem.ac.uk/tsujii/GENIA/SharedTask/detail.shtml#
dist
http://www.bx.psu.edu/miller_lab/dist/
distributions
http://bozeman.mbt.washington.edu/consed/distributions/
dl-acm-org
http://dl.acm.org/
doap
http://usefulinc.com/ns/doap#
doc
http://home.cc.umanitoba.ca/~psgendb/birchhomedir/local/pkg/gde/doc/
docs
http://www.thegpm.org/docs/
docs-karrlab-org
http://docs.karrlab.org/
documents
http://co.mbine.org/documents/
doku-php
https://wiki.thebiogrid.org/doku.php/
drafts
http://www.jcamp-dx.org/drafts/
edam
http://purl.obolibrary.org/obo/edam#
edamontology
http://edamontology.org/
faqformat
http://genome.ucsc.edu/FAQ/FAQformat#
fastg-sourceforge-net
http://fastg.sourceforge.net/
file-extension
http://filext.com/file-extension/
file-formats-html
http://manual.gromacs.org/documentation/2018/user-guide/file-formats.html#
foaf
http://xmlns.com/foaf/0.1/
format
http://www.isa-tools.org/format/
format-examples-shtml
http://www.compbio.ox.ac.uk/bioinformatics_faq/format_examples.shtml#
formats
https://www.coolutils.com/Formats/
formats-html
http://ambermd.org/formats.html#
galaxy-datatypes-html?highlight=datatypes%20graph
http://galaxy.readthedocs.org/en/latest/lib/galaxy.datatypes.html?highlight=datatypes%20graph#
gcos-agcc
http://media.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/
gene-mapping
https://en.wikipedia.org/wiki/Gene_mapping#
gene-prediction
https://en.wikipedia.org/wiki/Gene_prediction#
genome
http://jcomeau.freeshell.org/www/genome/
gff
http://www.sanger.ac.uk/resources/software/gff/
gsuite
https://github.com/gtrack/gtrack/tree/master/gsuite/
gtrack
https://github.com/gtrack/
gwas
http://www.stats.ox.ac.uk/~marchini/software/gwas/
h
https://hyperbrowser.uio.no/hb/u/hb-superuser/h/
handbook
http://pillow.readthedocs.org/en/latest/handbook/
help
https://www.uniprot.org/help/
hmmer
https://en.wikipedia.org/wiki/HMMER#
home
http://2011.bionlp-st.org/home/
html
https://tools.ietf.org/html/
hts-specs
https://samtools.github.io/hts-specs/
hyperbrowser-uio-no
https://hyperbrowser.uio.no/
igv
http://www.broadinstitute.org/software/igv/
immunology
https://en.wikipedia.org/wiki/Immunology#
immunoprecipitation
https://en.wikipedia.org/wiki/Immunoprecipitation#
import-export
http://uk.mathworks.com/help/matlab/import_export/
inc
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/inc/
index-php
https://wiki.reactome.org/index.php/
jalview-github-io
http://jalview.github.io/
jpeg
http://www.fileformat.info/format/jpeg/
latest
http://sourceforge.net/projects/poamsa/files/latest/
lib
http://galaxy.readthedocs.org/en/latest/lib/
library
https://msdn.microsoft.com/en-us/library/
libsbgn
http://www.sbgn.org/LibSBGN#
mage
http://www.mged.org/Workgroups/MAGE/
manual
http://staden.sourceforge.net/manual/
mass-spectrometry-data-format
https://en.wikipedia.org/wiki/Mass_spectrometry_data_format#
master
https://github.com/The-Sequence-Ontology/Specifications/blob/master/
mblab-wustl-edu
http://mblab.wustl.edu/
metaio
http://www.itk.org/Wiki/ITK/MetaIO/
microscopy
https://en.wikipedia.org/wiki/Microscopy#
mirtop
https://github.com/miRTop/
misi
http://visant.bu.edu/misi/
multipart
http://www.iana.org/assignments/media-types/multipart/
namd-tutorial-unix-html
http://www.ks.uiuc.edu/Training/TutorialsOverview/namd/namd-tutorial-unix-html/
nar
http://doi.org/10.1093/nar/
network-theory
https://en.wikipedia.org/wiki/Network_theory#
nifti-nimh-nih-gov
http://nifti.nimh.nih.gov/
nmrml
https://github.com/nmrML/
nrrd
http://teem.sourceforge.net/nrrd/
obo
http://purl.obolibrary.org/obo/
oboInOwl
http://www.geneontology.org/formats/oboInOwl#
ome-tiff
http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/
online
http://manual.gromacs.org/online/
owl
http://www.w3.org/2002/07/owl#
p
http://code.google.com/archive/p/
pangeo-io
https://pangeo.io/
pdfs
https://www.bioversityinternational.org/fileadmin/user_upload/online_library/publications/pdfs/
primer-(molecular-biology)
https://en.wikipedia.org/wiki/Primer_(molecular_biology)#
protxml
http://tools.proteomecenter.org/formats/protXML/
psd
http://www.fileformat.info/format/psd/
psicquic-github-io
http://psicquic.github.io/
psidev-info
http://psidev.info/
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
regulatory-affairs
https://en.wikipedia.org/wiki/Regulatory_affairs#
related
http://mdc.custhelp.com/app/answers/detail/a_id/17120/related/
samtools-sourceforge-net
http://samtools.sourceforge.net/
schema
http://www.ebi.ac.uk/Tools/common/schema/
semantics
https://linnarssonlab.org/loompy/semantics/
sequence-alignment
https://en.wikipedia.org/wiki/Sequence_alignment#
sequenceontology-org
http://sequenceontology.org/
ssbd-qbic-riken-jp
http://ssbd.qbic.riken.jp/
stable
https://zarr.readthedocs.io/en/stable/
standards
http://www.astm.org/Standards/
static
http://www.ibi.vu.nl/programs/k2nwww/static/
submission
http://www.ebi.ac.uk/pride/help/archive/submission/
subsubsection3-18-2-5-html
http://www.compbio.dundee.ac.uk/manuals/amps/subsubsection3_18_2_5.html#
tdwg
https://github.com/tdwg/
text
http://rna.urmc.rochester.edu/Text/
theory
http://www.daylight.com/dayhtml/doc/theory/
tiff
http://www.fileformat.info/format/tiff/
tr
http://www.w3.org/TR/
trace-cgi?cmd=show&f=formats&m=doc&s=format
http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#
tree
http://sandbox.karrlab.org/tree/
tutorials-html
https://mash.readthedocs.io/en/latest/tutorials.html#
tx-news
https://www.bioversityinternational.org/fileadmin/_migrated/uploads/tx_news/
typon
http://purl.phyloviz.net/ontology/typon#
upload
http://www.ensembl.org/info/website/upload/
user-guide
http://darlinglab.org/mauve/user-guide/
v1-0
https://github.com/common-workflow-language/common-workflow-language/tree/master/v1.0/
v2-html
https://zarr.readthedocs.io/en/stable/spec/v2.html#
v4-2-1
http://dmg.org/pmml/v4-2-1/
vcftools-sourceforge-net
http://vcftools.sourceforge.net/
w
https://en.wikipedia.org/w/
weka
http://www.cs.waikato.ac.nz/ml/weka/
wiki
https://en.wikipedia.org/wiki/
www-bpforms-org
https://www.bpforms.org/
www-comp-sys-bio-org
http://www.comp-sys-bio.org/
www-copasi-org
http://www.copasi.org/
www-imzml-org
http://www.imzml.org/
www-mged-org
http://www.mged.org/
www-psidev-info
http://www.psidev.info/
www-sqlite-org
https://www.sqlite.org/
www-uniprot-org
http://www.uniprot.org/
xbm
http://www.fileformat.info/format/xbm/
xml-coverpages-org
http://xml.coverpages.org/
xpm
http://www.fileformat.info/format/xpm/
xrna
http://rna.ucsc.edu/rnacenter/xrna/
xsd
http://www.w3.org/2001/XMLSchema#

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.