GENO ontology

An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence).

is equivalent to: genomic feature^c and (varies_with^op some genomic feature^c)
has super-classes: genomic feature^c; varies_with^op some genomic feature^c
has sub-classes: gene allele^c, polymorphic allele^c, reference allele^c, sequence_alteration^c, variant allele^c, wild-type allele^c

allele origin^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000877

has super-classes: sequence feature attribute^c
has sub-classes: de novo allele origin^c, inherited allele origin^c, somatic allele origin^c, unknown allele origin^c

allele set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000954

'Sets' are used to model entities that can be comprised of multiple discrete elements - but which can also contain zero or a single member. An "Allele Set' represents any collection of 0 or more discrete alleles found within a particular genome. The alleles in such a set can be located at distant or close locations in the genome, and if on the same chromosome can be in trans, in cis, or even overlapping When the members of such a set are found 'in cis' on the same chromosome, they may constitute a 'haplotype'. When found 'in trans' at the same location on homologous chromosomes, they may constitute a 'single locus complement'.

has super-classes: genomic feature set^c

allelic cellular distribution^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000926

has super-classes: sequence feature attribute^c
has sub-classes: clonal^c, constitutional^c

allelic genotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000823

An 'allelic genotype' describes the set of alleles present at a particular location in the genome. This use of the term 'genotype' reflects its use in clinical genetics where variation has historically been assessed at a specific locus, and a genotype describes the allelic state at that particular location. This contrasts to the use of the term 'genotype in model orgnaism communities where it commonly describes the allelic state at all loci in a genome known to vary from an established reference or background.

is equivalent to: intrinsic genotype^c and (denotes^op some single locus complement^c)
has super-classes: intrinsic genotype^c; genomic entity^c; denotes^op some single locus complement^c
has sub-classes: diplotype^c

allelic phase^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000886

has super-classes: sequence feature attribute^c
has sub-classes: in cis^c, in trans^c

allelic state^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000875

has super-classes: sequence feature attribute^c
has sub-classes: organellar plasmy^c, zygosity^c

allosomal inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000935

has super-classes: monogenic inheritance^c
has sub-classes: W-linked inheritance^c, X-linked inheritance^c, Y-linked inheritance^c, Z-linked inheritance^c

amino acid residue^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000782

has super-classes: biological sequence unit^c

amino acid sequence^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000722

is equivalent to: biological sequence^c and (has_sequence_unit^op some amino acid residue^c) and (has_sequence_unit^op only amino acid residue^c)
has super-classes: biological sequence^c; has_sequence_unit^op some amino acid residue^c

Amniota^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_32524

has super-classes: Tetrapoda^c
has sub-classes: Mammalia^c

analysis subset ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000008

has super-classes: subset ontology module^c

anatomical entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001062

is equivalent to: is anatomical entity^op
has super-classes: organismal entity^c; derives from^op some organism^c
has sub-classes: material anatomical entity^c
is in domain of: has developmental contribution from^op, has developmental potential involving^op, is anatomical entity^op
is in range of: has developmental contribution from^op, has developmental potential involving^op, results in developmental progression of^op

anatomical structure^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000061

has super-classes: material anatomical entity^c
has sub-classes: cell^c

ancestral polymorphic allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000500

has super-classes: polymorphic allele^c

aneusomic^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000513

has super-classes: variation attribute^c

aneusomic chromosomal part^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000343

Aneusomic chromosomal parts are examples of "partial aneuploidy" as described in http://en.wikipedia.org/wiki/Aneuploidy: "The terms "partial monosomy" and "partial trisomy" are used to describe an imbalance of genetic material caused by loss or gain of part of a chromosome. In particular, these terms would be used in the situation of an unbalanced translocation, where an individual carries a derivative chromosome formed through the breakage and fusion of two different chromosomes. In this situation, the individual would have three copies of part of one chromosome (two normal copies and the portion that exists on the derivative chromosome) and only one copy of part of the other chromosome involved in the derivative chromosome."

has super-classes: chromosome part^c; sequence_alteration^c; has_sequence_attribute^op some aneusomic^c
has sub-classes: gained aneusomic chromosomal segment^c, lost aneusomic chromosomal segment^c

aneusomic chromosome^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000346

Large sequence features gained in a genome are considered to be sequence alterations (akin to insertions), including aneusomic chromosome segments gained through unbalanced translocation events, entrie aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable gneme of a cell or organism. Similarly, large sequence features lost from genome are akin to deletions and therefore also considered sequence alterations. This includes the loss of chromosomal segments through unbalanced translocation events, and the loss of entire chromosomes through a non-disjunction event during replication.

has super-classes: chromosome^c; sequence_alteration^c; has_sequence_attribute^op some aneusomic^c
has sub-classes: gained aneusomic chromosome^c, lost aneusomic chromosome^c

aneusomic zygosity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000392

has super-classes: zygosity^c
has sub-classes: trisomic heterozygous^c, trisomic homozygous^c

Archaea^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_2157

has super-classes: organism^c

assembly^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001248

has super-classes: experimental_feature^c
has sub-classes: sequence_assembly^c

association^c back to ToC or Class ToC

IRI: http://purl.org/oban/association

has super-classes: information content entity^c
has sub-classes: genotype-phenotype association^c

autosomal dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000147

has super-classes: autosomal inheritance^c
has sub-classes: co-dominant autosomal inheritance^c, complete autosomal dominant inheritance^c, incomplete autosomal dominant inheritance^c, sex-limited autosomal dominant inheritance^c

autosomal inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000934

has super-classes: monogenic inheritance^c
has sub-classes: autosomal dominant inheritance^c, autosomal recessive inheritance^c

autosomal recessive inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000148

has super-classes: autosomal inheritance^c
has sub-classes: sex-limited autosomal recessive inheritance^c

B cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000236

has super-classes: lymphocyte^c

background genome^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000010

has super-classes: reference genome^c

Bacteria^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_2

has super-classes: organism^c

base ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000001

has super-classes: ontology module^c

Bilateria^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_33213

has super-classes: Metazoa^c
has sub-classes: Vertebrata <vertebrates>^c

biological process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000351

has super-classes: process^c
has sub-classes: developmental process^c, human life cycle stage^c, life cycle stage^c, phenotypic inheritance process^c

biological process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0008150

has super-classes: process^c
has sub-classes: life cycle stage^c
is in domain of: results in developmental progression of^op
is disjoint with: planned process^c

biological sequence^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000702

'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome.

has super-classes: biological sequence or set^c; has_string^dp some string
has sub-classes: DNA sequence^c, RNA sequence^c, amino acid sequence^c, biological sequence unit^c, genomic sequence^c, reference sequence^c
is in domain of: has_string^dp, is_sequence_of^op
is in range of: has_defining_sequence^op, has_sequence^op
is disjoint with: sequence feature location^c, sequence_feature^c

biological sequence or set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000921

has super-classes: generically dependent continuant^c
has sub-classes: biological sequence^c, biological sequence set^c

biological sequence set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000922

has super-classes: biological sequence or set^c
has sub-classes: genomic sequence set^c

biological sequence unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000779

is equivalent to: biological sequence^c and (has_extent^dp value 1)
has super-classes: biological sequence^c
has sub-classes: DNA residue^c, RNA residue^c, amino acid residue^c

biological sex^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000047

has super-classes: organismal quality^c
has sub-classes: phenotypic sex^c

biparental allele origin^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000976

Biparental inheritance of alleles is typical of normal mendelian inheritance, where offspring inherit a maternal and a paternal copies of a given gene.

has super-classes: inherited allele origin^c

Both strands^c back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#BothStrandsPosition

has super-classes: Stranded position^c

bridge ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000004

has super-classes: ontology module^c
has sub-classes: taxonomic bridge ontology module^c

C_to_A_transversion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000019

has super-classes: pyrimidine_to_purine_transversion^c

C_to_G_transversion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000020

has super-classes: pyrimidine_to_purine_transversion^c

C_to_T_transition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000011

has super-classes: pyrimidine_transition^c
has sub-classes: C_to_T_transition_at_pCpG_site^c

C_to_T_transition_at_pCpG_site^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000012

has super-classes: C_to_T_transition^c

CART^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000749

has super-classes: decision tree building data transformation^c
has members: GenePattern CARTⁿⁱ

categorical label^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000963

has super-classes: datum label^c
has members: ambidexterousⁿⁱ, left handedⁿⁱ, right handedⁿⁱ

categorical value specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001930

has super-classes: value specification^c
has sub-classes: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c, International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c, clinical tumor stage group according to AJCC 7th edition^c, histologic grade according to AJCC 7th edition^c, histologic grade according to the Fuhrman Nuclear Grading System^c, histologic grade for ovarian tumor^c, pathologic distant metastases stage for colon according to AJCC 7th edition^c, pathologic distant metastases stage for kidney according to AJCC 7th edition^c, pathologic distant metastases stage for lung according to AJCC 7th edition^c, pathologic distant metastases stage for ovary according to AJCC 7th edition^c, pathologic lymph node stage for colon and rectum according to AJCC 7th edition^c, pathologic lymph node stage for kidney according to AJCC 7th edition^c, pathologic lymph node stage for lung according to AJCC 7th edition^c, pathologic lymph node stage for ovary according to AJCC 7th edition^c, pathologic primary tumor stage for colon and rectum according to AJCC 7th edition^c, pathologic primary tumor stage for kidney according to AJCC 7th edition^c, pathologic primary tumor stage for lung according to AJCC 7th edition^c, pathologic primary tumor stage for ovary according to AJCC 7th edition^c, performance status value specification^c

cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000000

Stub class to serve as root of hierarchy for imports of cell types from CL or other cell terminologies.

has super-classes: anatomical structure^c
has sub-classes: experimentally modified cell in vitro^c, mononuclear cell^c

cell culture splitting^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600037

An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone.

has super-classes: material component separation^c; has_specified_input^op some cultured cell population^c; has_specified_output^op some cultured cell population^c; achieves_planned_objective^op some portioning objective^c

cell freezing medium^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001912

has super-classes: processed material^c

cell line^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0000031

has super-classes: organismal entity^c; secondary cultured cell population^c; has grain^op some cell line cell^c; derives from^op some organism^c; has grain^op only cell line cell^c

cell line cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0000001

has super-classes: secondary cultured cell^c; (is_specified_output_of^op some establishing cell line^c) or (derives from^op some is_specified_output_of^op some establishing cell line^c)

centromere^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000577

has super-classes: chromosome part^c

chromosomal band intensity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000618

has super-classes: sequence feature attribute^c
has sub-classes: gneg^c, gpos^c, gvar^c

chromosomal deletion inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000970

has super-classes: chromosomal inheritance^c

chromosomal duplication inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000971

has super-classes: chromosomal inheritance^c

chromosomal inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000969

has super-classes: inheritance pattern^c
has sub-classes: chromosomal deletion inheritance^c, chromosomal duplication inheritance^c, chromosomal rearrangement inheritance^c

chromosomal rearrangement inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000972

has super-classes: chromosomal inheritance^c

chromosomal region^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000614

has super-classes: chromosome part^c; part of^op some chromosome arm^c

chromosome^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000340

A complete chromosome sequence.

has super-classes: genomic feature^c
has sub-classes: aneusomic chromosome^c

chromosome arm^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000105

has super-classes: chromosome part^c; part of^op some chromosome part^c
has sub-classes: long chromosome arm^c, short chromosome arm^c

chromosome band^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000341

"Band' is a term of convenience in order to hierarchically organize morphologically defined chromosome features: chromosome > arm > region > band > sub-band.

has super-classes: chromosome part^c; part of^op some chromosomal region^c; has_sequence_attribute^op some chromosomal band intensity^c

chromosome part^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000830

is equivalent to: genomic feature^c and (is_proper_part_of^op some chromosome^c)
has super-classes: genomic feature^c; is_proper_part_of^op some chromosome^c
has sub-classes: aneusomic chromosomal part^c, centromere^c, chromosomal region^c, chromosome arm^c, chromosome band^c, chromosome sub-band^c

chromosome sub-band^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000616

has super-classes: chromosome part^c; part of^op some chromosome band^c; has_sequence_attribute^op some chromosomal band intensity^c

class discovery data transformation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200175

is equivalent to: (has_specified_output^op some clustered data set^c) or (achieves_planned_objective^op some class discovery objective^c)
has super-classes: data transformation^c
has sub-classes: dimensionality reduction^c, hierarchical clustering^c, k-means clustering^c, k-nearest neighbors^c

class discovery objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200178

has super-classes: data transformation objective^c

class prediction data transformation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000663

is equivalent to: (has_specified_output^op some classified data set^c) or (achieves_planned_objective^op some class prediction objective^c)
has super-classes: data transformation^c
has sub-classes: support vector machine^c

class prediction objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200179

has super-classes: data transformation objective^c

classified data set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000023

is equivalent to: is_specified_output_of^op some class prediction data transformation^c
has super-classes: data set^c; is_specified_output_of^op some class prediction data transformation^c

clinical tumor stage group according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002314

has super-classes: categorical value specification^c
has members: Occult Carcinoma (AJCC 7th)ⁿⁱ, Stage 0 (AJCC 7th)ⁿⁱ, Stage I (AJCC 7th)ⁿⁱ, Stage IIA (AJCC 7th)ⁿⁱ, Stage IIB (AJCC 7th)ⁿⁱ, Stage IIC (AJCC 7th)ⁿⁱ, Stage IIIA (AJCC 7th)ⁿⁱ, Stage IIIB (AJCC 7th)ⁿⁱ, Stage IIIC (AJCC 7th)ⁿⁱ, Stage IVA (AJCC 7th)ⁿⁱ, Stage IVB (AJCC 7th)ⁿⁱ

clonal^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000928

has super-classes: allelic cellular distribution^c
has sub-classes: mosaic^c

clustered data set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000648

is equivalent to: is_specified_output_of^op some class discovery data transformation^c
has super-classes: data set^c; is_specified_output_of^op some class discovery data transformation^c

clustered data visualization^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200190

has super-classes: data visualization^c; has_specified_output^op some dot plot^c or histogram^c or heatmap^c or dendrogram^c or scatter plot^c; has_specified_input^op only clustered data set^c
has members: GenePattern HeatMapViewer data visualizationⁿⁱ, GenePattern HierarchicalClusteringViewer data visualizationⁿⁱ

co-dominant autosomal inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000143

has super-classes: autosomal dominant inheritance^c

co-dominant X-linked inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000939

has super-classes: X-linked dominant inheritance^c

co-dominant Z-linked inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000946

has super-classes: Z-linked dominant inheritance^c

collection of organisms^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PCO_0000000

A group of organisms of the same taxonomic group grouped together in virtue of their sharing some commonality (either an inherent attribute or an externally assigned role).

has super-classes: organismal entity^c; has member^op some organism^c
has sub-classes: family^c, taxonomic group^c

collection of specimens^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002076

is equivalent to: material entity^c and (has member^op only specimen^c)
has super-classes: material entity^c

complete autosomal dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000144

has super-classes: autosomal dominant inheritance^c

complete X-linked dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000937

has super-classes: X-linked dominant inheritance^c

complete Z-linked dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000944

has super-classes: Z-linked dominant inheritance^c

complex_structural_alteration^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001784

has super-classes: structural_alteration^c

complex_substitution^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000005

has super-classes: substitution^c

compound heterozygous^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000402

has super-classes: heterozygous^c

concentration unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000051

has super-classes: measurement unit label^c
has members: colony forming unit per volumeⁿⁱ, gram per deciliterⁿⁱ, gram per literⁿⁱ, mass percentageⁿⁱ, mass volume percentageⁿⁱ, microgram per literⁿⁱ, micromolarⁿⁱ, milligram per milliliterⁿⁱ, milliliter per literⁿⁱ, millimolarⁿⁱ, molarⁿⁱ, nanomolarⁿⁱ, pHⁿⁱ, picomolarⁿⁱ, volume percentageⁿⁱ

constitutional^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000927

has super-classes: allelic cellular distribution^c

contig^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000149

has super-classes: sequence_assembly^c

continuant^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000002

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: entity^c; part of^op only continuant^c
has sub-classes: generically dependent continuant^c, independent continuant^c, specifically dependent continuant^c
is in domain of: causal relation between entities^op, causally influences^op, developmentally preceded by^op, participates in^op
is in range of: causal relation between entities^op, causally influences^op, developmentally preceded by^op, has participant^op
is disjoint with: occurrent^c

copy number complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000961

The count of how many of a particular sequences are found in a genome is the sequences 'copy number'. In diploid organisms, the normal copy number for sequences at most locations is 2 (a notable exception being those on the X-chromosome where normal copy number is 1). Variations in copy number occur if this count increases due to a duplication of the gene/region, or decreases due to a deletion of a gene/region. A driving use case for representing copy number is to support associations between variation in copy number of a particular sequence, and phenotypes or diseases that can result. A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as 'copy number complements' representing the set of all copies of a particular sequence in a genome. The fact that we are counting how many copies of the same *sequence* exist in a genome here, as opposed to how many of the same *feature*, is what sets sequence-level concepts like 'copy number complement' apart from feature-level concepts like 'single locus complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.

has super-classes: genomic sequence set^c
has sub-classes: variant copy number complement^c

copy_number_gain^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001742

has super-classes: copy_number_variation^c

copy_number_loss^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001743

has super-classes: copy_number_variation^c

copy_number_variation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001019

has super-classes: sequence_alteration^c
has sub-classes: copy_number_gain^c, copy_number_loss^c

cross validation objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200188

has super-classes: partitioning objective^c

culture medium^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000079

has super-classes: processed material^c

cultured cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000010

has super-classes: experimentally modified cell in vitro^c; (is_specified_output_of^op some establishing cell culture^c) or (derives from^op some is_specified_output_of^op some establishing cell culture^c)
has sub-classes: primary cultured cell^c, secondary cultured cell^c

cultured cell population^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100060

The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

has super-classes: processed material^c; is_specified_output_of^op some maintaining cell culture^c; has grain^op some cultured cell^c; has grain^op only cultured cell^c
has sub-classes: secondary cultured cell population^c

curation status specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000078

is equivalent to: { example to be eventually removed , metadata complete , organizational term , ready for release , metadata incomplete , uncurated , pending final vetting , to be replaced with external ontology term , requires discussion }
has super-classes: data about an ontology part^c
has members: example to be eventually removedⁿⁱ, metadata completeⁿⁱ, metadata incompleteⁿⁱ, organizational termⁿⁱ, pending final vettingⁿⁱ, ready for releaseⁿⁱ, requires discussionⁿⁱ, to be replaced with external ontology termⁿⁱ, uncuratedⁿⁱ

curation subset ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000007

has super-classes: subset ontology module^c

Danio rerio^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_7955

has super-classes: Euteleostomi^c

danio rerio cdkn1ca gene^c back to ToC or Class ToC

IRI: http://www.ncbi.nlm.nih.gov/gene/399483

has super-classes: danio rerio gene^c

danio rerio gene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000047

is equivalent to: gene^c and (in taxon^op some Danio rerio^c)
has super-classes: gene^c; in taxon^op some Danio rerio^c
has sub-classes: danio rerio cdkn1ca gene^c, danio rerio shha gene^c

danio rerio shha gene^c back to ToC or Class ToC

IRI: http://www.ncbi.nlm.nih.gov/gene/30269

has super-classes: danio rerio gene^c

danio rerio strain^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000119

has super-classes: strain or breed^c; has member^op some Danio rerio^c; has member^op only Danio rerio^c

data about an ontology part^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000102

has super-classes: data item^c
has sub-classes: curation status specification^c, denotator type^c, obsolescence reason specification^c, ontology module^c
has members: exemplar termⁿⁱ, exploratory termⁿⁱ

data format specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000098

has super-classes: directive information entity^c
has members: ACSⁿⁱ, Compensation-MLⁿⁱ, FCSⁿⁱ, Gating-MLⁿⁱ, OWLⁿⁱ, RDFⁿⁱ, Transformation-MLⁿⁱ, XMLⁿⁱ, tarⁿⁱ, zipⁿⁱ

data item^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000027

has super-classes: information content entity^c
has sub-classes: data about an ontology part^c, data set^c

data set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000100

has super-classes: data item^c
has sub-classes: classified data set^c, clustered data set^c

data transformation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200000

is equivalent to: achieves_planned_objective^op some data transformation objective^c
has super-classes: planned process^c; realizes^op some concretizes^op some algorithm^c and (has part^op some objective specification^c); achieves_planned_objective^op some data transformation objective^c; has_specified_input^op only data item^c
has sub-classes: class discovery data transformation^c, class prediction data transformation^c, decision tree building data transformation^c, partitioning data transformation^c, peak matching^c

data transformation objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200166

has super-classes: objective specification^c
has sub-classes: class discovery objective^c, class prediction objective^c, decision tree induction objective^c, partitioning objective^c

data visualization^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200111

has super-classes: planned process^c; has_specified_input^op some data item^c; has_specified_output^op some graph^c or image^c; has_specified_input^op only data item^c; has_specified_output^op only graph^c or image^c
has sub-classes: clustered data visualization^c

dataset creating^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/APOLLO_SV_00000796

is equivalent to: planned process^c and (has_specified_output^op some data set^c)
has super-classes: planned process^c; has_specified_output^op some data set^c
has sub-classes: dimensionality reduction^c, hierarchical clustering^c, k-means clustering^c, k-nearest neighbors^c

datum label^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000009

has super-classes: information content entity^c
has sub-classes: categorical label^c, measurement unit label^c

de novo allele origin^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000880

We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. De novo variants are *heritable* but not *inherited* - as they are not observed constitutively in either parent, but can be passed to offspring in virtue of their being present in the individual's germ cells. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring), and somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. De novo variants appear for the first time in one family member. They often explain genetic disorders in which an affected child has a mutation in every cell in the body but the parents do not, and there is no family history of the disorder.

has super-classes: allele origin^c

decision tree building data transformation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000707

is equivalent to: achieves_planned_objective^op some decision tree induction objective^c
has super-classes: data transformation^c; achieves_planned_objective^op some decision tree induction objective^c
has sub-classes: CART^c

decision tree induction objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000704

has super-classes: data transformation objective^c

deletion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000159

has super-classes: sequence_alteration^c; has_extent^dp value 0

dendrogram^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000183

has super-classes: graph^c

denotator type^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000409

is equivalent to: { universal , defined class , named class expression }
has super-classes: data about an ontology part^c
has members: defined classⁿⁱ, named class expressionⁿⁱ, universalⁿⁱ

developmental process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0032502

has super-classes: biological process^c

diagram^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000309

has super-classes: figure^c
has sub-classes: graph^c

digenic inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000930

has super-classes: multifactorial inheritance^c

dimensionality reduction^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200050

has super-classes: dataset creating^c; class discovery data transformation^c; (has_specified_output^op some clustered data set^c) and (achieves_planned_objective^op some class discovery objective^c)
has sub-classes: principal components analysis dimensionality reduction^c

diplotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000885

"Humans are diploid organisms; they have paired homologous chromosomes in their somatic cells, which contain two copies of each gene. An allele is one member of a pair of genes occupying a specific spot on a chromosome (called locus). Two alleles at the same locus on homologous chromosomes make up the individual’s genotype. A haplotype (a contraction of the term ‘haploid genotype’) is a combination of alleles at multiple loci that are transmitted together on the same chromosome. Haplotype may refer to as few as two loci or to an entire chromosome depending on the number of recombination events that have occurred between a given set of loci. Genewise haplotypes are established with markers within a gene; familywise haplotypes are established with markers within members of a gene family; and regionwise haplotypes are established within different genes in a region at the same chromosome. Finally, a diplotype is a matched pair of haplotypes on homologous chromosomes." From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4118015/figure/sap-26-03-165-g002/

is equivalent to: allelic genotype^c and (denotes^op some single locus complement^c and (has member^op exactly 2 allele^c))
has super-classes: allelic genotype^c; denotes^op some single locus complement^c and (has member^op exactly 2 allele^c)

direct_tandem_duplication^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000039

has super-classes: tandem_duplication^c

directive information entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000033

has super-classes: information content entity^c; is about^op some realizable entity^c
has sub-classes: action specification^c, data format specification^c, objective specification^c, plan specification^c, source code module^c

disease^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000031

has super-classes: disposition^c

disomic zygosity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000391

has super-classes: zygosity^c
has sub-classes: hemizygous^c, heterozygous^c, homozygous^c, nullizygous^c

disposition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000016

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: realizable entity^c
has sub-classes: disease^c, function^c, heritabililty^c, inheritance pattern^c
is in range of: has disposition^op
is disjoint with: role^c

DNA residue^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000780

has super-classes: biological sequence unit^c

DNA sequence^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000720

is equivalent to: biological sequence^c and (has_sequence_unit^op some DNA residue^c) and (has_sequence_unit^op only DNA residue^c)
has super-classes: biological sequence^c; has_sequence_unit^op some DNA residue^c

document^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000310

has super-classes: information content entity^c
has sub-classes: questionnaire^c

dot plot^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000037

has super-classes: graph^c

duplication^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000035

has super-classes: insertion^c
has sub-classes: tandem_duplication^c

Eastern Cooperative Oncology Group score value specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002357

has super-classes: performance status value specification^c
has members: 0: asymptomaticⁿⁱ, 1: symptomatic but fully ambulatoryⁿⁱ, 2: symptomatic but in bed less than 50% of the dayⁿⁱ, 3: symptomatic in bed more than 50% of the day but not bed riddenⁿⁱ, 4: bed riddenⁿⁱ

editors ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000002

has super-classes: ontology module^c

effective genotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000525

An effective genotype is meant to summarize all factors related to genes and their expression that influence an observed phenotype - including 'intrinsic' alterations in genomic sequence, and gene-specific 'extrinsic' alterations in expression transiently introduced at the time of the phenotypic assessment.

has super-classes: genotype^c; has part^op some extrinsic genotype^c; has part^op some intrinsic genotype^c

EL++ ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000020

has super-classes: ontology module subsetted by OWL profile^c

engineered^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000783

has super-classes: sequence feature attribute^c

engineered genetic construct^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000856

Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells. Constructs are typically packaged as part of delivery systems such as plasmids or viral vectors.

has super-classes: engineered_region^c
has sub-classes: P-element construct^c, enhancer_trap_construct^c, expression construct^c, gene_trap_construct^c, promoter_trap_construct^c

engineered_foreign_gene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000281

has super-classes: gene^c; engineered_region^c

engineered_region^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000804

is equivalent to: sequence_feature^c and (has_sequence_attribute^op some engineered^c)
has super-classes: sequence_feature^c; has_sequence_attribute^op some engineered^c
has sub-classes: engineered genetic construct^c, engineered_foreign_gene^c, gene knockdown reagent^c, reporter transgene^c, selectable marker transgene^c

enhancer^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000165

has super-classes: regulatory_region^c

enhancer_trap_construct^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001479

has super-classes: engineered genetic construct^c

entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000001

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has sub-classes: continuant^c, occurrent^c
is in domain of: denoted by^op
is in range of: denotes^op

environmental system^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01000254

In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised.

has super-classes: system^c

Epstein Barr virus transformed B cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100010

is equivalent to: (is_specified_output_of^op some establishing cell culture^c and (has_specified_input^op some Viruses^c)) and (derives from^op only B cell^c)
has super-classes: processed material^c; is_specified_output_of^op some establishing cell culture^c and (has_specified_input^op some Viruses^c)

establishing cell culture^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600036

A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.

has super-classes: material processing^c; has_specified_input^op some cell^c; has_specified_input^op some culture medium^c; has_specified_output^op some cultured cell population^c
has sub-classes: establishing cell line^c

establishing cell line^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001867

has super-classes: establishing cell culture^c; has_specified_output^op some cell line^c

Euarchontoglires^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_314146

has super-classes: Mammalia^c
has sub-classes: Homo sapiens^c, Rodentia^c

Eukaryota^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_2759

has super-classes: organism^c
has sub-classes: Opisthokonta^c

Euteleostomi^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_117571

has super-classes: Vertebrata <vertebrates>^c
has sub-classes: Danio rerio^c, Tetrapoda^c

Exact position^c back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#ExactPosition

has super-classes: Position^c

exclusion subset ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000010

has super-classes: subset ontology module^c

experimental_feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001410

has super-classes: region^c
has sub-classes: assembly^c

experimentally modified cell in vitro^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000578

has super-classes: cell^c; processed material^c
has sub-classes: cultured cell^c

expressed transgene region^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000638

has super-classes: transgene part^c
has sub-classes: reporter region^c, selectable marker region^c

expression construct^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000495

has super-classes: engineered genetic construct^c

expression-qualified sequence feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000737

has super-classes: qualified genomic feature^c
has sub-classes: expression-variant gene^c, reagent-targeted gene subregion^c

expression-variant gene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000529

Expression-variant genes are altered in their expression level through some modification or intervention external to its sequence and position. These may include endogenous mechanisms (e.g. direct epigentic modification that impact expression level, or altered regulatory networks controlling gene expression), or experimental interventions (e.g. targeting by a gene-knockdown reagent, or being transiently expressed as part of a transgenic construct in a host cell or organism). The identity of a given instance of a experssion-variant gene is dependent on how its level of expression is manipulated in a biological system (i.e. via targeting by gene-knockdown reagents, or being transiently overexpressed). So expression-variant genes have the additional identity criteria of a genetic context of its material bearer (external to its sequence and position) that impacts its level of expression in a biological system.

has super-classes: expression-qualified sequence feature^c; is_expression_variant_of^op some gene^c
has sub-classes: reagent targeted gene^c, transiently-expressed transgene^c

external import ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000011

has super-classes: import ontology module^c

extra-chromosomal transgene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000861

has super-classes: transgene^c

extrachromosomal replicon^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000494

is equivalent to: genomic feature^c and (not (is_proper_part_of^op some chromosome^c)) and (has_sequence_attribute^op some heritable^c)
has super-classes: genomic feature^c; has_sequence_attribute^op some heritable^c
has sub-classes: novel extrachromosomal replicon^c

extrinsic genotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000524

An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment. The 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations.

has super-classes: genotype^c

family^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PCO_0000020

has super-classes: collection of organisms^c

female^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000383

has super-classes: phenotypic sex^c

female intrinsic genotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000647

has super-classes: genomic genotype (sex-qualified)^c

figure^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000308

has super-classes: information content entity^c
has sub-classes: diagram^c, image^c

frequency unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000105

has super-classes: measurement unit label^c
has members: hertzⁿⁱ

function^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000034

has super-classes: disposition^c
is in domain of: function of^op
is in range of: has function^op

functional copy complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000963

A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a set may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features, such as the set of all functional copies of a particular sequence in a genome. This is known as the 'functional copy number' or 'genetic dosage' of the sequence. 'Functional copies' of a sequence are those that exhibit normal activity and/or produce gene products that exhibit normal activity associated with the sequence. The count of functional copies of a gene is often referred to as its 'dosage'. In diploid organisms, the normal 'dosage' is 2 for autosomal genes/regions. Dosage increases if there is a duplication of a functional gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of a 'copy number complement', which reflects how many copies of a sequence exist in a genome, regardless of their functionality. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. As we saw for 'copy number complement', the defining sequence here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a 'functional' copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify as functional if that alteration eliminates the activity of the allele.

has super-classes: genomic sequence set^c

G_to_A_transition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000016

has super-classes: purine_transition^c

G_to_C_transversion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000026

has super-classes: purine_to_pyrimidine_transversion^c

G_to_T_transversion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000027

has super-classes: purine_to_pyrimidine_transversion^c

gained aneusomic chromosomal segment^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000344

Such additions of translocated chromosomal parts confer a trisomic condition to the duplicated region of the chromsome, and are thus considered to be 'variant single locus complements' in virtue of an abnormal number of features at a particular genomic location, rather than abnormal sequence within the location.

has super-classes: aneusomic chromosomal part^c

gained aneusomic chromosome^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000338

This 'gained' chromosome is conceptually an 'insertion' in a genome that received two copies of a chromosome in a cell division following a non-disjunction event. As such, it qualifies as a type of sequence_alteration, and as a 'extra' chromosome.

has super-classes: aneusomic chromosome^c; has_sequence_attribute^op some novel^c

gene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000704

A gene is any 'gene allele' that produces a functional transcript (ie one capable of translation into a protein, or independent functioning as an RNA), when encoded in the genome of some cell or virion.

has super-classes: genomic feature^c
has sub-classes: danio rerio gene^c, engineered_foreign_gene^c, homo sapiens gene^c, mus musculus gene^c, transgene^c, wild-type gene^c

gene allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000014

In SO, the concept of a 'gene' is functionally defined, in that a gene necessarily produces a functional product. By contrast, the concept of a 'gene allele' here is positionally defined - representing the sequence present at the location a gene resides in a reference genome (based on sequence alignment). An Shh gene allele, for example, may be a fully functional wild-type version of the gene, a non-functional version carrying a deleterious point mutation, a truncated version of the gene, or even a complete deletion. In all these cases, an 'Shh gene allele' exists at the position where the canonical gene resides in the reference genome - even if the extent of this allele different than the wild-type, or even zero in the case of the complete deletion. A genomic feature being an allele_of a gene is based on its location in a host genome - not on its sequence. This means, for example, that the insertion of the human SMN2 gene into the genome of a mouse (see http://www.informatics.jax.org/allele/MGI:3056903) DOES NOT represent an allele_of the human SMN2 gene according to the GENO model - because it is located in a mouse genome, not a human one. Rather, this is a transgenic insertion that derives_sequence_from the human SMN2 gene. If this human SMN2 gene is inserted within the mouse SMN2 gene locus (e.g. used to replace mouse SMN2 gene), the feature it creates is an allele_of the mouse SMN2 gene (one that happens to match the sequence of the human ortholog of the gene). But again, it is not an allele_of the human SMN2 gene.

has super-classes: allele^c; is_allele_of^op some gene^c
has sub-classes: variant gene allele^c

gene knockdown reagent^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000533

has super-classes: engineered_region^c
has sub-classes: RNAi_reagent^c, morpholino_oligo^c

gene part^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000666

is equivalent to: genomic feature^c and (is subsequence of^op some gene allele^c)
has super-classes: genomic feature^c; sequentially ordered entity^c; is subsequence of^op some gene allele^c
has sub-classes: regulatory_region^c, transgene part^c

gene product^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000907

has super-classes: sequence_feature^c

gene product or complex activity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0003674

has super-classes: process^c
has sub-classes: kinase activity^c

gene trap insertion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000092

has super-classes: insertion^c

gene_trap_construct^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001477

has super-classes: engineered genetic construct^c

GenePattern software^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000713

has super-classes: software^c
has members: GenePattern module CARTXValidationⁿⁱ, GenePattern module HeatMapViewerⁿⁱ, GenePattern module HierarchicalClusteringⁿⁱ, GenePattern module HierarchicalClusteringViewerⁿⁱ, GenePattern module KMeansClusteringⁿⁱ, GenePattern module KNNⁿⁱ, GenePattern module KNNXValidationⁿⁱ, GenePattern module PCAⁿⁱ, GenePattern module PeakMatchⁿⁱ, GenePattern module SVMⁿⁱ

generated ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000014

has super-classes: ontology module^c
has sub-classes: template generated ontology module^c

generically dependent continuant^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000031

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: continuant^c; part of^op only generically dependent continuant^c
has sub-classes: biological sequence or set^c, genomic entity^c, information content entity^c, qualified sequence feature or collection^c, region^c, sequence feature location^c, sequence feature or set^c
is in domain of: generically depends on^op, is concretized as^op
is in range of: concretizes^op, is carrier of^op
is disjoint with: independent continuant^c, specifically dependent continuant^c, independent continuant^c, specifically dependent continuant^c

genetic material^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000482

This class is different from genomic material in that genomic material is necessarily heritable, while genetic material includes genomic material, as well as any additional nucleic acids that participate in gene expression resulting in a cellular or organismal phenotype. So things like transiently transfected expression constructs would qualify as 'genetic material but not 'genomic material'. Things like siRNAs and morpholinos affect gene expression indirectly, (ie are not templates for gene expression), and therefore do not qualify as genetic material.

has super-classes: nucleic acid^c
has sub-classes: genomic material^c

genome^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001026

A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'.

has super-classes: genomic feature set^c
has sub-classes: reference genome^c, variant genome^c

genomic background^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000611

is equivalent to: genomic genotype^c and (sequence role^op some reference^c)
has super-classes: genomic genotype^c; sequence role^op some reference^c; denotes^op some background genome^c
has sub-classes: unspecified genomic background^c

genomic entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000897

is equivalent to: genomic feature^c or (has part^op some genomic feature^c) or (has_sequence_feature^op some genomic feature^c or genomic feature set^c) or (denotes^op some genomic feature^c or genomic feature set^c or qualified genomic feature set^c)
has super-classes: generically dependent continuant^c; in taxon^op some organism^c
has sub-classes: allelic genotype^c, genomic feature^c, genomic feature set^c, genomic genotype^c, qualified genomic feature^c, qualified genomic feature set^c

genomic feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000481

1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. 2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). 3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome.

is equivalent to: sequence_feature^c and (has_location^op some genomic feature location^c)
has super-classes: genomic entity^c; sequence_feature^c; part of^op some genome^c; has_sequence^op some genomic sequence^c; has_location^op some genomic feature location^c
has sub-classes: QTL^c, allele^c, chromosome^c, chromosome part^c, extrachromosomal replicon^c, gene^c, gene part^c, haplotype block^c, heritable_phenotypic_marker^c, microsatellite^c
is in domain of: is_allele_of^op

genomic feature location^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000902

1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. 2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. 3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there.

has super-classes: sequence feature location^c
has sub-classes: Position^c

genomic feature set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000660

A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside.

has super-classes: sequence feature set^c; genomic entity^c; has member^op some genomic feature^c
has sub-classes: allele set^c, genome^c, genomic variation complement^c, haplotype^c, single locus complement^c

genomic genotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000899

1. A genomic genotype is a short-hand specification of a genome that uses a representational syntax comprised of information about a reference genome ('genomic background'), and all specific variants from this reference (the 'genomic variation complement'). Conceptually, this variant genome sequence can be resolved by substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the reference 'genomic background' sequence. 2. 'Heritable' genomic sequence is that which is passed on to subsequent generations of cells/organisms, and includes all chromosomal sequences, the mitochondrial genome, and any transmissable extrachromosomal replicons.

is equivalent to: intrinsic genotype^c and (denotes^op some genome^c)
has super-classes: intrinsic genotype^c; genomic entity^c; has_reference_part^op some genomic background^c; denotes^op some genome^c
has sub-classes: genomic background^c, genomic genotype (sex-agnostic)^c, genomic genotype (sex-qualified)^c, karyotype^c, variant genomic genotype^c

genomic genotype (sex-agnostic)^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000000

In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances).

has super-classes: genomic genotype^c

genomic genotype (sex-qualified)^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000645

We distinguish the notion of a sex-agnostic intrinsic genotype, which does not specify whether the portion of the genome defining organismal sex is male or female, from the notion of a sex-qualified intrinsic genotype, which does. Male and female mice that contain the same background and genetic variation complement will have the same 'sex-agnostic intrinsic genotype', despite their genomes varying in their sex-chromosome complement. By contrast, these two mice would have different 'sex-qualified intrinsic genotypes', as this class takes background sex chromosome sequences into account in the identity criteria for its instances. Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome.

has super-classes: genomic genotype^c; has_sex_agnostic_part^op some genomic genotype (sex-agnostic)^c
has sub-classes: female intrinsic genotype^c, male intrinsic genotype^c

genomic material^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000106

1. Genomic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. Genetic material is necessarily part of some 'material genome', and both are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some genome. 2. Genomic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but such cases must be capable of being inherited by progeny cells or organisms.

has super-classes: genetic material^c; has disposition^op some heritable^c

genomic sequence^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000960

A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome.

is equivalent to: is_sequence_of^op some genomic feature^c
has super-classes: biological sequence^c; is_sequence_of^op some genomic feature^c

genomic sequence set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000872

A 'genomic *sequence* set' differs from a 'genomic *feature* set' in that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *sequence feature*. 'Genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside. By contrast, 'genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location.

has super-classes: biological sequence set^c
has sub-classes: copy number complement^c, functional copy complement^c

genomic variation complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000009

is equivalent to: genomic feature set^c and (has_variant_part^op some variant single locus complement^c)
has super-classes: genomic feature set^c; has_variant_part^op some variant single locus complement^c

genotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000536

1. Scope of 'Genetic State': 'Genetic state' is considered quite broadly in GENO to describe two general kinds of 'states'. First, is traditional notion of 'allelic state' - defined as the complement of alleles present at a particular location or locations in a genome (i.e. across all homologous chromosomes containing this location). Here, a genotype can describe allelic state at a specific locus in a genome (an 'allelic genotype'), or describe the allelic state across the entire genome ('genomic genotype'). Second, this concept can also describe states of genomic features 'extrinsic' to their intrinsic sequence, such as the expression status of a gene as a result of being specifically targeted by experimental interventions such as RNAi, morpholinos, or CRISPRs. 2. Genotype Subtypes: In GENO, we use the term 'intrinsic' for genotypes describing variation in genomic sequence, and 'extrinsic' for genotypes describing variation in gene expression (e.g. resulting from the targeted experimental knock-down or over-expression of endogenous genes). We use the term 'effective genotype' to describe the total intrinsic and extrinsic variation in a cell or organism at the time a phenotypic assessment is performed. Two more precise conccepts are subsumed by the notion of an 'intrinsic genotype': (1) 'allelic genotypes', which specify allelic state at a single genomic location; and (2) 'genomic genotypes', which specify allelic state across an entire genome. In both cases, allelic state is typically specified in terms of a differential between a reference and a set of 1 or more known variant features. 3. The Genotype Partonomy: 'Genomic genotypes' describing sequence variation across an entire genome are 'decomposed' in GENO into a partonomy of more granular levels of variation. These levels are defined to be meaningful to biologists in their attempts to relate genetic variation to phenotypic features. They include 'genomic variation complement' (GVC), 'variant single locus complement' (VSLC), 'allele', 'haplotype', 'sequence alteration', and 'genomic background' classes. For example, the components of the zebrafish genotype "fgf8a<ti282a/ti282a>; fgf3<t24149/+>[AB]", described at zfin.org/ZDB-FISH-150901-9362, include the following elements: - GVC: fgf8a<ti282a/ti282a>; fgf3<t24149/+> (total intrinsic variation in the genome) - Genomic Background: AB (the reference against which the GVC is variant) - VSLC1: fgf8a<ti282a/ti282a> (homozygous complement of gene alleles at one known variant locus) - VSLC2: fgf3<t24149/+> (heterozygous complement of gene alleles at another known variant locus) - Allele 1: fgf8a<ti282a> (variant version of the fgf8a gene, present in two copies) - Allele 2: fgf3<t24149> (variant version of the fgf3 gene, present in one copy) - Allele 3: fgf3<+> (wild-type version of the fgf3 gene, present in one copy) - Sequence Alteration1: <ti282a> (the specific mutation within the fgf8a gene that makes it variant) - Sequence Alteration2: <t24149> (the specific mutation within the fgf3 gene that makes it variant) A graphical representation of this decomposition that maps each element to a visual depiction of the portion of a genome it denotes can be found here: https://github.com/monarch-initiative/GENO-ontology/blob/develop/README.md One reason that explicit representation of these levels is important is because it is at these levels that phenotypic features are annotated to genetic variations in different clinical and model organism databases For example, ZFIN typically annotates phenotypes to effective genotypes, MGI to intrinsic genotypes, Wormbase to variant alleles, and ClinVar to haplotypes and sequence alterations. The ability to decompose a genotype into representations at these levels allows us to "propagate phenotypes" up or down the partonomy (e.g. infer associations of phenotypes annotated to a genotype to its more granular levels of variation and the gene(s) affected). This helps to supporting integrated analysis of G2P data.

has super-classes: information content entity^c; denotes^op some genomic feature set^c or qualified genomic feature set^c
has sub-classes: effective genotype^c, extrinsic genotype^c, intrinsic genotype^c

genotype-phenotype association^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000833

has super-classes: association^c; has_qualifier^op some environmental system^c; has_qualifier^op some developmental process^c and ((starts during^op some life cycle stage^c) and (ends during^op some life cycle stage^c)); association has object^op some phenotype^c; association has subject^op some genotype^c or (part of^op some genotype^c)

germline allele origin^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000888

We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Germline variants are both *inherited* (present constitutively in a parent and passed down to offspring) and *heritable* (passable down to future offspring). By contrast, somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. Traits caused by de novo mutations in germ cells are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present a germ cells.

has super-classes: inherited allele origin^c
has sub-classes: maternal allele origin^c, paternal allele origin^c

gneg^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000620

has super-classes: chromosomal band intensity^c

gpos^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000619

has super-classes: chromosomal band intensity^c
has sub-classes: gpos100^c, gpos25^c, gpos33^c, gpos50^c, gpos66^c, gpos75^c

gpos100^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000622

has super-classes: gpos^c

gpos25^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000625

has super-classes: gpos^c

gpos33^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000633

has super-classes: gpos^c

gpos50^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000624

has super-classes: gpos^c

gpos66^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000632

has super-classes: gpos^c

gpos75^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000623

has super-classes: gpos^c

graph^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000038

has super-classes: diagram^c
has sub-classes: dendrogram^c, dot plot^c, heatmap^c, histogram^c, scatter plot^c

gvar^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000621

has super-classes: chromosomal band intensity^c

haplotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000871

A haplotype is a set of non-overlapping alleles that reside in close proximity on the same DNA strand. We model them as 'complements' because they include all known/relevant alleles within a defined region in the genome (e.g. a 'gene', or a 'haplotype block') - where this set may consist of 0, 1, or more alterations from some reference. Because they are genetically linked, the alleles comprising a haplotype are likely to be co-inherited and survive descent across many generations of reproduction. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': 1. The 'alleles' comprising the haplotype are 'single nucleotide polymorphisms' (SNPs) or other small alterations, which collectively tend to occur together on a chromosomal strand). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. 2. The 'alleles' comprising the haplotype are SNPs or other short alterations, which collectively define a specific version of a gene. In this case, the locaiton bounding the haplotype corresponds to a gene locus, and the haplotype defines a specific allele of that gene (i.e 'gene allele'). "Star alleles" of PGx genes are examples of this category of haplotype (e.g. https://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele_hgvs.cgi?A*33:01:01, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724253/). 3. Each of the 'alleles' comprising the haplotype is itself a 'gene allele' (i.e. a specific version of an entire gene), such that the haolotype contains multiple complete 'gene alleles' that are co-inherited because they reside in tightly linked clusters on a single chromosome. Each of these more specific definition serves a purpose for a particular type of genetic analysis or use case. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.

has super-classes: genomic feature set^c; has member^op some allele^c

haplotype block^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000898

A particular haplotype block is defined by the set of sequence alterations it is known to contain, which collectively represent a 'haplotype'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype.

has super-classes: genomic feature^c

heatmap^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000180

has super-classes: graph^c

hemizygous^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000134

has super-classes: disomic zygosity^c
has sub-classes: hemizygous X-linked^c, hemizygous Y-linked^c, hemizygous insertion-linked^c

hemizygous insertion-linked^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000606

has super-classes: hemizygous^c

hemizygous X-linked^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000604

has super-classes: hemizygous^c

hemizygous Y-linked^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000605

has super-classes: hemizygous^c

heritabililty^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000138

We can use these terms to describe the heritability of genetic matieral or sequence features - e.g. chromosomal DNA or genes are heritable in that they are passed on to child cells/organisms). Such genetic material has a heritable disposition in a cell or virion, in virtue of its being replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells). We can also use these terms to describe the heritability of phenotypes/conditions - e.g. the passage of a particular trait or disease across generations of reproducing cells/organisms.

has super-classes: disposition^c
has sub-classes: heritable^c, non-heritable^c

heritable^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000139

has super-classes: heritabililty^c

heritable_phenotypic_marker^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001500

has super-classes: genomic feature^c

heteroplasmic^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000603

has super-classes: organellar plasmy^c

heteroplasmic mitochondrial inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000892

has super-classes: mitochondrial inheritance^c

heterozygous^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000135

has super-classes: disomic zygosity^c
has sub-classes: compound heterozygous^c, simple heterozygous^c

hierarchical clustering^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200042

has super-classes: dataset creating^c; class discovery data transformation^c; (has_specified_output^op some clustered data set^c) and (achieves_planned_objective^op some class discovery objective^c)
has members: GenePattern hierarchical clusteringⁿⁱ

histogram^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000179

has super-classes: graph^c

histologic grade according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002205

has super-classes: categorical value specification^c
has members: G1: Well differentiatedⁿⁱ, G2: Moderately differentiatedⁿⁱ, G3: Poorly differentiatedⁿⁱ, G4: Undifferentiatedⁿⁱ

histologic grade according to the Fuhrman Nuclear Grading System^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002210

has super-classes: categorical value specification^c
has members: G1 (Fuhrman)ⁿⁱ, G2 (Fuhrman)ⁿⁱ, G3 (Fuhrman)ⁿⁱ, G4 (Fuhrman)ⁿⁱ

histologic grade for ovarian tumor^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002215

has super-classes: categorical value specification^c
has sub-classes: histologic grade for ovarian tumor according to a two-tier grading system^c, histologic grade for ovarian tumor according to the World Health Organization^c

histologic grade for ovarian tumor according to a two-tier grading system^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002216

has super-classes: histologic grade for ovarian tumor^c
has members: High grade ovarian tumorⁿⁱ, Low grade ovarian tumorⁿⁱ

histologic grade for ovarian tumor according to the World Health Organization^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002219

has super-classes: histologic grade for ovarian tumor^c
has members: G1 (WHO)ⁿⁱ, G2 (WHO)ⁿⁱ, G3 (WHO)ⁿⁱ, G4 (WHO)ⁿⁱ

Homo sapiens^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_9606

has super-classes: Euarchontoglires^c

homo sapiens gene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000054

is equivalent to: gene^c and (in taxon^op some Homo sapiens^c)
has super-classes: gene^c; in taxon^op some Homo sapiens^c
has sub-classes: homo sapiens SHH gene^c

homo sapiens SHH gene^c back to ToC or Class ToC

IRI: http://www.ncbi.nlm.nih.gov/gene/6469

Equivalent to: http://www.ensembl.org/Gene/Summary?g=ENSG00000164690 Codes for: http://www.uniprot.org/uniprot/Q15465

has super-classes: homo sapiens gene^c

homoplasmic^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000602

has super-classes: organellar plasmy^c

homoplasmic mitochondrial inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000893

has super-classes: mitochondrial inheritance^c

homozygous^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000136

has super-classes: disomic zygosity^c

human life cycle stage^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/HsapDv_0000000

has super-classes: biological process^c

human phenotypic abnormality^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/HP_0000118

pulling in HP 'phenotypic abnormality' root here

has super-classes: phenotype^c

human population^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000111

has super-classes: population^c

image^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000101

has super-classes: figure^c

import ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000005

has super-classes: subset ontology module^c
has sub-classes: external import ontology module^c

in cis^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000131

has super-classes: allelic phase^c

in trans^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000132

has super-classes: allelic phase^c

incomplete autosomal dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000145

has super-classes: autosomal dominant inheritance^c

incomplete X-linked dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000938

has super-classes: X-linked dominant inheritance^c

incomplete Z-linked dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000945

has super-classes: Z-linked dominant inheritance^c

indel^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000032

Indels can have a different number of bases than the corresponding reference sequence.

has super-classes: sequence_alteration^c

independent continuant^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000004

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: continuant^c; part of^op only independent continuant^c
has sub-classes: material entity^c
is in domain of: capable of^op, derives from^op, develops from^op, has disposition^op, has function^op, has role^op, is carrier of^op
is in range of: derives from^op, develops from^op, generically depends on^op
is disjoint with: specifically dependent continuant^c, generically dependent continuant^c, specifically dependent continuant^c, generically dependent continuant^c

information carrier^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000015

is equivalent to: quality^c and (concretizes^op some information content entity^c)
has super-classes: quality^c; concretizes^op some information content entity^c

information content entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000030

has super-classes: generically dependent continuant^c; is about^op some entity^c
has sub-classes: association^c, data item^c, datum label^c, directive information entity^c, document^c, figure^c, genotype^c, sequence interval^c, value specification^c
is in domain of: denotes^op, is about^op
is in range of: denoted by^op

inheritance pattern^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000141

An inheritance pattern results from the disposition of a genetic variant to cause a particular trait or phenotype when it is present in a particular genetic and environmental context. Here, "genetic context" refers to the allelic state of the variant, which depends on what other alleles exist at the same location/locus in the genome. Zygosities such as heterozygous and homozygous are simple, common examples of 'states' of an allele. These genetic and environmental "interactions" of alleles play out at the level of the gene products produced by the causal alleles, and are observable in the pattern with which the trait caused by an allele is inherited across generations of individuals. Thus, an inheritance pattern such as dominance is not inherent to a single allele or its phenotype, but rather a result of the relationship between two alleles of a gene and the phenotype that results in a given environment. This also means that the 'dominance' of an allele is context dependent - Allele 1 can be dominant over Allele 2 in the context of Phenotype X, but recessive to Allele 3 in the context of Phenotype Y.

has super-classes: disposition^c
has sub-classes: chromosomal inheritance^c, mitochondrial inheritance^c, monogenic inheritance^c, multifactorial inheritance^c, undetermined inheritance^c
is in range of: obsolete_participates_in_inheritance_process^op

inherited allele origin^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000974

has super-classes: allele origin^c
has sub-classes: biparental allele origin^c, germline allele origin^c, uniparental allele origin^c

insertion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000667

has super-classes: sequence_alteration^c
has sub-classes: duplication^c, gene trap insertion^c, transgenic_insertion^c

integrated transgene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000093

An integrated transgene differs from a transgenic insertion in that a transgenic insertion may contain single transgene, a partial transgene that needs endognous sequences from the host genome to become functional (e.g. an enhancer trap), or multiple transgenes (i.e. be polycistronic). Fiurthermore, the transgenic insertion may contain sequences in addition to its transgene(s - e.g. sequences flanking the transgene reqired for integration or replicaiton/maintenance in the host genome. The term 'integrated transgene' covers individual transgenes that were delivered in whole or in part by a transgenic insertion. An 'integrated transgene' differs from its parent 'transgene' in that transgenes can include genes introduced into a cell/organism on an extra-chromosomal plasmid that is never integrated into the host genome.

has super-classes: transgene^c; part of^op some transgenic_insertion^c

International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002326

has super-classes: categorical value specification^c
has members: Stage IA (FIGO)ⁿⁱ, Stage IA1 (FIGO)ⁿⁱ, Stage IA2 (FIGO)ⁿⁱ, Stage IB (FIGO)ⁿⁱ, Stage IB1 (FIGO)ⁿⁱ, Stage IB2 (FIGO)ⁿⁱ, Stage IIA (FIGO)ⁿⁱ, Stage IIA1 (FIGO)ⁿⁱ, Stage IIA2 (FIGO)ⁿⁱ, Stage IIB (FIGO)ⁿⁱ, Stage IIIA (FIGO)ⁿⁱ, Stage IIIB (FIGO)ⁿⁱ, Stage IVA (FIGO)ⁿⁱ, Stage IVB (FIGO)ⁿⁱ

International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002341

has super-classes: categorical value specification^c
has members: Stage 1 (FIGO)ⁿⁱ, Stage 1A (FIGO)ⁿⁱ, Stage 1B (FIGO)ⁿⁱ, Stage 1C (FIGO)ⁿⁱ, Stage 2 (FIGO)ⁿⁱ, Stage 2A (FIGO)ⁿⁱ, Stage 2B (FIGO)ⁿⁱ, Stage 2C (FIGO)ⁿⁱ, Stage 3 (FIGO)ⁿⁱ, Stage 3A (FIGO)ⁿⁱ, Stage 3B (FIGO)ⁿⁱ, Stage 3C (FIGO)ⁿⁱ, Stage 4 (FIGO)ⁿⁱ, Stage Unknown (FIGO)ⁿⁱ

intrinsic genotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000719

has super-classes: genotype^c; denotes^op some single locus complement^c or genome^c
has sub-classes: allelic genotype^c, genomic genotype^c

inversion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000036

has super-classes: sequence_alteration^c

inverted_tandem_duplication^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000040

has super-classes: tandem_duplication^c

junction^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000699

A junction is a boundary between regions. A boundary has an extent of zero.

has super-classes: sequence_feature^c

k-means clustering^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200041

has super-classes: dataset creating^c; partitioning data transformation^c; class discovery data transformation^c; (has_specified_output^op some clustered data set^c) and (achieves_planned_objective^op some class discovery objective^c)
has members: GenePattern k-means clusteringⁿⁱ

k-nearest neighbors^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000727

has super-classes: dataset creating^c; partitioning data transformation^c; class discovery data transformation^c; (has_specified_output^op some clustered data set^c) and (achieves_planned_objective^op some class discovery objective^c)
has members: GenePattern k-nearest neighborsⁿⁱ

Karnofsky score vaue specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002363

has super-classes: performance status value specification^c
has members: 100: asymptomaticⁿⁱ, 40-50: symptomatic, in bed more than 50% of the day, but not bed riddenⁿⁱ, 60-70: symptomatic but in bed less than 50% of the dayⁿⁱ, 80-90: symptomatic but fully ambulatoryⁿⁱ

karyotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000644

Karyotypes describe structural variation across a genome at the level of chromosomal morphology and banding patterns detectable in stained chromosomal spreads. This coarser level does not capture more granular levels of variation commonly represented in other forms of genotypes (e.g. specific alleles and sequence alterations). A base karyotype representing a genome with no known structural variation can be as simple as '46XY', but karyotypes typically contains some gross variant component (such as a chromosome duplication or translocation).

has super-classes: genomic genotype^c

kinase activity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0016301

has super-classes: gene product or complex activity^c; is kinase activity^op

knockdown reagent targeted gene complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000839

has super-classes: reagent-targeted gene complement^c; has_variant_part^op some reagent targeted gene^c

leave one out cross validation method^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200033

has super-classes: statistical model validation^c
has members: GenePattern LOOCVⁿⁱ

length unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000001

has super-classes: measurement unit label^c
has members: angstromⁿⁱ, centimeterⁿⁱ, meterⁿⁱ, micrometerⁿⁱ, millimeterⁿⁱ, nanometerⁿⁱ

life cycle stage^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000105

has super-classes: biological process^c; biological process^c
has sub-classes: unspecified life cycle stage^c

location-qualified sequence feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000736

As a qualified sequence feature, the BRCA1c.5096G>A variant as materialized in a somatic breast epithelial cell could be distinguished as a separate entity from a BRCA1c.5096G>A variant in a different cell type or location (e.g. germline BRCA1 varaint in a sperm cell).

has super-classes: qualified genomic feature^c

long chromosome arm^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000629

has super-classes: chromosome arm^c

lost aneusomic chromosomal segment^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000345

This is not a deletion in the sense defined by the Sequence Ontology in that it is not the result of an 'excision' of nucleotides, but an unbalanced translocation event. The allelic complement that results is comprised of the terminus or junction represented by this lost chromosomal segment, and the remaining normal segment in the homologous chromosome. The lost aneusommic chromosomal segment is typically accommpanied by a gained aneusomic chromosomal segment from another chromosome. Loss of translocated chromosomal parts can confer a monosomic condition to a region of the chromsome. This results in a 'variant single locus complement' - in virtue of an abnormal number of features at a particular locus, rather than abnormal sequence within the locus.

has super-classes: aneusomic chromosomal part^c; has_extent^dp value 0

lost aneusomic chromosome^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000339

has super-classes: aneusomic chromosome^c; has_extent^dp value 0

lymphocyte^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000542

has super-classes: mononuclear cell^c
has sub-classes: B cell^c

macromolecule^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33839

has super-classes: molecular entity^c
has sub-classes: nucleic acid^c

main release ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000003

has super-classes: ontology module^c

maintaining cell culture^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600024

has super-classes: material maintenance^c; has_specified_input^op some cultured cell population^c; has_specified_input^op some culture medium^c or cell freezing medium^c; has_specified_output^op some cultured cell population^c

major polymorphic allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000498

has super-classes: polymorphic allele^c

male^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000384

has super-classes: phenotypic sex^c

male intrinsic genotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000646

has super-classes: genomic genotype (sex-qualified)^c

Mammalia^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_40674

has super-classes: Amniota^c
has sub-classes: Euarchontoglires^c

mammalian phenotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MP_0000001

where to place this depends on if we take the organismal view or the quality centric view.

has super-classes: phenotype^c

manufacturer^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000835

is equivalent to: (Homo sapiens^c or organization^c) and (has role^op some manufacturer role^c)
has super-classes: material entity^c; has role^op some manufacturer role^c
has members: AES Chemunexⁿⁱ, Advanced Instruments Inc. (AI Companies)ⁿⁱ, Affymetrixⁿⁱ, Agilentⁿⁱ, Ambionⁿⁱ, Antigenixⁿⁱ, Apogee Flow Systemsⁿⁱ, Applied Biosystemsⁿⁱ, BIO-RADⁿⁱ, Beckman Coulterⁿⁱ, Becton Dickinson (BD Biosciences)ⁿⁱ, Bentley Instrumentsⁿⁱ, BioGentsⁿⁱ, Bruker Corporationⁿⁱ, Bruker Daltonicsⁿⁱ, CytoBuoyⁿⁱ, Cytopeiaⁿⁱ, Dako Cytomationⁿⁱ, Exalpha Biologicalⁿⁱ, Exbio Antibodiesⁿⁱ, Helicosⁿⁱ, Illuminaⁿⁱ, Invitrogenⁿⁱ, Li-Corⁿⁱ, Luminexⁿⁱ, Milliporeⁿⁱ, Miltenyi Biotecⁿⁱ, NanoString Technologiesⁿⁱ, Nimblegenⁿⁱ, Oxford Nanopore Technologiesⁿⁱ, Pacific Biosciencesⁿⁱ, Partecⁿⁱ, Rocheⁿⁱ, Sysmex Corporation, Kobe, Japanⁿⁱ, Thermoⁿⁱ, Watersⁿⁱ, eBioscienceⁿⁱ

manufacturer role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000571

has super-classes: role^c; characteristic of^op some Homo sapiens^c or organization^c; realized in^op only manufacturing^c

manufacturing^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000457

is equivalent to: achieves_planned_objective^op some manufacturing objective^c
has super-classes: material processing^c; has_specified_input^op some material entity^c; achieves_planned_objective^op some manufacturing objective^c

manufacturing objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000458

has super-classes: material transformation objective^c

mass unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000002

has super-classes: measurement unit label^c
has members: gramⁿⁱ, kilogramⁿⁱ, microgramⁿⁱ, milligramⁿⁱ, nanogramⁿⁱ, picogramⁿⁱ

material anatomical entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000465

has super-classes: anatomical entity^c
has sub-classes: anatomical structure^c

material component separation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600014

is equivalent to: achieves_planned_objective^op some material separation objective^c
has super-classes: material processing^c; has_specified_input^op some material entity^c; achieves_planned_objective^op some material separation objective^c
has sub-classes: cell culture splitting^c

material entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000040

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: independent continuant^c
has sub-classes: collection of specimens^c, manufacturer^c, material genome^c, material information bearer^c, material supplier^c, molecular entity^c, organismal entity^c, organization^c, processed material^c, specimen^c, system^c
is in domain of: causal relation between material entity and a process^op, directly negatively regulates activity of^op, directly positively regulates activity of^op, directly regulates activity of^op, interacts with^op, regulates activity of^op
is in range of: directly negatively regulates activity of^op, directly positively regulates activity of^op, directly regulates activity of^op, interacts with^op, regulates activity of^op

material genome^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000108

A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNA, but many viruses have RNA genomes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), and can in addition contain non-chromosomal elements such as replicative viruses, plasmids, and transposable elements. Note that at present, a material genome and genetic material are necessarily part of some cell or virion. So a genomic library is not considered a material genome/genetic material - rather, we could say that this genomic library is a 'genomic material sample' that bears the concretization of some SO:genome.

has super-classes: material entity^c

material information bearer^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000178

is equivalent to: material entity^c and (bearer of^op some concretizes^op some information content entity^c)
has super-classes: material entity^c; bearer of^op some concretizes^op some information content entity^c

material maintenance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000838

is equivalent to: achieves_planned_objective^op some material maintenance objective^c
has super-classes: planned process^c; achieves_planned_objective^op some material maintenance objective^c
has sub-classes: maintaining cell culture^c

material maintenance objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000806

has super-classes: objective specification^c

material processing^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000094

is equivalent to: achieves_planned_objective^op some material transformation objective^c
has super-classes: planned process^c; has_specified_output^op some processed material^c; achieves_planned_objective^op some material transformation objective^c; has_specified_input^op only material entity^c
has sub-classes: establishing cell culture^c, manufacturing^c, material component separation^c

material separation objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000639

is equivalent to: portioning objective^c or separation into different composition objective^c
has super-classes: material transformation objective^c
has sub-classes: portioning objective^c, separation into different composition objective^c

material supplier^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002989

is equivalent to: (Homo sapiens^c or organization^c) and (has role^op some material supplier role^c)
has super-classes: material entity^c; has role^op some material supplier role^c
has members: Affymetrixⁿⁱ

material supplier role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000018

has super-classes: service provider role^c

material transformation objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000456

has super-classes: objective specification^c
has sub-classes: manufacturing objective^c, material separation objective^c

maternal allele origin^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000878

has super-classes: germline allele origin^c

maternal_uniparental_disomy^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001745

has super-classes: UPD^c

measurement unit label^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000003

has super-classes: datum label^c
has sub-classes: concentration unit^c, frequency unit^c, length unit^c, mass unit^c, rate unit^c, substance unit^c, temperature unit^c, time unit^c, volume unit^c, volumetric flow rate unit^c

Metazoa^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_33208

has super-classes: Opisthokonta^c
has sub-classes: Bilateria^c

microsatellite^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000289

A defined feature that includes any type of VNTR or SSLP locus.

has super-classes: genomic feature^c

microsatellite alteration^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000873

has super-classes: repeat region alteration^c

minor polymorphic allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000499

has super-classes: polymorphic allele^c

mitochondrial inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000949

Because the mitochondrial genome is essentially always maternally inherited, a mitochondrial condition can only be transmitted by females, although the condition can affect both sexes. The proportion of mutant mitochondria can vary (heteroplasmy).

has super-classes: inheritance pattern^c
has sub-classes: heteroplasmic mitochondrial inheritance^c, homoplasmic mitochondrial inheritance^c

MNP^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001013

has super-classes: substitution^c

modification-qualified sequence feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000818

has super-classes: qualified genomic feature^c

molecular entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_23367

has super-classes: material entity^c
has sub-classes: macromolecule^c

monogenic inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000933

has super-classes: inheritance pattern^c
has sub-classes: allosomal inheritance^c, autosomal inheritance^c

mononuclear cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000842

has super-classes: cell^c
has sub-classes: lymphocyte^c

morpholino_oligo^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000034

has super-classes: gene knockdown reagent^c

mosaic^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000964

A clonal distribution in which an allele arose during embryogenesis and is present in a subset of tissues derived from some common developmental cell or tissue type.

has super-classes: clonal^c

multifactorial inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000929

Diseases inherited in this manner are termed 'complex diseases'.

has super-classes: inheritance pattern^c
has sub-classes: digenic inheritance^c, oligogenic inheritance^c, polygenic inheritance^c

Murinae^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_39107

has super-classes: Rodentia^c
has sub-classes: Mus musculus^c

Mus musculus^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_10090

has super-classes: Murinae^c

mus musculus gene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000057

is equivalent to: gene^c and (in taxon^op some Mus musculus^c)
has super-classes: gene^c; in taxon^op some Mus musculus^c
has sub-classes: mus musculus shh gene^c

mus musculus shh gene^c back to ToC or Class ToC

IRI: http://www.ncbi.nlm.nih.gov/gene/20423

Equivalent to: http://www.informatics.jax.org/marker/MGI:98297

has super-classes: mus musculus gene^c

mus musculus strain^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000118

has super-classes: strain or breed^c

mutant^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000480

has super-classes: variation attribute^c

mutation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000492

has super-classes: sequence_alteration^c; varies_with^op some wild-type allele^c

Negative strand^c back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#ReverseStrandPosition

has super-classes: Stranded position^c

non-heritable^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000140

has super-classes: heritabililty^c

novel^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000685

has super-classes: variation attribute^c

novel extrachromosomal replicon^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000681

Extrachromosomal replicons are replicated and passed on to descendents, and thus part of the heritable genome of a cell or organism. In cases where the presence of such a replicon is exogenous or aberrant (i.e. not included in the reference for that genome), the replicon is considered a 'sequence alteration'.

has super-classes: extrachromosomal replicon^c; novel replicon^c; not (is_proper_part_of^op some chromosome^c)

novel replicon^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000684

Novel replicons are considered as an 'insertion' in a genome, and as such, qualify as types of sequence_alterations and variant alleles. There is no pre-existing locus that it modifies, however, and thus it is not really an 'allele of' a named locus. But conceptually, we still consider these to represent genetic variants and classify them as variant alleles.

has super-classes: sequence_alteration^c; has_sequence_attribute^op some novel^c
has sub-classes: novel extrachromosomal replicon^c

nucleic acid^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33696

has super-classes: macromolecule^c
has sub-classes: genetic material^c

nullizygous^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000978

has super-classes: disomic zygosity^c

objective specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000005

has super-classes: directive information entity^c
has sub-classes: data transformation objective^c, material maintenance objective^c, material transformation objective^c, specimen collection objective^c
is in domain of: objective_achieved_by^op
is in range of: achieves_planned_objective^op

obo basic subset ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000018

has super-classes: ontology module subsetted by expressivity^c

obsolescence reason specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000225

is equivalent to: { failed exploratory term , placeholder removed , terms merged , term imported , term split }; { failed exploratory term , placeholder removed , terms merged , term imported , term split , out of scope }
has super-classes: data about an ontology part^c
has members: failed exploratory termⁿⁱ, out of scopeⁿⁱ, placeholder removedⁿⁱ, term importedⁿⁱ, term splitⁿⁱ, terms mergedⁿⁱ

obsolete allele cellular context^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000901

Cellular context of an allele is typically defined in the context of evaluating an individual organism, as alleles that are somatic in one organism can be germline in others.

obsolete assembly_component^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000143

obsolete autosomal recessive inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000150

obsolete biological sequence collection^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000725

obsolete biological sequence or collection^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000724

obsolete canonical allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000890

As a 'sequence feature or collection' (sensu SO), a 'canonical allele' is considered here as an extent of biological sequence encoded in nucleic acid molecules of a cell or organism (as opposed to an information artifact that is about such a sequence). Canonical alleles can include haplotypes that contain more than one discontinuous sequence alteration that exist in cis on the same chromosomal strand. In the ClinGen allele model, 'canonical alleles are contrasted with 'contextual alleles'. Contextual alleles are informational representation that describe a canonical allele using a particular reference sequence. A single canonical allele can be described by many contextual alleles that each use a different reference sequence in their representation (e.g. different chromosomal or transcript references)

obsolete chromosome complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000324

obsolete coding sequence alteration^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000848

obsolete color brightness^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000016

obsolete contextual allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000891

The notion of a 'contextual allele' derives from the ClinGen Allele model. Here, each genetic allele in a patient corresponds to a single 'canonical allele', which in turn may aggregate any number of 'contextual allele' representations that are may be defined against different reference sequences. Accordingly, many contextual alleles can describe a single canonical allele. For example, the contextual alleles “NC_000013.11:g.32319070T>A” and “NG_012772.3:g.8591T>A” both describe the same underlying canonical allele, a single nucleotide variation, in the BRCA2 gene.

obsolete copy number complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000956

1. Features described by 'copy number' are larger regions of sequence spanning one or more complete genes, or large chromosomal segment. Copies of these regions often become distributed across a genome at unknown locations. By contrast, short repeats, such as tri-nucelotide 'CAG' repeats in the Huntingtin gene, occur at defined locations (adjacent to the originating 'CAG' sequence), and can therefore be modeled as proper alleles. 2. A copy number complement, like any sequence feature complement, is a set of features in a particular genome that meet some criterion. The criterion in this case is that their sequence maps to that of a particular location in a reference sequence. So a copy number complement is the set of all features that share or align with a specified sequence defined on some reference. The sequence of member sequences need not exactly match that of the reference, as copies may accrue some alterations. What is important is that conceptually they represent exact or inexact copies of the reference sequence at a defining location. 3. In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). In GENO, a 'copy number variation' refers to a copy number complement' that has an abnormal number of members.

obsolete dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000142

obsolete engineered_plasmid^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000637

obsolete enhancer trapping technique^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000171

obsolete experimental insertion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000091

obsolete extrinsic sequence feature attribute^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000925

obsolete functional copy number complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000923

As for copy number complements, the defining 'sequence' here is specified in terms of a location on a reference sequence - typically the location where a gene or set of genes resides. But the criteria for membership in a functional copy number complement require only that the feature can perform the functions associated with the gene or genes at the defining location. A gene allele that varies by only one nucleotide from the wild-type gene may not qualify if that alteration eliminates the function of the allele. This represents an important distinction between 'copy number' and 'functional copy number'. The former is not concerned with the functionality of sequence copies - only that there is a duplication of sequence in the genome. Thus, the addition of a non-functional allele of a gene will increase its copy number, but not increase its 'functional copy number (aka its dosage).

obsolete gametic^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000883

obsolete gene trapping technique^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000172

obsolete genetic dosage^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000876

Genetic dosage reflects how many 'functional' copies of a sequence are present in a genome. In diploid organisms, the normal dosage is 2 for autosomal genes/regions. Dosage increases if there is a duplication of the gene/region. Dosage decreases if there is either a deletion of a gene/region, or an inactivating mutation that eliminates gene function. This sets it apart from the notion of 'copy number', which reflects how many actual copies of a sequence exist in a genome. Addition of a non-functional allele of a gene will increase its copy number, but not increase its dosage. Duplications of a sequence can occur at new locations in the genome, such that the resulting sequence represents a distinct sequence feature from the copy at its native locus. For example, duplication of a region containing the human APOE gene on a different chromosome creates a sequence feature that shares sequence from the original gene, but not location, and therefore represents a different sequence feature. The notions of dosage and copy number are therefore concerned with sequence-level entities (how many copies of a 'sequence' exist), as opposed to sequence feature-level entities. The notion of a single-locus complement would be used to describe how many of a particular features are present in a genome - and describe which alleles of this feature are found.

obsolete genetic insertion technique^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000164

obsolete genomic feature collection^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000022

Conceptually, members of this collection are meant to be about the sum total genetic material in a single cell or organism. But these members need not be associated with an actual material in a real cell or organism individual. For example, things like a 'reference genome' may not actually represent the material genome of any individual cell or organism in reality. Here, there may be no genomic material referents of the sequences in such a collection because the genome is tied to an idealized, hypothetical cell or organism instance. The key is that conceptually, they are still tied to the idea of being contained in a single genome. In the case of a genotype, the individual seqeunce members are not all about the genetic material of a singel cell or organism. Rather, it is the resolved sequence contained in the genotype that is meant to be about the total genomic sequence content of a genome - which we deem acceptable for classifying as a genetic locus collection.

obsolete genomic position^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000768

obsolete haplotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000915

1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene': a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene). 2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand. GENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. 3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles': a. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. b. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand. c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. The GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.

obsolete haplotype block^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000916

A haplotype block is a class of genomic sequence defined by a lack of evidence for historical recombination, such that sequence alterations within it tend to be co-inherited across successive generations. A haplotype is considered to be one of many possible versions of a 'haplotype block' - defined by the set of co-inherited alterations it contains. In this sense, the relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene'* - a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'. The boundaries of haplotype blocks are defined in efforts to identify haplotypes that exist in organisms or populations. A haplotype block may span any number of sequence alterations, and may cover small or large chromosomal regions - depending on the number of recombination events that have occurred between the alterations defining the haplotype. ----------------------- * One difference however is that gene instnaces are necessarily 'functional' - so non-functional alleles of a gene locus wont qualify as gene instances. no such requirement exists for haplotype block instnaces.

obsolete intrinsic sequence feature attribute^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000924

obsolete mutagen treatment technique^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000165

obsolete mutant allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000491

'Mutant' is typically contrasted with 'wild-type', where 'mutant' indicates a natural but very rare allele in a population (typically <1%), or an experimentally-induced variation that derives from a wild-type background locus for a given strain, which can be selected for in establishing a mutant line.

is in domain of: is_mutant_allele_of^op

obsolete null feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000680

obsolete promoter trapping technique^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000173

obsolete random genetic insertion technique^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000169

obsolete random transgene insertion technique^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000175

obsolete reagent sequence feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000415

obsolete reference gene allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000060

Being a 'reference gene' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common version/allele in a population, being an ancestral allele, or being indentified first as a prototypical example of a gene. In model organism datasets, 'reference' genes are typically the 'wild-type' allele for a given gene, representing a functional and unaltered version of the gene that is part of a defined genomic background, and against which natural or experimentally-induced versions are compared.

obsolete reference junction^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000042

In the case of a transgenic insertion that creates a hemizygous locus, the refernce locus that this insertion is variant_with is the junction on the homologous chromosome at the same position where the insertion occurred. This is the 'hemizygous reference' junction. The junction-insertion pair represents the allelic complement at that locus, which is considered to be hemizygous. Most genotype syntaxes represent this hemizygous state with a ' /0' notation.

obsolete reference single locus complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000029

obsolete sequence feature collection^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000019

1. Note that members of this class can be features with extents of zero (e.g. junctions). This is likely different than the SO:sequence feature class which has members that are regions.

obsolete sequence feature collection^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000870

obsolete sequence feature collection attribute^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000125

obsolete sequence information entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000778

obsolete targeted gene mutation technique^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000166

obsolete targeted genetic insertion technique^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000170

obsolete targeted knock-in technique^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000174

obsolete unspecified^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000772

obsolete unspecified feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000037

An unspecified feature is known to exist as the partner of a characterized allele when the zygosity at that locus is not known. Its specific sequence/identity, however, is unknown (ie whether it is a reference or variant allele).

obsolete variant copy number complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000955

In a 'normal' diploid genome, the copy number complement for any feature (on a non-Y chromosome) contains two members. A copy number variation occurs when a complement contains more or less than two members - as the result of deletion or duplication event(s). Note that the 'copy number variation' class in GENO is related to but ontologically distinct form the SO 'copy_number_variation' class. The GENO class refers to a *set* of all copies of a sequence in a genome, where the number of members in the set is in conflict with the genome's normal ploidy (e.g. not two for a diploid genome). The SO class, which is defined as a sequence feature level concept and therefore represents a single continuous extent of sequence, refers to a single copy of duplicated (or deleted) sequence that comprises the set defined by the GENO CNV class.

occurrent^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000003

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: entity^c; part of^op only occurrent^c
has sub-classes: process^c
is in domain of: causal relation between processes^op, has participant^op, preceded by^op, precedes^op, starts during^op, temporal relation^op
is in range of: causal relation between processes^op, participates in^op, preceded by^op, precedes^op, starts during^op, temporal relation^op
is disjoint with: continuant^c

oligogenic inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000931

It is recommended this term be used for traits governed by three gene loci, although it is noted that usage of this term in the literature is not uniform.

has super-classes: multifactorial inheritance^c

ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000000

has super-classes: data about an ontology part^c
has sub-classes: base ontology module^c, bridge ontology module^c, editors ontology module^c, generated ontology module^c, main release ontology module^c, reasoned ontology module^c, subset ontology module^c

ontology module subsetted by expressivity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000017

has super-classes: subset ontology module^c
has sub-classes: obo basic subset ontology module^c, ontology module subsetted by OWL profile^c

ontology module subsetted by OWL profile^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000019

has super-classes: ontology module subsetted by expressivity^c
has sub-classes: EL++ ontology module^c

Opisthokonta^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_33154

has super-classes: Eukaryota^c
has sub-classes: Metazoa^c

organellar plasmy^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000918

Cells with a population of organelles from a single origin that all share the same organellar genome will contain only one allele of each organellar gene, while cells with populations of organelles of different origins may contain more than one allele of a given organellar gene.

has super-classes: allelic state^c
has sub-classes: heteroplasmic^c, homoplasmic^c

organism^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100026

is equivalent to: Viruses^c or Bacteria^c or Archaea^c or Eukaryota^c
has super-classes: organismal entity^c
has sub-classes: Archaea^c, Bacteria^c, Eukaryota^c, Oryzias latipes^c, Viruses^c
is in range of: in taxon^op

organismal entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000904

is equivalent to: organism^c or (derives from^op some organism^c) or (has member^op some organism^c)
has super-classes: material entity^c
has sub-classes: anatomical entity^c, cell line^c, collection of organisms^c, organism^c

organismal quality^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001995

has super-classes: physical object quality^c
has sub-classes: biological sex^c

organization^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000245

has super-classes: material entity^c
has sub-classes: regulatory agency^c
has members: Thermo Fisher Scientificⁿⁱ

Oryzias latipes^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_8090

has super-classes: organism^c

oryzias latipes strain^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000887

has super-classes: strain or breed^c; has member^op some Oryzias latipes^c; has member^op only Oryzias latipes^c

P-element construct^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000850

has super-classes: engineered genetic construct^c

partitioning data transformation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200171

is equivalent to: achieves_planned_objective^op some partitioning objective^c
has super-classes: data transformation^c; achieves_planned_objective^op some partitioning objective^c
has sub-classes: k-means clustering^c, k-nearest neighbors^c, statistical model validation^c

partitioning objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200172

has super-classes: data transformation objective^c
has sub-classes: cross validation objective^c

paternal allele origin^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000879

has super-classes: germline allele origin^c

paternal_uniparental_disomy^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001746

has super-classes: UPD^c

pathologic distant metastases stage for colon according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002290

has super-classes: categorical value specification^c
has members: cM0 (colon)ⁿⁱ, cM1 (colon)ⁿⁱ, cM1a (colon)ⁿⁱ, cM1b (colon)ⁿⁱ, pM1 (colon)ⁿⁱ, pM1a (colon)ⁿⁱ, pM1b (colon)ⁿⁱ

pathologic distant metastases stage for kidney according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002306

has super-classes: categorical value specification^c
has members: cM0 (kidney)ⁿⁱ, cM1 (kidney)ⁿⁱ, pM1 (kidney)ⁿⁱ

pathologic distant metastases stage for lung according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002298

has super-classes: categorical value specification^c
has members: cM0 (lung)ⁿⁱ, cM1 (lung)ⁿⁱ, cM1a (lung)ⁿⁱ, cM1b (lung)ⁿⁱ, pM1 (lung)ⁿⁱ, pM1a (lung)ⁿⁱ, pM1b (lung)ⁿⁱ

pathologic distant metastases stage for ovary according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002310

has super-classes: categorical value specification^c
has members: cM0 (ovary)ⁿⁱ, cM1 (ovary)ⁿⁱ, pM1 (ovary)ⁿⁱ

pathologic lymph node stage for colon and rectum according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002270

has super-classes: categorical value specification^c
has members: pN0 (colon)ⁿⁱ, pN1 (colon)ⁿⁱ, pN1a (colon)ⁿⁱ, pN1b (colon)ⁿⁱ, pN1c (colon)ⁿⁱ, pN2 (colon)ⁿⁱ, pN2a (colon)ⁿⁱ, pN2b (colon)ⁿⁱ

pathologic lymph node stage for kidney according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002284

has super-classes: categorical value specification^c
has members: pN0 (kidney)ⁿⁱ, pN1 (kidney)ⁿⁱ

pathologic lymph node stage for lung according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002279

has super-classes: categorical value specification^c
has members: pN0 (lung)ⁿⁱ, pN1 (lung)ⁿⁱ, pN2 (lung)ⁿⁱ, pN3 (lung)ⁿⁱ

pathologic lymph node stage for ovary according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002287

has super-classes: categorical value specification^c
has members: pN0 (ovary)ⁿⁱ, pN1 (ovary)ⁿⁱ

pathologic primary tumor stage for colon and rectum according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002224

has super-classes: categorical value specification^c
has members: pT0 (colon)ⁿⁱ, pT1 (colon)ⁿⁱ, pT2 (colon)ⁿⁱ, pT3 (colon)ⁿⁱ, pT4a (colon)ⁿⁱ, pT4b (colon)ⁿⁱ, pTis (colon)ⁿⁱ

pathologic primary tumor stage for kidney according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002243

has super-classes: categorical value specification^c
has members: pT0 (kidney)ⁿⁱ, pT1 (kidney)ⁿⁱ, pT1a (kidney)ⁿⁱ, pT1b (kidney)ⁿⁱ, pT2 (kidney)ⁿⁱ, pT2a (kidney)ⁿⁱ, pT2b (kidney)ⁿⁱ, pT3 (kidney)ⁿⁱ, pT3a (kidney)ⁿⁱ, pT3b (kidney)ⁿⁱ, pT3c (kidney)ⁿⁱ, pT4 (kidney)ⁿⁱ

pathologic primary tumor stage for lung according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002232

has super-classes: categorical value specification^c
has members: pT0 (lung)ⁿⁱ, pT1 (lung)ⁿⁱ, pT1a (lung)ⁿⁱ, pT1b (lung)ⁿⁱ, pT2 (lung)ⁿⁱ, pT2a (lung)ⁿⁱ, pT2b (lung)ⁿⁱ, pT3 (lung)ⁿⁱ, pT4 (lung)ⁿⁱ, pTis (lung)ⁿⁱ

pathologic primary tumor stage for ovary according to AJCC 7th edition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002256

has super-classes: categorical value specification^c
has members: pT0 (ovary)ⁿⁱ, pT1 (ovary)ⁿⁱ, pT1a (ovary)ⁿⁱ, pT1b (ovary)ⁿⁱ, pT1c (ovary)ⁿⁱ, pT2 (ovary)ⁿⁱ, pT2a (ovary)ⁿⁱ, pT2b (ovary)ⁿⁱ, pT2c (ovary)ⁿⁱ, pT3 (ovary)ⁿⁱ, pT3a (ovary)ⁿⁱ, pT3b (ovary)ⁿⁱ, pT3c (ovary)ⁿⁱ

peak matching^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000726

has super-classes: data transformation^c
has members: GenePattern peak matchingⁿⁱ

performance status value specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002356

has super-classes: categorical value specification^c
has sub-classes: Eastern Cooperative Oncology Group score value specification^c, Karnofsky score vaue specification^c

phenotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UPHENO_0001001

1. From OGMS: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species (from OGMS, and used in OBI, but treatment as a quality is at odds with previous OBI discussions and their treatemnt of 'comparative phenotype assessment, where a phenotype is described as a quality or disposition) 2. From OBI calls: quality or disposition inheres in organism or part of an organism towards some growth environment

has super-classes: quality^c
has sub-classes: human phenotypic abnormality^c, mammalian phenotype^c, worm phenotype^c, zebrafish phenotype^c
is in domain of: phenotype of^op
is in range of: has phenotype^op

phenotypic inheritance process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000770

has super-classes: biological process^c

phenotypic sex^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001894

has super-classes: biological sex^c
has sub-classes: female^c, male^c

physical object quality^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0001241

has super-classes: quality^c
has sub-classes: organismal quality^c

plan specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000104

2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

has super-classes: directive information entity^c; has part^op some objective specification^c; has part^op some action specification^c
has sub-classes: algorithm^c, software^c

planned process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000011

is equivalent to: realizes^op some concretizes^op some plan specification^c
has super-classes: process^c; realizes^op some concretizes^op some plan specification^c
has sub-classes: data transformation^c, data visualization^c, dataset creating^c, material maintenance^c, material processing^c, software development^c, specimen collection process^c
is in domain of: achieves_planned_objective^op, has_specified_input^op, has_specified_output^op
is in range of: is_specified_input_of^op, is_specified_output_of^op, objective_achieved_by^op
is disjoint with: biological process^c

point_mutation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000008

has super-classes: SNV^c

polygenic inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000932

Typically used for traits/conditions governed by more than three gene loci.

has super-classes: multifactorial inheritance^c

polymorphic^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000477

has super-classes: variation attribute^c

polymorphic allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000497

Polymorphic alleles are contrasted with mutant alleles (extremely rare variants that exist in <1% of a population), and 'wild-type alleles' (extremenly common variants present in >99% of a population). Polymorphic alleles exist in equilibrium in a given population somewhere between these two extremes (i.e. >1% and <99%).

has super-classes: allele^c
has sub-classes: ancestral polymorphic allele^c, major polymorphic allele^c, minor polymorphic allele^c
is in domain of: is_polymorphic_allele_of^op

population^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000181

has super-classes: taxonomic group^c
has sub-classes: human population^c

portioning objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000678

has super-classes: material separation objective^c
is disjoint with: separation into different composition objective^c

Position^c back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#Position

has super-classes: genomic feature location^c
has sub-classes: Exact position^c, Stranded position^c

Positive strand^c back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#ForwardStrandPosition

has super-classes: Stranded position^c

primary cultured cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000001

has super-classes: cultured cell^c; not (is_specified_output_of^op some cell culture splitting^c); not (derives from^op some cultured cell^c and (is_specified_output_of^op some cell culture splitting^c))

principal components analysis dimensionality reduction^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200051

has super-classes: dimensionality reduction^c
has members: GenePattern PCAⁿⁱ

process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000015

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: occurrent^c
has sub-classes: biological process^c, biological process^c, gene product or complex activity^c, planned process^c
is in domain of: has component process^op, has input^op, realizes^op, regulated by^op, regulates^op, regulates characteristic^op, transitively provides input for^op
is in range of: capable of^op, causal relation between material entity and a process^op, has component process^op, realized in^op, regulated by^op, regulates^op, transitively provides input for^op

processed material^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000047

is equivalent to: material entity^c and (is_specified_output_of^op some material processing^c)
has super-classes: material entity^c; is_specified_output_of^op some material processing^c
has sub-classes: Epstein Barr virus transformed B cell^c, cell freezing medium^c, culture medium^c, cultured cell population^c, experimentally modified cell in vitro^c, processed specimen^c, reagent^c

processed specimen^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000953

A tissue sample that has been sliced and stained for a histology study.

is equivalent to: processed material^c and specimen^c
has super-classes: processed material^c; specimen^c

promoter^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000167

has super-classes: regulatory_region^c

promoter_trap_construct^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001478

has super-classes: engineered genetic construct^c

purine_to_pyrimidine_transversion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000023

has super-classes: transversion^c
has sub-classes: A_to_C_transversion^c, A_to_T_transversion^c, G_to_C_transversion^c, G_to_T_transversion^c

purine_transition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000014

has super-classes: transition^c
has sub-classes: A_to_G_transition^c, G_to_A_transition^c

pyrimidine_to_purine_transversion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000018

has super-classes: transversion^c
has sub-classes: C_to_A_transversion^c, C_to_G_transversion^c, T_to_A_transversion^c, T_to_G_transversion^c

pyrimidine_transition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000010

has super-classes: transition^c
has sub-classes: C_to_T_transition^c, T_to_C_transition^c

QTL^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000771

has super-classes: genomic feature^c

qualified genomic feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000714

has super-classes: genomic entity^c; qualified sequence feature^c; has_qualifier^op some thing^c; has_sequence_feature^op some genomic feature^c
has sub-classes: expression-qualified sequence feature^c, location-qualified sequence feature^c, modification-qualified sequence feature^c

qualified genomic feature set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000715

A 'complement' refers to an exhaustive collection of all objects that make up some well-defined set. This notion is useful for defining biologically-relevant sets of sequence features. For example, a haplotype is defined as the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele. A complements may contain 0, 1, or more than one members. For example, the complement of alleles at a defined locus across homologous chromosomes in an individual's genome will consist of two members for autosomal locations, and one member for non-homologous locations on the X and Y chromosome.

has super-classes: genomic entity^c; qualified sequence feature set^c; has_sequence_feature^op some genomic feature set^c; has member^op some qualified genomic feature^c
has sub-classes: reagent-targeted gene complement^c, transiently-expressed transgene complement^c

qualified sequence feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000919

GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical state or context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).

has super-classes: qualified sequence feature or collection^c
has sub-classes: qualified genomic feature^c

qualified sequence feature or collection^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000713

has super-classes: generically dependent continuant^c
has sub-classes: qualified sequence feature^c, qualified sequence feature set^c

qualified sequence feature set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000920

has super-classes: qualified sequence feature or collection^c; has part^op some qualified sequence feature^c; has_sequence_feature^op some sequence feature set^c
has sub-classes: qualified genomic feature set^c

quality^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000019

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: specifically dependent continuant^c; part of^op only quality^c
has sub-classes: information carrier^c, physical object quality^c
is in range of: has quality^op
is disjoint with: realizable entity^c

quality^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/PATO_0000001

has super-classes: specifically dependent continuant^c
has sub-classes: phenotype^c
is in range of: regulates characteristic^op

questionnaire^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001000

has super-classes: document^c
has members: Edingburgh handedness inventoryⁿⁱ

rate unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000280

has super-classes: measurement unit label^c
has members: count per molarⁿⁱ, count per molar secondⁿⁱ, count per nanomolarⁿⁱ, count per nanomolar secondⁿⁱ

reagent^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001879

(copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).

is equivalent to: material entity^c and (has role^op some reagent role^c)
has super-classes: processed material^c; has role^op some reagent role^c

reagent role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000086

(copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).

has super-classes: role^c

reagent targeted gene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000504

The identity of a given instance of a reagent-targeted gene is dependent on the experimental context of its knock-down - specifically what reagent was used and at what level. For example, the wild-type shha zebrafish gene targeted in epxeriment 1 by morpholino1 annd in experiment 2 by morpholino 2 represent two distinct instances of a 'reagent-targeted gene', despite sharing the same sequence and position.

has super-classes: expression-variant gene^c; has_proper_part^op some reagent-targeted gene subregion^c; is_gene_target_of^op some gene knockdown reagent^c

reagent-targeted gene complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000527

has super-classes: qualified genomic feature set^c; has member^op some reagent targeted gene^c
has sub-classes: knockdown reagent targeted gene complement^c

reagent-targeted gene subregion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000534

has super-classes: expression-qualified sequence feature^c

realizable entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000017

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: specifically dependent continuant^c; part of^op only realizable entity^c
has sub-classes: disposition^c, role^c
is in domain of: realized in^op
is in range of: realizes^op
is disjoint with: quality^c

reasoned ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000013

has super-classes: ontology module^c

reference^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000152

Being 'reference' is a role or status assigned in the context of a data set or analysis framework. A given allele can be reference on one context and variant in another.

has super-classes: variation attribute^c

reference allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000036

Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population. In model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared.

is equivalent to: allele^c and (sequence role^op some reference^c)
has super-classes: allele^c; sequence role^op some reference^c
is in domain of: is_reference_allele_of^op

reference genome^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000914

has super-classes: genome^c; has_sequence^op some reference genome sequence^c
has sub-classes: background genome^c

reference genome sequence^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001505

has super-classes: reference sequence^c

reference sequence^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000017

A reference sequence is one that serves as a standard against which 'variant' versions of the feature are compared, or against which located sequence features within the reference region are aligned in order to assign position information. Being 'reference' does not imply anything about the frequency or function of features bearing the sequence. Only that some agent has used it to serve a reference role in defining a variant or locating a sequence.

is equivalent to: biological sequence^c and (sequence role^op some reference^c)
has super-classes: biological sequence^c; sequence role^op some reference^c
has sub-classes: reference genome sequence^c

Region^c back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#Region

has super-classes: sequence_feature^c; (begin^op exactly 1 Position^c) and (end^op exactly 1 Position^c); begin^op some Position^c; end^op some Position^c

region^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000001

has super-classes: generically dependent continuant^c
has sub-classes: experimental_feature^c, regulatory_region^c

regulator role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000014

has super-classes: regulatory role^c

regulatory agency^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000450

is equivalent to: organization^c and (has role^op some regulator role^c)
has super-classes: organization^c; has role^op some regulator role^c
has members: U.S. Food and Drug Administrationⁿⁱ

regulatory role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000017

has super-classes: role^c
has sub-classes: regulator role^c

regulatory transgene region^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000637

has super-classes: transgene part^c; regulatory_region^c

regulatory_region^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0005836

has super-classes: gene part^c; region^c
has sub-classes: enhancer^c, promoter^c, regulatory transgene region^c

repeat region alteration^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000874

has super-classes: sequence_alteration^c
has sub-classes: microsatellite alteration^c

reporter^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000910

has super-classes: sequence feature attribute^c

reporter region^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000640

has super-classes: expressed transgene region^c

reporter transgene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000667

is equivalent to: transgene^c and (has_sequence_attribute^op some reporter^c)
has super-classes: engineered_region^c; transgene^c; has part^op some reporter region^c; has_sequence_attribute^op some reporter^c

RNA residue^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000781

has super-classes: biological sequence unit^c

RNA sequence^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000721

is equivalent to: biological sequence^c and (has_sequence_unit^op some RNA residue^c) and (has_sequence_unit^op only RNA residue^c)
has super-classes: biological sequence^c; has_sequence_unit^op some RNA residue^c

RNAi_reagent^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000337

has super-classes: gene knockdown reagent^c

Rodentia^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_9989

has super-classes: Euarchontoglires^c
has sub-classes: Murinae^c

role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000023

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: realizable entity^c
has sub-classes: manufacturer role^c, reagent role^c, regulatory role^c, service provider role^c, specimen role^c
is in range of: has role^op
is disjoint with: disposition^c

scatter plot^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000184

has super-classes: graph^c

secondary cultured cell^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001866

A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.

has super-classes: cultured cell^c; (is_specified_output_of^op some cell culture splitting^c) or (derives from^op some is_specified_output_of^op some cell culture splitting^c); derives from^op some primary cultured cell^c
has sub-classes: cell line cell^c

secondary cultured cell population^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001905

The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally.

has super-classes: cultured cell population^c; is_specified_output_of^op some cell culture splitting^c; has grain^op some secondary cultured cell^c; has grain^op only secondary cultured cell^c
has sub-classes: cell line^c

selectable marker^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000911

has super-classes: sequence feature attribute^c

selectable marker region^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000912

has super-classes: expressed transgene region^c

selectable marker transgene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000642

is equivalent to: transgene^c and (has_sequence_attribute^op some selectable marker^c)
has super-classes: engineered_region^c; transgene^c; has_sequence_attribute^op some selectable marker^c

separation into different composition objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000681

has super-classes: material separation objective^c
is disjoint with: portioning objective^c

sequence atomic unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/RO_0002533

has super-classes: sequentially ordered entity^c

sequence feature attribute^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000788

Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity.

has super-classes: specifically dependent continuant^c
has sub-classes: allele origin^c, allelic cellular distribution^c, allelic phase^c, allelic state^c, chromosomal band intensity^c, engineered^c, reporter^c, selectable marker^c, variation attribute^c

sequence feature location^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000815

1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). 2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there.

has super-classes: generically dependent continuant^c
has sub-classes: genomic feature location^c
is in domain of: has_interval^op
is in range of: has_defining_location^op, has_location^op
is disjoint with: biological sequence^c, sequence_feature^c

sequence feature or set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000701

GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.

is equivalent to: sequence feature or set^c or sequence_feature^c
has super-classes: generically dependent continuant^c
has sub-classes: sequence feature set^c, sequence_feature^c

sequence feature set^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000659

'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. [1] https://www.snpedia.com/index.php/APOE-%CE%B54 [2] https://www.snpedia.com/index.php/APOE-%CE%B52 [3] https://www.snpedia.com/index.php/Gs270

has super-classes: sequence feature or set^c; has member^op some sequence_feature^c; has_member_count^dp some int
has sub-classes: genomic feature set^c

sequence interval^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000965

has super-classes: information content entity^c

sequence_alteration^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001059

1. A 'sequence alteration' is an allele whose sequence deviates in its entirety from that of other features found at the same genomic location (i.e. it deviates along its entire extent). In this sense, 'sequence alterations' represent the minimal extent an allele can take - i.e. that which is variable with some other feature along its entire sequence). An example is a SNP or insertion. Alleles whose extent goes beyond the specific sequence that is known to be variable are not sequence alterations. These are alleles that represent alternate versions of some larger, named feature. The classic example here is a 'gene allele', which spans the extent of an entire gene, and contains one or more sequence alterations (regions known to vary) as part. 2. Sequence alterations are not necessarily 'variant' in the sense defined in GENO (i.e. being 'variant with' some reference sequence). In any comparison of alleles at a particular location, the choice of a 'reference' is context-dependent - as comparisons in other contexts might consider a different allele to be the reference. So while sequence alterations are usually considered 'variant' in the context in which they are considered, this variant status may not hold at all times. For this reason, the 'sequence alteration' class is not made an rdfs:subClassOf 'variant allele'. For a particular instance of a sequence alteration, howver, we may in some cases be able to rdf:type it as a 'varaint allele' and a 'sequence alteration', in situations where we can be confident that the feature will *never* be considered a reference. For example, experimentally generated mutations in model organism genes that are created expressly to vary from an established reference. 3. Note that we consider novel features gained in a genome to be sequence alterations, including aneusomic chromosomes gained through a non-disjunction event during replication, or extrachromosomal replicons that become part of the heritable genome of a cell or organism.

is equivalent to: allele^c and (completely_varies_with^op some genomic feature^c)
has super-classes: allele^c; completely_varies_with^op some genomic feature^c
has sub-classes: UPD^c, aneusomic chromosomal part^c, aneusomic chromosome^c, copy_number_variation^c, deletion^c, indel^c, insertion^c, inversion^c, mutation^c, novel replicon^c, repeat region alteration^c, structural_alteration^c, substitution^c, translocation^c

sequence_assembly^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000353

has super-classes: assembly^c
has sub-classes: contig^c

sequence_feature^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000110

A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome.

has super-classes: sequence feature or set^c; has_sequence^op some biological sequence^c; has_location^op some sequence feature location^c
has sub-classes: Region^c, engineered_region^c, gene product^c, genomic feature^c, junction^c, terminus^c
is in domain of: has_location^op, has_sequence_string^dp
is in range of: has_defining_feature^op, has_sequence_feature^op
is disjoint with: biological sequence^c, sequence feature location^c

sequence_length_variation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000248

has super-classes: substitution^c
has sub-classes: simple_sequence_length_variation^c

sequentially ordered entity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/RO_0002532

has super-classes: has subsequence^op some sequence atomic unit^c
has sub-classes: gene part^c, sequence atomic unit^c
is in domain of: sequentially related to^op
is in range of: sequentially related to^op

service provider role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000947

has super-classes: role^c; characteristic of^op some Homo sapiens^c or organization^c; realized in^op only planned process^c
has sub-classes: material supplier role^c

sex-limited autosomal dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000952

has super-classes: autosomal dominant inheritance^c

sex-limited autosomal recessive inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000953

has super-classes: autosomal recessive inheritance^c

short chromosome arm^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000628

has super-classes: chromosome arm^c

simple heterozygous^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000458

a heterozygous quality inhering in a single locus complement comprised of one variant allele and one wild-type/reference allele (e.g.fgf8a<ti282a/+>)

has super-classes: heterozygous^c

simple_sequence_length_variation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000207

has super-classes: sequence_length_variation^c

single layer subset ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000009

has super-classes: subset ontology module^c

single locus complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000516

A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. The fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.

has super-classes: genomic feature set^c
has sub-classes: variant single locus complement^c
is in domain of: has_zygosity^op

SNP^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000694

has super-classes: SNV^c

SNV^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001483

has super-classes: substitution^c
has sub-classes: SNP^c, point_mutation^c, transition^c, transversion^c

software^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000010

has super-classes: plan specification^c
has sub-classes: GenePattern software^c

software development^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/APOLLO_SV_00000008

is equivalent to: planned process^c and (has_specified_output^op some software^c or source code module^c)
has super-classes: planned process^c; has_specified_output^op some software^c or source code module^c

somatic allele origin^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000882

We distinguish germline, somatic, and de novo allele origin based on a combination two key criteria - whether the allele *inherited* from a parent, and whether it is *heritble' by offspring. Somatic variants are neither inherited or heritable - having originated via a spontaneous mutation in a non-germ cell. By contrast, germline variants are both inherited (passed down from a parent) and heritable (passable down to offspring). De novo mutations are not inherited but are typically heritable, as they originated through a spontaneous mutation that made them present in germ cells. These acquired mutations are called 'somatic' because they typically affect somatic (non-germ) cells. But when spontaneous do mutations occur in the germ cells of an organism, these can be passed on to offspring in whom they will be considered de novo mutations.

has super-classes: allele origin^c

source code module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000096

has super-classes: directive information entity^c

species subset ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000012

has super-classes: subset ontology module^c

specifically dependent continuant^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000020

is defined by: http://purl.obolibrary.org/obo/bfo.owl

has super-classes: continuant^c; part of^op only specifically dependent continuant^c
has sub-classes: quality^c, quality^c, realizable entity^c, sequence feature attribute^c
is in domain of: concretizes^op
is in range of: bearer of^op, is concretized as^op
is disjoint with: independent continuant^c, generically dependent continuant^c, independent continuant^c, generically dependent continuant^c

specimen^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100051

is equivalent to: material entity^c and (has role^op some specimen role^c)
has super-classes: material entity^c; has role^op some specimen role^c
has sub-classes: processed specimen^c

specimen collection objective^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000684

has super-classes: objective specification^c

specimen collection process^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000659

is equivalent to: planned process^c and (achieves_planned_objective^op some specimen collection objective^c)
has super-classes: planned process^c; has_specified_input^op some material entity^c; has_specified_output^op some specimen^c; achieves_planned_objective^op some specimen collection objective^c

specimen role^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000112

has super-classes: role^c; characteristic of^op some material entity^c and (is_specified_output_of^op some specimen collection process^c)

statistical model validation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000792

is equivalent to: achieves_planned_objective^op some cross validation objective^c
has super-classes: partitioning data transformation^c; achieves_planned_objective^op some cross validation objective^c
has sub-classes: leave one out cross validation method^c

strain or breed^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000112

Two mice colonies with the same genotype information, but maintained in different labs, are different strains (many examples of this in MGI/IMSR)

has super-classes: taxonomic group^c; in taxon^op some organism^c
has sub-classes: danio rerio strain^c, mus musculus strain^c, oryzias latipes strain^c

Stranded position^c back to ToC or Class ToC

IRI: http://biohackathon.org/resource/faldo#StrandedPosition

Part of the coordinate system denoting on which strand the feature can be found. If you do not yet know which stand the feature is on, you should tag the position with just this class. If you know more you should use one of the subclasses. This means a region described with a '.' in GFF3. A GFF3 unstranded position does not have this type in FALDO -- those are just a 'position'.

has super-classes: Position^c
has sub-classes: Both strands^c, Negative strand^c, Positive strand^c

structural_alteration^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001785

has super-classes: sequence_alteration^c
has sub-classes: complex_structural_alteration^c

subset ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000006

has super-classes: ontology module^c
has sub-classes: analysis subset ontology module^c, curation subset ontology module^c, exclusion subset ontology module^c, import ontology module^c, ontology module subsetted by expressivity^c, single layer subset ontology module^c, species subset ontology module^c

substance unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000006

has super-classes: measurement unit label^c
has members: micromoleⁿⁱ, nanomoleⁿⁱ, picomoleⁿⁱ

substitution^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000002

has super-classes: sequence_alteration^c
has sub-classes: MNP^c, SNV^c, complex_substitution^c, sequence_length_variation^c

support vector machine^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000700

has super-classes: class prediction data transformation^c; achieves_planned_objective^op some class prediction objective^c
has members: GenePattern SVMⁿⁱ

system^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/RO_0002577

has super-classes: material entity^c
has sub-classes: environmental system^c

T_to_A_transversion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000021

has super-classes: pyrimidine_to_purine_transversion^c

T_to_C_transition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000013

has super-classes: pyrimidine_transition^c

T_to_G_transversion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000022

has super-classes: pyrimidine_to_purine_transversion^c

tandem_duplication^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000173

has super-classes: duplication^c
has sub-classes: direct_tandem_duplication^c, inverted_tandem_duplication^c

taxonomic bridge ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000016

has super-classes: bridge ontology module^c

taxonomic group^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000113

has super-classes: collection of organisms^c
has sub-classes: population^c, strain or breed^c

temperature unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000005

has super-classes: measurement unit label^c
has members: degree Celsiusⁿⁱ, degree Fahrenheitⁿⁱ

template generated ontology module^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_8000015

has super-classes: generated ontology module^c

terminus^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000688

has super-classes: sequence_feature^c

Tetrapoda^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_32523

has super-classes: Euteleostomi^c
has sub-classes: Amniota^c

time unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000003

has super-classes: measurement unit label^c
has members: dayⁿⁱ, hourⁿⁱ, minuteⁿⁱ, monthⁿⁱ, secondⁿⁱ, weekⁿⁱ, yearⁿⁱ

transgene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000902

On the relationship between 'transgenic insertions', 'transgenes', and 'alleles' Transgenic insertions are sequence alterations comprised of foreign/exogenous sequence. This sequence can be from the same or different species as the host cell or genome - it is exogenous in virtue of it being additional sequence inserted into the original host genome. A given transgenic insertion may create one or more transgenes when introduced into a host genome. The extent of a transgene is spans all features needed to drive its expression in the host genome. In most cases a transgenic insertion completely contains one or more transgenes that are fully competent to drive expression in the host genome. But in some cases, a transgenic insertion may carry only part of the final transgene it creates - which requires additional endogenous sequences in the vicinity of its insertion site to complete a functional gene (e.g. this is the case for enhancer traps or gene traps) to complete. In addition to the transgenes they create upon genomic integration, transgenic insertions can create variant alleles by disrupting a known endogenous gene/locus. Variant alleles are versions of a particular genomic features (typically genes), that are altered in their sequence relative to some reference. An insertion that disrupts an endogenous gene would be considered a 'sequence alteration' (sensu SO) which creates a 'variant gene allele'. From the perspective of this disrupted gene, the origin or transgenic nature of this insertion is irrelevant - what matters here is that the gene's sequence has been altered to create an allele. For the purposes of modeling, any transgene(s) created when an endogenous gene is interrupted by an insertion is considered/modeled separately from the allele of the endogenous gene that is created by the insertion. The transgenic insertion, which is simply a sequence alteration in the host genome, is then linked to any transgenes that it contributes to or overlaps with or contains. The model of the Flybase example HERE illustrates this approach.

has super-classes: gene^c
has sub-classes: extra-chromosomal transgene^c, integrated transgene^c, reporter transgene^c, selectable marker transgene^c

transgene part^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000460

is equivalent to: gene part^c and (is subsequence of^op some transgene^c)
has super-classes: gene part^c; is subsequence of^op some transgene^c
has sub-classes: expressed transgene region^c, regulatory transgene region^c

transgenic_insertion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001218

has super-classes: insertion^c; has part^op some integrated transgene^c

transiently-expressed transgene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000506

has super-classes: expression-variant gene^c

transiently-expressed transgene complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000528

has super-classes: qualified genomic feature set^c; has_variant_part^op some transiently-expressed transgene^c

transition^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000009

has super-classes: SNV^c
has sub-classes: purine_transition^c, pyrimidine_transition^c

translocation^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0000199

has super-classes: sequence_alteration^c

transversion^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_1000017

has super-classes: SNV^c
has sub-classes: purine_to_pyrimidine_transversion^c, pyrimidine_to_purine_transversion^c

trisomic heterozygous^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000394

has super-classes: aneusomic zygosity^c

trisomic homozygous^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000393

has super-classes: aneusomic zygosity^c

undetermined inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000889

has super-classes: inheritance pattern^c

uniparental allele origin^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000975

From Wikidedia: Uniparental inheritance is a non-mendelian form of inheritance that consists of the transmission of genotypes from one parental type to all progeny. That is, all the genes in offspring will originate from only the mother or only the father. This phenomenon is most commonly observed in eukaryotic organelles such as mitochondria and chloroplasts. https://en.wikipedia.org/wiki/Uniparental_inheritance

has super-classes: inherited allele origin^c

unknown allele origin^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000881

has super-classes: allele origin^c

unspecified genomic background^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000649

has super-classes: genomic background^c

unspecified life cycle stage^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000160

has super-classes: life cycle stage^c

unspecified zygosity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000137

has super-classes: zygosity^c

UPD^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/SO_0001744

has super-classes: sequence_alteration^c
has sub-classes: maternal_uniparental_disomy^c, paternal_uniparental_disomy^c

value specification^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001933

has super-classes: information content entity^c
has sub-classes: categorical value specification^c

variant^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000476

has super-classes: variation attribute^c

variant allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000002

Note that what is considered the 'reference' vs. 'variant' sequence at a given locus may be context-dependent - so being 'variant' is more a role played in a particular situation. A 'variant allele' contains a 'sequence alteration', or is itself a 'sequence alteration', that makes it vary_with some other allele to which it is being compared. But in any comparison of alternative sequences at a particular genomic location, the choice of a 'reference' vs the 'variant' is context-dependent - as comparisons in other contexts might consider a different feature to be the reference. So being 'variant' is more a role played in a particular situation - as an allele that is variant in one context/analysis may be considered reference in another. A variant allele can be variant along its entire extent, in which case it is considered a 'sequence alteration', or it can span a broader extent of sequence contains sequence alteration(s) as part. And example of the former is a SNP, and an example of the latter is a variant gene allele that contains one or more point mutations in its sequence.

is equivalent to: allele^c and (varies_with^op some reference allele^c)
has super-classes: allele^c; sequence_alteration^c or (has subsequence^op some sequence_alteration^c); varies_with^op some reference allele^c
has sub-classes: variant gene allele^c
is in domain of: is_variant_allele_of^op

variant copy number complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000962

'Abnormal' is typically more or less than two members for an autosomal sequence in a diploid genome, and more or less than one member for a sequence in a non-homologous region of a sex-chromosome.

has super-classes: copy number complement^c

variant gene allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000515

A gene allele is 'variant' in virtue of its containing a sequence alteration that varies from some reference gene standard. But note that a gene allele that is variant in one context/dataset can be considered a reference in another context/dataset.

is equivalent to: gene allele^c and (varies_with^op some reference allele^c)
has super-classes: variant allele^c; gene allele^c; has_variant_part^op some sequence_alteration^c; is_variant_allele_of^op some gene^c

variant genome^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000033

is equivalent to: genome^c and (varies_with^op some reference genome^c)
has super-classes: genome^c; has_variant_part^op some sequence_alteration^c; varies_with^op some reference genome^c

variant genomic genotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000777

is equivalent to: genomic genotype^c and (denotes^op some variant genome^c)
has super-classes: genomic genotype^c; denotes^op some variant genome^c

variant single locus complement^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000030

Instances of this class are sets comprised of all allels at a specified genomic location where at least one allele is variant (non-reference). In diploid genomes this complement typically has two members. Note that this class also covers cases where deviant numbers of genes or chromosomes are present in a genome (e.g. trisomy of chromosome 21), even if their sequence is not variant.

is equivalent to: single locus complement^c and (has_variant_part^op some variant allele^c)
has super-classes: single locus complement^c; has_variant_part^op some variant allele^c

variation attribute^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000773

has super-classes: sequence feature attribute^c
has sub-classes: aneusomic^c, mutant^c, novel^c, polymorphic^c, reference^c, variant^c, wild-type^c

Vertebrata <vertebrates>^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_7742

has super-classes: Bilateria^c
has sub-classes: Euteleostomi^c

Viruses^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_10239

Stub class to serve as root of hierarchy for imports of virus types from relevant ontologies or terminologies.

has super-classes: organism^c

volume unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000095

has super-classes: measurement unit label^c
has members: cubic centimeterⁿⁱ, cubic decimeterⁿⁱ, literⁿⁱ, microliterⁿⁱ, milliliterⁿⁱ, nanoliterⁿⁱ, picoliterⁿⁱ

volumetric flow rate unit^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UO_0000270

has super-classes: measurement unit label^c
has members: microliters per minuteⁿⁱ

W-linked inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000948

has super-classes: allosomal inheritance^c

wild-type^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000511

has super-classes: variation attribute^c

wild-type allele^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000501

'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain. The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis.

has super-classes: allele^c
has sub-classes: wild-type gene^c
is in domain of: is_wild_type_allele_of^op

wild-type gene^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000502

A gene allele representing the most common varaint in a population (typically >99% frequency), that exhibits canonical function, and against which rare and/or non-functional mutant gene alleles are compared in characterizing the phenotypic consequences of genetic variation.

has super-classes: wild-type allele^c; gene^c

worm phenotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/WBPhenotype_0000886

has super-classes: phenotype^c

X-linked dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000146

has super-classes: X-linked inheritance^c
has sub-classes: co-dominant X-linked inheritance^c, complete X-linked dominant inheritance^c, incomplete X-linked dominant inheritance^c

X-linked inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000936

has super-classes: allosomal inheritance^c
has sub-classes: X-linked dominant inheritance^c, X-linked recessive inheritance^c

X-linked recessive inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000149

has super-classes: X-linked inheritance^c

Y-linked inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000941

has super-classes: allosomal inheritance^c

Z-linked dominant inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000943

has super-classes: Z-linked inheritance^c
has sub-classes: co-dominant Z-linked inheritance^c, complete Z-linked dominant inheritance^c, incomplete Z-linked dominant inheritance^c

Z-linked inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000942

has super-classes: allosomal inheritance^c
has sub-classes: Z-linked dominant inheritance^c, Z-linked reccessive inheritance^c

Z-linked reccessive inheritance^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000947

has super-classes: Z-linked inheritance^c

zebrafish phenotype^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000575

ZFIN do not annotate with a pre-composed phenotype ontology - all annotations compose phenotypes on-the-fly using a combination of PATO, ZFA, GO and other ontologies. So while there is no manually curated zebrafish phenotype ontology, the Upheno pipeline generates one automatically here: http://purl.obolibrary.org/obo/upheno/zp.owl This ontology does not have a root 'phenotype' class, however, and so we generate our own in GENO as a stub placeholder for import of needed zebrafish phenotype classes.

has super-classes: phenotype^c
has sub-classes: abnormal(ly) absent adaxial cell^c, abnormal(ly) absent dorso-rostral cluster^c, abnormal(ly) disrupted diencephalon development^c, abnormal(ly) disrupted neutrophil aggregation^c, abnormal(ly) malformed endocardium cell^c

zygosity^c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000133

has super-classes: allelic state^c; characteristic of^op some single locus complement^c
has sub-classes: aneusomic zygosity^c, disomic zygosity^c, unspecified zygosity^c
is in range of: has_zygosity^op

Object Properties

achieves_planned_objective
acts upstream of
acts upstream of or within
acts upstream of or within, negative effect
acts upstream of or within, positive effect
acts upstream of, negative effect
acts upstream of, positive effect
ameliorates condition
association has object
association has predicate
association has subject
bearer of
bears_concretization_of
begin
benign_for_condition
bounds sequence of
capable of
capable of negatively regulating
capable of part of
capable of positively regulating
capable of regulating
causal agent in process
causal relation between entities
causal relation between material entity and a process
causal relation between processes
causally downstream of
causally downstream of or within
causally influenced by
causally influences
causally related to
causally upstream of
causally upstream of or within
causally upstream of or within, negative effect
causally upstream of or within, positive effect
causally upstream of, negative effect
causally upstream of, positive effect
causes condition
causes or contributes to condition
characteristic of
characteristic of part of
completely_varies_with
concretizes
contributes to condition
contributes to frequency of condition
contributes to severity of condition
correlated with
correlated with condition
denoted by
denotes
depends on
derives from
derives into
developmentally contributes to
developmentally preceded by
developmentally related to
developmentally succeeded by
develops from
develops into
device utilizes material
directly negatively regulated by
directly negatively regulates
directly negatively regulates activity of
directly positively regulated by
directly positively regulates
directly positively regulates activity of
directly regulated by
directly regulates
directly regulates activity of
disposition of
does not overlap sequence of
during which ends
during which starts
enabled by
enables
enables subfunction
end
ends after
ends during
evolutionarily related to
faldo properties
formed as result of
function of
functionally related to
generically depends on
has component
has component activity
has component process
has developmental contribution from
has developmental potential involving
has disposition
has effector activity
has function
has grain
has input
has member
has model
has negative regulatory component activity
has output
has part
has part structure that is capable of
has participant
has phenotype
has phenotype or disease
has positive regulatory component activity
has potential to develop into
has potential to developmentally contribute to
has potential to directly develop into
has quality
has regulatory component activity
has role
has role in modeling
has subsequence
has_affected_feature
has_allele
has_asserted_phenotype
has_defining_feature
has_defining_location
has_defining_sequence
has_expression_variant
has_genotype
has_inferred_phenotype
has_interval
has_location
has_proper_part
has_qualifier
has_qualifying_environment
has_qualifying_process
has_reference_part
has_reference_sequence
has_sequence
has_sequence_attribute
has_sequence_feature
has_sequence_part
has_sequence_unit
has_sex_agnostic_part
has_specified_input
has_specified_output
has_staining_intensity
has_uncertain_significance_for_condition
has_variant_part
has_zygosity
helper property (not for use in curation)
immediately causally downstream of
immediately causally upstream of
immediately preceded by
immediately precedes
in taxon
indirectly causally upstream of
indirectly negatively regulates
indirectly positively regulates
indirectly regulates
inferred_to_cause_condition
inferred_to_contribute_to_condition
inferred_to_correlate_with_condition
input of
interaction relation helper property
interacts with
involved in
involved in negative regulation of
involved in or involved in regulation of
involved in positive regulation of
involved in regulation of
is about
is anatomical entity
is bound by sequence of
is carrier of
is concretized as
is downstream of sequence of
is kinase activity
is subsequence of
is upstream of sequence of
is_allele_of
is_candidate_variant_for
is_expression_variant_of
is_feature_affected_by
is_gene_target_of
is_genotype_of
is_mutant_allele_of
is_polymorphic_allele_of
is_proper_part_of
is_reference_allele_of
is_reference_part_of
is_regulatory_part_of
is_sequence_of
is_sequence_part_of
is_sex_agnostic_part_of
is_specified_input_of
is_specified_output_of
is_subject_of
is_targeted_by
is_variant_allele_of
is_variant_part_of
is_wild_type_allele_of
likely_benign_for_condition
likely_pathogenic_for_condition
location
member of
mereotopologically related to
molecular interaction relation helper property
molecularly controls
molecularly interacts with
negatively regulated by
negatively regulates
negatively regulates characteristic
non-causal_for_condition
objective_achieved_by
obsolete_approximates_sequence
obsolete_has_genetic_variant
obsolete_has_position_component
obsolete_has_regulatory_part
obsolete_is_alteration_within
obsolete_is_expression_variant_with
obsolete_is_genetic_variant_of
obsolete_is_phenotype_of_genotype
obsolete_is_specified_by
obsolete_is_variant_with
obsolete_participates_in_inheritance_process
obsolete_resolves_to_sequence
obsolete_specifies
on strand
output of
overlaps
overlaps sequence of
part of
part of structure that is capable of
participates in
pathogenic_for_condition
phenotype of
phosphorylates
positively regulated by
positively regulates
positively regulates characteristic
preceded by
precedes
process has causal agent
provides input for
quality of
realized in
realizes
reference (faldo)
regulated by
regulates
regulates activity of
regulates characteristic
related_condition
results in developmental progression of
results in formation of anatomical entity
role of
sequence role
sequence_derives_from
sequentially related to
starts during
targets_gene
temporal relation
transitively provides input for
varies_with

achieves_planned_objective^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000417

has domain: planned process^c
has range: objective specification^c
is inverse of: objective_achieved_by^op

acts upstream of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002263

has super-properties: acts upstream of or within^op
has sub-properties: acts upstream of, negative effect^op, acts upstream of, positive effect^op, involved in regulation of^op
has sub-property chains: enables^op o causally upstream of^op

acts upstream of or within^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002264

has super-properties: causal agent in process^op
has sub-properties: acts upstream of^op, acts upstream of or within, negative effect^op, acts upstream of or within, positive effect^op, involved in or involved in regulation of^op
has sub-property chains: enables^op o causally upstream of or within^op

acts upstream of or within, negative effect^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0004033

has super-properties: acts upstream of or within^op
has sub-properties: acts upstream of, negative effect^op
has sub-property chains: enables^op o causally upstream of or within, negative effect^op

acts upstream of or within, positive effect^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0004032

has super-properties: acts upstream of or within^op
has sub-properties: acts upstream of, positive effect^op
has sub-property chains: enables^op o causally upstream of or within, positive effect^op

acts upstream of, negative effect^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0004035

has super-properties: acts upstream of^op; acts upstream of or within, negative effect^op
has sub-property chains: enables^op o causally upstream of, negative effect^op

acts upstream of, positive effect^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0004034

has super-properties: acts upstream of^op; acts upstream of or within, positive effect^op
has sub-property chains: enables^op o causally upstream of, positive effect^op

ameliorates condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003307

Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environments include natural environments or exposures, experimentally applied conditions, or clinical interventions.

has super-properties: related_condition^op; contributes to severity of condition^op

association has object^op back to ToC or Object Property ToC

IRI: http://purl.org/oban/association_has_object

association has predicate^op back to ToC or Object Property ToC

IRI: http://purl.org/oban/association_has_predicate

association has subject^op back to ToC or Object Property ToC

IRI: http://purl.org/oban/association_has_subject

bearer of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000053

has characteristics : inverse functional

has sub-properties: has disposition^op, has function^op, has quality^op, has role^op, sequence role^op
has range: specifically dependent continuant^c
is inverse of: characteristic of^op

bears_concretization_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000211

Shortcut relation expanding to bearer_of some (concretizes some . . . ), linking a material information bearer or sequence macromolecule to some ICE or GDC sequence.

has sub-property chains: bearer of^op o concretizes^op

begin^op back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#begin

has super-properties: faldo properties^op

benign_for_condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000843

has super-properties: non-causal_for_condition^op

bounds sequence of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002522

has characteristics : transitive

has super-properties: has_sequence_part^op; sequentially related to^op
has sub-properties: has subsequence^op
is inverse of: is bound by sequence of^op

capable of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002215

has super-properties: capable of part of^op
has sub-properties: enables^op
has domain: independent continuant^c
has range: process^c

capable of negatively regulating^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002597

has super-properties: capable of regulating^op
has sub-property chains: capable of^op o negatively regulates^op

capable of part of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002216

has super-properties: functionally related to^op; causal agent in process^op
has sub-properties: capable of^op

capable of positively regulating^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002598

has super-properties: capable of regulating^op
has sub-property chains: capable of^op o positively regulates^op

capable of regulating^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002596

has super-properties: causal agent in process^op
has sub-properties: capable of negatively regulating^op, capable of positively regulating^op
has sub-property chains: capable of^op o regulates^op

causal agent in process^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002500

has super-properties: causal relation between material entity and a process^op
has sub-properties: acts upstream of or within^op, capable of part of^op, capable of regulating^op, involved in or involved in regulation of^op
is inverse of: process has causal agent^op

causal relation between entities^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002506

has super-properties: causally related to^op
has sub-properties: causally influenced by^op, causally influences^op
has domain: continuant^c
has range: continuant^c

causal relation between material entity and a process^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002595

has super-properties: causally related to^op
has sub-properties: causal agent in process^op, has part structure that is capable of^op
has domain: material entity^c
has range: process^c

causal relation between processes^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002501

has super-properties: causally related to^op
has sub-properties: causally downstream of or within^op, causally upstream of or within^op
has domain: occurrent^c
has range: occurrent^c

causally downstream of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002404

has super-properties: preceded by^op; causally downstream of or within^op
has sub-properties: immediately causally downstream of^op
is inverse of: causally upstream of^op

causally downstream of or within^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002427

has characteristics : transitive

has super-properties: causal relation between processes^op
has sub-properties: causally downstream of^op, regulated by^op
is inverse of: causally upstream of or within^op

causally influenced by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002559

has super-properties: causal relation between entities^op
is inverse of: causally influences^op

causally influences^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002566

has super-properties: causal relation between entities^op
has sub-properties: regulates activity of^op
has domain: continuant^c
has range: continuant^c
is inverse of: causally influenced by^op
has sub-property chains: enables^op o causally upstream of^op o has input^op; enables^op o causally upstream of^op o enabled by^op

causally related to^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002410

has sub-properties: causal relation between entities^op, causal relation between material entity and a process^op, causal relation between processes^op, causes or contributes to condition^op, process has causal agent^op, regulates characteristic^op

causally upstream of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002411

has characteristics : transitive

has super-properties: precedes^op; causally upstream of or within^op
has sub-properties: causally upstream of, negative effect^op, causally upstream of, positive effect^op, immediately causally upstream of^op, indirectly causally upstream of^op, regulates^op
is inverse of: causally downstream of^op

causally upstream of or within^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002418

has characteristics : transitive

has super-properties: causal relation between processes^op
has sub-properties: causally upstream of^op, causally upstream of or within, negative effect^op, causally upstream of or within, positive effect^op
is inverse of: causally downstream of or within^op
has sub-property chains: causally upstream of or within^op o part of^op

causally upstream of or within, negative effect^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0004046

has super-properties: causally upstream of or within^op
has sub-properties: causally upstream of, negative effect^op

causally upstream of or within, positive effect^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0004047

has super-properties: causally upstream of or within^op
has sub-properties: causally upstream of, positive effect^op, transitively provides input for^op

causally upstream of, negative effect^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002305

has super-properties: causally upstream of^op; causally upstream of or within, negative effect^op
has sub-properties: negatively regulates^op

causally upstream of, positive effect^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002304

has super-properties: causally upstream of^op; causally upstream of or within, positive effect^op
has sub-properties: positively regulates^op

causes condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003303

has super-properties: causes or contributes to condition^op
has sub-properties: likely_pathogenic_for_condition^op, pathogenic_for_condition^op

causes or contributes to condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003302

has super-properties: related_condition^op; causally related to^op
has sub-properties: causes condition^op, contributes to condition^op

characteristic of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000052

has characteristics : functional

has super-properties: characteristic of part of^op
has sub-properties: disposition of^op, function of^op, quality of^op, role of^op
is inverse of: bearer of^op

characteristic of part of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002314

has super-properties: depends on^op
has sub-properties: characteristic of^op
has sub-property chains: characteristic of part of^op o part of^op

completely_varies_with^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000784

has characteristics : symmetric

has super-properties: varies_with^op

concretizes^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000059

has domain: specifically dependent continuant^c; process^c or specifically dependent continuant^c
has range: generically dependent continuant^c
is inverse of: is concretized as^op

contributes to condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003304

has super-properties: causes or contributes to condition^op
has sub-properties: contributes to frequency of condition^op, contributes to severity of condition^op

contributes to frequency of condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003306

has super-properties: contributes to condition^op

contributes to severity of condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003305

has super-properties: contributes to condition^op
has sub-properties: ameliorates condition^op

correlated with^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002610

has sub-properties: correlated with condition^op

correlated with condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003308

has super-properties: related_condition^op; correlated with^op

denoted by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000235

has domain: entity^c
has range: information content entity^c
is inverse of: denotes^op

denotes^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000219

has super-properties: is about^op
has domain: information content entity^c
has range: entity^c
is inverse of: denoted by^op

depends on^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002502

has sub-properties: characteristic of part of^op

derives from^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001000

has super-properties: top object property
has domain: independent continuant^c
has range: independent continuant^c
is inverse of: derives into^op

derives into^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001001

is inverse of: derives from^op

developmentally contributes to^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002255

has super-properties: developmentally succeeded by^op; has potential to developmentally contribute to^op
is inverse of: has developmental contribution from^op
has sub-property chains: develops into^op o part of^op

developmentally preceded by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002258

has super-properties: developmentally related to^op
has sub-properties: develops from^op, has developmental contribution from^op
has domain: continuant^c
has range: continuant^c
is inverse of: developmentally succeeded by^op

developmentally related to^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002324

has sub-properties: developmentally preceded by^op, has developmental potential involving^op, results in developmental progression of^op

developmentally succeeded by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002286

has super-properties: has developmental potential involving^op
has sub-properties: developmentally contributes to^op, develops into^op
is inverse of: developmentally preceded by^op

develops from^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002202

has characteristics : transitive

has super-properties: has developmental contribution from^op; developmentally preceded by^op
has domain: independent continuant^c
has range: independent continuant^c
is inverse of: develops into^op

develops into^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002203

has characteristics : transitive

has super-properties: developmentally succeeded by^op; has potential to develop into^op; has potential to directly develop into^op
is inverse of: develops from^op

device utilizes material^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0017001

has sub-property chains: capable of^op o has input^op

directly negatively regulated by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002023

has super-properties: directly regulated by^op
is inverse of: directly negatively regulates^op

directly negatively regulates^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002630

has super-properties: negatively regulates^op; directly regulates^op
is inverse of: directly negatively regulated by^op

directly negatively regulates activity of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002449

has super-properties: directly regulates activity of^op
has domain: material entity^c
has range: material entity^c
has sub-property chains: enables^op o directly negatively regulates^op o enabled by^op

directly positively regulated by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002024

has super-properties: directly regulated by^op
is inverse of: directly positively regulates^op

directly positively regulates^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002629

has super-properties: positively regulates^op; directly regulates^op
is inverse of: directly positively regulated by^op

directly positively regulates activity of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002450

has super-properties: directly regulates activity of^op
has domain: material entity^c
has range: material entity^c
has sub-property chains: enables^op o directly positively regulates^op o enabled by^op

directly regulated by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002022

has super-properties: regulated by^op
has sub-properties: directly negatively regulated by^op, directly positively regulated by^op
is inverse of: directly regulates^op

directly regulates^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002578

has super-properties: regulates^op; immediately causally upstream of^op
has sub-properties: directly negatively regulates^op, directly positively regulates^op
is inverse of: directly regulated by^op

directly regulates activity of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002448

has super-properties: molecularly interacts with^op; regulates activity of^op
has sub-properties: directly negatively regulates activity of^op, directly positively regulates activity of^op
has domain: material entity^c
has range: material entity^c
has sub-property chains: enables^op o regulates^op o enabled by^op

disposition of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000092

has super-properties: characteristic of^op
is inverse of: has disposition^op

does not overlap sequence of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002527

has characteristics : symmetric

has super-properties: sequentially related to^op
has sub-properties: is downstream of sequence of^op, is upstream of sequence of^op

during which ends^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002084

has super-properties: temporal relation^op
is inverse of: ends during^op

during which starts^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002088

has super-properties: temporal relation^op
is inverse of: starts during^op

enabled by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002333

has super-properties: has participant^op; functionally related to^op
is inverse of: enables^op

enables^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002327

has super-properties: capable of^op
is inverse of: enabled by^op
has sub-property chains: enables^op o has part^op; enables^op o has component activity^op

enables subfunction^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0004031

has super-properties: functionally related to^op
has sub-property chains: enables^op o has part^op

end^op back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#end

has super-properties: faldo properties^op

ends after^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002086

has characteristics : transitive

has super-properties: temporal relation^op
has sub-properties: preceded by^op
has sub-property chains: ends during^op o preceded by^op

ends during^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002093

has super-properties: temporal relation^op
is inverse of: during which ends^op

evolutionarily related to^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002320

has sub-properties: in taxon^op

faldo properties^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000708

organizational property to hold imports from faldo.

has sub-properties: begin^op, end^op, location^op, reference (faldo)^op

formed as result of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002354

has super-properties: output of^op; obsolete property^op
is inverse of: results in formation of anatomical entity^op

function of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000079

has super-properties: characteristic of^op
has domain: function^c
is inverse of: has function^op

functionally related to^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002328

has sub-properties: capable of part of^op, enabled by^op, enables subfunction^op, has part structure that is capable of^op, input of^op, involved in or involved in regulation of^op, output of^op, part of structure that is capable of^op

generically depends on^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0010001

has domain: generically dependent continuant^c
has range: independent continuant^c
is inverse of: is carrier of^op
has sub-property chains: characteristic of^op o is concretized as^op

has component^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002180

has super-properties: has part^op
has sub-properties: has component process^op

has component activity^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002017

has super-properties: has component process^op
has sub-properties: has effector activity^op, has regulatory component activity^op

has component process^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002018

has super-properties: has component^op
has sub-properties: has component activity^op
has domain: process^c
has range: process^c

has developmental contribution from^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002254

has super-properties: developmentally preceded by^op
has sub-properties: develops from^op
has domain: anatomical entity^c
has range: anatomical entity^c
is inverse of: developmentally contributes to^op
has sub-property chains: has part^op o has developmental contribution from^op

has developmental potential involving^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002384

has super-properties: developmentally related to^op
has sub-properties: developmentally succeeded by^op, has potential to develop into^op, has potential to developmentally contribute to^op
has domain: anatomical entity^c
has range: anatomical entity^c

has disposition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000091

has super-properties: bearer of^op
has domain: independent continuant^c
has range: disposition^c
is inverse of: disposition of^op

has effector activity^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002025

has characteristics : functional

has super-properties: has component activity^op

has function^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000085

has super-properties: bearer of^op
has domain: independent continuant^c
has range: function^c
is inverse of: function of^op

has grain^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000643

has super-properties: has part^op

has input^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002233

has super-properties: has participant^op
has sub-properties: has_specified_input^op
has domain: process^c
is inverse of: input of^op

has member^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002351

has characteristics : irreflexive

has super-properties: has part^op
is inverse of: member of^op

has model^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002615

is inverse of: has role in modeling^op

has negative regulatory component activity^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002014

has super-properties: has regulatory component activity^op; negatively regulated by^op

has output^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002234

has super-properties: has participant^op
has sub-properties: has_specified_output^op, results in formation of anatomical entity^op
is inverse of: output of^op

has part^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000051

has characteristics : transitive

has super-properties: overlaps^op
has sub-properties: has component^op, has grain^op, has member^op, has subsequence^op, has_proper_part^op, has_sequence_part^op
is inverse of: part of^op

has part structure that is capable of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002584

has super-properties: functionally related to^op; causal relation between material entity and a process^op
has sub-property chains: has part^op o capable of^op

has participant^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000057

has sub-properties: enabled by^op, has input^op, has output^op, has_specified_input^op, has_specified_output^op
has domain: occurrent^c
has range: continuant^c
is inverse of: participates in^op
has sub-property chains: has part^op o has participant^op

has phenotype^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002200

has super-properties: has phenotype or disease^op
has sub-properties: has_asserted_phenotype^op
has domain: generically dependent continuant^c or disease^c or material anatomical entity^c
has range: phenotype^c
is inverse of: phenotype of^op

has phenotype or disease^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0016001

has sub-properties: has phenotype^op

has positive regulatory component activity^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002015

has super-properties: has regulatory component activity^op; positively regulated by^op

has potential to develop into^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002387

has super-properties: has developmental potential involving^op
has sub-properties: develops into^op, has potential to directly develop into^op

has potential to developmentally contribute to^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002385

has super-properties: has developmental potential involving^op
has sub-properties: developmentally contributes to^op

has potential to directly develop into^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002388

has super-properties: has potential to develop into^op
has sub-properties: develops into^op

has quality^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000086

has super-properties: bearer of^op
has range: quality^c
is inverse of: quality of^op

has regulatory component activity^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002013

has super-properties: has component activity^op; regulated by^op
has sub-properties: has negative regulatory component activity^op, has positive regulatory component activity^op

has role^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000087

has super-properties: bearer of^op
has domain: independent continuant^c
has range: role^c
is inverse of: role of^op

has role in modeling^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0003301

The driving use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest.

has characteristics : asymmetric, irreflexive

is inverse of: has model^op

has subsequence^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002524

has characteristics : transitive

has super-properties: has part^op; has_sequence_part^op; bounds sequence of^op; overlaps sequence of^op
is inverse of: is subsequence of^op

has_affected_feature^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000418

This class to organizes all relations used to link genetic variation instances of any type to genomic feature classes they effect. For example, is_allele_of links a gene allele instance to its gene class (genes are represented as classes in our OWL model). Such links support phenotype propagation from alleles to genes for Monarch Initiative use cases. Use of these properties effectively puns gene class IRIs into owl:individuals in a given rdf datset.

has sub-properties: is_allele_of^op, is_expression_variant_of^op, targets_gene^op
is inverse of: is_feature_affected_by^op
has sub-property chains: has_variant_part^op o has_affected_feature^op; is_variant_part_of^op o has_affected_feature^op

has_allele^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000413

has super-properties: is_feature_affected_by^op
is inverse of: is_allele_of^op

has_asserted_phenotype^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000743

has super-properties: has phenotype^op

has_defining_feature^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000959

Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_feature property is used to specify the sequence defining a copy number complement - by using a 'sequence feature' as a proxy for the specific sequence of this feature on some reference. For copy number complements, it is the sequence of this proxy feature on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence of this proxy feature (typically a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement.

has domain: copy number complement^c or functional copy complement^c
has range: sequence_feature^c

has_defining_location^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000957

Copy number complements represent sets of all copies of a particular biological sequence present in a particular genome. Their "identity" is based on their defining sequence, and the count of this sequence in the genome.The has_defining_location property is used to specify the sequence defining a copy number complement - by using a 'sequence location' as a proxy for a specific sequence that is found at this location. For copy number complements, it is the sequence at this location on some reference that defines sequences in a genome of interest that qualify for membership in the complement. For functional copy number complements (aka genetic dosage), it is the canonical function(s) performed by the sequence at this location (typically that of a gene) that helps to define sequences in a genome of interest that qualify for membership in the complement.

has domain: copy number complement^c or functional copy complement^c
has range: sequence feature location^c

has_defining_sequence^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000958

has domain: copy number complement^c or functional copy complement^c
has range: biological sequence^c

has_expression_variant^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000449

has super-properties: is_feature_affected_by^op
is inverse of: is_expression_variant_of^op

has_genotype^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000222

The biological entity can be an organism, a group of organism that share common genotype, or organism-derived entities such as cell lines or biospecimens. The genotype can be any of the various flavors of genotypes/allelotypes defined in GENO (intrinsic genotype, extrinsic genotype, effective genotype), or any genetic variation component of a genotype including variant alleles or sequence alterations.

has domain: genotype^c or (part of^op some genotype^c)
is inverse of: is_genotype_of^op

has_inferred_phenotype^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000740

has sub-property chains: has_variant_part^op o has_asserted_phenotype^op; is_variant_part_of^op o is_sex_agnostic_part_of^op o has_asserted_phenotype^op; is_variant_part_of^op o has_asserted_phenotype^op; has_allele^op o is_variant_part_of^op o has_asserted_phenotype^op; has_allele^op o has_asserted_phenotype^op; has_expression_variant^op o is_variant_part_of^op o has_asserted_phenotype^op; has_expression_variant^op o has_asserted_phenotype^op; is_sex_agnostic_part_of^op o has_asserted_phenotype^op

has_interval^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000966

Can be used when Interval objects are employed in representing sequence location. But start and end positions can also be directly attached to a location, avoiding the use of Interval objects.

has domain: sequence feature location^c

has_location^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000903

has domain: sequence_feature^c
has range: sequence feature location^c

has_proper_part^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000231

has characteristics : transitive

has super-properties: has part^op
is inverse of: is_proper_part_of^op

has_qualifier^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000580

has sub-properties: has_qualifying_environment^op, has_qualifying_process^op

has_qualifying_environment^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000847

has super-properties: has_qualifier^op

has_qualifying_process^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000846

has super-properties: has_qualifier^op

has_reference_part^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000385

has characteristics : transitive

has super-properties: has_sequence_part^op
is inverse of: is_reference_part_of^op

has_reference_sequence^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000967

has_sequence^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000239

'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule.

has range: biological sequence^c
is inverse of: is_sequence_of^op

has_sequence_attribute^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000207

has super-properties: top object property
has sub-properties: has_staining_intensity^op, has_zygosity^op
has domain: sequence feature or set^c or biological sequence^c or qualified sequence feature or collection^c

has_sequence_feature^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000726

In GENO we define three levels of sequence artifacts: (1) biological sequences, (2) sequence features, and (3) qualified sequence features. The identify criteria for a 'biological sequence' include only its inherent sequence (the ordered string of units that comprise it). The identity criteria for a 'sequence feature' include its sequence and position (where it resides - i.e. its location based on how it maps to a reference or standard) The identity criteria for a 'qualified sequence feature' include its component sequence feature (defined by its sequence and position), and the material context of its bearer in a cell or organism. This context can include direct epigenetic modification, or being targeted by gene knockdown reagents such as morpholinos or RNAi, or being transiently overexpressed from a transgenic construct in a cell or organism.

has domain: qualified sequence feature^c or qualified sequence feature set^c
has range: sequence_feature^c

has_sequence_part^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000654

has super-properties: has part^op
has sub-properties: bounds sequence of^op, has subsequence^op, has_reference_part^op, has_sequence_unit^op, has_sex_agnostic_part^op, has_variant_part^op
is inverse of: is_sequence_part_of^op

has_sequence_unit^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000783

has super-properties: has_sequence_part^op

has_sex_agnostic_part^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000650

has super-properties: has_sequence_part^op
is inverse of: is_sex_agnostic_part_of^op

has_specified_input^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000293

has super-properties: has participant^op; has input^op
has domain: planned process^c
is inverse of: is_specified_input_of^op

has_specified_output^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000299

has super-properties: has participant^op; has output^op
has domain: planned process^c
is inverse of: is_specified_output_of^op

has_staining_intensity^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000626

Used to link a gross chromosomal sequence feature (chromosome part) to a color value quality that inheres in the sequence feature in virtue of the staining pattern of the chromosomal DNA in which the sequence is materialized.

has super-properties: has_sequence_attribute^op

has_uncertain_significance_for_condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000845

has super-properties: related_condition^op

has_variant_part^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000382

has characteristics : transitive

has super-properties: has_sequence_part^op
is inverse of: is_variant_part_of^op

has_zygosity^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000608

has super-properties: has_sequence_attribute^op
has domain: single locus complement^c
has range: zygosity^c

helper property (not for use in curation)^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002464

has sub-properties: interaction relation helper property^op

immediately causally downstream of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002405

has super-properties: immediately preceded by^op; causally downstream of^op
is inverse of: immediately causally upstream of^op

immediately causally upstream of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002412

has super-properties: immediately precedes^op; causally upstream of^op
has sub-properties: directly regulates^op, provides input for^op
is inverse of: immediately causally downstream of^op

immediately preceded by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002087

has super-properties: preceded by^op
has sub-properties: immediately causally downstream of^op
is inverse of: immediately precedes^op

immediately precedes^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002090

has super-properties: precedes^op
has sub-properties: immediately causally upstream of^op
is inverse of: immediately preceded by^op

in taxon^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002162

has super-properties: evolutionarily related to^op
has range: organism^c
has sub-property chains: overlaps^op o in taxon^op; regulates^op o in taxon^op; capable of^op o in taxon^op; has developmental contribution from^op o in taxon^op; results in developmental progression of^op o in taxon^op; has potential to develop into^op o in taxon^op

indirectly causally upstream of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0012011

has super-properties: causally upstream of^op
has sub-properties: indirectly regulates^op

indirectly negatively regulates^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002409

has characteristics : transitive

has super-properties: negatively regulates^op; indirectly regulates^op
has sub-property chains: indirectly negatively regulates^op o directly negatively regulates^op; directly negatively regulates^op o indirectly negatively regulates^op; directly negatively regulates^op o directly negatively regulates^op

indirectly positively regulates^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002407

has characteristics : transitive

has super-properties: positively regulates^op; indirectly regulates^op
has sub-property chains: indirectly positively regulates^op o directly positively regulates^op; indirectly negatively regulates^op o indirectly negatively regulates^op; directly positively regulates^op o indirectly positively regulates^op; directly positively regulates^op o directly positively regulates^op

indirectly regulates^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0012012

has super-properties: regulates^op; indirectly causally upstream of^op
has sub-properties: indirectly negatively regulates^op, indirectly positively regulates^op

inferred_to_cause_condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000791

has super-properties: related_condition^op
has sub-property chains: is_sex_agnostic_part_of^op o causes condition^op; has_variant_part^op o is_sex_agnostic_part_of^op o causes condition^op; has_variant_part^op o causes condition^op; is_variant_part_of^op o is_sex_agnostic_part_of^op o is_variant_part_of^op o causes condition^op; is_variant_part_of^op o is_sex_agnostic_part_of^op o causes condition^op; is_variant_part_of^op o causes condition^op; has_allele^op o is_variant_part_of^op o is_sex_agnostic_part_of^op o is_variant_part_of^op o causes condition^op; has_allele^op o is_variant_part_of^op o is_sex_agnostic_part_of^op o causes condition^op; is_feature_affected_by^op o has_variant_part^op o causes condition^op; is_feature_affected_by^op o is_variant_part_of^op o causes condition^op; is_feature_affected_by^op o causes condition^op; is_sex_agnostic_part_of^op o is_variant_part_of^op o causes condition^op

inferred_to_contribute_to_condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000793

has super-properties: related_condition^op

inferred_to_correlate_with_condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000794

has super-properties: related_condition^op

input of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002352

has super-properties: participates in^op; functionally related to^op
is inverse of: has input^op

interaction relation helper property^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002563

has super-properties: helper property (not for use in curation)^op
has sub-properties: molecular interaction relation helper property^op

interacts with^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002434

has characteristics : symmetric

has sub-properties: molecularly interacts with^op
has domain: material entity^c
has range: material entity^c

involved in^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002331

has super-properties: participates in^op; involved in or involved in regulation of^op
has sub-property chains: enables^op o part of^op; involved in^op o part of^op

involved in negative regulation of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002430

has super-properties: involved in regulation of^op
has sub-property chains: enables^op o negatively regulates^op; involved in^op o negatively regulates^op

involved in or involved in regulation of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002431

has super-properties: acts upstream of or within^op; functionally related to^op; causal agent in process^op
has sub-properties: involved in^op, involved in regulation of^op

involved in positive regulation of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002429

has super-properties: involved in regulation of^op
has sub-property chains: enables^op o positively regulates^op; involved in^op o positively regulates^op

involved in regulation of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002428

has super-properties: acts upstream of^op; involved in or involved in regulation of^op
has sub-properties: involved in negative regulation of^op, involved in positive regulation of^op
has sub-property chains: enables^op o regulates^op; involved in^op o regulates^op

is about^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000136

has sub-properties: denotes^op
has domain: information content entity^c
is inverse of: is_subject_of^op

is anatomical entity^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0020105

has domain: anatomical entity^c

is bound by sequence of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002523

has characteristics : transitive

has super-properties: sequentially related to^op
has sub-properties: is subsequence of^op
is inverse of: bounds sequence of^op

is carrier of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0010002

has domain: independent continuant^c
has range: generically dependent continuant^c
is inverse of: generically depends on^op
has sub-property chains: concretizes^op o bearer of^op

is concretized as^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000058

has domain: generically dependent continuant^c
has range: specifically dependent continuant^c; process^c or specifically dependent continuant^c
is inverse of: concretizes^op

is downstream of sequence of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002529

has characteristics : transitive

has super-properties: does not overlap sequence of^op
is inverse of: is downstream of sequence of^op, is downstream of sequence of^op

is kinase activity^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002481

has super-properties: molecular interaction relation helper property^op

is subsequence of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002525

has characteristics : transitive

has super-properties: part of^op; is_sequence_part_of^op; is bound by sequence of^op; overlaps sequence of^op
is inverse of: has subsequence^op

is upstream of sequence of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002528

has characteristics : transitive

has super-properties: does not overlap sequence of^op

is_allele_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000408

To allow users to make important distinctions in discourse and modeling, GENO clearly separates the notions/levels of 'biological sequence', 'sequence feature', and 'sequence location' ('genomic locus' when found in a genome). This sets up an important terminological nuance when it comes to alleles, where we believe it correct to say that a particular genomic feature is an alleles_of some genomic locus (as opposed to an allele_of some sequence or some feature). This is typically a gene locus, but even insertions falling outside of genes are considered alleles_of the locus they alter (e.g. alleles of other types of named loci such as QTLs, or alleles of some unnamed locus of arbitrary size). While conceptually it is most correct to say features are alleles_of some genomic locus, it is common practice to say that they are alleles of the class of feature defined to reside at that locus (typically a gene). Accordingly, we may write things like "fgf8a<ti282a> is an allele of the Danio rerio fgf8a gene", and we may create data where fgf8a<ti282a> is asserted as an allele_of the fgf8a gene class IRI. But here we mean more precisely that it is an allele of the locus at which the fgf8a gene resides. Allowing for this means that we dont have to create 'feature-based location/locus' terms mirroing all feature class terms already in exiistence (e.g. for every gene). It is important to be clear that the location/locus that a feature is an allele_of is defined exclusively by its genomic position, and not on the sequence it may contains. This is particularly relevant when considering transgenic insertions. For example, this means that the insertion of the S. cerevisiae GAL4 gene sequence within the D. melanogaster Bx gene locus would create an allele of the D. melanogaster Bx gene, but not an allele of the S. cerevisiae GAL4 gene. The transgene that results from such an insertion, while expressing S. cerevisiae GAL4 gene sequence, is not an allele of this gene because it does not reside at the S. cerevisiae GAL4 locus. This departs from how some databases use the term 'allele' - where transgenes expressing an exogenous gene are considered to be alleles of the exogenous genes they carry. For example, in the example above, Flybase describes the S. cerevisiae GAL4 transgene as an allele_of the S. cerevisiae GAL4 gene (and gives it the allele identifier FBal0040476). A GENO representation on the other hand would say that the S. cerevisiae GAL4 transgene derives_sequence_from the S. cerevisiae GAL4 gene, but is not an allele_of this gene. In a GENO model, FBal0040476 would be typed as a transgene insertion, but not considered an allele_of the Scer\GAL4 gene. At the end of the day, it's just semantics, but worth clarifying given the ubiquity and variable use of the term 'allele'. The GENO model attempts to define and adhere to the principled notion of positionally-defined 'alleles', and functionally-defined 'transgenes'.

has super-properties: has_affected_feature^op
has sub-properties: is_reference_allele_of^op, is_variant_allele_of^op, is_wild_type_allele_of^op
has domain: genomic feature^c
is inverse of: has_allele^op

is_candidate_variant_for^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000849

has super-properties: related_condition^op

is_expression_variant_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000443

This relation links an expression-variant gene instance (targeted or transgenic) to the class of gene that it preresents. For transient transgenes, this is the gene, the coding sequence need only to contain as part an expressed region from a given gene to stand in an is_expression_variant_of relation to the gene class.

has super-properties: has_affected_feature^op
is inverse of: has_expression_variant^op

is_feature_affected_by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000445

This is an organizational grouping class to collect all relations used to link genomic feature classes (typically genes) to instance of a genomic feature sequence feature or qualified sequence feature. For example, linking a gene class IRI to an instance of an allele of that gene class. Such links support phenotype propagation from features/variants to genes (e.g. for Monarch Initiative use cases)

has sub-properties: has_allele^op, has_expression_variant^op, is_gene_target_of^op
is inverse of: has_affected_feature^op

is_gene_target_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000447

Domain = punned gene class Range = gene knockdown reagent

has super-properties: is_feature_affected_by^op
is inverse of: targets_gene^op

is_genotype_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000220

is inverse of: has_genotype^op

is_mutant_allele_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000651

A relation between a mutant allele (ie rare variant present in less than 1% of a population, or an experimentally-altered variant such as a knocked-out gene in a model organism), and the gene it is a variant of.

has super-properties: is_variant_allele_of^op
has domain: obsolete mutant allele^c

is_polymorphic_allele_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000652

has super-properties: is_variant_allele_of^op
has domain: polymorphic allele^c

is_proper_part_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000248

has super-properties: part of^op
is inverse of: has_proper_part^op

is_reference_allele_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000610

has super-properties: is_allele_of^op
has domain: reference allele^c

is_reference_part_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000387

has super-properties: is_sequence_part_of^op
is inverse of: has_reference_part^op

is_regulatory_part_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000761

has super-properties: is_sequence_part_of^op

is_sequence_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000251

has domain: biological sequence^c
is inverse of: has_sequence^op

is_sequence_part_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000655

has super-properties: part of^op
has sub-properties: is subsequence of^op, is_reference_part_of^op, is_regulatory_part_of^op, is_sex_agnostic_part_of^op, is_variant_part_of^op
is inverse of: has_sequence_part^op

is_sex_agnostic_part_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000661

has super-properties: is_sequence_part_of^op
is inverse of: has_sex_agnostic_part^op

is_specified_input_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000295

has super-properties: participates in^op
has range: planned process^c
is inverse of: has_specified_input^op

is_specified_output_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000312

has super-properties: participates in^op
has range: planned process^c
is inverse of: has_specified_output^op

is_subject_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000252

is inverse of: is about^op

is_targeted_by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000634

is_variant_allele_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000641

has super-properties: is_allele_of^op
has sub-properties: is_mutant_allele_of^op, is_polymorphic_allele_of^op
has domain: variant allele^c

is_variant_part_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000383

has characteristics : transitive

has super-properties: is_sequence_part_of^op
is inverse of: has_variant_part^op

is_wild_type_allele_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000653

has super-properties: is_allele_of^op
has domain: wild-type allele^c

likely_benign_for_condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000844

has super-properties: non-causal_for_condition^op

likely_pathogenic_for_condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000841

has super-properties: causes condition^op

location^op back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#location

has super-properties: faldo properties^op

member of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002350

has super-properties: part of^op
is inverse of: has member^op

mereotopologically related to^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002323

has sub-properties: overlaps^op

molecular interaction relation helper property^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002564

has super-properties: interaction relation helper property^op
has sub-properties: is kinase activity^op

molecularly controls^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_000244

molecularly interacts with^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002436

has characteristics : symmetric

has super-properties: interacts with^op
has sub-properties: directly regulates activity of^op, phosphorylates^op

negatively regulated by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002335

has super-properties: regulated by^op
has sub-properties: has negative regulatory component activity^op
is inverse of: negatively regulates^op

negatively regulates^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002212

has super-properties: regulates^op; causally upstream of, negative effect^op
has sub-properties: directly negatively regulates^op, indirectly negatively regulates^op
is inverse of: negatively regulated by^op

negatively regulates characteristic^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0019002

has super-properties: regulates characteristic^op
has sub-property chains: negatively regulates^op o positively regulates characteristic^op; positively regulates^op o negatively regulates characteristic^op

non-causal_for_condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000842

has super-properties: related_condition^op
has sub-properties: benign_for_condition^op, likely_benign_for_condition^op

objective_achieved_by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000833

has domain: objective specification^c
has range: planned process^c
is inverse of: achieves_planned_objective^op

obsolete_approximates_sequence^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000243

has super-properties: obsolete property^op

obsolete_has_genetic_variant^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000411

Domain = punned gene class Range = genomic feature

has super-properties: obsolete property^op

obsolete_has_position_component^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000767

has super-properties: obsolete property^op

obsolete_has_regulatory_part^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000741

Proposal for a property linking variants to smaller components that are regulatory, and therefore should not inherit phenotypes.

has super-properties: obsolete property^op

obsolete_is_alteration_within^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000742

has super-properties: obsolete property^op
has sub-property chains: is_variant_part_of^op o is_allele_of^op

obsolete_is_expression_variant_with^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000488

has super-properties: obsolete property^op

obsolete_is_genetic_variant_of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000410

Domain = genomic feature instance Range = punned gene class IRI

has super-properties: obsolete property^op

obsolete_is_phenotype_of_genotype^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000359

Might expand to something like: phenotype and (is_phenotype_of some (organism and (has_part some ('material genome' and (is_subject_of some (genome and (is_specified_by some genotype)))))))

has super-properties: obsolete property^op

obsolete_is_specified_by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000253

has super-properties: obsolete property^op

obsolete_is_variant_with^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000486

This proeprty is most commonly used to relate two different alleles of a given gene. It is not a relation between an allele and the gene it is a variant of.

has super-properties: obsolete property^op

obsolete_participates_in_inheritance_process^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000368

has super-properties: obsolete property^op
has range: inheritance pattern^c

obsolete_resolves_to_sequence^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000244

has super-properties: obsolete property^op

obsolete_specifies^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000242

has super-properties: obsolete property^op

on strand^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000906

Can be used to a genomic feature to the chromosomal strand it resides on in the genome (+ or - strand, or both strands). Commonly used to link a gene to the strand it is transcribed from.

output of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002353

has super-properties: participates in^op; functionally related to^op
has sub-properties: formed as result of^op
is inverse of: has output^op

overlaps^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002131

has characteristics : symmetric

has super-properties: mereotopologically related to^op
has sub-properties: has part^op, overlaps sequence of^op, part of^op
has sub-property chains: part of^op o part of^op; has part^op o overlaps^op; overlaps^op o part of^op

overlaps sequence of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002526

has characteristics : symmetric

has super-properties: overlaps^op; sequentially related to^op
has sub-properties: has subsequence^op, is subsequence of^op
has sub-property chains: has subsequence^op o is subsequence of^op

part of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000050

has characteristics : transitive

has super-properties: overlaps^op
has sub-properties: is subsequence of^op, is_proper_part_of^op, is_sequence_part_of^op, member of^op
is inverse of: has part^op

part of structure that is capable of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002329

has super-properties: functionally related to^op

participates in^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000056

has sub-properties: input of^op, involved in^op, is_specified_input_of^op, is_specified_output_of^op, output of^op
has domain: continuant^c
has range: occurrent^c
is inverse of: has participant^op

pathogenic_for_condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000840

has super-properties: causes condition^op

phenotype of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002201

has characteristics : functional

has domain: phenotype^c
is inverse of: has phenotype^op

phosphorylates^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002447

has super-properties: molecularly interacts with^op

positively regulated by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002336

has super-properties: regulated by^op
has sub-properties: has positive regulatory component activity^op
is inverse of: positively regulates^op

positively regulates^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002213

has characteristics : transitive

has super-properties: regulates^op; causally upstream of, positive effect^op
has sub-properties: directly positively regulates^op, indirectly positively regulates^op
is inverse of: positively regulated by^op
has sub-property chains: negatively regulates^op o negatively regulates^op

positively regulates characteristic^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0019001

has super-properties: regulates characteristic^op
has sub-property chains: positively regulates^op o positively regulates characteristic^op

preceded by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000062

has characteristics : transitive

has super-properties: ends after^op
has sub-properties: causally downstream of^op, immediately preceded by^op
has domain: occurrent^c
has range: occurrent^c
is inverse of: precedes^op
has sub-property chains: part of^op o preceded by^op; starts during^op o preceded by^op

precedes^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000063

has characteristics : transitive

has super-properties: temporal relation^op
has sub-properties: causally upstream of^op, immediately precedes^op
has domain: occurrent^c
has range: occurrent^c
is inverse of: preceded by^op
has sub-property chains: part of^op o precedes^op

process has causal agent^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002608

has super-properties: causally related to^op
is inverse of: causal agent in process^op

provides input for^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002413

has super-properties: immediately causally upstream of^op; transitively provides input for^op
has sub-property chains: has output^op o has input^op

quality of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000080

has super-properties: characteristic of^op
is inverse of: has quality^op

realized in^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000054

is defined by: http://purl.obolibrary.org/obo/bfo.owl

Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

has domain: realizable entity^c
has range: process^c
is inverse of: realizes^op

realizes^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000055

is defined by: http://purl.obolibrary.org/obo/iao.owl

Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

has domain: process^c
has range: realizable entity^c
is inverse of: realized in^op

reference (faldo)^op back to ToC or Object Property ToC

IRI: http://biohackathon.org/resource/faldo#reference

has super-properties: faldo properties^op

regulated by^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002334

has characteristics : transitive

has super-properties: causally downstream of or within^op
has sub-properties: directly regulated by^op, has regulatory component activity^op, negatively regulated by^op, positively regulated by^op
has domain: process^c
has range: process^c
is inverse of: regulates^op

regulates^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002211

has characteristics : transitive

has super-properties: causally upstream of^op
has sub-properties: directly regulates^op, indirectly regulates^op, negatively regulates^op, positively regulates^op
has domain: process^c
has range: process^c
is inverse of: regulated by^op
has sub-property chains: regulates^op o has effector activity^op; directly regulates^op o directly regulates^op

regulates activity of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0011002

has super-properties: causally influences^op
has sub-properties: directly regulates activity of^op
has domain: material entity^c
has range: material entity^c

regulates characteristic^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0019000

has super-properties: causally related to^op
has sub-properties: negatively regulates characteristic^op, positively regulates characteristic^op
has domain: process^c
has range: quality^c
has sub-property chains: regulates^op o regulates characteristic^op

related_condition^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000790

has sub-properties: ameliorates condition^op, causes or contributes to condition^op, correlated with condition^op, has_uncertain_significance_for_condition^op, inferred_to_cause_condition^op, inferred_to_contribute_to_condition^op, inferred_to_correlate_with_condition^op, is_candidate_variant_for^op, non-causal_for_condition^op

results in developmental progression of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002295

has super-properties: developmentally related to^op
has sub-properties: results in formation of anatomical entity^op
has domain: biological process^c
has range: anatomical entity^c

results in formation of anatomical entity^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002297

has super-properties: has output^op; results in developmental progression of^op
is inverse of: formed as result of^op

role of^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000081

has super-properties: characteristic of^op
is inverse of: has role^op

sequence role^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000968

The RO:0000087 (has role) property cannot be used here because its domain is explicitly constrained to independent continuants, and sequence features in GENO are generically dependent contnuants.

has super-properties: bearer of^op

sequence_derives_from^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000639

has super-properties: top object property
has sub-property chains: has part^op o sequence_derives_from^op

sequentially related to^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002514

has sub-properties: bounds sequence of^op, does not overlap sequence of^op, is bound by sequence of^op, overlaps sequence of^op
has domain: sequentially ordered entity^c
has range: sequentially ordered entity^c

starts during^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002091

has super-properties: temporal relation^op
has domain: occurrent^c
has range: occurrent^c
is inverse of: during which starts^op

targets_gene^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000414

This is intended to be used as an instance-class relation, used for linking an instance of a gene targeting reagent to the class of gene whose instances it targets.

has super-properties: has_affected_feature^op
is inverse of: is_gene_target_of^op

temporal relation^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002222

A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has sub-properties: during which ends^op, during which starts^op, ends after^op, ends during^op, precedes^op, starts during^op
has domain: occurrent^c
has range: occurrent^c

transitively provides input for^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002414

has characteristics : transitive

has super-properties: causally upstream of or within, positive effect^op
has sub-properties: provides input for^op
has domain: process^c
has range: process^c

varies_with^op back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000683

This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of)

has characteristics : symmetric

has sub-properties: completely_varies_with^op

Named Individuals

0: asymptomatic
100: asymptomatic
1: symptomatic but fully ambulatory
2: symptomatic but in bed less than 50% of the day
3: symptomatic in bed more than 50% of the day but not bed ridden
40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
4: bed ridden
60-70: symptomatic but in bed less than 50% of the day
80-90: symptomatic but fully ambulatory
ACS
Advanced Instruments Inc. (AI Companies)
AES Chemunex
Affymetrix
Afrotropical Ecoregion
Agilent
Aldabra Island Xeric Scrub Ecoregion
ambidexterous
Ambion
angstrom
Antigenix
Apogee Flow Systems
Applied Biosystems
Australasia Ecoregion
Beckman Coulter
Becton Dickinson (BD Biosciences)
Bentley Instruments
BIO-RAD
BioGents
Bruker Corporation
Bruker Daltonics
Carnarvon Xeric Shrublands Ecoregion
centimeter
Central Ranges Xeric Shrub Ecoregion
cM0 (colon)
cM0 (kidney)
cM0 (lung)
cM0 (ovary)
cM1 (colon)
cM1 (kidney)
cM1 (lung)
cM1 (ovary)
cM1a (colon)
cM1a (lung)
cM1b (colon)
cM1b (lung)
colony forming unit per volume
Compensation-ML
count per molar
count per molar second
count per nanomolar
count per nanomolar second
cubic centimeter
cubic decimeter
CytoBuoy
Cytopeia
Dako Cytomation
day
defined class
degree Celsius
degree Fahrenheit
East Saharan Montane Xeric Woodland Ecoregion
eBioscience
Edingburgh handedness inventory
Eritrean Coastal Desert Ecoregion
Ethiopian Xeric Grasslands and Shrublands Ecoregion
Exalpha Biological
example to be eventually removed
Exbio Antibodies
exemplar term
exploratory term
failed exploratory term
FCS
G1 (Fuhrman)
G1 (WHO)
G1: Well differentiated
G2 (Fuhrman)
G2 (WHO)
G2: Moderately differentiated
G3 (Fuhrman)
G3 (WHO)
G3: Poorly differentiated
G4 (Fuhrman)
G4 (WHO)
G4: Undifferentiated
Gating-ML
GenePattern CART
GenePattern HeatMapViewer data visualization
GenePattern hierarchical clustering
GenePattern HierarchicalClusteringViewer data visualization
GenePattern k-means clustering
GenePattern k-nearest neighbors
GenePattern LOOCV
GenePattern module CARTXValidation
GenePattern module HeatMapViewer
GenePattern module HierarchicalClustering
GenePattern module HierarchicalClusteringViewer
GenePattern module KMeansClustering
GenePattern module KNN
GenePattern module KNNXValidation
GenePattern module PCA
GenePattern module PeakMatch
GenePattern module SVM
GenePattern PCA
GenePattern peak matching
GenePattern SVM
Gibson Desert Ecoregion
gram
gram per deciliter
gram per liter
Great Victoria Desert Ecoregion
Helicos
hertz
High grade ovarian tumor
Hobyo Grassland and Shrubland Ecoregion
hour
Ile Europa and Bassas da India Ecoregion
Illumina
Indo-Malay Ecoregion
Invitrogen
Kalahari Xeric Savanna Ecoregion
Kaokoveld Desert Ecoregion
kilogram
left handed
Li-Cor
liter
Low grade ovarian tumor
Luminex
Madagascar Spiny Thickets Ecoregion
Madagascar Succulent Woodlands Ecoregion
Masai Xeric Grasslands and Shrublands Ecoregion
mass percentage
mass volume percentage
metadata complete
metadata incomplete
meter
microgram
microgram per liter
microliter
microliters per minute
micrometer
micromolar
micromole
milligram
milligram per milliliter
milliliter
milliliter per liter
millimeter
millimolar
Millipore
Miltenyi Biotec
minute
molar
month
Nama Karoo Ecoregion
named class expression
Namib Desert Ecoregion
Namibian Savanna Woodland Ecoregion
nanogram
nanoliter
nanometer
nanomolar
nanomole
NanoString Technologies
Nimblegen
Northwestern Thorn Scrub Forests
Nullarbor Plains Xeric Shrubland Ecoregion
obsolete_core
Occult Carcinoma (AJCC 7th)
Oman and United Arab Emirates Ecoregion
Oman, Yemen, and Saudi Arabia Ecoregion
organizational term
out of scope
OWL
Oxford Nanopore Technologies
Pacific Biosciences
Partec
pending final vetting
pH
picogram
picoliter
picomolar
picomole
Pilbara Shrublands Ecoregion
placeholder removed
pM1 (colon)
pM1 (kidney)
pM1 (lung)
pM1 (ovary)
pM1a (colon)
pM1a (lung)
pM1b (colon)
pM1b (lung)
pN0 (colon)
pN0 (kidney)
pN0 (lung)
pN0 (ovary)
pN1 (colon)
pN1 (kidney)
pN1 (lung)
pN1 (ovary)
pN1a (colon)
pN1b (colon)
pN1c (colon)
pN2 (colon)
pN2 (lung)
pN2a (colon)
pN2b (colon)
pN3 (lung)
pT0 (colon)
pT0 (kidney)
pT0 (lung)
pT0 (ovary)
pT1 (colon)
pT1 (kidney)
pT1 (lung)
pT1 (ovary)
pT1a (kidney)
pT1a (lung)
pT1a (ovary)
pT1b (kidney)
pT1b (lung)
pT1b (ovary)
pT1c (ovary)
pT2 (colon)
pT2 (kidney)
pT2 (lung)
pT2 (ovary)
pT2a (kidney)
pT2a (lung)
pT2a (ovary)
pT2b (kidney)
pT2b (lung)
pT2b (ovary)
pT2c (ovary)
pT3 (colon)
pT3 (kidney)
pT3 (lung)
pT3 (ovary)
pT3a (kidney)
pT3a (ovary)
pT3b (kidney)
pT3b (ovary)
pT3c (kidney)
pT3c (ovary)
pT4 (kidney)
pT4 (lung)
pT4a (colon)
pT4b (colon)
pTis (colon)
pTis (lung)
RDF
ready for release
Red Sea Coastal Desert Ecoregion
requires discussion
right handed
Roche
second
Simpson Desert Region
Socotran Archipelago Ecoregion
Solar radiation
Somali Montane Xeric Woodland Ecoregion
Stage 0 (AJCC 7th)
Stage 1 (FIGO)
Stage 1A (FIGO)
Stage 1B (FIGO)
Stage 1C (FIGO)
Stage 2 (FIGO)
Stage 2A (FIGO)
Stage 2B (FIGO)
Stage 2C (FIGO)
Stage 3 (FIGO)
Stage 3A (FIGO)
Stage 3B (FIGO)
Stage 3C (FIGO)
Stage 4 (FIGO)
Stage I (AJCC 7th)
Stage IA (FIGO)
Stage IA1 (FIGO)
Stage IA2 (FIGO)
Stage IB (FIGO)
Stage IB1 (FIGO)
Stage IB2 (FIGO)
Stage IIA (AJCC 7th)
Stage IIA (FIGO)
Stage IIA1 (FIGO)
Stage IIA2 (FIGO)
Stage IIB (AJCC 7th)
Stage IIB (FIGO)
Stage IIC (AJCC 7th)
Stage IIIA (AJCC 7th)
Stage IIIA (FIGO)
Stage IIIB (AJCC 7th)
Stage IIIB (FIGO)
Stage IIIC (AJCC 7th)
Stage IVA (AJCC 7th)
Stage IVA (FIGO)
Stage IVB (AJCC 7th)
Stage IVB (FIGO)
Stage Unknown (FIGO)
Succulent Karoo Ecoregion
Sysmex Corporation, Kobe, Japan
tar
term imported
term split
terms merged
Thar Desert
The Great Sandy-Tanami Desert Ecoregion
Thermo
Thermo Fisher Scientific
Tirari-Sturt Stony Desert Ecoregion
to be replaced with external ontology term
Transformation-ML
U.S. Food and Drug Administration
uncurated
universal
volume percentage
Waters
week
Western Australian Mulga Shrublands Ecoregion
XML
year
Yemen and Saudi Arabia Ecoregion
Yemen, Saudi Arabia, and Oman Ecoregion
zip

0: asymptomaticⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002361

belongs to: Eastern Cooperative Oncology Group score value specification^c

100: asymptomaticⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002364

belongs to: Karnofsky score vaue specification^c

1: symptomatic but fully ambulatoryⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002362

belongs to: Eastern Cooperative Oncology Group score value specification^c

2: symptomatic but in bed less than 50% of the dayⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002359

belongs to: Eastern Cooperative Oncology Group score value specification^c

3: symptomatic in bed more than 50% of the day but not bed riddenⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002358

belongs to: Eastern Cooperative Oncology Group score value specification^c

40-50: symptomatic, in bed more than 50% of the day, but not bed riddenⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002367

belongs to: Karnofsky score vaue specification^c

4: bed riddenⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002360

belongs to: Eastern Cooperative Oncology Group score value specification^c

60-70: symptomatic but in bed less than 50% of the dayⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002366

belongs to: Karnofsky score vaue specification^c

80-90: symptomatic but fully ambulatoryⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002365

belongs to: Karnofsky score vaue specification^c

ACSⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000321

belongs to: data format specification^c

Advanced Instruments Inc. (AI Companies)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001375

belongs to: manufacturer^c

AES Chemunexⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001428

belongs to: manufacturer^c

Affymetrixⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000462

belongs to: manufacturer^c; material supplier^c

Afrotropical Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001583

Agilentⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000765

belongs to: manufacturer^c

Aldabra Island Xeric Scrub Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001605

has facts: part of^op Afrotropical Ecoregion

ambidexterousⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000979

belongs to: categorical label^c

Ambionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000756

belongs to: manufacturer^c

angstromⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000019

belongs to: length unit^c

Antigenixⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001347

belongs to: manufacturer^c

Apogee Flow Systemsⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001312

belongs to: manufacturer^c

Applied Biosystemsⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000776

belongs to: manufacturer^c

Australasia Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001571

Beckman Coulterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001372

belongs to: manufacturer^c

Becton Dickinson (BD Biosciences)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001321

belongs to: manufacturer^c

Bentley Instrumentsⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001431

belongs to: manufacturer^c

BIO-RADⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000754

belongs to: manufacturer^c

BioGentsⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002903

belongs to: manufacturer^c

Bruker Corporationⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000770

belongs to: manufacturer^c

Bruker Daltonicsⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000779

belongs to: manufacturer^c

Carnarvon Xeric Shrublands Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001575

has facts: part of^op Australasia Ecoregion

centimeterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000015

belongs to: length unit^c

Central Ranges Xeric Shrub Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001576

has facts: part of^op Australasia Ecoregion

cM0 (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002291

belongs to: pathologic distant metastases stage for colon according to AJCC 7th edition^c

cM0 (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002307

belongs to: pathologic distant metastases stage for kidney according to AJCC 7th edition^c

cM0 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002299

belongs to: pathologic distant metastases stage for lung according to AJCC 7th edition^c

cM0 (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002311

belongs to: pathologic distant metastases stage for ovary according to AJCC 7th edition^c

cM1 (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002292

belongs to: pathologic distant metastases stage for colon according to AJCC 7th edition^c

cM1 (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002308

belongs to: pathologic distant metastases stage for kidney according to AJCC 7th edition^c

cM1 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002300

belongs to: pathologic distant metastases stage for lung according to AJCC 7th edition^c

cM1 (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002312

belongs to: pathologic distant metastases stage for ovary according to AJCC 7th edition^c

cM1a (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002293

belongs to: pathologic distant metastases stage for colon according to AJCC 7th edition^c

cM1a (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002301

belongs to: pathologic distant metastases stage for lung according to AJCC 7th edition^c

cM1b (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002294

belongs to: pathologic distant metastases stage for colon according to AJCC 7th edition^c

cM1b (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002302

belongs to: pathologic distant metastases stage for lung according to AJCC 7th edition^c

colony forming unit per volumeⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000212

belongs to: concentration unit^c

Compensation-MLⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000329

belongs to: data format specification^c

count per molarⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000285

belongs to: rate unit^c

count per molar secondⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000282

belongs to: rate unit^c

count per nanomolarⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000284

belongs to: rate unit^c

count per nanomolar secondⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000281

belongs to: rate unit^c

cubic centimeterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000097

belongs to: volume unit^c

cubic decimeterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000100

belongs to: volume unit^c

CytoBuoyⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001458

belongs to: manufacturer^c

Cytopeiaⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001224

belongs to: manufacturer^c

Dako Cytomationⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001338

belongs to: manufacturer^c

dayⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000033

belongs to: time unit^c

defined classⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000420

belongs to: denotator type^c

degree Celsiusⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000027

belongs to: temperature unit^c

degree Fahrenheitⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000195

belongs to: temperature unit^c

East Saharan Montane Xeric Woodland Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001603

has facts: part of^op Afrotropical Ecoregion

eBioscienceⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001213

belongs to: manufacturer^c

Edingburgh handedness inventoryⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001004

belongs to: questionnaire^c

Eritrean Coastal Desert Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001602

has facts: part of^op Afrotropical Ecoregion

Ethiopian Xeric Grasslands and Shrublands Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001601

has facts: part of^op Afrotropical Ecoregion

Exalpha Biologicalⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001287

belongs to: manufacturer^c

example to be eventually removedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000002

belongs to: curation status specification^c

Exbio Antibodiesⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001320

belongs to: manufacturer^c

exemplar termⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000514

belongs to: data about an ontology part^c

exploratory termⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GENO_0000484

belongs to: data about an ontology part^c

failed exploratory termⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000103

belongs to: obsolescence reason specification^c

FCSⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000327

belongs to: data format specification^c

G1 (Fuhrman)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002211

belongs to: histologic grade according to the Fuhrman Nuclear Grading System^c

G1 (WHO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002220

belongs to: histologic grade for ovarian tumor according to the World Health Organization^c

G1: Well differentiatedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002206

belongs to: histologic grade according to AJCC 7th edition^c

G2 (Fuhrman)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002212

belongs to: histologic grade according to the Fuhrman Nuclear Grading System^c

G2 (WHO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002221

belongs to: histologic grade for ovarian tumor according to the World Health Organization^c

G2: Moderately differentiatedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002207

belongs to: histologic grade according to AJCC 7th edition^c

G3 (Fuhrman)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002213

belongs to: histologic grade according to the Fuhrman Nuclear Grading System^c

G3 (WHO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002222

belongs to: histologic grade for ovarian tumor according to the World Health Organization^c

G3: Poorly differentiatedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002208

belongs to: histologic grade according to AJCC 7th edition^c

G4 (Fuhrman)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002214

belongs to: histologic grade according to the Fuhrman Nuclear Grading System^c

G4 (WHO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002223

belongs to: histologic grade for ovarian tumor according to the World Health Organization^c

G4: Undifferentiatedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002209

belongs to: histologic grade according to AJCC 7th edition^c

Gating-MLⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000330

belongs to: data format specification^c

GenePattern CARTⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000767

belongs to: CART^c

GenePattern HeatMapViewer data visualizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000780

belongs to: clustered data visualization^c

GenePattern hierarchical clusteringⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000755

belongs to: hierarchical clustering^c

GenePattern HierarchicalClusteringViewer data visualizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000781

belongs to: clustered data visualization^c

GenePattern k-means clusteringⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000764

belongs to: k-means clustering^c

GenePattern k-nearest neighborsⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000762

belongs to: k-nearest neighbors^c

GenePattern LOOCVⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000763

belongs to: leave one out cross validation method^c

GenePattern module CARTXValidationⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000768

belongs to: GenePattern software^c
has facts: is about^op GenePattern LOOCV; is about^op GenePattern CART

GenePattern module HeatMapViewerⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000782

belongs to: GenePattern software^c
has facts: is about^op GenePattern HeatMapViewer data visualization

GenePattern module HierarchicalClusteringⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000774

belongs to: GenePattern software^c
has facts: is about^op GenePattern hierarchical clustering

GenePattern module HierarchicalClusteringViewerⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000783

belongs to: GenePattern software^c
has facts: is about^op GenePattern HierarchicalClusteringViewer data visualization

GenePattern module KMeansClusteringⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000766

belongs to: GenePattern software^c
has facts: is about^op GenePattern k-means clustering

GenePattern module KNNⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000773

belongs to: GenePattern software^c
has facts: is about^op GenePattern k-nearest neighbors

GenePattern module KNNXValidationⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000771

belongs to: GenePattern software^c

GenePattern module PCAⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000777

belongs to: GenePattern software^c
has facts: is about^op GenePattern PCA

GenePattern module PeakMatchⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000772

belongs to: GenePattern software^c
has facts: is about^op GenePattern peak matching

GenePattern module SVMⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000761

belongs to: GenePattern software^c
has facts: is about^op GenePattern SVM

GenePattern PCAⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000760

belongs to: principal components analysis dimensionality reduction^c

GenePattern peak matchingⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000778

belongs to: peak matching^c

GenePattern SVMⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000775

belongs to: support vector machine^c

Gibson Desert Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001577

has facts: part of^op Australasia Ecoregion

gramⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000021

belongs to: mass unit^c

gram per deciliterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000208

belongs to: concentration unit^c

gram per literⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000175

belongs to: concentration unit^c

Great Victoria Desert Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001579

has facts: part of^op Australasia Ecoregion

Helicosⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000757

belongs to: manufacturer^c

hertzⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000106

belongs to: frequency unit^c

High grade ovarian tumorⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002218

belongs to: histologic grade for ovarian tumor according to a two-tier grading system^c

Hobyo Grassland and Shrubland Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001599

has facts: part of^op Afrotropical Ecoregion

hourⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000032

belongs to: time unit^c

Ile Europa and Bassas da India Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001598

has facts: part of^op Afrotropical Ecoregion

Illuminaⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000759

belongs to: manufacturer^c

Indo-Malay Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001626

Invitrogenⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001434

belongs to: manufacturer^c

Kalahari Xeric Savanna Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001597

has facts: part of^op Afrotropical Ecoregion

Kaokoveld Desert Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001596

has facts: part of^op Afrotropical Ecoregion

kilogramⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000009

belongs to: mass unit^c

left handedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000998

belongs to: categorical label^c

Li-Corⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000769

belongs to: manufacturer^c

literⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000099

belongs to: volume unit^c

Low grade ovarian tumorⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002217

belongs to: histologic grade for ovarian tumor according to a two-tier grading system^c

Luminexⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001443

belongs to: manufacturer^c

Madagascar Spiny Thickets Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001595

has facts: part of^op Afrotropical Ecoregion

Madagascar Succulent Woodlands Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001594

has facts: part of^op Afrotropical Ecoregion

Masai Xeric Grasslands and Shrublands Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001593

has facts: part of^op Afrotropical Ecoregion

mass percentageⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000163

belongs to: concentration unit^c

mass volume percentageⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000164

belongs to: concentration unit^c

metadata completeⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000120

belongs to: curation status specification^c

metadata incompleteⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000123

belongs to: curation status specification^c

meterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000008

belongs to: length unit^c

microgramⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000023

belongs to: mass unit^c

microgram per literⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000301

belongs to: concentration unit^c

microliterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000101

belongs to: volume unit^c

microliters per minuteⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000271

belongs to: volumetric flow rate unit^c

micrometerⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000017

belongs to: length unit^c

micromolarⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000064

belongs to: concentration unit^c

micromoleⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000039

belongs to: substance unit^c

milligramⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000022

belongs to: mass unit^c

milligram per milliliterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000176

belongs to: concentration unit^c

milliliterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000098

belongs to: volume unit^c

milliliter per literⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000207

belongs to: concentration unit^c

millimeterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000016

belongs to: length unit^c

millimolarⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000063

belongs to: concentration unit^c

Milliporeⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001340

belongs to: manufacturer^c

Miltenyi Biotecⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001424

belongs to: manufacturer^c

minuteⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000031

belongs to: time unit^c

molarⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000062

belongs to: concentration unit^c

monthⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000035

belongs to: time unit^c

Nama Karoo Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001592

has facts: part of^op Afrotropical Ecoregion

named class expressionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000421

belongs to: denotator type^c

Namib Desert Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001591

has facts: part of^op Afrotropical Ecoregion

Namibian Savanna Woodland Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001590

has facts: part of^op Afrotropical Ecoregion

nanogramⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000024

belongs to: mass unit^c

nanoliterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000102

belongs to: volume unit^c

nanometerⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000018

belongs to: length unit^c

nanomolarⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000065

belongs to: concentration unit^c

nanomoleⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000041

belongs to: substance unit^c

NanoString Technologiesⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001860

belongs to: manufacturer^c

Nimblegenⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001855

belongs to: manufacturer^c

Northwestern Thorn Scrub Forestsⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001628

has facts: part of^op Indo-Malay Ecoregion

Nullarbor Plains Xeric Shrubland Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001580

has facts: part of^op Australasia Ecoregion

obsolete_coreⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000224

Occult Carcinoma (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002315

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Oman and United Arab Emirates Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001600

has facts: part of^op Afrotropical Ecoregion

Oman, Yemen, and Saudi Arabia Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001604

has facts: part of^op Afrotropical Ecoregion

organizational termⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000121

belongs to: curation status specification^c

out of scopeⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OMO_0001000

belongs to: obsolescence reason specification^c

OWLⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000332

belongs to: data format specification^c

Oxford Nanopore Technologiesⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002755

belongs to: manufacturer^c

Pacific Biosciencesⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001856

belongs to: manufacturer^c

Partecⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001355

belongs to: manufacturer^c

pending final vettingⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000125

belongs to: curation status specification^c

pHⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000196

belongs to: concentration unit^c

picogramⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000025

belongs to: mass unit^c

picoliterⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000103

belongs to: volume unit^c

picomolarⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000066

belongs to: concentration unit^c

picomoleⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000042

belongs to: substance unit^c

Pilbara Shrublands Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001574

has facts: part of^op Australasia Ecoregion

placeholder removedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000226

belongs to: obsolescence reason specification^c

pM1 (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002295

belongs to: pathologic distant metastases stage for colon according to AJCC 7th edition^c

pM1 (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002309

belongs to: pathologic distant metastases stage for kidney according to AJCC 7th edition^c

pM1 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002303

belongs to: pathologic distant metastases stage for lung according to AJCC 7th edition^c

pM1 (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002313

belongs to: pathologic distant metastases stage for ovary according to AJCC 7th edition^c

pM1a (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002296

belongs to: pathologic distant metastases stage for colon according to AJCC 7th edition^c

pM1a (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002304

belongs to: pathologic distant metastases stage for lung according to AJCC 7th edition^c

pM1b (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002297

belongs to: pathologic distant metastases stage for colon according to AJCC 7th edition^c

pM1b (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002305

belongs to: pathologic distant metastases stage for lung according to AJCC 7th edition^c

pN0 (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002271

belongs to: pathologic lymph node stage for colon and rectum according to AJCC 7th edition^c

pN0 (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002285

belongs to: pathologic lymph node stage for kidney according to AJCC 7th edition^c

pN0 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002280

belongs to: pathologic lymph node stage for lung according to AJCC 7th edition^c

pN0 (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002288

belongs to: pathologic lymph node stage for ovary according to AJCC 7th edition^c

pN1 (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002272

belongs to: pathologic lymph node stage for colon and rectum according to AJCC 7th edition^c

pN1 (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002286

belongs to: pathologic lymph node stage for kidney according to AJCC 7th edition^c

pN1 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002281

belongs to: pathologic lymph node stage for lung according to AJCC 7th edition^c

pN1 (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002289

belongs to: pathologic lymph node stage for ovary according to AJCC 7th edition^c

pN1a (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002273

belongs to: pathologic lymph node stage for colon and rectum according to AJCC 7th edition^c

pN1b (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002274

belongs to: pathologic lymph node stage for colon and rectum according to AJCC 7th edition^c

pN1c (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002275

belongs to: pathologic lymph node stage for colon and rectum according to AJCC 7th edition^c

pN2 (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002276

belongs to: pathologic lymph node stage for colon and rectum according to AJCC 7th edition^c

pN2 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002282

belongs to: pathologic lymph node stage for lung according to AJCC 7th edition^c

pN2a (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002277

belongs to: pathologic lymph node stage for colon and rectum according to AJCC 7th edition^c

pN2b (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002278

belongs to: pathologic lymph node stage for colon and rectum according to AJCC 7th edition^c

pN3 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002283

belongs to: pathologic lymph node stage for lung according to AJCC 7th edition^c

pT0 (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002225

belongs to: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition^c

pT0 (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002244

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT0 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002233

belongs to: pathologic primary tumor stage for lung according to AJCC 7th edition^c

pT0 (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002257

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT1 (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002227

belongs to: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition^c

pT1 (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002245

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT1 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002235

belongs to: pathologic primary tumor stage for lung according to AJCC 7th edition^c

pT1 (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002258

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT1a (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002246

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT1a (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002236

belongs to: pathologic primary tumor stage for lung according to AJCC 7th edition^c

pT1a (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002259

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT1b (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002247

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT1b (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002237

belongs to: pathologic primary tumor stage for lung according to AJCC 7th edition^c

pT1b (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002260

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT1c (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002261

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT2 (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002228

belongs to: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition^c

pT2 (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002248

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT2 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002238

belongs to: pathologic primary tumor stage for lung according to AJCC 7th edition^c

pT2 (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002262

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT2a (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002249

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT2a (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002239

belongs to: pathologic primary tumor stage for lung according to AJCC 7th edition^c

pT2a (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002263

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT2b (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002250

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT2b (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002240

belongs to: pathologic primary tumor stage for lung according to AJCC 7th edition^c

pT2b (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002264

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT2c (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002265

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT3 (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002229

belongs to: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition^c

pT3 (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002251

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT3 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002241

belongs to: pathologic primary tumor stage for lung according to AJCC 7th edition^c

pT3 (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002266

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT3a (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002252

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT3a (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002267

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT3b (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002253

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT3b (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002268

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT3c (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002254

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT3c (ovary)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002269

belongs to: pathologic primary tumor stage for ovary according to AJCC 7th edition^c

pT4 (kidney)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002255

belongs to: pathologic primary tumor stage for kidney according to AJCC 7th edition^c

pT4 (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002242

belongs to: pathologic primary tumor stage for lung according to AJCC 7th edition^c

pT4a (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002230

belongs to: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition^c

pT4b (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002231

belongs to: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition^c

pTis (colon)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002226

belongs to: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition^c

pTis (lung)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002234

belongs to: pathologic primary tumor stage for lung according to AJCC 7th edition^c

RDFⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000324

belongs to: data format specification^c

ready for releaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000122

belongs to: curation status specification^c

Red Sea Coastal Desert Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001589

has facts: part of^op Afrotropical Ecoregion

requires discussionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000428

belongs to: curation status specification^c

right handedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000958

belongs to: categorical label^c

Rocheⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000758

belongs to: manufacturer^c

secondⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000010

belongs to: time unit^c

Simpson Desert Regionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001573

has facts: part of^op Australasia Ecoregion

Socotran Archipelago Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001588

has facts: part of^op Afrotropical Ecoregion

Solar radiationⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001862

has facts: process has causal agent^op q525

Somali Montane Xeric Woodland Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001587

has facts: part of^op Afrotropical Ecoregion

Stage 0 (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002316

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Stage 1 (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002342

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 1A (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002343

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 1B (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002344

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 1C (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002345

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 2 (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002346

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 2A (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002347

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 2B (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002348

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 2C (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002349

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 3 (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002350

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 3A (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002351

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 3B (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002352

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 3C (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002353

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage 4 (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002354

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Stage I (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002317

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Stage IA (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002327

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IA1 (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002328

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IA2 (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002329

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IB (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002330

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IB1 (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002331

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IB2 (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002332

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IIA (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002318

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Stage IIA (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002333

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IIA1 (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002334

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IIA2 (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002335

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IIB (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002319

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Stage IIB (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002336

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IIC (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002320

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Stage IIIA (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002321

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Stage IIIA (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002337

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IIIB (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002322

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Stage IIIB (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002338

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IIIC (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002323

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Stage IVA (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002324

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Stage IVA (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002339

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage IVB (AJCC 7th)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002325

belongs to: clinical tumor stage group according to AJCC 7th edition^c

Stage IVB (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002340

belongs to: International Federation of Gynecology and Obstetrics cervical cancer stage value specification^c

Stage Unknown (FIGO)ⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002355

belongs to: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification^c

Succulent Karoo Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001584

has facts: part of^op Afrotropical Ecoregion

Sysmex Corporation, Kobe, Japanⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000829

belongs to: manufacturer^c

tarⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000326

belongs to: data format specification^c

term importedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000228

belongs to: obsolescence reason specification^c

term splitⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000229

belongs to: obsolescence reason specification^c

terms mergedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000227

belongs to: obsolescence reason specification^c

Thar Desertⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001627

has facts: part of^op Indo-Malay Ecoregion

The Great Sandy-Tanami Desert Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001578

has facts: part of^op Australasia Ecoregion

Thermoⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000752

belongs to: manufacturer^c

Thermo Fisher Scientificⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002193

belongs to: organization^c

Tirari-Sturt Stony Desert Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001572

has facts: part of^op Australasia Ecoregion

to be replaced with external ontology termⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000423

belongs to: curation status specification^c

Transformation-MLⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000317

belongs to: data format specification^c

U.S. Food and Drug Administrationⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000901

belongs to: regulatory agency^c

uncuratedⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000124

belongs to: curation status specification^c

universalⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000410

belongs to: denotator type^c

volume percentageⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000165

belongs to: concentration unit^c

Watersⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000753

belongs to: manufacturer^c

weekⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000034

belongs to: time unit^c

Western Australian Mulga Shrublands Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001569

has facts: part of^op Australasia Ecoregion

XMLⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000322

belongs to: data format specification^c

yearⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UO_0000036

belongs to: time unit^c

Yemen and Saudi Arabia Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001585

has facts: part of^op Afrotropical Ecoregion

Yemen, Saudi Arabia, and Oman Ecoregionⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/ENVO_01001586

has facts: part of^op Afrotropical Ecoregion

zipⁿⁱ back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000325

belongs to: data format specification^c

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni .

GENO ontology

Table of Content

Introduction

Classes

A_to_C_transversionc back to ToC or Class ToC

A_to_G_transitionc back to ToC or Class ToC

A_to_T_transversionc back to ToC or Class ToC

abnormal(ly) absent adaxial cellc back to ToC or Class ToC

abnormal(ly) absent dorso-rostral clusterc back to ToC or Class ToC

abnormal(ly) disrupted diencephalon developmentc back to ToC or Class ToC

abnormal(ly) disrupted neutrophil aggregationc back to ToC or Class ToC

abnormal(ly) malformed endocardium cellc back to ToC or Class ToC

action specificationc back to ToC or Class ToC

algorithmc back to ToC or Class ToC

allelec back to ToC or Class ToC

allele originc back to ToC or Class ToC

allele setc back to ToC or Class ToC

allelic cellular distributionc back to ToC or Class ToC

allelic genotypec back to ToC or Class ToC

allelic phasec back to ToC or Class ToC

allelic statec back to ToC or Class ToC

allosomal inheritancec back to ToC or Class ToC

amino acid residuec back to ToC or Class ToC

amino acid sequencec back to ToC or Class ToC

Amniotac back to ToC or Class ToC

analysis subset ontology modulec back to ToC or Class ToC

anatomical entityc back to ToC or Class ToC

anatomical structurec back to ToC or Class ToC

ancestral polymorphic allelec back to ToC or Class ToC

aneusomicc back to ToC or Class ToC

aneusomic chromosomal partc back to ToC or Class ToC

aneusomic chromosomec back to ToC or Class ToC

aneusomic zygosityc back to ToC or Class ToC

Archaeac back to ToC or Class ToC

assemblyc back to ToC or Class ToC

associationc back to ToC or Class ToC

autosomal dominant inheritancec back to ToC or Class ToC

autosomal inheritancec back to ToC or Class ToC

autosomal recessive inheritancec back to ToC or Class ToC

B cellc back to ToC or Class ToC

background genomec back to ToC or Class ToC

Bacteriac back to ToC or Class ToC

base ontology modulec back to ToC or Class ToC

Bilateriac back to ToC or Class ToC

biological processc back to ToC or Class ToC

biological processc back to ToC or Class ToC

biological sequencec back to ToC or Class ToC

biological sequence or setc back to ToC or Class ToC

biological sequence setc back to ToC or Class ToC

biological sequence unitc back to ToC or Class ToC

biological sexc back to ToC or Class ToC

biparental allele originc back to ToC or Class ToC

Both strandsc back to ToC or Class ToC

bridge ontology modulec back to ToC or Class ToC

C_to_A_transversionc back to ToC or Class ToC

C_to_G_transversionc back to ToC or Class ToC

C_to_T_transitionc back to ToC or Class ToC

C_to_T_transition_at_pCpG_sitec back to ToC or Class ToC

CARTc back to ToC or Class ToC

categorical labelc back to ToC or Class ToC

categorical value specificationc back to ToC or Class ToC

cellc back to ToC or Class ToC

cell culture splittingc back to ToC or Class ToC

cell freezing mediumc back to ToC or Class ToC

cell linec back to ToC or Class ToC

cell line cellc back to ToC or Class ToC

centromerec back to ToC or Class ToC

chromosomal band intensityc back to ToC or Class ToC

chromosomal deletion inheritancec back to ToC or Class ToC

chromosomal duplication inheritancec back to ToC or Class ToC

chromosomal inheritancec back to ToC or Class ToC

chromosomal rearrangement inheritancec back to ToC or Class ToC

chromosomal regionc back to ToC or Class ToC

chromosomec back to ToC or Class ToC

chromosome armc back to ToC or Class ToC

chromosome bandc back to ToC or Class ToC

chromosome partc back to ToC or Class ToC

chromosome sub-bandc back to ToC or Class ToC

class discovery data transformationc back to ToC or Class ToC

class discovery objectivec back to ToC or Class ToC

A_to_C_transversion^c back to ToC or Class ToC

A_to_G_transition^c back to ToC or Class ToC

A_to_T_transversion^c back to ToC or Class ToC

abnormal(ly) absent adaxial cell^c back to ToC or Class ToC

abnormal(ly) absent dorso-rostral cluster^c back to ToC or Class ToC

abnormal(ly) disrupted diencephalon development^c back to ToC or Class ToC

abnormal(ly) disrupted neutrophil aggregation^c back to ToC or Class ToC

abnormal(ly) malformed endocardium cell^c back to ToC or Class ToC

action specification^c back to ToC or Class ToC

algorithm^c back to ToC or Class ToC

allele^c back to ToC or Class ToC

allele origin^c back to ToC or Class ToC

allele set^c back to ToC or Class ToC

allelic cellular distribution^c back to ToC or Class ToC

allelic genotype^c back to ToC or Class ToC

allelic phase^c back to ToC or Class ToC

allelic state^c back to ToC or Class ToC

allosomal inheritance^c back to ToC or Class ToC

amino acid residue^c back to ToC or Class ToC

amino acid sequence^c back to ToC or Class ToC

Amniota^c back to ToC or Class ToC

analysis subset ontology module^c back to ToC or Class ToC

anatomical entity^c back to ToC or Class ToC

anatomical structure^c back to ToC or Class ToC

ancestral polymorphic allele^c back to ToC or Class ToC

aneusomic^c back to ToC or Class ToC

aneusomic chromosomal part^c back to ToC or Class ToC

aneusomic chromosome^c back to ToC or Class ToC

aneusomic zygosity^c back to ToC or Class ToC

Archaea^c back to ToC or Class ToC

assembly^c back to ToC or Class ToC

association^c back to ToC or Class ToC

autosomal dominant inheritance^c back to ToC or Class ToC

autosomal inheritance^c back to ToC or Class ToC

autosomal recessive inheritance^c back to ToC or Class ToC

B cell^c back to ToC or Class ToC

background genome^c back to ToC or Class ToC

Bacteria^c back to ToC or Class ToC

base ontology module^c back to ToC or Class ToC

Bilateria^c back to ToC or Class ToC

biological process^c back to ToC or Class ToC

biological process^c back to ToC or Class ToC

biological sequence^c back to ToC or Class ToC

biological sequence or set^c back to ToC or Class ToC

biological sequence set^c back to ToC or Class ToC

biological sequence unit^c back to ToC or Class ToC

biological sex^c back to ToC or Class ToC

biparental allele origin^c back to ToC or Class ToC

Both strands^c back to ToC or Class ToC

bridge ontology module^c back to ToC or Class ToC

C_to_A_transversion^c back to ToC or Class ToC

C_to_G_transversion^c back to ToC or Class ToC

C_to_T_transition^c back to ToC or Class ToC

C_to_T_transition_at_pCpG_site^c back to ToC or Class ToC

CART^c back to ToC or Class ToC

categorical label^c back to ToC or Class ToC

categorical value specification^c back to ToC or Class ToC

cell^c back to ToC or Class ToC

cell culture splitting^c back to ToC or Class ToC

cell freezing medium^c back to ToC or Class ToC

cell line^c back to ToC or Class ToC

cell line cell^c back to ToC or Class ToC

centromere^c back to ToC or Class ToC

chromosomal band intensity^c back to ToC or Class ToC

chromosomal deletion inheritance^c back to ToC or Class ToC

chromosomal duplication inheritance^c back to ToC or Class ToC

chromosomal inheritance^c back to ToC or Class ToC

chromosomal rearrangement inheritance^c back to ToC or Class ToC

chromosomal region^c back to ToC or Class ToC

chromosome^c back to ToC or Class ToC

chromosome arm^c back to ToC or Class ToC

chromosome band^c back to ToC or Class ToC

chromosome part^c back to ToC or Class ToC

chromosome sub-band^c back to ToC or Class ToC

class discovery data transformation^c back to ToC or Class ToC

class discovery objective^c back to ToC or Class ToC

class prediction data transformation^c back to ToC or Class ToC

class prediction objective^c back to ToC or Class ToC

classified data set^c back to ToC or Class ToC

clinical tumor stage group according to AJCC 7th edition^c back to ToC or Class ToC