The MGED Ontology

Classes

action
age
allele
array design package
array group
array package
atmosphere
atomic action
audit and security package
barrier facility
bedding
bibliographic reference
bio assay
bio assay data
bio assay data cluster
bio assay data package
bio assay package
bio material
bio material characteristic category
bio material characteristics
bio material package
bio material purity
bio molecular annotation
bio sample
bio sample type
bio sequence
bio sequence package
bio sequence type
bio source
bio source provider
bio source type
biological factor category
biological property
biometrics
cancer site
cell line
cell line database
cell type
cell type database
cellular component
cellular component database
chromosomal aberration
chromosomal aberration classification
clinical history
clinical treatment
clinical treatment database
complex action
compound
compound database
concentration unit
concentration unit other
contact
control type
cultivar
data transformation protocol type
data type
database
database entry type
defect type
delivery method
deprecated terms
deprecation reason
derived bio assay
derived bio assay type
description package
design element
design element group
design element group type
design element package
developmental stage
developmental stage database
disease location
disease staging
disease staging database
disease state
disease state database
distance unit
distance unit other
ecotype
environmental factor category
environmental history
environmental stress
epidemiological design
experiment
experiment design
experiment design type
experiment package
experimental factor
experimental factor category
experimental protocol type
factor value
factor value dependency
factor value set
fail type
family history
family member
family relationship
feature defect
feature group
feature shape
fiducial
fiducial type
generation
genetic material
genetic modification
genotype
geographic location
geographic location database
growth condition
haplotype
hardware
hardware type
hardware variation
higher level analysis package
higher level analysis protocol type
histology
histology database
history factor
host
humidity
image
image format
individual
individual chromosomal abnormality
individual genetic characteristics
initial time point
label compound
labeled extract
light
light unit
m g e d core ontology
m g e d extended ontology
m g e d ontology
m g e d ontology version
mass unit
mass unit other
material type
measurement
measurement package
measurement type
media
methodological design
methodological factor category
node
node value
node value type
normalization description
normalization description type
nutrients
observation
observation database
ontology entry
operator variation
organism
organism database
organism part
organism part database
organism status
organization
other unit
parameter
pathogen test
person
perturbational design
phenotype
phenotype database
physical array design
physical bio assay
physical bio sequence type
ploidy
polymer type
population density
preservation
preservation type
protocol
protocol package
protocol parameter type
protocol type
protocol variation
publication type
quality control description
quality control description type
quantitation type
quantitation type package
quantity unit
quantity unit other
radiation unit
replicate description
replicate description type
reporter
result
roles
sampling time point
scale
seq feature basis
sequence ontology bio sequence type
sequence ontology database
serotype
sex
software
software type
software variation
somatic modification
strain or line
strain or line database
strand type
substrate type
surface type
targeted cell type
targeted cell type database
technological design
technology type
temperature
temperature unit
test
test result
test type
test type database
theoretical bio sequence type
time unit
time unit other
transformation
treatment
tumor grading
tumor grading database
u r i
unit
user
volume unit
volume unit other
warning type
water
zone defect

action^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Action

Procedures used during treatment.

has super-classes: bio material package^c; biological factor category^c
has sub-classes: atomic action^c, complex action^c

age^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Age

The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting).

has super-classes: bio material characteristics^c; has maximum measurement^op some measurement^c; has measurement^op some measurement^c; has initial time point^op some initial time point^c
is in domain of: has initial time point^op, has maximum measurement^op

allele^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Allele

One of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on phenotype or sequence. Polymorphisms are included in this definition.

has super-classes: individual genetic characteristics^c
has members: wild typeⁿⁱ

array design package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ArrayDesignPackage

MAGE package that describes the array layout and design. The array may be physical or virtual.

has super-classes: m g e d core ontology^c
has sub-classes: design element group^c, design element group type^c, feature shape^c, physical array design^c, surface type^c, technology type^c

array group^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ArrayGroup

An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays.

has super-classes: array package^c; has type^op some substrate type^c; has fiducials^op some fiducial^c

array package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ArrayPackage

MAGE package for describing the process by which arrays were manufactured.

has super-classes: m g e d core ontology^c
has sub-classes: array group^c, defect type^c, feature defect^c, fiducial^c, fiducial type^c, substrate type^c, zone defect^c

atmosphere^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Atmosphere

The atmospheric conditions used to culture or grow an organism.

has super-classes: growth condition^c; has atmospheric component^op some compound^c

atomic action^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#AtomicAction

An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add

has super-classes: action^c
has members: addⁿⁱ, change humidityⁿⁱ, change lightⁿⁱ, change temperatureⁿⁱ, concentrateⁿⁱ, diluteⁿⁱ, mix by inversionⁿⁱ, mix by pipetteⁿⁱ, mix by vortexⁿⁱ, mix generalⁿⁱ, placeⁿⁱ, removeⁿⁱ, resuspendⁿⁱ, set temperatureⁿⁱ, specified biomaterial actionⁿⁱ, spinⁿⁱ, waitⁿⁱ

audit and security package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#AuditAndSecurityPackage

MAGE package for contacts including organizations and people.

has super-classes: m g e d core ontology^c
has sub-classes: contact^c, roles^c

barrier facility^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BarrierFacility

Rating of containment system for the protection of organisms from infectious agents.

has super-classes: growth condition^c

bedding^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Bedding

Refers to the bedding material present in an animals housing.

has super-classes: environmental history^c

bibliographic reference^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BibliographicReference

A bibliographic reference is a published citation in a journal, book, other format e.g. web resource

has super-classes: description package^c; has title^dp some string; has publisher^dp some string; has authors^dp some string; has editor^dp some string; has pages^dp some string; has issue^dp some string; has publication^dp some string; has type^op some publication type^c; has u r i^op some u r i^c; has volume^dp some string; has year^dp some date
is in domain of: has issue^dp, has pages^dp, has volume^dp

bio assay^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioAssay

A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays.

has super-classes: bio assay package^c
has sub-classes: derived bio assay^c, physical bio assay^c

bio assay data^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioAssayData

BioAssayData refers to the data files including images generated from one or more BioAssays.

has super-classes: bio assay data package^c

bio assay data cluster^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioAssayDataCluster

A grouping of bioassay data that has been organized by one or more mathematical functions into nodes.

has super-classes: higher level analysis package^c; has nodes^op some node^c

bio assay data package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioAssayDataPackage

MAGE package for BioAssayData.

has super-classes: m g e d extended ontology^c
has sub-classes: bio assay data^c, transformation^c

bio assay package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioAssayPackage

MAGE package for bioassay.

has super-classes: m g e d core ontology^c
has sub-classes: bio assay^c, derived bio assay type^c, image format^c

bio material^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioMaterial

Description of the processing state of the biomaterial for use in the microarray hybridization.

has super-classes: bio material package^c; has type^op some material type^c; has biomaterial characteristics^op some bio material characteristics^c
has sub-classes: bio sample^c, bio source^c, labeled extract^c

bio material characteristic category^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioMaterialCharacteristicCategory

General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue.

has super-classes: biological factor category^c
has members: ageⁿⁱ, biomaterial providerⁿⁱ, cell lineⁿⁱ, cell typeⁿⁱ, clinical informationⁿⁱ, clinical treatmentⁿⁱ, developmental stageⁿⁱ, disease stagingⁿⁱ, disease stateⁿⁱ, individualⁿⁱ, individual genetic characteristicⁿⁱ, organismⁿⁱ, organism partⁿⁱ, organism statusⁿⁱ, physical characteristicsⁿⁱ, sampling time pointⁿⁱ, sexⁿⁱ, strain or lineⁿⁱ, tumor gradingⁿⁱ
is also defined as: named individual

bio material characteristics^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioMaterialCharacteristics

Properties of the biomaterial before treated in any manner for the purposes of the experiment.

has super-classes: bio material package^c; biological factor category^c
has sub-classes: age^c, bio material purity^c, bio source provider^c, bio source type^c, biometrics^c, cell line^c, cell type^c, cellular component^c, chromosomal aberration classification^c, clinical treatment^c, developmental stage^c, disease staging^c, disease state^c, environmental history^c, genetic modification^c, histology^c, individual^c, individual genetic characteristics^c, observation^c, organism^c, organism part^c, organism status^c, phenotype^c, serotype^c, sex^c, strain or line^c, targeted cell type^c, test^c, test result^c, test type^c, tumor grading^c

bio material package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioMaterialPackage

Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.

has super-classes: m g e d core ontology^c
has sub-classes: action^c, bio material^c, bio material characteristics^c, bio sample type^c, family member^c, family relationship^c, initial time point^c, material type^c, treatment^c

bio material purity^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioMaterialPurity

A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells.

has super-classes: bio material characteristics^c

bio molecular annotation^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioMolecularAnnotation

BioMolecularAnnotation experiment design types are those which are designed to investigate functions, processes, locations and identity at the molecular level e.g. binding site identification, genotyping.

has super-classes: experiment design type^c
has members: binding site identification designⁿⁱ, co expression designⁿⁱ, comparative genome hybridization designⁿⁱ, genotyping designⁿⁱ, operon identification designⁿⁱ, r n a stability designⁿⁱ, secreted protein identification designⁿⁱ, tiling path designⁿⁱ, transcript identification designⁿⁱ, translational bias designⁿⁱ, unknown experiment design typeⁿⁱ

bio sample^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSample

The BioSource after any treatment.

has super-classes: bio material^c; has been treated^op some treatment^c; has type^op some bio sample type^c

bio sample type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSampleType

Used to tell when the BioSample is an extract or not.

has super-classes: bio material package^c
has members: extractⁿⁱ, not extractⁿⁱ

bio sequence^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSequence

A representation of a DNA, RNA, or protein sequence.

has super-classes: bio sequence package^c; has species^op some organism^c; has type^op some polymer type^c; has type^op some bio sequence type^c

bio sequence package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSequencePackage

MAGE package for biological sequences (biosequence).

has super-classes: m g e d core ontology^c
has sub-classes: bio sequence^c, bio sequence type^c, polymer type^c, seq feature basis^c

bio sequence type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSequenceType

Controlled terms for descriptors indicating the type of biosequence. Types may be physical (e.g. BAC, cDNA clone), or computational (e.g. unigene cluster, consensus).

has super-classes: bio sequence package^c
has sub-classes: physical bio sequence type^c, theoretical bio sequence type^c

bio source^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSource

The BioSource is the original source material before any treatment events.

has super-classes: bio material^c

bio source provider^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSourceProvider

The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial.

has super-classes: bio material characteristics^c; has donor^op some organization^c; has owner^op some person^c
is in domain of: has biosource type^op

bio source type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSourceType

The form in which the BioMaterial was obtained/maintained e.g. frozen, fresh etc. Note can be used to describe BioSamples as well as BioSources.

has super-classes: bio material characteristics^c
has members: agar stabⁿⁱ, freeze dried sampleⁿⁱ, fresh sampleⁿⁱ, frozen sampleⁿⁱ, paraffin sampleⁿⁱ, urineⁿⁱ
is also defined as: named individual

biological factor category^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BiologicalFactorCategory

Factors that relate to properties of the biomaterial, its treatment, or its growth.

has super-classes: experimental factor category^c
has sub-classes: action^c, bio material characteristic category^c, bio material characteristics^c, compound^c

biological property^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BiologicalProperty

A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined.

has super-classes: experiment design type^c
has members: cell component comparison designⁿⁱ, cell cycle designⁿⁱ, cell type comparison designⁿⁱ, cellular process designⁿⁱ, development or differentiation designⁿⁱ, imprinting designⁿⁱ, individual genetic characteristics designⁿⁱ, innate behavior designⁿⁱ, is expressed designⁿⁱ, organism part comparison designⁿⁱ, organism status designⁿⁱ, physiological process designⁿⁱ, sex designⁿⁱ, species designⁿⁱ, strain or line designⁿⁱ, unknown experiment design typeⁿⁱ
is also defined as: named individual

biometrics^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Biometrics

Physical properties of the BioMaterial e. g. mass or height

has super-classes: bio material characteristics^c; has length^op some measurement^c; has mass^op some measurement^c; has individual^op some individual^c; has diameter^op some measurement^c; has height^op some measurement^c; has organism part^op some organism part^c; has cubic volume^op some measurement^c

cancer site^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CancerSite

class to hold instances used as the filler for the property has_cancer_site

has super-classes: m g e d core ontology^c
has members: metastatic siteⁿⁱ, primary siteⁿⁱ

cell line^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CellLine

The identifier for the established culture of a metazoan cell if one was used as a biomaterial.

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some cell line database^c

cell line database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CellLineDatabase

Database of cell line information.

has super-classes: database^c
has members: a t c c culturesⁿⁱ, c a b r i h l a typed b cell linesⁿⁱ, c a b r i human and animal cell linesⁿⁱ, c a b r i hybridomasⁿⁱ, c l d b human and animal cell lineⁿⁱ

cell type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CellType

CellType, the type of cell used in the experiment if non mixed, if mixed the TargetedCellType should be used, example of instances, epithelial, glial etc.

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some cell type database^c

cell type database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CellTypeDatabase

Database of cell type information.

has super-classes: database^c
has members: c b i l c vⁿⁱ, cell ontologyⁿⁱ, e v o cⁿⁱ, n c i cell type databaseⁿⁱ, t a i rⁿⁱ

cellular component^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CellularComponent

A structure within a cell, such as an anatomical structure (e.g. rough endoplasmic reticulum or nucleus) or a gene product group (e.g. ribosome, proteasome or a protein dimer).

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some cellular component database^c

cellular component database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CellularComponentDatabase

A resource for terms to describe cellular components, e.g. GO Cellular Component ontology.

has super-classes: database^c
has members: gene ontologyⁿⁱ

chromosomal aberration^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ChromosomalAberration

An abnormality of a chromosome's number or structure, which excludes simple changes in sequence and is usually detectable by cytogenetic and microscopic techniques such as FISH.

has super-classes: deprecated terms^c; deprecated from version^op value version 1.1.7; has chromosomal aberration classification^op some chromosomal aberration classification^c; has reason for deprecation^op value deleted term
is also defined as: named individual

chromosomal aberration classification^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ChromosomalAberrationClassification

An irregularity in the number or structure of chromosomes, usually in the form of a gain (duplication), loss (deletion), exchange (translocation), or alteration in sequence (inversion) of genetic material. Excludes simple changes in sequence such as mutations, and is usually detectable by cytogenetic and microscopic techniques such as FISH.

has super-classes: bio material characteristics^c
has members: chromosomal deletionⁿⁱ, chromosomal duplicationⁿⁱ, chromosomal insertionⁿⁱ, chromosomal inversionⁿⁱ, chromosomal translocationⁿⁱ, genomic region amplificationⁿⁱ, oligosomyⁿⁱ, polysomyⁿⁱ
is also defined as: named individual

clinical history^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ClinicalHistory

The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.

has super-classes: environmental history^c; has clinical finding^op some test result^c; has clinical treatment^op some clinical treatment^c; has clinical record^op some ontology entry^c; has prior disease state^op some disease state^c; has test type^op some test type^c

clinical treatment^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ClinicalTreatment

The current clinical treatment(s) of the patient from which the biosource is derived.

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some clinical treatment database^c

clinical treatment database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ClinicalTreatmentDatabase

Database of clinical treatment information

has super-classes: database^c

complex action^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ComplexAction

Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification.

has super-classes: action^c
has members: acclimatizationⁿⁱ, behavioral stimulusⁿⁱ, biological fluid collectionⁿⁱ, biopsyⁿⁱ, change biomaterial characteristicsⁿⁱ, compound based treatmentⁿⁱ, decontaminateⁿⁱ, dissectⁿⁱ, fractionateⁿⁱ, genetic modificationⁿⁱ, growⁿⁱ, harvestⁿⁱ, histological slide preparationⁿⁱ, hybridizationⁿⁱ, incubateⁿⁱ, inoculateⁿⁱ, irradiateⁿⁱ, labelingⁿⁱ, linear amplificationⁿⁱ, nucleic acid extractionⁿⁱ, p c r amplificationⁿⁱ, poolⁿⁱ, preservationⁿⁱ, purifyⁿⁱ, reverse transcriptionⁿⁱ, sacrificeⁿⁱ, specified biomaterial actionⁿⁱ, splitⁿⁱ, starvationⁿⁱ, storeⁿⁱ, timepointⁿⁱ, transfectⁿⁱ, washⁿⁱ
is also defined as: named individual

compound^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Compound

A drug, solvent, chemical, etc., with a property that can be measured such as concentration.

has super-classes: biological factor category^c; ontology entry^c; has measurement^op some compound^c; is solvent^dp some boolean; has database^op some compound database^c
has sub-classes: label compound^c

compound database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CompoundDatabase

Database of compound information.

has super-classes: database^c
has members: ch e b iⁿⁱ, chem i dⁿⁱ, n c i compound databaseⁿⁱ

concentration unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ConcentrationUnit

Units used for concentration measurements.

has super-classes: unit^c
has sub-classes: concentration unit other^c
has members: f mⁿⁱ, g per lⁿⁱ, gram percentⁿⁱ, mⁿⁱ, m l per lⁿⁱ, m mⁿⁱ, mg per mlⁿⁱ, p mⁿⁱ, percent vol per volⁿⁱ, percent weight per volⁿⁱ, percent weight per weightⁿⁱ, u mⁿⁱ, u per lⁿⁱ

concentration unit other^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ConcentrationUnitOther

Concentration units not specified in MAGE.

has super-classes: concentration unit^c
has members: cells per mlⁿⁱ, cfu per mlⁿⁱ, kat per lⁿⁱ, m osm per kg h2 oⁿⁱ, mg per kg per dayⁿⁱ, ml per kgⁿⁱ, p hⁿⁱ, percent confluenceⁿⁱ, percent purityⁿⁱ, pfu per mlⁿⁱ, x timesⁿⁱ

contact^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Contact

Organizations or individuals that may be contacted.

has super-classes: audit and security package^c; has u r i^op some u r i^c; has toll free phone^dp some string; has type^op some roles^c; has fax^dp some string; has address^dp some string; has phone^dp some string; has email^dp some string
has sub-classes: organization^c, person^c

control type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ControlType

Controlled terms for descriptors for the type of control design element.

has super-classes: design element package^c
has members: control biosequenceⁿⁱ, control bufferⁿⁱ, control emptyⁿⁱ, control genomic d n aⁿⁱ, control hybridization qualityⁿⁱ, control labelⁿⁱ, control reporter sizeⁿⁱ, control spike calibrationⁿⁱ, control unknown typeⁿⁱ

cultivar^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Cultivar

a plant variety obtained in agriculture in horticulture

has super-classes: strain or line^c; has database^op some strain or line database^c

data transformation protocol type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DataTransformationProtocolType

The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays.

has super-classes: protocol type^c
has members: across bioassay data set functionⁿⁱ, dye swap mergeⁿⁱ, flag filterⁿⁱ, linlog transformationⁿⁱ, loess global normalizationⁿⁱ, loess group normalizationⁿⁱ, loess scaled group normalizationⁿⁱ, lowess global normalizationⁿⁱ, lowess group normalizationⁿⁱ, lowess scaled group normalizationⁿⁱ, mean log normalizationⁿⁱ, median log normalizationⁿⁱ, moving averageⁿⁱ, quantile normalization protocol typeⁿⁱ, replicate analysisⁿⁱ, total intensity normalization pairedⁿⁱ, total intensity normalization singleⁿⁱ, within bioassay data set functionⁿⁱ

data type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DataType

Primitive data types found in computing languages such as float, boolean, etc.

has super-classes: m g e d core ontology^c
has members: booleanⁿⁱ, dateⁿⁱ, floatⁿⁱ, integerⁿⁱ, list of booleansⁿⁱ, list of floatsⁿⁱ, list of integersⁿⁱ, list of negative floatsⁿⁱ, list of negative integersⁿⁱ, list of nonnegative floatsⁿⁱ, list of nonnegative integersⁿⁱ, list of nonpositive floatsⁿⁱ, list of nonpositive integersⁿⁱ, list of positive floatsⁿⁱ, list of positive integersⁿⁱ, list of stringsⁿⁱ, negative floatⁿⁱ, negative integerⁿⁱ, nonnegative floatⁿⁱ, nonnegative integerⁿⁱ, nonpositive floatⁿⁱ, nonpositive integerⁿⁱ, positive floatⁿⁱ, positive integerⁿⁱ, string datatypeⁿⁱ

database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Database

Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.

has super-classes: description package^c; has version^dp some string; has u r i^op some u r i^c
has sub-classes: cell line database^c, cell type database^c, cellular component database^c, clinical treatment database^c, compound database^c, developmental stage database^c, disease staging database^c, disease state database^c, geographic location database^c, histology database^c, observation database^c, organism database^c, organism part database^c, phenotype database^c, sequence ontology database^c, strain or line database^c, targeted cell type database^c, test type database^c, tumor grading database^c

database entry type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DatabaseEntryType

Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD).

has super-classes: description package^c
has members: amino acid primary sequence recordⁿⁱ, bibliographic recordⁿⁱ, biological resource recordⁿⁱ, clinical recordⁿⁱ, compound recordⁿⁱ, computed amino acid sequence feature recordⁿⁱ, computed nucleic acid sequence feature recordⁿⁱ, computed protein structure recordⁿⁱ, curated amino acid sequence recordⁿⁱ, curated gene recordⁿⁱ, curated nucleic acid sequence feature recordⁿⁱ, function recordⁿⁱ, image recordⁿⁱ, microarray experiment recordⁿⁱ, nucleic acid primary sequence recordⁿⁱ, ontology recordⁿⁱ, pathway recordⁿⁱ, pedigree recordⁿⁱ, phylogeny recordⁿⁱ, primary protein structure recordⁿⁱ

defect type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DefectType

Defects associated with features or zones such as those that are missing or moved.

has super-classes: array package^c
has members: diameter aberrationⁿⁱ, displaced feature or zoneⁿⁱ, heavy backgroundⁿⁱ, irregular shapeⁿⁱ, missing feature or zoneⁿⁱ, not uniformⁿⁱ

delivery method^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DeliveryMethod

Method used to deliver a compound for treatment.

has super-classes: m g e d extended ontology^c
has members: ad libitumⁿⁱ, feedingⁿⁱ, in mediumⁿⁱ, intramuscular injectionⁿⁱ, intraperitoneal injectionⁿⁱ, intravenousⁿⁱ, oral gavageⁿⁱ, subcutaneousⁿⁱ

deprecated terms^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DeprecatedTerms

Class to hold deprecated instances and classes.

has super-classes: m g e d core ontology^c; has reason for deprecation^op some deprecation reason^c
has sub-classes: chromosomal aberration^c, factor value dependency^c, factor value set^c, individual chromosomal abnormality^c
has members: b a cⁿⁱ, beddingⁿⁱ, behavior designⁿⁱ, behavioral design typeⁿⁱ, bloodⁿⁱ, c d n a cloneⁿⁱ, chromosomeⁿⁱ, circadian rhythm designⁿⁱ, consensus d n aⁿⁱ, consensus m r n aⁿⁱ, cosmidⁿⁱ, ct d n aⁿⁱ, ds oligoⁿⁱ, e s tⁿⁱ, exemplar m r n aⁿⁱ, exonⁿⁱ, fecesⁿⁱ, geneⁿⁱ, gene fragmentⁿⁱ, genetic variationⁿⁱ, hfrⁿⁱ, infectⁿⁱ, intergenicⁿⁱ, intronⁿⁱ, low intensity filterⁿⁱ, m r n aⁿⁱ, mean and confidence indicatorsⁿⁱ, monosomyⁿⁱ, mt d n aⁿⁱ, n c i thesaurusⁿⁱ, noⁿⁱ, o r fⁿⁱ, operonⁿⁱ, p a cⁿⁱ, p c r ampliconⁿⁱ, p c r primerⁿⁱ, p c r primer forwardⁿⁱ, p c r primer reverseⁿⁱ, plasmidⁿⁱ, polypeptideⁿⁱ, predicted geneⁿⁱ, promoterⁿⁱ, r r n a geneⁿⁱ, signal log ratioⁿⁱ, slice analysisⁿⁱ, sn r n a geneⁿⁱ, ss oligoⁿⁱ, t r n a geneⁿⁱ, tau rank correlationⁿⁱ, total intensity normalizationⁿⁱ, transcriptⁿⁱ, trisomyⁿⁱ, vectorⁿⁱ, y a cⁿⁱ, yesⁿⁱ

deprecation reason^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DeprecationReason

class to hold instances used as the filler for the property has_reason_for_deprecation

has super-classes: m g e d core ontology^c
has members: deleted termⁿⁱ, merged termⁿⁱ, replaced termⁿⁱ, split termⁿⁱ

derived bio assay^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DerivedBioAssay

A BioAssay that is created by the transformation of measured or derived BioAssays.

has super-classes: bio assay^c; has type^op some derived bio assay type^c

derived bio assay type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DerivedBioAssayType

Controlled set of descriptors for the type of derivation of the BioAssay such as averaging features, taking ratios of signal QuantitationTypes, and normalizing BioAssay data.

has super-classes: bio assay package^c
has members: across bio assay mean and coefficient of variationⁿⁱ, across bio assay mean and p valuesⁿⁱ, across bio assay mean and standard deviationⁿⁱ, across bio assay mean and varianceⁿⁱ, affymetrix average differenceⁿⁱ, averaged intensityⁿⁱ, bioassay replicate reductionⁿⁱ, clustered dataⁿⁱ, collapsed spot replicateⁿⁱ, dye swap replicate reductionⁿⁱ, filtered dataⁿⁱ, log ratioⁿⁱ, m a s4 average differenceⁿⁱ, m a s5 signalⁿⁱ, m a s5 signal log ratioⁿⁱ, m b e iⁿⁱ, mean and coefficient of variationⁿⁱ, mean and p valuesⁿⁱ, mean and standard deviationⁿⁱ, mean and varianceⁿⁱ, normalized intensitiesⁿⁱ, normalized ratiosⁿⁱ, r m aⁿⁱ, ratioⁿⁱ, signalⁿⁱ
is also defined as: named individual

description package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DescriptionPackage

MAGE package for description of annotations and references to annotations.

has super-classes: m g e d core ontology^c
has sub-classes: bibliographic reference^c, database^c, database entry type^c, image^c, ontology entry^c, publication type^c

design element^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DesignElement

Design elements are reporters, features, and composite elements as defined by MAGE.

has super-classes: design element package^c; has type^op some control type^c
has sub-classes: reporter^c
has members: long oligoⁿⁱ, p c rⁿⁱ, short oligoⁿⁱ

design element group^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DesignElementGroup

A DesignElementGroup holds information on Features, Reporters, or CompositeSequences.

has super-classes: array design package^c; has species^op some organism^c; has type^op some design element group type^c
has sub-classes: feature group^c

design element group type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DesignElementGroupType

Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence.

has super-classes: array design package^c
has members: control design element group typeⁿⁱ, experimental design element group typeⁿⁱ, mixed design element group typeⁿⁱ, species specific design element group typeⁿⁱ

design element package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DesignElementPackage

The MAGE package for describing the elements located on the array.

has super-classes: m g e d core ontology^c
has sub-classes: control type^c, design element^c, fail type^c, warning type^c

developmental stage^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DevelopmentalStage

The developmental stage of the organism's life cycle during which the biomaterial was extracted.

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some developmental stage database^c

developmental stage database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DevelopmentalStageDatabase

Database of developmental stage information.

has super-classes: database^c
has members: e m a pⁿⁱ, e v o cⁿⁱ, fly base developmental stage databaseⁿⁱ, h u m a tⁿⁱ, m a d stageⁿⁱ, t a i r arabidopsis development ontologyⁿⁱ

disease location^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DiseaseLocation

Anatomical location(s) of disease.

has super-classes: organism part^c; has cancer site^op some cancer site^c

disease staging^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DiseaseStaging

The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some disease staging database^c

disease staging database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DiseaseStagingDatabase

Database of disease staging information

has super-classes: database^c
has members: n c i disease staging databaseⁿⁱ

disease state^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DiseaseState

The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed.

has super-classes: bio material characteristics^c; ontology entry^c; has disease location^op some disease location^c; has disease staging^op some disease staging^c; has database^op some disease state database^c

disease state database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DiseaseStateDatabase

Database of disease state information.

has super-classes: database^c
has members: e v o cⁿⁱ, i c d 9 c mⁿⁱ, m e s hⁿⁱ, m t b databaseⁿⁱ, n c i disease state databaseⁿⁱ, t d m sⁿⁱ, u m l sⁿⁱ, web r e n iⁿⁱ

distance unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DistanceUnit

Units used for distance measurements.

has super-classes: unit^c
has sub-classes: distance unit other^c
has members: aⁿⁱ, cmⁿⁱ, mⁿⁱ, mmⁿⁱ, nmⁿⁱ, umⁿⁱ

distance unit other^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DistanceUnitOther

Distance units not specified in MAGE.

has super-classes: distance unit^c

ecotype^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Ecotype

a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler

has super-classes: strain or line^c; has database^op some strain or line database^c

environmental factor category^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#EnvironmentalFactorCategory

Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth.

has super-classes: experimental factor category^c
has members: atmosphereⁿⁱ, barrier facilityⁿⁱ, light durationⁿⁱ, light intensityⁿⁱ, mediaⁿⁱ, nutrientsⁿⁱ, population densityⁿⁱ, relative humidityⁿⁱ, temperatureⁿⁱ, waterⁿⁱ

environmental history^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#EnvironmentalHistory

A description of the conditions the organism has been exposed to that are not one of the variables under study.

has super-classes: bio material characteristics^c
has sub-classes: bedding^c, clinical history^c, family history^c, generation^c, geographic location^c, growth condition^c, host^c, pathogen test^c, sampling time point^c
has members: environmental history designⁿⁱ

environmental stress^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#EnvironmentalStress

Environmental stress is a treatment where some aspect of the environment is perturbed in order to stress the organism or culture, e.g. temperature shock, osmotic shock

has super-classes: m g e d extended ontology^c; has measurement^op some measurement^c

epidemiological design^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#EpidemiologicalDesign

An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history.

has super-classes: experiment design type^c
has members: clinical history designⁿⁱ, disease state designⁿⁱ, family history designⁿⁱ, unknown experiment design typeⁿⁱ

experiment^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Experiment

The complete set of bioassays (hybridizations) and their descriptions performed as an experiment for a common purpose. Here we take experiment to mean an observational or perturbing study. An experiment will be often equivalent to a publication.

has super-classes: experiment package^c; has bioassays^op some bio assay^c; has experiment design^op some experiment design^c; has bioassay data^op some bio assay data^c; has citation^op some bibliographic reference^c; has providers^op some contact^c

experiment design^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ExperimentDesign

ExperimentDesign refers to both observational and experimental (perturbational) studies. The organizing principles of the study including the relationships between assays and the steps taken to interpret the data.

has super-classes: experiment package^c; has m a g e description^op some replicate description^c; has description^dp some string; has experiment factors^op some experimental factor^c; has m a g e description^op some normalization description^c; has m a g e description^op some quality control description^c; has bioassays^op some bio assay^c; has experiment design type^op some experiment design type^c

experiment design type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ExperimentDesignType

The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc.

has super-classes: experiment package^c
has sub-classes: bio molecular annotation^c, biological property^c, epidemiological design^c, methodological design^c, perturbational design^c, technological design^c

experiment package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ExperimentPackage

The descriptions associated with the Experiment package of MAGE

has super-classes: m g e d core ontology^c
has sub-classes: experiment^c, experiment design^c, experiment design type^c, experimental factor^c, experimental factor category^c, factor value^c, factor value dependency^c, factor value set^c, normalization description^c, normalization description type^c, quality control description^c, quality control description type^c, replicate description^c, replicate description type^c
is also defined as: named individual

experimental factor^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ExperimentalFactor

The factors in the study that are experimental parameters or regarded as influencing the experimental results.

has super-classes: experiment package^c; has category^op some methodological factor category^c; has category^op some biological factor category^c; has factor value^op some factor value^c

experimental factor category^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ExperimentalFactorCategory

A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML.

has super-classes: experiment package^c
has sub-classes: biological factor category^c, environmental factor category^c, methodological factor category^c

experimental protocol type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ExperimentalProtocolType

All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment.

has super-classes: protocol type^c
has members: acclimatizationⁿⁱ, array manufacturingⁿⁱ, behavioral stimulusⁿⁱ, biological fluid collectionⁿⁱ, change biomaterial characteristicsⁿⁱ, compound based treatmentⁿⁱ, decontaminateⁿⁱ, dissectⁿⁱ, element designⁿⁱ, feature extractionⁿⁱ, fractionateⁿⁱ, genetic modificationⁿⁱ, growⁿⁱ, harvestⁿⁱ, histological slide preparationⁿⁱ, hybridizationⁿⁱ, image acquisitionⁿⁱ, incubateⁿⁱ, inoculateⁿⁱ, irradiateⁿⁱ, labelingⁿⁱ, linear amplificationⁿⁱ, nucleic acid extractionⁿⁱ, p c r amplificationⁿⁱ, poolⁿⁱ, preservationⁿⁱ, purifyⁿⁱ, reverse transcriptionⁿⁱ, sacrificeⁿⁱ, specified biomaterial actionⁿⁱ, splitⁿⁱ, starvationⁿⁱ, storeⁿⁱ, transfectⁿⁱ, unknown protocol typeⁿⁱ, washⁿⁱ
is also defined as: named individual

factor value^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FactorValue

The value of an ExperimentFactor.

has super-classes: experiment package^c; has property set^op some factor value set^c; has factor value ontology entry^op some experimental factor category^c; has measurement^op some measurement^c; has property set^op some factor value dependency^c

factor value dependency^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FactorValueDependency

A group of FactorValues which refer to the same condition used to treat or describe a BioMaterial, e.g. 10% glucose, 1 hour OR larval stage, age 24 hours.

has super-classes: deprecated terms^c; experiment package^c; has reason for deprecation^op value deleted term; deprecated from version^op value version 1.1.9; has value^dp some string
is also defined as: named individual

factor value set^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FactorValueSet

A super grouping of FactorValueDependencies or FactorValues which describes combinations of conditions used to treat or describe a BioMaterial applied to a BioAssay, typically separating things on the basis of channels or the concepts of measured and reference samples e.g. 10% glucose, 1 hour AND 10mm NaCl, 2 hours in channel 1.

has super-classes: deprecated terms^c; experiment package^c; has reason for deprecation^op value deleted term; has value^dp some string; deprecated from version^op value version 1.1.9
is also defined as: named individual

fail type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FailType

Controlled terms for descriptors of failures (as in PCR) associated with reporters.

has super-classes: design element package^c
has members: p c r failⁿⁱ, p c r questionableⁿⁱ

family history^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FamilyHistory

Relevant aspects of genetic preconditions or family member's clinical history.

has super-classes: environmental history^c; has family member^op some family member^c

family member^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FamilyMember

Member of the biosource's family.

has super-classes: bio material package^c; has family relationship^op some family relationship^c; has disease state^op some disease state^c; has individual genetic characteristics^op some individual genetic characteristics^c; has clinical record^op some ontology entry^c

family relationship^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FamilyRelationship

A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother.

has super-classes: bio material package^c
has members: auntⁿⁱ, brotherⁿⁱ, daughterⁿⁱ, fatherⁿⁱ, granddaughterⁿⁱ, grandfatherⁿⁱ, grandmotherⁿⁱ, grandsonⁿⁱ, motherⁿⁱ, sisterⁿⁱ, sonⁿⁱ, uncleⁿⁱ

feature defect^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FeatureDefect

A technical manufacturer described defect for features.

has super-classes: array package^c; has type^op some defect type^c

feature group^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FeatureGroup

Technology-based grouping of features representing individual locations on the array.

has super-classes: design element group^c; has type^op some technology type^c; has feature shape^op some feature shape^c

feature shape^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FeatureShape

The expected shape of the feature on the array.

has super-classes: array design package^c
has members: ellipsoid featureⁿⁱ, rectangular featureⁿⁱ, square featureⁿⁱ

fiducial^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Fiducial

A marking on the surface of the array that can be used to identify the origin of the array.

has super-classes: array package^c; has type^op some fiducial type^c

fiducial type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FiducialType

A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark.

has super-classes: array package^c
has members: chrome borderⁿⁱ, laser ablation markⁿⁱ

generation^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Generation

The number of cell passages if the organism or organism part that is cultured is unicellular or a cell culture otherwise the number of generations.

has super-classes: environmental history^c

genetic material^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#GeneticMaterial

Genetic material may be DNA or RNA and identifiable as an entry in a public external database such as EMBL/DDBJ/GenBank or one of the model organism databases.

has super-classes: m g e d extended ontology^c

genetic modification^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#GeneticModification

The genetic modification introduced into the organism from which the biomaterial was derived. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.

has super-classes: bio material characteristics^c
has members: chromosomal substitutionⁿⁱ, gene knock inⁿⁱ, gene knock outⁿⁱ, induced mutationⁿⁱ, transfectionⁿⁱ

genotype^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Genotype

The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.

has super-classes: individual genetic characteristics^c
has members: wild typeⁿⁱ

geographic location^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#GeographicLocation

A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference.

has super-classes: environmental history^c; ontology entry^c; has database^op some geographic location database^c

geographic location database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#GeographicLocationDatabase

Database of geographic locations.

has super-classes: database^c
has members: n c i geographic location databaseⁿⁱ

growth condition^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#GrowthCondition

A description of the conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures and open environments such as field studies.

has super-classes: environmental history^c; has maximum measurement^op some measurement^c; has value^dp some string; has measurement^op some measurement^c
has sub-classes: atmosphere^c, barrier facility^c, humidity^c, light^c, media^c, nutrients^c, population density^c, temperature^c, water^c

haplotype^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Haplotype

The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed.

has super-classes: individual genetic characteristics^c

hardware^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Hardware

The machine or instrument used.

has super-classes: protocol package^c; has software^op some software^c; has model^dp some string; has type^op some hardware type^c; has make^dp some string; has manufacturer^op some contact^c
is in domain of: has make^dp, has model^dp

hardware type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#HardwareType

Controlled terms for descriptors of types of hardware.

has super-classes: protocol package^c
has members: array scannerⁿⁱ, arrayerⁿⁱ, centrifugeⁿⁱ, computerⁿⁱ, d n a sequencerⁿⁱ, heating blockⁿⁱ, homogenizerⁿⁱ, hybridization chamberⁿⁱ, hybridization stationⁿⁱ, liquid handlerⁿⁱ, oligo synthesizerⁿⁱ, sonicatorⁿⁱ, spectrophotometerⁿⁱ, thermal cyclerⁿⁱ, vacuum dryerⁿⁱ, vortexerⁿⁱ, wash stationⁿⁱ, waterbathⁿⁱ

hardware variation^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#HardwareVariation

The effects of different hardware, types of hardware, or models of hardware on experimental results are studied.

has super-classes: methodological factor category^c

higher level analysis package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#HigherLevelAnalysisPackage

MAGE package for HigherLevelAnalysis

has super-classes: m g e d core ontology^c
has sub-classes: bio assay data cluster^c, node^c, node value^c, node value type^c

higher level analysis protocol type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#HigherLevelAnalysisProtocolType

A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging).

has super-classes: protocol type^c
has members: condition specificityⁿⁱ, differential expressionⁿⁱ, multiple testing correctionⁿⁱ

histology^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Histology

Microscopic morphology of tissues.

has super-classes: bio material characteristics^c; ontology entry^c; has performer^op some contact^c; has organism part^op some organism part^c; has database^op some histology database^c

histology database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#HistologyDatabase

Database of histology information.

has super-classes: database^c
has members: n c i histology databaseⁿⁱ, pathbaseⁿⁱ, t d m sⁿⁱ

history factor^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#HistoryFactor

Factors that are measured or observed parts of the study but not induced or under the control of the experiment. These factors do not have protocols (e.g., epidemiology factors).

has super-classes: m g e d extended ontology^c

host^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Host

Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells).

has super-classes: environmental history^c; has host^op some organism^c; has host part^op some organism part^c
is in domain of: has host^op, has host part^op

humidity^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Humidity

The humidity that the biosource is exposed to.

has super-classes: growth condition^c

image^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Image

has super-classes: description package^c; has u r i^op some u r i^c; has image format^op some image format^c; has database^op some database^c

image format^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ImageFormat

Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.)

has super-classes: bio assay package^c
has members: affymetrix d a tⁿⁱ, g i fⁿⁱ, j p e gⁿⁱ, p n gⁿⁱ, t i f fⁿⁱ

individual^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Individual

Identifier or name of the individual organism from which the biomaterial was derived.

has super-classes: bio material characteristics^c

individual chromosomal abnormality^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#IndividualChromosomalAbnormality

An abnormality in the number or structure of chromosomes in the biomaterial from an individual organism, detected by karyotyping or other methods. E.g., a B-cell lymphoma from a patient has an abnormal karyotype 48,XY,t(1;2)(p22;p11),+3,+12.

has super-classes: deprecated terms^c; individual genetic characteristics^c; has reason for deprecation^op value deleted term; deprecated from version^op value version 1.2.0
is also defined as: named individual

individual genetic characteristics^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#IndividualGeneticCharacteristics

The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.

has super-classes: bio material characteristics^c; has value^dp some string
has sub-classes: allele^c, genotype^c, haplotype^c, individual chromosomal abnormality^c, ploidy^c
is also defined as: named individual

initial time point^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#InitialTimePoint

The point from which measurements of age were taken.

has super-classes: bio material package^c
has members: beginning of stageⁿⁱ, birthⁿⁱ, coitusⁿⁱ, eclosionⁿⁱ, egg layingⁿⁱ, fertilizationⁿⁱ, germinationⁿⁱ, hatchingⁿⁱ, plantingⁿⁱ, sowingⁿⁱ

label compound^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#LabelCompound

Compounds that are used for labeling extracts.

has super-classes: compound^c
has members: 32 pⁿⁱ, 33 pⁿⁱ, alexa 350ⁿⁱ, alexa 430ⁿⁱ, alexa 488ⁿⁱ, alexa 532ⁿⁱ, alexa 546ⁿⁱ, alexa 568ⁿⁱ, alexa 594ⁿⁱ, alexa 633ⁿⁱ, alexa 660ⁿⁱ, alexa 680ⁿⁱ, biotinⁿⁱ, cy3ⁿⁱ, cy5ⁿⁱ

labeled extract^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#LabeledExtract

The BioSample after labeling for detection of the nucleic acids.

has super-classes: bio material^c; has been treated^op some treatment^c; has compound^op some label compound^c

light^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Light

The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.

has super-classes: growth condition^c

light unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#LightUnit

Units for measuring the intensity of light.

has super-classes: other unit^c
has members: candelaⁿⁱ, candelas per square meterⁿⁱ, lumenⁿⁱ, luxⁿⁱ, microeinstein per minute and square meterⁿⁱ, microeinstein per second and square meterⁿⁱ

m g e d core ontology^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MGEDCoreOntology

An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents.

has super-classes: m g e d ontology^c; has i d^dp some string
has sub-classes: array design package^c, array package^c, audit and security package^c, bio assay package^c, bio material package^c, bio sequence package^c, cancer site^c, data type^c, deprecated terms^c, deprecation reason^c, description package^c, design element package^c, experiment package^c, higher level analysis package^c, m g e d ontology version^c, measurement package^c, measurement type^c, protocol package^c, quantitation type package^c, result^c, scale^c, u r i^c

m g e d extended ontology^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MGEDExtendedOntology

Location for those classes that are not in the Core ontology as they do are not containable in MAGE. It is not yet structured to work with the Core ontology

has super-classes: m g e d ontology^c
has sub-classes: bio assay data package^c, delivery method^c, environmental stress^c, genetic material^c, history factor^c, preservation^c, preservation type^c, protocol parameter type^c, protocol variation^c, somatic modification^c, strand type^c, user^c

m g e d ontology^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MGEDOntology

The MGED Ontology is a top level container for the MGEDCoreOntology and the MGEDExtendedOntology. The MGED ontology describes microarray experiments and is split into the MGEDCoreOntology, which supports MAGE-OM v1.0 and is organized consistently with MAGE, and the MGEDExtendedOntology, which expands MAGE v1.0 and contains concepts and relationships which are not included in MAGE.

has super-classes: thing^c; is user defined^op some contact^c; is user defined^op some bibliographic reference^c
has sub-classes: m g e d core ontology^c, m g e d extended ontology^c

m g e d ontology version^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MGEDOntologyVersion

The version of the MGED Ontology.

has super-classes: m g e d core ontology^c
has members: version 1.1.7ⁿⁱ, version 1.1.8ⁿⁱ, version 1.1.9ⁿⁱ, version 1.2.0ⁿⁱ, version 1.3.0ⁿⁱ, version 1.3.1ⁿⁱ

mass unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MassUnit

Units used for mass measurements.

has super-classes: unit^c
has sub-classes: mass unit other^c
has members: fgⁿⁱ, gⁿⁱ, kgⁿⁱ, mgⁿⁱ, ngⁿⁱ, pgⁿⁱ, ugⁿⁱ

mass unit other^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MassUnitOther

Mass units not specified in MAGE.

has super-classes: mass unit^c

material type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MaterialType

Controlled terms for the state of the BioMaterial. Each state (BioSource, different BioSamples, and LabeledExtract) have MaterialTypes. Examples are population of an organism, organism, organism part, cell, etc.

has super-classes: bio material package^c
has members: cellⁿⁱ, cell lysateⁿⁱ, cytoplasmic r n aⁿⁱ, d n aⁿⁱ, genomic d n aⁿⁱ, molecular mixtureⁿⁱ, nuclear r n aⁿⁱ, organellar d n aⁿⁱ, organellar r n aⁿⁱ, organism partⁿⁱ, poly a r n aⁿⁱ, proteinⁿⁱ, synthetic d n aⁿⁱ, synthetic r n aⁿⁱ, total r n aⁿⁱ, virusⁿⁱ, whole organismⁿⁱ

measurement^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Measurement

Measured values and units.

has super-classes: measurement package^c; has value^dp some string; has units^op some unit^c; has measurement type^op some measurement type^c
is in domain of: has measurement type^op

measurement package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MeasurementPackage

MAGE package for measurement.

has super-classes: m g e d core ontology^c
has sub-classes: measurement^c, unit^c

measurement type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MeasurementType

class to hold instances used as the filler for the property has_measurement_type

has super-classes: m g e d core ontology^c
has members: absoluteⁿⁱ, relativeⁿⁱ

media^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Media

The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) .

has super-classes: growth condition^c
has members: agarⁿⁱ, liquidⁿⁱ, semisolidⁿⁱ, soilⁿⁱ

methodological design^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MethodologicalDesign

A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop.

has super-classes: experiment design type^c
has members: all pairsⁿⁱ, array platform variation designⁿⁱ, dye swap designⁿⁱ, ex vivo designⁿⁱ, hardware variation designⁿⁱ, in vitro designⁿⁱ, in vivo designⁿⁱ, loop designⁿⁱ, normalization testing designⁿⁱ, operator variation designⁿⁱ, optimization designⁿⁱ, quality control testing designⁿⁱ, reference designⁿⁱ, replicate designⁿⁱ, self vs self designⁿⁱ, software variation designⁿⁱ, time series designⁿⁱ, unknown experiment design typeⁿⁱ

methodological factor category^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MethodologicalFactorCategory

The effects on results of changing protocols, hardware, software, or people performing the experiments are studied Examples are comparison of data across different labeling protocols, scanners, image quantification software, or laboratories.

has super-classes: experimental factor category^c
has sub-classes: hardware variation^c, operator variation^c, protocol type^c, software variation^c

node^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Node

A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes.

has super-classes: higher level analysis package^c; has node value^op some node value^c

node value^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NodeValue

Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm.

has super-classes: higher level analysis package^c; has node value type^op some node value type^c; has scale^op some scale^c; has type^op some data type^c

node value type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NodeValueType

Controlled set of terms for describing the type of values (e.g., Euclidean distance).

has super-classes: higher level analysis package^c
has members: cosine distanceⁿⁱ, euclidean distanceⁿⁱ, french railway distanceⁿⁱ, jackknife pearson correlationⁿⁱ, manhattan distanceⁿⁱ, pearson correlationⁿⁱ, pearson correlation coefficientⁿⁱ, spearmans rank correlationⁿⁱ, uncentered pearson correlationⁿⁱ

normalization description^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NormalizationDescription

NormalizationDescription provides details of the normalization strategy for the experiment.

has super-classes: experiment package^c; has type^op some normalization description type^c

normalization description type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NormalizationDescriptionType

Controlled descriptors for the normalization strategy used for the experiment.

has super-classes: experiment package^c
has members: flip dye consistencyⁿⁱ, iterative mean log centeringⁿⁱ, linear regression normalizationⁿⁱ, linlog normalizationⁿⁱ, loess normalizationⁿⁱ, lowess normalizationⁿⁱ, mean log centeringⁿⁱ, median log centeringⁿⁱ, quantile normalizationⁿⁱ, ratio statistics normalizationⁿⁱ
is also defined as: named individual

nutrients^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Nutrients

The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).

has super-classes: growth condition^c; has nutrient component^op some compound^c

observation^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Observation

Observation will record the macroscopic examination of the biomaterial.

has super-classes: bio material characteristics^c; has database^op some observation database^c; has performer^op some contact^c

observation database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ObservationDatabase

Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations.

has super-classes: database^c
has members: mammalian phenotype ontologyⁿⁱ

ontology entry^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#OntologyEntry

External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology.

has super-classes: description package^c; has database^op some database^c; has accession version^dp some string; has accession^dp some string; has value^dp some string; has database entry type^op some database entry type^c; has description^dp some string
has sub-classes: cell line^c, cell type^c, cellular component^c, clinical treatment^c, compound^c, developmental stage^c, disease staging^c, disease state^c, geographic location^c, histology^c, organism^c, organism part^c, phenotype^c, sequence ontology bio sequence type^c, strain or line^c, targeted cell type^c, test type^c, tumor grading^c

operator variation^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#OperatorVariation

The effects of different investigators, laboratories, or organizations on experimental results are studied.

has super-classes: methodological factor category^c

organism^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Organism

The genus and species (and subspecies) of the organism from which the biomaterial is derived from.

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some organism database^c

organism database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#OrganismDatabase

Database of taxonomic information.

has super-classes: database^c
has members: n c b i taxonomyⁿⁱ

organism part^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#OrganismPart

The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some organism part database^c
has sub-classes: disease location^c

organism part database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#OrganismPartDatabase

Database of organism part information.

has super-classes: database^c
has members: adult mouse anatomyⁿⁱ, c b i l c vⁿⁱ, cell m lⁿⁱ, e v o cⁿⁱ, f m aⁿⁱ, fly base organism part databaseⁿⁱ, m a d stageⁿⁱ, n c i organism part databaseⁿⁱ, open g a l e nⁿⁱ, t a i r arabidopsis anatomy ontologyⁿⁱ, t d m sⁿⁱ

organism status^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#OrganismStatus

The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.

has super-classes: bio material characteristics^c
has members: postmortemⁿⁱ, premortemⁿⁱ

organization^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Organization

The organization (e.g. company, hospital) to contact to obtain or purchase something.

has super-classes: contact^c; has name^dp some string; has parent organization^op some organization^c

other unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#OtherUnit

Other units are those types not specified in MAGE such as lumens, radioactivity, etc.

has super-classes: unit^c
has sub-classes: light unit^c, radiation unit^c
has members: activity units per mlⁿⁱ, kg per m2ⁿⁱ, micromole per second and square meterⁿⁱ, number per dayⁿⁱ, u per weekⁿⁱ

parameter^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Parameter

A parameter is a variable within a protocol.

has super-classes: protocol package^c; has units^op some unit^c; has type^op some data type^c

pathogen test^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PathogenTest

Tests and results for pathogens infecting organism from which the biosource is derived

has super-classes: environmental history^c; has result^op some result^c; was tested for^op some organism^c

person^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Person

The individual to contact regarding something provided such as a biomaterial.

has super-classes: contact^c; has affiliation^op some organization^c; has first name^dp some string; has last name^dp some string; has mid initials^dp some string

perturbational design^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PerturbationalDesign

A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification

has super-classes: experiment design type^c
has members: cellular modification designⁿⁱ, compound treatment designⁿⁱ, disease state designⁿⁱ, dose response designⁿⁱ, genetic modification designⁿⁱ, growth condition designⁿⁱ, injury designⁿⁱ, non targeted transgenic variation designⁿⁱ, pathogenicity designⁿⁱ, stimulated design typeⁿⁱ, stimulus or stress designⁿⁱ, unknown experiment design typeⁿⁱ
is also defined as: named individual

phenotype^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Phenotype

The observable form taken by some character (or group of characters) in an individual or an organism, excluding pathology and disease. The detectable outward manifestations of a specific genotype.

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some phenotype database^c

phenotype database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PhenotypeDatabase

Database of phenotype information

has super-classes: database^c

physical array design^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PhysicalArrayDesign

Descriptions pertaining to the array.

has super-classes: array design package^c; has type^op some surface type^c

physical bio assay^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PhysicalBioAssay

A physical bioassay is the combination of arrays and biomaterials as in a hybridization.

has super-classes: bio assay^c; has image format^op some image format^c
is in domain of: has image format^op

physical bio sequence type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PhysicalBioSequenceType

A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC.

has super-classes: bio sequence type^c
has sub-classes: sequence ontology bio sequence type^c
has members: antibodyⁿⁱ, clone of unknown sourceⁿⁱ, unknown sequenceⁿⁱ
is also defined as: named individual

ploidy^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Ploidy

The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.

has super-classes: individual genetic characteristics^c
has members: aneuploidⁿⁱ, diploidⁿⁱ, haploidⁿⁱ, polyploidⁿⁱ

polymer type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PolymerType

Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence.

has super-classes: bio sequence package^c
has members: d n aⁿⁱ, proteinⁿⁱ, r n aⁿⁱ

population density^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PopulationDensity

The concentration range of the organism.

has super-classes: growth condition^c

preservation^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Preservation

Method and type of preserving the organism or biosource (i.e. keeping it in stasis).

has super-classes: m g e d extended ontology^c; has protocol^op some protocol^c; has type^op some preservation type^c

preservation type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PreservationType

The type of method used to preserve (keep in stasis) the organism or biosource.

has super-classes: m g e d extended ontology^c
has members: frozen storageⁿⁱ, seed dormancyⁿⁱ

protocol^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Protocol

Documentation of the set of steps taken in a procedure.

has super-classes: protocol package^c; has hardware^op some hardware^c; has title^dp some string; has software^op some software^c; has text^dp some string; has u r i^op some u r i^c; has description^dp some string; has citation^op some bibliographic reference^c; has type^op some protocol type^c

protocol package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ProtocolPackage

The MAGE package for protocols.

has super-classes: m g e d core ontology^c
has sub-classes: hardware^c, hardware type^c, parameter^c, protocol^c, protocol type^c, software^c, software type^c

protocol parameter type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ProtocolParameterType

Descriptors for protocol parameter types, e.g. compound concentration, media type.

has super-classes: m g e d extended ontology^c

protocol type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ProtocolType

A controlled set of terms to provide a descriptor for the type of protocol.

has super-classes: methodological factor category^c; protocol package^c
has sub-classes: data transformation protocol type^c, experimental protocol type^c, higher level analysis protocol type^c

protocol variation^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ProtocolVariation

The effects of different protocols or changes in protocols on experimental results are studied.

has super-classes: m g e d extended ontology^c

publication type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PublicationType

Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.).

has super-classes: description package^c
has members: bookⁿⁱ, journal articleⁿⁱ, online resourceⁿⁱ

quality control description^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#QualityControlDescription

QualityControlDescription provides details of the quality control aspects of the experiment.

has super-classes: experiment package^c; has type^op some quality control description type^c

quality control description type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#QualityControlDescriptionType

Controlled descriptors for the quality control strategy for an experiment.

has super-classes: experiment package^c
has members: biological replicateⁿⁱ, dye swap quality controlⁿⁱ, peer review quality controlⁿⁱ, real time p c r quality controlⁿⁱ, reverse transcription p c r quality controlⁿⁱ, spike quality controlⁿⁱ, technical replicateⁿⁱ

quantitation type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#QuantitationType

The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix.

has super-classes: quantitation type package^c; has type^op some data type^c; has scale^op some scale^c

quantitation type package^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#QuantitationTypePackage

The MAGE package for defining classes for quantitation.

has super-classes: m g e d core ontology^c
has sub-classes: quantitation type^c

quantity unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#QuantityUnit

Units used for quantity measurements.

has super-classes: unit^c
has sub-classes: quantity unit other^c
has members: amolⁿⁱ, fmolⁿⁱ, i uⁿⁱ, molⁿⁱ, moleculesⁿⁱ, nmolⁿⁱ, pmolⁿⁱ, umolⁿⁱ

quantity unit other^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#QuantityUnitOther

Quantity units not specified in MAGE.

has super-classes: quantity unit^c
has members: countⁿⁱ

radiation unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#RadiationUnit

Units for measuring decay of a radioactive isotope over time.

has super-classes: other unit^c
has members: ciⁿⁱ, cpmⁿⁱ, dpmⁿⁱ, rⁿⁱ, radⁿⁱ, remⁿⁱ

replicate description^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ReplicateDescription

ReplicateDescription provides details about the type of replication used in the experiment.

has super-classes: experiment package^c; has type^op some replicate description type^c

replicate description type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ReplicateDescriptionType

Controlled descriptors for the type of replication.

has super-classes: experiment package^c
has members: biological replicateⁿⁱ, dye swap replicateⁿⁱ, technical replicateⁿⁱ

reporter^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Reporter

Description of the material placed on a feature (spot).

has super-classes: design element^c; has type^op some fail type^c; has type^op some warning type^c

result^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Result

class to hold instances used as the filler for the property has_result

has super-classes: m g e d core ontology^c
has members: inconclusiveⁿⁱ, negativeⁿⁱ, positiveⁿⁱ

roles^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Roles

Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider.

has super-classes: audit and security package^c
has members: array manufacturerⁿⁱ, biomaterial providerⁿⁱ, biosequence providerⁿⁱ, consortium memberⁿⁱ, consultantⁿⁱ, curatorⁿⁱ, data analystⁿⁱ, data coderⁿⁱ, funderⁿⁱ, hardware manufacturerⁿⁱ, institutionⁿⁱ, investigatorⁿⁱ, software manufacturerⁿⁱ, submitterⁿⁱ

sampling time point^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SamplingTimePoint

A descriptor of the time point that a sample was taken. Not to be used where the sample is part of a time course. SamplingTimePoint is not related to age. An instance could be summer, a date, a time, or a range value.

has super-classes: environmental history^c

scale^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Scale

The scale (linear, log10, ln, etc) used to represent the value.

has super-classes: m g e d core ontology^c
has members: linear scaleⁿⁱ, log base 10ⁿⁱ, log base 2ⁿⁱ, log base eⁿⁱ, unscaledⁿⁱ

seq feature basis^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SeqFeatureBasis

Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.)

has super-classes: bio sequence package^c
has members: computational featureⁿⁱ, experimental and computational featureⁿⁱ, experimental featureⁿⁱ, unknown basis featureⁿⁱ

sequence ontology bio sequence type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SequenceOntologyBioSequenceType

Descriptors of biosequence based on the Sequence Ontology (SO) project.

has super-classes: ontology entry^c; physical bio sequence type^c; theoretical bio sequence type^c; has database^op some sequence ontology database^c

sequence ontology database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SequenceOntologyDatabase

Database for sequence annotation information.

has super-classes: database^c
has members: sequence ontologyⁿⁱ

serotype^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Serotype

An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods

has super-classes: bio material characteristics^c

sex^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Sex

Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.

has super-classes: bio material characteristics^c
has members: fⁿⁱ, f minusⁿⁱ, femaleⁿⁱ, hermaphroditeⁿⁱ, maleⁿⁱ, mating type aⁿⁱ, mating type alphaⁿⁱ, mating type h minusⁿⁱ, mating type h plusⁿⁱ, mixed sexⁿⁱ, unknown sexⁿⁱ

software^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Software

The software application used.

has super-classes: protocol package^c; has type^op some software type^c; has hardware^op some hardware^c; has software^op some software^c; has manufacturer^op some contact^c

software type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SoftwareType

Controlled terms that provide descriptors for the type of software.

has super-classes: protocol package^c
has members: array manufacture softwareⁿⁱ, bioassay data transformation softwareⁿⁱ, clustering softwareⁿⁱ, differential expression softwareⁿⁱ, feature extraction softwareⁿⁱ, image acquisition softwareⁿⁱ, liquid handler softwareⁿⁱ, operating systemⁿⁱ

software variation^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SoftwareVariation

The effects of different software, software packages, or software versions on experimental results are studied.

has super-classes: methodological factor category^c

somatic modification^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SomaticModification

The organism has had non-genetic parts removed, added, or rearranged.

has super-classes: m g e d extended ontology^c; has part modified^op some organism part^c

strain or line^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#StrainOrLine

A strain or line is an animal or plant offspring that has a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings. This class is extended to include F1 offspring and established breeding lines. For microbes, these are isolates derived from nature or in the laboratory.

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some strain or line database^c; has species^op some organism^c
has sub-classes: cultivar^c, ecotype^c

strain or line database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#StrainOrLineDatabase

Database of strain, line, cultivar or ecotype information.

has super-classes: database^c
has members: a t c c culturesⁿⁱ, c a b r i bacteria and archaea strainsⁿⁱ, c a b r i filamentous fungi strainsⁿⁱ, c a b r i yeasts strainsⁿⁱ, g r a m e n eⁿⁱ, j a x mouse strainsⁿⁱ, n a s cⁿⁱ, n c b i taxonomyⁿⁱ, n c i strain or line databaseⁿⁱ, t a i rⁿⁱ

strand type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#StrandType

A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse

has super-classes: m g e d extended ontology^c
has members: double strandedⁿⁱ, forwardⁿⁱ, reverseⁿⁱ, single strandedⁿⁱ

substrate type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType

Controlled terms for descriptors of types of array substrates.

has super-classes: array package^c
has members: glassⁿⁱ, nitrocelluloseⁿⁱ, nylonⁿⁱ, siliconⁿⁱ, unknown substrate typeⁿⁱ

surface type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SurfaceType

Controlled terms for descriptors for coating of the substrate.

has super-classes: array design package^c
has members: aminosilaneⁿⁱ, polylysineⁿⁱ, unknown surface typeⁿⁱ

targeted cell type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TargetedCellType

The target cell type is the cell of primary interest. The biomaterial may be derived from a mixed population of cells although only one cell type is of interest.

has super-classes: bio material characteristics^c; ontology entry^c

targeted cell type database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TargetedCellTypeDatabase

Database of targeted cell type information.

has super-classes: database^c
has members: c b i l c vⁿⁱ, cell ontologyⁿⁱ, m a d stageⁿⁱ, n c i targeted cell type databaseⁿⁱ

technological design^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TechnologicalDesign

The purpose(s) for which the array is used within an experiment, e.g. to assess the transcriptome, the genomic content, or to identify transcription factor binding sites.

has super-classes: experiment design type^c
has members: binding site identification designⁿⁱ, cellular modification designⁿⁱ, comparative genome hybridization designⁿⁱ, transcript identification designⁿⁱ

technology type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TechnologyType

The technology type or platform of the reporters on the array.

has super-classes: array design package^c
has members: in situ oligo featuresⁿⁱ, spotted antibody featuresⁿⁱ, spotted colony featuresⁿⁱ, spotted ds d n a featuresⁿⁱ, spotted protein featuresⁿⁱ, spotted ss oligo featuresⁿⁱ, spotted ss p c r amplicon featuresⁿⁱ

temperature^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Temperature

The temperature that a biosource is exposed to.

has super-classes: growth condition^c

temperature unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TemperatureUnit

Units used for temperature measurements.

has super-classes: unit^c
has members: degrees cⁿⁱ, degrees fⁿⁱ, kⁿⁱ

test^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Test

An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry.

has super-classes: bio material characteristics^c; has test result^op some test result^c; has performer^op some contact^c; has test type^op some test type^c

test result^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TestResult

TestResult is the recorded value of the test outcome.

has super-classes: bio material characteristics^c; has measurement^op some measurement^c

test type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TestType

Descriptor of the Test performed e.g. Leukocyte count

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some test type database^c

test type database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TestTypeDatabase

Database of codes for clinical findings.

has super-classes: database^c
has members: i u p a c clinical chemistry guidelinesⁿⁱ, l o i n cⁿⁱ, t d m sⁿⁱ

theoretical bio sequence type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TheoreticalBioSequenceType

A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron.

has super-classes: bio sequence type^c
has sub-classes: sequence ontology bio sequence type^c
has members: unknown sequenceⁿⁱ
is also defined as: named individual

time unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TimeUnit

Units used for time measurements.

has super-classes: unit^c
has sub-classes: time unit other^c
has members: daysⁿⁱ, hoursⁿⁱ, minutesⁿⁱ, monthsⁿⁱ, msⁿⁱ, secondsⁿⁱ, usⁿⁱ, weeksⁿⁱ, yearsⁿⁱ

time unit other^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TimeUnitOther

Time units not specified in MAGE.

has super-classes: time unit^c
has members: half lifeⁿⁱ

transformation^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Transformation

The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data.

has super-classes: bio assay data package^c; has protocol^op some protocol^c

treatment^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Treatment

A treatment is the process or action by which a biomaterial is created from an input biomaterial.

has super-classes: bio material package^c; has order^dp some int; has protocol^op some protocol^c; has action^op some action^c

tumor grading^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TumorGrading

A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus.

has super-classes: bio material characteristics^c; ontology entry^c; has database^op some tumor grading database^c

tumor grading database^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TumorGradingDatabase

Database of tumor grading information

has super-classes: database^c
has members: n c i tumor grading databaseⁿⁱ

u r i^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#URI

Uniform Resource Identifier

has super-classes: m g e d core ontology^c

unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Unit

Units of measure.

has super-classes: measurement package^c
has sub-classes: concentration unit^c, distance unit^c, mass unit^c, other unit^c, quantity unit^c, temperature unit^c, time unit^c, volume unit^c

user^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#User

User is a way to id a person in a database

has super-classes: m g e d extended ontology^c; has i d^dp some string

volume unit^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#VolumeUnit

Units used for volume measurements.

has super-classes: unit^c
has sub-classes: volume unit other^c
has members: ccⁿⁱ, dlⁿⁱ, flⁿⁱ, lⁿⁱ, mlⁿⁱ, nlⁿⁱ, plⁿⁱ, ulⁿⁱ

volume unit other^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#VolumeUnitOther

Volume units not specified in MAGE.

has super-classes: volume unit^c

warning type^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#WarningType

Controlled terms for descriptors of the warnings associated with reporters.

has super-classes: design element package^c
has members: is contaminatedⁿⁱ, not sequence verifiedⁿⁱ

water^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Water

Water consumed by or enveloping the organism that the biosource is derived from.

has super-classes: growth condition^c; has additive^op some compound^c; has treatment^op some protocol^c

zone defect^c back to ToC or Class ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ZoneDefect

A technical manufactured described defect for zones.

has super-classes: array package^c; has type^op some defect type^c

Named Individuals

32 p
33 p
a
a t c c cultures
absolute
acclimatization
across bio assay mean and coefficient of variation
across bio assay mean and p values
across bio assay mean and standard deviation
across bio assay mean and variance
across bioassay data set function
activity units per ml
ad libitum
add
adult mouse anatomy
affymetrix average difference
affymetrix d a t
agar
agar stab
age
alexa 350
alexa 430
alexa 488
alexa 532
alexa 546
alexa 568
alexa 594
alexa 633
alexa 660
alexa 680
all pairs
amino acid primary sequence record
aminosilane
amol
aneuploid
antibody
array manufacture software
array manufacturer
array manufacturing
array platform variation design
array scanner
arrayer
atmosphere
aunt
averaged intensity
b a c
barrier facility
bedding
beginning of stage
behavior design
behavioral design type
behavioral stimulus
bibliographic record
binding site identification design
bioassay data transformation software
bioassay replicate reduction
biological fluid collection
biological replicate
biological resource record
biomaterial provider
biopsy
biosequence provider
biotin
birth
blood
book
boolean
brother
c a b r i bacteria and archaea strains
c a b r i filamentous fungi strains
c a b r i h l a typed b cell lines
c a b r i human and animal cell lines
c a b r i hybridomas
c a b r i yeasts strains
c b i l c v
c d n a clone
c l d b human and animal cell line
candela
candelas per square meter
cc
cell
cell component comparison design
cell cycle design
cell line
cell lysate
cell m l
cell ontology
cell type
cell type comparison design
cells per ml
cellular modification design
cellular process design
centrifuge
cfu per ml
ch e b i
change biomaterial characteristics
change humidity
change light
change temperature
chem i d
chrome border
chromosomal aberration
chromosomal deletion
chromosomal duplication
chromosomal insertion
chromosomal inversion
chromosomal substitution
chromosomal translocation
chromosome
ci
circadian rhythm design
clinical history design
clinical information
clinical record
clinical treatment
clone of unknown source
clustered data
clustering software
cm
co expression design
coitus
collapsed spot replicate
comparative genome hybridization design
compound based treatment
compound record
compound treatment design
computational feature
computed amino acid sequence feature record
computed nucleic acid sequence feature record
computed protein structure record
computer
concentrate
condition specificity
consensus d n a
consensus m r n a
consortium member
consultant
control biosequence
control buffer
control design element group type
control empty
control genomic d n a
control hybridization quality
control label
control reporter size
control spike calibration
control unknown type
cosine distance
cosmid
count
cpm
ct d n a
curated amino acid sequence record
curated gene record
curated nucleic acid sequence feature record
curator
cy3
cy5
cytoplasmic r n a
d n a
d n a sequencer
data analyst
data coder
date
daughter
days
decontaminate
degrees c
degrees f
deleted term
development or differentiation design
developmental stage
diameter aberration
differential expression
differential expression software
dilute
diploid
disease staging
disease state
disease state design
displaced feature or zone
dissect
dl
dose response design
double stranded
dpm
ds oligo
dye swap design
dye swap merge
dye swap quality control
dye swap replicate
dye swap replicate reduction
e m a p
e s t
e v o c
eclosion
egg laying
element design
ellipsoid feature
environmental history design
euclidean distance
ex vivo design
exemplar m r n a
exon
experimental and computational feature
experimental design element group type
experimental feature
extract
f
f m
f m a
f minus
factor value dependency
factor value set
family history design
father
feature extraction
feature extraction software
feces
feeding
female
fertilization
fg
filtered data
fl
flag filter
flip dye consistency
float
fly base developmental stage database
fly base organism part database
fmol
forward
fractionate
freeze dried sample
french railway distance
fresh sample
frozen sample
frozen storage
function record
funder
g
g i f
g per l
g r a m e n e
gene
gene fragment
gene knock in
gene knock out
gene ontology
genetic modification
genetic modification design
genetic variation
genomic d n a
genomic region amplification
genotyping design
germination
glass
gram percent
granddaughter
grandfather
grandmother
grandson
grow
growth condition design
h u m a t
half life
haploid
hardware manufacturer
hardware variation design
harvest
hatching
heating block
heavy background
hermaphrodite
hfr
histological slide preparation
homogenizer
hours
hybridization
hybridization chamber
hybridization station
i c d 9 c m
i u
i u p a c clinical chemistry guidelines
image acquisition
image acquisition software
image record
imprinting design
in medium
in situ oligo features
in vitro design
in vivo design
inconclusive
incubate
individual
individual chromosomal abnormality
individual genetic characteristic
individual genetic characteristics design
induced mutation
infect
injury design
innate behavior design
inoculate
institution
integer
intergenic
intramuscular injection
intraperitoneal injection
intravenous
intron
investigator
irradiate
irregular shape
is contaminated
is expressed design
iterative mean log centering
j a x mouse strains
j p e g
jackknife pearson correlation
journal article
k
kat per l
kg
kg per m2
l
l o i n c
labeling
laser ablation mark
light duration
light intensity
linear amplification
linear regression normalization
linear scale
linlog normalization
linlog transformation
liquid
liquid handler
liquid handler software
list of booleans
list of floats
list of integers
list of negative floats
list of negative integers
list of nonnegative floats
list of nonnegative integers
list of nonpositive floats
list of nonpositive integers
list of positive floats
list of positive integers
list of strings
loess global normalization
loess group normalization
loess normalization
loess scaled group normalization
log base 10
log base 2
log base e
log ratio
long oligo
loop design
low intensity filter
lowess global normalization
lowess group normalization
lowess normalization
lowess scaled group normalization
lumen
lux
m
m
m a d stage
m a s4 average difference
m a s5 signal
m a s5 signal log ratio
m b e i
m e s h
m l per l
m m
m osm per kg h2 o
m r n a
m t b database
male
mammalian phenotype ontology
manhattan distance
mating type a
mating type alpha
mating type h minus
mating type h plus
mean and coefficient of variation
mean and confidence indicators
mean and p values
mean and standard deviation
mean and variance
mean log centering
mean log normalization
media
median log centering
median log normalization
merged term
metastatic site
mg
mg per kg per day
mg per ml
microarray experiment record
microeinstein per minute and square meter
microeinstein per second and square meter
micromole per second and square meter
minutes
missing feature or zone
mix by inversion
mix by pipette
mix by vortex
mix general
mixed design element group type
mixed sex
ml
ml per kg
mm
mol
molecular mixture
molecules
monosomy
months
mother
moving average
ms
mt d n a
multiple testing correction
n a s c
n c b i taxonomy
n c i cell type database
n c i compound database
n c i disease staging database
n c i disease state database
n c i geographic location database
n c i histology database
n c i organism part database
n c i strain or line database
n c i targeted cell type database
n c i thesaurus
n c i tumor grading database
negative
negative float
negative integer
ng
nitrocellulose
nl
nm
nmol
no
non targeted transgenic variation design
nonnegative float
nonnegative integer
nonpositive float
nonpositive integer
normalization testing design
normalized intensities
normalized ratios
not extract
not sequence verified
not uniform
nuclear r n a
nucleic acid extraction
nucleic acid primary sequence record
number per day
nutrients
nylon
o r f
oligo synthesizer
oligosomy
online resource
ontology record
open g a l e n
operating system
operator variation design
operon
operon identification design
optimization design
oral gavage
organellar d n a
organellar r n a
organism
organism part
organism part comparison design
organism status
organism status design
p a c
p c r
p c r amplicon
p c r amplification
p c r fail
p c r primer
p c r primer forward
p c r primer reverse
p c r questionable
p h
p m
p n g
paraffin sample
pathbase
pathogenicity design
pathway record
pearson correlation
pearson correlation coefficient
pedigree record
peer review quality control
percent confluence
percent purity
percent vol per vol
percent weight per vol
percent weight per weight
pfu per ml
pg
phylogeny record
physical characteristics
physiological process design
pl
place
planting
plasmid
pmol
poly a r n a
polylysine
polypeptide
polyploid
polysomy
pool
population density
positive
positive float
positive integer
postmortem
predicted gene
premortem
preservation
primary protein structure record
primary site
promoter
protein
purify
quality control testing design
quantile normalization
quantile normalization protocol type
r
r m a
r n a
r n a stability design
r r n a gene
rad
ratio
ratio statistics normalization
real time p c r quality control
rectangular feature
reference design
relative
relative humidity
rem
remove
replaced term
replicate analysis
replicate design
resuspend
reverse
reverse transcription
reverse transcription p c r quality control
sacrifice
sampling time point
seconds
secreted protein identification design
seed dormancy
self vs self design
semisolid
sequence ontology
set temperature
sex
sex design
short oligo
signal
signal log ratio
silicon
single stranded
sister
slice analysis
sn r n a gene
software manufacturer
software variation design
soil
son
sonicator
sowing
spearmans rank correlation
species design
species specific design element group type
specified biomaterial action
spectrophotometer
spike quality control
spin
split
split term
spotted antibody features
spotted colony features
spotted ds d n a features
spotted protein features
spotted ss oligo features
spotted ss p c r amplicon features
square feature
ss oligo
starvation
stimulated design type
stimulus or stress design
store
strain or line
strain or line design
string datatype
subcutaneous
submitter
synthetic d n a
synthetic r n a
t a i r
t a i r arabidopsis anatomy ontology
t a i r arabidopsis development ontology
t d m s
t i f f
t r n a gene
tau rank correlation
technical replicate
temperature
thermal cycler
tiling path design
time series design
timepoint
total intensity normalization
total intensity normalization paired
total intensity normalization single
total r n a
transcript
transcript identification design
transfect
transfection
translational bias design
trisomy
tumor grading
u m
u m l s
u per l
u per week
ug
ul
um
umol
uncentered pearson correlation
uncle
unknown basis feature
unknown experiment design type
unknown protocol type
unknown sequence
unknown sex
unknown substrate type
unknown surface type
unscaled
urine
us
vacuum dryer
vector
version 1.1.7
version 1.1.8
version 1.1.9
version 1.2.0
version 1.3.0
version 1.3.1
virus
vortexer
wait
wash
wash station
water
waterbath
web r e n i
weeks
whole organism
wild type
within bioassay data set function
x times
y a c
years
yes

32 pⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#_32P

32 P, radioactive isotope of phosphorus used for labeling/detection purposes

belongs to: label compound^c
has facts: unique identifier^dp "MO_839"^^string

33 pⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#_33P

33 P, radioactive isotope of phosphorus, used for labeling/detection purposes.

belongs to: label compound^c
has facts: unique identifier^dp "MO_427"^^string

aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#A

Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer

belongs to: distance unit^c
has facts: unique identifier^dp "MO_515"^^string

a t c c culturesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ATCC_Cultures

database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses

belongs to: cell line database^c; strain or line database^c
has facts: unique identifier^dp "MO_979"^^string; has human readable u r i^dp "http://www.atcc.org/Cultures/Products.cfm"^^string

absoluteⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#absolute

a measurement where the value is independent of other measurements

belongs to: measurement type^c
has facts: unique identifier^dp "MO_741"^^string

acclimatizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#acclimatization

The action of stabilizing an organism prior to treatment

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_776"^^string

across bio assay mean and coefficient of variationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#acrossBioAssay_mean_and_coefficient_of_variation

The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_840"^^string

across bio assay mean and p valuesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#acrossBioAssay_mean_and_p_values

The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_671"^^string

across bio assay mean and standard deviationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#acrossBioAssay_mean_and_standard_deviation

The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_946"^^string

across bio assay mean and varianceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#acrossBioAssay_mean_and_variance

The mean and variance values resulting from computationally combining 2 or more sets of bioassay data.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_400"^^string

across bioassay data set functionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#across_bioassay_data_set_function

A function applied to corresponding values coming from a set of compatible Measured/Derived bioassay data sets. Two Measured/Derived bioassay data sets are compatible if there is a natural one-to-one correspondence between them.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_606"^^string

activity units per mlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#activity_units_per_ml

Units of defined biological activity, e.g. cytokine stimulation, per ml.

belongs to: other unit^c
has facts: unique identifier^dp "MO_870"^^string; has reason for deprecation^op deleted term; deprecated from version^op version 1.3.1

ad libitumⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ad_libitum

A delivery method for compounds/drugs where the compound or drug is freely available.

belongs to: delivery method^c
has facts: unique identifier^dp "MO_592"^^string

addⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#add

The procedure of placing one physical object in the same container/physical space as another.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_815"^^string

adult mouse anatomyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Adult_Mouse_Anatomy

This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28).

belongs to: organism part database^c
has facts: unique identifier^dp "MO_992"^^string; has machine readable u r i^dp "http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology?rev=1.1&view=markup"^^string

affymetrix average differenceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Affymetrix_average_difference

the method used by Affymetrix to obtain mean signal intensity from a group of related Features. This involves calculation of the overall sum of perfect match minus mismatch pairs divided by the number of pairs.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_649"^^string

affymetrix d a tⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Affymetrix_DAT

A proprietary image data format that is lossless and containing one channel of data.

belongs to: image format^c
has facts: unique identifier^dp "MO_786"^^string

agarⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#agar

A type of solid media commonly used for growing organisms

belongs to: media^c
has facts: unique identifier^dp "MO_935"^^string

agar stabⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#agar_stab

agar stab, a cell culture inoculated into agar for long term storage

belongs to: bio source type^c
has facts: unique identifier^dp "MO_971"^^string

ageⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#age

A descriptor for FactorValue where age is compared.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_467"^^string

alexa 350ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_350

Absorbs at 346 nm, emission maxima at 442 nm (blue). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

belongs to: label compound^c
has facts: unique identifier^dp "MO_512"^^string

alexa 430ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_430

Absorbs at 433 nm, emission maxima at 539 nm (yellow-green), Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

belongs to: label compound^c
has facts: unique identifier^dp "MO_401"^^string

alexa 488ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_488

Absorbs at 495 nm, emission maxima at 519 nm (green). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

belongs to: label compound^c
has facts: unique identifier^dp "MO_446"^^string

alexa 532ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_532

Absorbs at 532 nm, emission maxima at 554 nm (yellow). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

belongs to: label compound^c
has facts: unique identifier^dp "MO_375"^^string

alexa 546ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_546

Absorbs at 556 nm, emission maxima at 573 nm (orange). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

belongs to: label compound^c
has facts: unique identifier^dp "MO_493"^^string

alexa 568ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_568

Absorbs at 556 nm, emission maxima at 573 nm (orange). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

belongs to: label compound^c
has facts: unique identifier^dp "MO_736"^^string

alexa 594ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_594

Absorbs at 590 nm, emission maxima at 617 nm (red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

belongs to: label compound^c
has facts: unique identifier^dp "MO_461"^^string

alexa 633ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_633

Absorbs at 632 nm, emission maxima at 647 nm (red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

belongs to: label compound^c
has facts: unique identifier^dp "MO_345"^^string

alexa 660ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_660

Absorbs at 663 nm, emission maxima at 690 nm (far-red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

belongs to: label compound^c
has facts: unique identifier^dp "MO_547"^^string

alexa 680ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_680

Absorbs at 679 nm, emission maxima at 702 nm (far-red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble.

belongs to: label compound^c
has facts: unique identifier^dp "MO_799"^^string

all pairsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#all_pairs

An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_565"^^string

amino acid primary sequence recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#amino_acid_primary_sequence_record

A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record

belongs to: database entry type^c
has facts: unique identifier^dp "MO_829"^^string

aminosilaneⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#aminosilane

a surface coating type for immobilization with the compound aminosilane

belongs to: surface type^c
has facts: unique identifier^dp "MO_747"^^string

amolⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#amol

attomole, quantity unit

belongs to: quantity unit^c
has facts: unique identifier^dp "MO_977"^^string

aneuploidⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#aneuploid

Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n).

belongs to: ploidy^c
has facts: unique identifier^dp "MO_918"^^string

antibodyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#antibody

glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen

belongs to: physical bio sequence type^c
has facts: unique identifier^dp "MO_833"^^string

array manufacture softwareⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#array_manufacture_software

Software to control an arrayer.

belongs to: software type^c
has facts: unique identifier^dp "MO_502"^^string

array manufacturerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#array_manufacturer

Person or organization that manufactured the array.

belongs to: roles^c
has facts: unique identifier^dp "MO_890"^^string

array manufacturingⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#array_manufacturing

The process of physically creating the array.

belongs to: experimental protocol type^c
has facts: unique identifier^dp "MO_818"^^string

array platform variation designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#array_platform_variation_design

An experiment in which the array platform is compared, e.g. Agilent versus Affy.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_899"^^string

array scannerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#array_scanner

An instrument capable of acquiring images of arrays.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_824"^^string

arrayerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#arrayer

An instrument capable of manufacturing arrays by spotting material.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_697"^^string

atmosphereⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#atmosphere

The atmospheric conditions used to culture or grow an organism.

belongs to: environmental factor category^c
has facts: unique identifier^dp "MO_498"^^string

auntⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#aunt

The sister of one's father or mother.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_354"^^string

averaged intensityⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#averaged_intensity

Results of data reduction involving computation of the average of multiple intensities of identical type. These could include identical Features, Reporters or CompositeSequences in different microarray hybridizations, matched replicate spots on 2D gels run from the same sample, or repeat measurements of the same metabolite in replicate cell cultures.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_362"^^string

b a cⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BAC

sequence from a bacterial artificial chromosome exact synonym: bacterial artificial chromosome

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_985"^^string; synonym^dp "bacterial artificial chromosome"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

barrier facilityⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#barrier_facility

The rating of containment system used to protect organisms from infectious agents.

belongs to: environmental factor category^c
has facts: unique identifier^dp "MO_511"^^string

beddingⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#bedding

The material (e.g. straw) that an animal sleeps on

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.7"^^string; unique identifier^dp "MO_615"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op bio material characteristic category; deprecation replacement term^op bio material characteristic category; has reason for deprecation^op deleted term; deprecated from version^op version 1.1.7

beginning of stageⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#beginning_of_stage

time point that indicates the start of some developmental stage

belongs to: initial time point^c
has facts: unique identifier^dp "MO_608"^^string

behavior designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#behavior_design

The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.9"^^string; unique identifier^dp "MO_532"^^string; deprecation reason^dp "split_term"^^string; deprecation old parent^op biological property; split to term^op innate behavior design; has reason for deprecation^op split term; split to term^op stimulated design type; deprecated from version^op version 1.1.9

behavioral design typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#behavioral_design_type

A design type in which some behavior(s) of an organism is studied. The behavior can be innate, such as path finding in bees, or in response to an experimental behavioral stimulus such as sleep deprivation.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.9"^^string; unique identifier^dp "MO_766"^^string; deprecation reason^dp "replaced_term"^^string; deprecation old parent^op perturbational design; replaced with term^op innate behavior design; was replaced by^op innate behavior design; has reason for deprecation^op replaced term; deprecated from version^op version 1.1.9

behavioral stimulusⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#behavioral_stimulus

The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.)

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_674"^^string

bibliographic recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#bibliographic_record

A record which describes and identifies a paper publication e.g. a medline record

belongs to: database entry type^c
has facts: unique identifier^dp "MO_923"^^string

binding site identification designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#binding_site_identification_design

A binding site identification design type investigates protein binding sites on nucleic acids non-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP

belongs to: bio molecular annotation^c; technological design^c
has facts: synonym^dp "ChIP-chip"^^string; unique identifier^dp "MO_933"^^string; synonym^dp "chromatin IP"^^string; synonym^dp "chromatin immunoprecipitation"^^string; synonym^dp "chromatin_immunoprecipitation"^^string

bioassay data transformation softwareⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#bioassay_data_transformation_software

Software used to transform the Measured or DerivedBioAssay data e.g. normalization. Non-exact synonym: normalization software

belongs to: software type^c
has facts: unique identifier^dp "MO_672"^^string; synonym^dp "normalization software"^^string

bioassay replicate reductionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#bioassay_replicate_reduction

Results of data reduction involving computation of a representative value, e.g. averaging across a group of identical Features, Reporters or CompositeSequences from 2 or more hybridizations, matched replicate spots on 2D gels run from the same or an equivalent sample, or repeat measurements of the same metabolite in replicate cell cultures.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_976"^^string

biological fluid collectionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#biological_fluid_collection

The action of collecting biological fluids including bodily secretions, exudates, transudates etc. and sampling of cytoplasm. The purpose of sampling may range from collecting other organisms (i.e. pathogens) to studying fluid composition.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_685"^^string

biological replicateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#biological_replicate

A replicate that consists of independent biological replicates made from different individual BioSources.

belongs to: quality control description type^c; replicate description type^c
has facts: unique identifier^dp "MO_952"^^string

biological resource recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#biological_resource_record

A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list

belongs to: database entry type^c
has facts: unique identifier^dp "MO_989"^^string

biomaterial providerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#biomaterial_provider

Term used to describe a role or factor value for the person or organization that provides a BioMaterial.

belongs to: bio material characteristic category^c; roles^c
has facts: unique identifier^dp "MO_591"^^string

biopsyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#biopsy

The process of removing tissue from a living organism.

belongs to: complex action^c
has facts: unique identifier^dp "MO_711"^^string

biosequence providerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#biosequence_provider

Provider of biosequences (clones, oligos etc) for deposition on the array.

belongs to: roles^c
has facts: unique identifier^dp "MO_881"^^string

biotinⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#biotin

a compound used for labeling/detection purposes

belongs to: label compound^c
has facts: unique identifier^dp "MO_793"^^string

birthⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#birth

the action of emergence and separation of offspring from the mother.

belongs to: initial time point^c
has facts: unique identifier^dp "MO_710"^^string

bloodⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#blood

A biomaterial obtained as fluid consisting of plasma, blood cells and platelets.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.9"^^string; unique identifier^dp "MO_409"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op bio source type; deprecation old parent^op bio source type; has reason for deprecation^op deleted term; deprecated from version^op version 1.1.9

bookⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#book

A publication type which has an ISBN.

belongs to: publication type^c
has facts: unique identifier^dp "MO_627"^^string

booleanⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#boolean

The values are either TRUE or FALSE, which can be expressed as 1 and 0.

belongs to: data type^c
has facts: unique identifier^dp "MO_826"^^string

brotherⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#brother

A male having the same genetic parents as another, or one genetic parent in common with another.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_655"^^string

c a b r i bacteria and archaea strainsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CABRI_Bacteria_and_Archaea_Strains

List of CABRI bacteria and archaea strains sorted by genus and species. It includes more than 40,000 resources that are available from seven European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and strains of interest can be requested.

belongs to: strain or line database^c
has facts: unique identifier^dp "MO_1008"^^string; has human readable u r i^dp "http://www.cabri.org/HyperCat/bact/all_A.htm"^^string

c a b r i filamentous fungi strainsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CABRI_Filamentous_Fungi_Strains

List of CABRI filamentous fungi strains sorted by genus and species. It includes more than 30,000 resources that are available from five European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and strains of interest can be requested.

belongs to: strain or line database^c
has facts: unique identifier^dp "MO_1009"^^string; has human readable u r i^dp "http://www.cabri.org/HyperCat/fun/all_A.htm"^^string

c a b r i h l a typed b cell linesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CABRI_HLA_typed_B_Cell_lines

List of CABRI HLA typed B cell lines sorted by name. It includes 238 resources that are available from a European collection participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and cell lines of interest can be requested.

belongs to: cell line database^c
has facts: unique identifier^dp "MO_1005"^^string; has human readable u r i^dp "http://www.cabri.org/HyperCat/cells/hla.htm"^^string

c a b r i human and animal cell linesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CABRI_Human_and_Animal_Cell_lines

Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc.

belongs to: cell line database^c
has facts: unique identifier^dp "MO_536"^^string; has human readable u r i^dp "http://www.cabri.org/HyperCat/cells/all.htm"^^string

c a b r i hybridomasⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CABRI_Hybridomas

List of CABRI hybridomas sorted by name. It includes 397 resources that are available from European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and cell lines of interest can be requested.

belongs to: cell line database^c
has facts: unique identifier^dp "MO_1006"^^string; has human readable u r i^dp "http://www.cabri.org/HyperCat/cells/hybrid.htm"^^string

c a b r i yeasts strainsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CABRI_Yeasts_Strains

List of CABRI yeasts strains sorted by genus and species. It includes more than 30,000 resources that are available from four European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and strains of interest can be requested.

belongs to: strain or line database^c
has facts: unique identifier^dp "MO_1010"^^string; has human readable u r i^dp "http://www.cabri.org/HyperCat/yeast/all_A.htm"^^string

c b i l c vⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CBIL_CV

a controlled vocabulary provided by CBIL

belongs to: cell type database^c; organism part database^c; targeted cell type database^c
has facts: unique identifier^dp "MO_886"^^string; has human readable u r i^dp "http://www.cbil.upenn.edu/anatomy.php3"^^string

c d n a cloneⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cDNA_clone

sequence of complementary cDNA copy of an RNA molecule contained on a plasmid including the plasmid sequence, used when the entire clone is spotted non-exact synonym: cDNA, complementary DNA

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_966"^^string; synonym^dp "cDNA"^^string; synonym^dp "complementary DNA"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

c l d b human and animal cell lineⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CLDB_Human_and_Animal_Cell_Line

List of cell lines available in the Cell Line Database (CLDB), that includes more than 4,000 resources from many European collections and Italian laboratories. Indexes are given by species/strain, pathology, tumor, tissue/organ, and transforming agent.

belongs to: cell line database^c
has facts: has human readable u r i^dp ""^^string; unique identifier^dp "MO_1007"^^string

candelaⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#candela

One lumen per steradian. A steradian is a fraction of the surface area of a sphere that is equal to the square of the radius divided by the total surface area. This is approximately 8% of the total surface area. Exact synonym: candle power

belongs to: light unit^c
has facts: unique identifier^dp "MO_572"^^string; synonym^dp "candle power"^^string

candelas per square meterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#candelas_per_square_meter

Unit of brightness or luminance.

belongs to: light unit^c
has facts: unique identifier^dp "MO_813"^^string

ccⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cc

a cubic centimeter, volume unit

belongs to: volume unit^c
has facts: unique identifier^dp "MO_834"^^string

cellⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell

One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms.

belongs to: material type^c
has facts: unique identifier^dp "MO_612"^^string

cell component comparison designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_component_comparison_design

A design in which RNA from different cell components is examined.

belongs to: biological property^c
has facts: unique identifier^dp "MO_1019"^^string

cell cycle designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_cycle_design

A cell cycle design experiment design type is one that assays events that occurs in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.

belongs to: biological property^c
has facts: unique identifier^dp "MO_822"^^string

cell lineⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_line

A descriptor for FactorValue where CellLine is compared.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_562"^^string

cell lysateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_lysate

cell lysate, a collection of cells whose membranes have been disrupted

belongs to: material type^c
has facts: unique identifier^dp "MO_903"^^string

cell m lⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#CellML

Ontology describing anatomical and physiological relationships.

belongs to: organism part database^c
has facts: unique identifier^dp "MO_967"^^string; has human readable u r i^dp "http://portal.bioengineering.elyt.ods.org/ontology/"^^string

cell ontologyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_ontology

database of cell ontology terms

belongs to: cell type database^c; targeted cell type database^c
has facts: unique identifier^dp "MO_404"^^string; has machine readable u r i^dp "http://cvs.sourceforge.net/views.py/obo/obo/ontology/anatomy/cell_type/cell.ontology?rev=HEAD&content-type=text/vnd.viewcvs-markup"^^string

cell typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_type

A descriptor for FactorValue where CellType is compared.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_548"^^string

cell type comparison designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_type_comparison_design

A cell type comparison design experiment design type compares cells of different type for example different cell lines.

belongs to: biological property^c
has facts: unique identifier^dp "MO_764"^^string

cells per mlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cells_per_ml

the number of cells per ml

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_727"^^string

cellular modification designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cellular_modification_design

A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.

belongs to: perturbational design^c; technological design^c
has facts: unique identifier^dp "MO_392"^^string; synonym^dp "RNAi"^^string

cellular process designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cellular_process_design

Processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

belongs to: biological property^c
has facts: unique identifier^dp "MO_810"^^string

centrifugeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#centrifuge

An instrument capable of applying centrifugal force to tubes or microtiter plates.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_476"^^string

cfu per mlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cfu_per_ml

the number of colony forming units per ml

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_788"^^string

ch e b iⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ChEBI

A freely available dictionary of small molecular entities. The term molecular entity encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

belongs to: compound database^c
has facts: unique identifier^dp "MO_857"^^string; has human readable u r i^dp "http://www.ebi.ac.uk/chebi"^^string

change biomaterial characteristicsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#change_biomaterial_characteristics

Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. Non exact synonym: change growth condition, change environment

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_383"^^string; synonym^dp "change environment"^^string; synonym^dp "change growth condition"^^string

change humidityⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#change_humidity

The action of changing the relative humidity, e.g. from 1% to 10%.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_917"^^string

change lightⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#change_light

Change in light intensity or wavelength.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_549"^^string

change temperatureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#change_temperature

Change in temperature.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_677"^^string

chem i dⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ChemID

Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds.

belongs to: compound database^c
has facts: unique identifier^dp "MO_426"^^string; has human readable u r i^dp "http://chem.sis.nlm.nih.gov/chemidplus"^^string

chrome borderⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#chrome_border

the chrome border on an Affymetrix type array which is used as a point of reference for orientation (fiducial)

belongs to: fiducial type^c
has facts: unique identifier^dp "MO_491"^^string

chromosomal aberrationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ChromosomalAberration

has facts: deprecation replacement term^op chromosomal aberration
is also defined as: class

chromosomal deletionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#chromosomal_deletion

The loss of a segment of the genetic material from a chromosome.

belongs to: chromosomal aberration classification^c
has facts: unique identifier^dp "MO_922"^^string

chromosomal duplicationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#chromosomal_duplication

An irregularity in the number of chromosomes, usually in the form of a gain of genetic material.

belongs to: chromosomal aberration classification^c
has facts: unique identifier^dp "MO_1002"^^string

chromosomal insertionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#chromosomal_insertion

The gain of a segment of the genetic material in a chromosome by fragmentation of a chromosome and transfer of the broken-off portion of another chromosome or other sources.

belongs to: chromosomal aberration classification^c
has facts: unique identifier^dp "MO_518"^^string

chromosomal inversionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#chromosomal_inversion

Chromosome segments that have been turned through 180 degrees with the result that the gene sequence for the segment is reversed with respect to the rest of the chromosome.

belongs to: chromosomal aberration classification^c
has facts: unique identifier^dp "MO_622"^^string

chromosomal substitutionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#chromosomal_substitution

A state/condition describing a cell, or organism, in which all, or part, of a chromosome from a donor replaces that of the recipient. Examples include strains created by repeated backcrossing as well as those created by recombinant methods. For single gene insertion, use the term gene_knock_in.

belongs to: genetic modification^c
has facts: unique identifier^dp "MO_995"^^string

chromosomal translocationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#chromosomal_translocation

A type of aberration characterized by fragmentation of a chromosome and transfer of the broken-off portion to another chromosome, often of a different pair.

belongs to: chromosomal aberration classification^c
has facts: unique identifier^dp "MO_368"^^string

chromosomeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#chromosome

Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_578"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op physical bio sequence type; deprecation replacement term^op physical bio sequence type; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

ciⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Ci

Curie. Unit of the rate of radioactive decay, i.e., the activity of that quantity of radioactive material in which the number of disintegrations per second is 3.7E10. 1 Ci = 3.75 x1010 atom disintegrations per second (dps).

belongs to: radiation unit^c
has facts: unique identifier^dp "MO_642"^^string

circadian rhythm designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#circadian_rhythm_design

A circadian rhythm experiment design type assays the events associated with the circadian rhythm which is a biological activity that exhibits an endogenous periodicity independently of any daily variation in the environment.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.7"^^string; unique identifier^dp "MO_539"^^string; deprecation reason^dp "replaced_term"^^string; deprecation old parent^op biological property; was replaced by^op physiological process design; replaced with term^op physiological process design; has reason for deprecation^op replaced term; deprecated from version^op version 1.1.7

clinical history designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#clinical_history_design

A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.

belongs to: epidemiological design^c
has facts: unique identifier^dp "MO_832"^^string

clinical informationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#clinical_information

A descriptor for FactorValue where ClinicalInformation is compared.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_816"^^string

clinical recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#clinical_record

record which describes and identifies clinical information about an organism

belongs to: database entry type^c
has facts: unique identifier^dp "MO_852"^^string

clinical treatmentⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#clinical_treatment

A descriptor for a clinical treatment for a patient.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_384"^^string

clone of unknown sourceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#clone_of_unknown_source

Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown.

belongs to: physical bio sequence type^c
has facts: unique identifier^dp "MO_371"^^string

clustered dataⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#clustered_data

Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_418"^^string

clustering softwareⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#clustering_software

Software used to cluster the data.

belongs to: software type^c
has facts: unique identifier^dp "MO_464"^^string

cmⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cm

centimeter, a unit of distance

belongs to: distance unit^c
has facts: unique identifier^dp "MO_837"^^string

co expression designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#co-expression_design

A co-expression experiment design type identifies genes which are coordinately expressed and are potentially used to infer a role in a biological process(es) non-exact synonym: guilt by association

belongs to: bio molecular annotation^c
has facts: unique identifier^dp "MO_904"^^string; synonym^dp "guilt by association"^^string

coitusⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#coitus

the physical act of copulation that occurs during the process of sexual reproduction synonyms: copulation, insemination

belongs to: initial time point^c
has facts: unique identifier^dp "MO_783"^^string; synonym^dp "copulation"^^string; synonym^dp "insemination"^^string

collapsed spot replicateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#collapsed_spot_replicate

Results of data reduction involving computation of a representative value, e.g. by averaging, for a group of replicated Features, Reporters or CompositeSequences from a single hybridization.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_789"^^string

comparative genome hybridization designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#comparative_genome_hybridization_design

Experiment design type in which genomic content is studied using an array based assay.

belongs to: bio molecular annotation^c; technological design^c
has facts: synonym^dp "CGH"^^string; unique identifier^dp "MO_856"^^string; synonym^dp "array CGH"^^string; synonym^dp "array_CGH"^^string

compound based treatmentⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#compound_based_treatment

The treatment is effected by a defined chemical or biological compound. The compound may be a drug, solvent, chemical, etc., with a property that can be measured such as concentration.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_798"^^string

compound recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#compound_record

a record which describes and identifies a compound e.g. drug record part of NCI thesaurus

belongs to: database entry type^c
has facts: unique identifier^dp "MO_546"^^string

compound treatment designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#compound_treatment_design

A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.

belongs to: perturbational design^c
has facts: unique identifier^dp "MO_555"^^string

computational featureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#computational_feature

Computationally derived sequence feature.

belongs to: seq feature basis^c
has facts: unique identifier^dp "MO_411"^^string

computed amino acid sequence feature recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#computed_amino_acid_sequence_feature_record

a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM

belongs to: database entry type^c
has facts: unique identifier^dp "MO_797"^^string

computed nucleic acid sequence feature recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#computed_nucleic_acid_sequence_feature_record

A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record

belongs to: database entry type^c
has facts: unique identifier^dp "MO_774"^^string

computed protein structure recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#computed_protein_structure_record

a record which describes and identifies a protein structure e.g. PDB

belongs to: database entry type^c
has facts: unique identifier^dp "MO_765"^^string

computerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#computer

A device capable of applying software.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_510"^^string

concentrateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#concentrate

Increasing the concentration of solutes in a solution or suspension.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_883"^^string

condition specificityⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#condition_specificity

An analysis aimed at ranking genes or transcripts according to the uniformity of expression across a set of conditions. For example, the analysis can be used to rank genes according to the degree of tissue or developmental stage specificity.

belongs to: higher level analysis protocol type^c
has facts: unique identifier^dp "MO_417"^^string

consensus d n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#consensus_DNA

DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.3.1.1"^^string; unique identifier^dp "MO_361"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type

consensus m r n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#consensus_mRNA

mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.3.1.1"^^string; unique identifier^dp "MO_423"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op theoretical bio sequence type; deprecation old parent^op theoretical bio sequence type

consortium memberⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#consortium_member

A member of a consortium of institutions.

belongs to: roles^c
has facts: unique identifier^dp "MO_778"^^string

consultantⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#consultant

A contact who provides some service related to some aspect of the experiment which is not data coding or analysis. E.g. help with an experimental design.

belongs to: roles^c
has facts: unique identifier^dp "MO_984"^^string

control biosequenceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#control_biosequence

A Reporter associated with a BioSequence that has a context dependent predicted signal. e.g. a yeast reporter on a human array is a control_biosequence expected to be of low signal if no spikes are used. If spikes are used, the signal is expected to be high.

belongs to: control type^c
has facts: unique identifier^dp "MO_940"^^string

control bufferⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#control_buffer

A Reporter where only buffer was deposited on the array

belongs to: control type^c
has facts: unique identifier^dp "MO_505"^^string

control design element group typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#control_design_element_group_type

A grouping of DesignElements features/Reporters/Composites which are not designed to detect a signal in the biomaterial and which are on the array for control purposes e.g. a grouping of controls used for spiking.

belongs to: design element group type^c
has facts: unique identifier^dp "MO_414"^^string

control emptyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#control_empty

A Reporter where no material or buffer was deposited on the array

belongs to: control type^c
has facts: unique identifier^dp "MO_830"^^string

control genomic d n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#control_genomic_DNA

A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA.

belongs to: control type^c
has facts: unique identifier^dp "MO_449"^^string

control hybridization qualityⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#control_hybridization_quality

A Reporter that could be used to determine the quality and general performance of the labeled extract. An example is a pool of BioSequences representing widely-expressed genes (i.e., housekeeping genes).

belongs to: control type^c
has facts: unique identifier^dp "MO_385"^^string

control labelⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#control_label

Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone.

belongs to: control type^c
has facts: unique identifier^dp "MO_708"^^string

control reporter sizeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#control_reporter_size

A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency.

belongs to: control type^c
has facts: unique identifier^dp "MO_431"^^string

control spike calibrationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#control_spike_calibration

A Reporter that could be hybridized to an exogenously added nucleic acid or protein (spike) before or during hybridization and is used as a control for data processing. It may be deposited at one or more known concentrations (calibration). A reporter may be a spike, a calibration control or both.

belongs to: control type^c
has facts: unique identifier^dp "MO_364"^^string

control unknown typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#control_unknown_type

A Reporter indicated as being a control of unknown type.

belongs to: control type^c
has facts: unique identifier^dp "MO_925"^^string

cosine distanceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cosine_distance

The cosine distance of two vectors is the cosine of the angle between them. This measures the difference in direction between two vectors, irrespective of their lengths.

belongs to: node value type^c
has facts: unique identifier^dp "MO_550"^^string

cosmidⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cosmid

sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_888"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

countⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#count

Unit for a simple count of things

belongs to: quantity unit other^c
has facts: unique identifier^dp "MO_500"^^string

cpmⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cpm

counts per minute, unit of light emissions produced by ionizing radiation.

belongs to: radiation unit^c
has facts: unique identifier^dp "MO_348"^^string

ct d n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ctDNA

ctDNA: sequence from the chloroplast synonym: chloroplast DNA

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.3.1.1"^^string; unique identifier^dp "MO_586"^^string; synonym^dp "chloroplast DNA"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type

curated amino acid sequence recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#curated_amino_acid_sequence_record

A record which describes and identifies an amino acid sequence which has been curated

belongs to: database entry type^c
has facts: unique identifier^dp "MO_451"^^string

curated gene recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#curated_gene_record

A record which describes and identifies nucleic acid sequence which has been identified as a gene by a curator. e.g. Flybase gene record

belongs to: database entry type^c
has facts: unique identifier^dp "MO_913"^^string

curated nucleic acid sequence feature recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#curated_nucleic_acid_sequence_feature_record

A record which identifies a nucleic acid sequence feature(s) and which has been curated.

belongs to: database entry type^c
has facts: unique identifier^dp "MO_644"^^string

curatorⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#curator

person who checks the consistency of the data and MAGE-ML file

belongs to: roles^c
has facts: unique identifier^dp "MO_893"^^string

cy3ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Cy3

fluorophore used for labeling/detection purposes

belongs to: label compound^c
has facts: unique identifier^dp "MO_739"^^string

cy5ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Cy5

fluorophore used for labeling/detection purposes

belongs to: label compound^c
has facts: unique identifier^dp "MO_646"^^string

cytoplasmic r n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cytoplasmic_RNA

RNA obtained from the cytoplasm.

belongs to: material type^c
has facts: unique identifier^dp "MO_978"^^string

d n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DNA

Deoxyribonucleic acid.

belongs to: material type^c; polymer type^c
has facts: unique identifier^dp "MO_945"^^string

d n a sequencerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DNA_sequencer

An instrument that produces DNA sequences.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_676"^^string

data analystⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#data_analyst

A contact who performs data analysis, e.g. statistician.

belongs to: roles^c
has facts: unique identifier^dp "MO_753"^^string

data coderⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#data_coder

person who prepares the MAGE-ML file

belongs to: roles^c
has facts: unique identifier^dp "MO_695"^^string

dateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#date

Time stated in terms of the day, month, and year.

belongs to: data type^c
has facts: unique identifier^dp "MO_587"^^string

daughterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#daughter

The female offspring of the patient or individual under study.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_665"^^string

daysⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#days

24 hours, time unit

belongs to: time unit^c
has facts: unique identifier^dp "MO_513"^^string; synonym^dp "d"^^string

decontaminateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#decontaminate

Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma).

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_389"^^string

degrees cⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#degrees_C

degrees celsius, unit of temperature

belongs to: temperature unit^c
has facts: unique identifier^dp "MO_980"^^string

degrees fⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#degrees_F

degrees Fahrenheit, unit of temperature

belongs to: temperature unit^c
has facts: unique identifier^dp "MO_812"^^string

deleted termⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#deleted_term

The term was deleted from the MGED CoreOntology.

belongs to: deprecation reason^c
has facts: unique identifier^dp "MO_1023"^^string

development or differentiation designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#development_or_differentiation_design

A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions.

belongs to: biological property^c
has facts: unique identifier^dp "MO_892"^^string

developmental stageⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#developmental_stage

A descriptor for FactorValue where DevelopmentalStage is compared.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_878"^^string

diameter aberrationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#diameter_aberration

The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.

belongs to: defect type^c
has facts: unique identifier^dp "MO_781"^^string

differential expressionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#differential_expression

An analysis aimed at identifying differentially expressed genes in two or more conditions.

belongs to: higher level analysis protocol type^c
has facts: unique identifier^dp "MO_874"^^string

differential expression softwareⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#differential_expression_software

A software implementing a Higher Level Analysis protocol of type differential_expresssion.

belongs to: software type^c
has facts: unique identifier^dp "MO_350"^^string

diluteⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dilute

Decreasing the concentration of solutes in a solution or suspension.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_962"^^string

diploidⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#diploid

Describes a cell, nucleus or an organism with two copies of each chromosome.

belongs to: ploidy^c
has facts: unique identifier^dp "MO_836"^^string

disease stagingⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#disease_staging

The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_792"^^string

disease stateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#disease_state

A descriptor for FactorValue where DiseaseState is compared.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_787"^^string

disease state designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#disease_state_design

An experiment design type in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.

belongs to: epidemiological design^c; perturbational design^c
has facts: unique identifier^dp "MO_902"^^string

displaced feature or zoneⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#displaced_feature_or_zone

The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).

belongs to: defect type^c
has facts: unique identifier^dp "MO_959"^^string

dissectⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dissect

The action of removing one or more organism parts.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_374"^^string

dlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dl

deciliter, unit of volume

belongs to: volume unit^c
has facts: unique identifier^dp "MO_624"^^string

dose response designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dose_response_design

A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s).

belongs to: perturbational design^c
has facts: unique identifier^dp "MO_485"^^string

double strandedⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#double_stranded

a nucleic acid consisting of two polynucleotide chains having antiparallel orientation and being bound together by hydrogen bonding between the chains. This would apply to DNA and some RNA genomes, but not to rRNA or tRNA, etc.

belongs to: strand type^c
has facts: unique identifier^dp "MO_828"^^string

dpmⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dpm

disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument.

belongs to: radiation unit^c
has facts: unique identifier^dp "MO_583"^^string

ds oligoⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ds_oligo

a double stranded oligonucleotide

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_344"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

dye swap designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dye_swap_design

An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip

belongs to: methodological design^c
has facts: unique identifier^dp "MO_858"^^string; synonym^dp "dye flip"^^string; synonym^dp "flip dye"^^string

dye swap mergeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dye_swap_merge

A method of merging expression results from 2 dye-swap hybridizations on a Feature by Feature basis, with possible flagging if the results do not pass consistency checking criteria.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_448"^^string

dye swap quality controlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dye_swap_quality_control

Indicates that a dye swap was performed for some or all hybridizations within an experiment

belongs to: quality control description type^c
has facts: unique identifier^dp "MO_524"^^string

dye swap replicateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dye_swap_replicate

One of a pair of replicate assays in which LabeledExtracts derived from the same BioMaterial used for both assays (e.g., a hybridization or a 2-D gel run) differ only in that the dyes used for labeling have been reversed, e.g., assay 1: A-Cy3 vs. B-Cy5, and assay 2: A-Cy5 vs. B-Cy3. The purpose of using dye-swap replicate pairs is to assess or remove dye-specific biases from the combined experimental results.

belongs to: replicate description type^c
has facts: unique identifier^dp "MO_901"^^string

dye swap replicate reductionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dye_swap_replicate_reduction

Results of data reduction involving computation of a representative value from identical reporters or features obtained from two, or more, hybridizations in which each LabelExtract is labeled with each of the labels or dyes. Computation of a representative value for reporter X using data from Hybridizations 1 and 2, where LabeledExtract A is labeled with Cy3 (and LabeledExtract B is labeled with Cy5) in Hybridization 1 and LabeledExtract A is labeled with Cy5 (and LabeledExtract B is labeled with Cy3) in Hybridization 2.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_750"^^string

e m a pⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#EMAP

The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth.

belongs to: developmental stage database^c
has facts: unique identifier^dp "MO_357"^^string; has human readable u r i^dp "http://genex.hgu.mrc.ac.uk"^^string

e s tⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#EST

Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_412"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

e v o cⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#eVOC

Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.

belongs to: cell type database^c; developmental stage database^c; disease state database^c; organism part database^c
has facts: unique identifier^dp "MO_684"^^string; has human readable u r i^dp "http://www.sanbi.ac.za/evoc/ontologies.html"^^string

eclosionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#eclosion

Emergence of an adult insect from its pupa or cocoon.

belongs to: initial time point^c
has facts: unique identifier^dp "MO_876"^^string

egg layingⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#egg_laying

The point at which the egg(s) is laid by an organism.

belongs to: initial time point^c
has facts: unique identifier^dp "MO_767"^^string

element designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#element_design

protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design

belongs to: experimental protocol type^c
has facts: unique identifier^dp "MO_523"^^string

ellipsoid featureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ellipsoid_feature

The shape of the feature on the array is circular or oval.

belongs to: feature shape^c
has facts: unique identifier^dp "MO_459"^^string

environmental history designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#environmental_history_design

An environmental history design type is where some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.

belongs to: environmental history^c
has facts: unique identifier^dp "MO_698"^^string

euclidean distanceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Euclidean_distance

The straight line distance between two points. In n dimensions, the Euclidean distance between two points p and q is square root of (sum (pi-qi)2) where pi (or qi) is the i-th coordinate of p (or q).

belongs to: node value type^c
has facts: unique identifier^dp "MO_932"^^string

ex vivo designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ex_vivo_design

An experiment design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_808"^^string

exemplar m r n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#exemplar_mRNA

An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.3.1.1"^^string; unique identifier^dp "MO_621"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type

exonⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#exon

sequence which represents regions of a transcript that are joined to another exon during splicing

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_619"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op theoretical bio sequence type; deprecation old parent^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

experimental and computational featureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#experimental_and_computational_feature

Sequence features derived by both computational and experimental methods.

belongs to: seq feature basis^c
has facts: unique identifier^dp "MO_516"^^string

experimental design element group typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#experimental_design_element_group_type

A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial.

belongs to: design element group type^c
has facts: unique identifier^dp "MO_755"^^string

experimental featureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#experimental_feature

An experimentally defined sequence feature.

belongs to: seq feature basis^c
has facts: unique identifier^dp "MO_452"^^string

extractⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#extract

The BioSample immediately before labeling.

belongs to: bio sample type^c
has facts: unique identifier^dp "MO_895"^^string

fⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#F

mating type indicating the presence of F plasmid in a bacterial cell

belongs to: sex^c
has facts: unique identifier^dp "MO_717"^^string

f mⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#fM

femtomolar, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_898"^^string

f m aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FMA

The Foundational Model of Anatomy (FMA) is concerned with the representation of concepts and relationships necessary for the symbolic modeling of the structure of the human body.

belongs to: organism part database^c
has facts: unique identifier^dp "MO_468"^^string; has human readable u r i^dp "http://sig.biostr.wahington.edu/projects/fm/"^^string

f minusⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#F_minus

mating type indicating the absence of F plasmid in a bacterial cell

belongs to: sex^c
has facts: unique identifier^dp "MO_682"^^string

factor value dependencyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FactorValueDependency

has facts: deprecation old parent^op experiment package
is also defined as: class

factor value setⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FactorValueSet

has facts: deprecation old parent^op experiment package; deprecation replacement term^op factor value set
is also defined as: class

family history designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#family_history_design

A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied

belongs to: epidemiological design^c
has facts: unique identifier^dp "MO_544"^^string

fatherⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#father

A male parent.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_762"^^string

feature extractionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction

The process of obtaining quantifiable values from the scanned image of the array. Exact synonyms: image analysis, image quantification

belongs to: experimental protocol type^c
has facts: unique identifier^dp "MO_928"^^string; synonym^dp "image analysis"^^string; synonym^dp "image quantification"^^string

feature extraction softwareⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction_software

Software to create MeasuredBioAssayData from images. Exact Synonym: image analysis software, image quantification software.

belongs to: software type^c
has facts: unique identifier^dp "MO_633"^^string; synonym^dp "image analysis software"^^string; synonym^dp "image quantification software"^^string

fecesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feces

A biosource obtained as fecal matter.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.9"^^string; unique identifier^dp "MO_636"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op bio source type; deprecation replacement term^op bio source type; has reason for deprecation^op deleted term; deprecated from version^op version 1.1.9

feedingⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feeding

Delivery method where a compound/drug is administered in food or water.

belongs to: delivery method^c
has facts: unique identifier^dp "MO_993"^^string

femaleⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#female

of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes.

belongs to: sex^c
has facts: unique identifier^dp "MO_506"^^string

fertilizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#fertilization

The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO)

belongs to: initial time point^c
has facts: unique identifier^dp "MO_701"^^string

fgⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#fg

femtogram, unit of mass

belongs to: mass unit^c
has facts: unique identifier^dp "MO_732"^^string

filtered dataⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#filtered_data

Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_625"^^string

flⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#fl

femtoliter, unit of volume

belongs to: volume unit^c
has facts: unique identifier^dp "MO_721"^^string

flag filterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#flag_filter

transformation method that involves removal of values in a data set based on visual or computed flags (e.g. the GenePix feature_extraction software standard flags). This includes low-intensity filtering methods, where the flag indicates low intensity values in the data set (for microarrays and gels the threshold for exclusion is usually based on some estimation of local or global background intensity; for mass spectrometry and NMR, it is usually based on the signal-to-noise ratio in the spectrum).

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_1024"^^string

flip dye consistencyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#flip-dye_consistency

A method of checking the consistency of expression levels between a pair of features from flip-dye hybridizations by studying the distribution of the logarithm of ratios of intensity ratios from the two spots.

belongs to: normalization description type^c
has facts: unique identifier^dp "MO_907"^^string; was replaced by^op dye swap merge; has reason for deprecation^op replaced term; deprecated from version^op version 1.2.0

floatⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#float

A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34).

belongs to: data type^c
has facts: unique identifier^dp "MO_860"^^string

fly base developmental stage databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FlyBase_developmental_stage_database

uri for FlyBase developmental stage terms

belongs to: developmental stage database^c
has facts: unique identifier^dp "MO_865"^^string; has machine readable u r i^dp "http://cvs.sourceforge.net/viewcvs.py/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.ontology?content-type=text/plain&rev=1.1"^^string

fly base organism part databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#FlyBase_organism_part_database

curated database containing information on Drosophila genes, alleles etc

belongs to: organism part database^c
has facts: unique identifier^dp "MO_504"^^string; has machine readable u r i^dp "http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/"^^string

fmolⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#fmol

femtomole, unit of quantity

belongs to: quantity unit^c
has facts: unique identifier^dp "MO_689"^^string

forwardⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#forward

the forward strand exact synonym: +

belongs to: strand type^c
has facts: synonym^dp "+"^^string; unique identifier^dp "MO_820"^^string

fractionateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#fractionate

The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify).

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_872"^^string

freeze dried sampleⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#freeze_dried_sample

A biomaterial that has been lyophilized or dried by freezing under a vacuum.

belongs to: bio source type^c
has facts: unique identifier^dp "MO_589"^^string

french railway distanceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#french_railway_distance

The "French railway distance" is based on the fact that (at least in the past) most of the railways in France headed straight to Paris. Thus, the French railway distance between two points is the usual distance if the straight line through them passes to a designated Paris point, or is the sum of their distances to the Paris point otherwise.

belongs to: node value type^c
has facts: unique identifier^dp "MO_964"^^string

fresh sampleⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#fresh_sample

A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat.

belongs to: bio source type^c
has facts: unique identifier^dp "MO_730"^^string

frozen sampleⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#frozen_sample

A biomaterial obtained frozen

belongs to: bio source type^c
has facts: unique identifier^dp "MO_610"^^string

frozen storageⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#frozen_storage

Storage where the thing stored is stored below 0 degrees celsius.

belongs to: preservation type^c
has facts: unique identifier^dp "MO_481"^^string

function recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#function_record

a record which identifies and describes the function of a gene product, e.g. E.C. record

belongs to: database entry type^c
has facts: unique identifier^dp "MO_538"^^string

funderⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#funder

Contact which provides funding for experiments.

belongs to: roles^c
has facts: unique identifier^dp "MO_520"^^string

gⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#g

gram, unit of mass

belongs to: mass unit^c
has facts: unique identifier^dp "MO_825"^^string

g i fⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#GIF

Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss.

belongs to: image format^c
has facts: unique identifier^dp "MO_963"^^string

g per lⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#g_per_L

grams per liter, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_805"^^string

g r a m e n eⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#GRAMENE

A Comparative Mapping Resource for Grains.

belongs to: strain or line database^c
has facts: unique identifier^dp "MO_678"^^string; has human readable u r i^dp "http://www.gramene.org/"^^string

geneⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#gene

genomic sequence which corresponds to the primary transcript and uses the furthest 5' and 3' UTR's, doesn't include non transcribed regulatory regions. Can be experimentally or computationally determined

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_503"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

gene fragmentⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#gene_fragment

sequence of part of a gene, which is missing one or both ends

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.3.1.1"^^string; unique identifier^dp "MO_853"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op theoretical bio sequence type; deprecation old parent^op theoretical bio sequence type

gene knock inⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#gene_knock_in

A modification whereby a functional gene, or a functional part of a gene, is inserted into an organism', e.g. by recombination, P-element insertion.

belongs to: genetic modification^c
has facts: unique identifier^dp "MO_437"^^string

gene knock outⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#gene_knock_out

The modification of an organism that renders a gene non-functional e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.

belongs to: genetic modification^c
has facts: unique identifier^dp "MO_771"^^string

gene ontologyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#GeneOntology

The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.

belongs to: cellular component database^c
has facts: unique identifier^dp "MO_1022"^^string; has machine readable u r i^dp "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"^^string

genetic modificationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#genetic_modification

An action whereby an organism(s) has had genetic material removed, added, or rearranged.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_927"^^string

genetic modification designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#genetic_modification_design

A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out

belongs to: perturbational design^c
has facts: unique identifier^dp "MO_447"^^string

genetic variationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#genetic_variation

A descriptor for FactorValue where GeneticVariation is compared.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.8"^^string; unique identifier^dp "MO_557"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op bio material characteristic category; deprecation replacement term^op bio material characteristic category; has reason for deprecation^op deleted term; deprecated from version^op version 1.1.8

genomic d n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#genomic_DNA

high molecular weight DNA

belongs to: material type^c
has facts: unique identifier^dp "MO_599"^^string

genomic region amplificationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#genomic_region_amplification

increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification

belongs to: chromosomal aberration classification^c
has facts: unique identifier^dp "MO_609"^^string

genotyping designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#genotyping_design

A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.

belongs to: bio molecular annotation^c
has facts: unique identifier^dp "MO_560"^^string

germinationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#germination

The physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth (from the GO).

belongs to: initial time point^c
has facts: unique identifier^dp "MO_590"^^string

glassⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass

The array is made on a glass slide.

belongs to: substrate type^c
has facts: unique identifier^dp "MO_742"^^string

gram percentⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#gram_percent

grams per deciliter, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_582"^^string

granddaughterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#granddaughter

A daughter of one's son or daughter.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_703"^^string

grandfatherⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#grandfather

The father of one's father or mother.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_478"^^string

grandmotherⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#grandmother

The mother of one's father or mother.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_924"^^string

grandsonⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#grandson

A son of one's son or daughter.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_831"^^string

growⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#grow

A ComplexAction or ProtocolType describing growth of an organism or cell culture.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_758"^^string

growth condition designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#growth_condition_design

A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients.

belongs to: perturbational design^c
has facts: unique identifier^dp "MO_588"^^string

h u m a tⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#HUMAT

Ontology of human developmental anatomy for Carnegie stages 1-20.

belongs to: developmental stage database^c
has facts: unique identifier^dp "MO_844"^^string; has machine readable u r i^dp "http://obo.sourceforge.net/list.shtml"^^string

half lifeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#half-life

t1/2. The period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration. Typically applied to the half-life of radioactive atoms but also applicable to any other situation where the population is of molecules of diminishing concentration or activity.

belongs to: time unit other^c
has facts: unique identifier^dp "MO_595"^^string

haploidⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#haploid

Describes a cell, nucleus or an organism with one copy of each chromosome.

belongs to: ploidy^c
has facts: unique identifier^dp "MO_719"^^string

hardware manufacturerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#hardware_manufacturer

Person or organization that manufactured the hardware.

belongs to: roles^c
has facts: unique identifier^dp "MO_763"^^string

hardware variation designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#hardware_variation_design

A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_734"^^string

harvestⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#harvest

The process of harvesting cells from culture.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_982"^^string

hatchingⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#hatching

The point at which an organism emerges from an egg.

belongs to: initial time point^c
has facts: unique identifier^dp "MO_745"^^string

heating blockⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#heating_block

A device for controlling temperature.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_663"^^string

heavy backgroundⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#heavy_background

The Zone is excluded due to smearing, streaking, or dense background in the Zone.

belongs to: defect type^c
has facts: unique identifier^dp "MO_571"^^string

hermaphroditeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#hermaphrodite

an organism with both male and female sexual organs in one individual synonym: intersex

belongs to: sex^c
has facts: unique identifier^dp "MO_356"^^string; synonym^dp "intersex"^^string

hfrⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Hfr

High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.7"^^string; unique identifier^dp "MO_419"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op sex; deprecation replacement term^op sex; has reason for deprecation^op deleted term; deprecated from version^op version 1.1.7

histological slide preparationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#histological_slide_preparation

The action of preparing a slide for the microscopical examination of organism parts or cell types.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_611"^^string

homogenizerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#homogenizer

An instrument which fragments tissues or other biomaterials.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_714"^^string

hoursⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#hours

60 minutes, time unit

belongs to: time unit^c
has facts: unique identifier^dp "MO_486"^^string; synonym^dp "h"^^string

hybridizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#hybridization

The process of incubating one or more labeled extracts with an array.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_884"^^string

hybridization chamberⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#hybridization_chamber

A chamber in which the hybridization is performed which maintains constant conditions.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_563"^^string

hybridization stationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#hybridization_station

An instrument which controls hybridization conditions, into which a hybridization chamber may fit.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_497"^^string

i c d 9 c mⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ICD-9-CM

Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.

belongs to: disease state database^c
has facts: unique identifier^dp "MO_654"^^string; has machine readable u r i^dp "ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2002"^^string

i uⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#IU

The International unit is a unit of measurement for the amount of a substance, based on measured biological activity. It is used for vitamins, hormones, some drugs, vaccines, blood products and similar biologically active substances. The precise definition of one IU differs from substance to substance and is established by international agreement and is based on a reference provided by the Committee on Biological Standardization of the World Health Organization.

belongs to: quantity unit^c
has facts: synonym^dp "International unit"^^string; unique identifier^dp "MO_1011"^^string; synonym^dp "UI"^^string

i u p a c clinical chemistry guidelinesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#IUPAC_Clinical_Chemistry_Guidelines

A resource of vocabularies for describing clinical tests, e.g. blood chemistry.

belongs to: test type database^c
has facts: unique identifier^dp "MO_593"^^string; has human readable u r i^dp "http://www.iupac.org/publications/pac/2000/205/205olesen.html"^^string

image acquisitionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#image_acquisition

The process of generating an image from the array.

belongs to: experimental protocol type^c
has facts: unique identifier^dp "MO_929"^^string

image acquisition softwareⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#image_acquisition_software

Software to control a scanner and manipulate and save images. Exact synonym: scanning software

belongs to: software type^c
has facts: unique identifier^dp "MO_1003"^^string; synonym^dp "scanning software"^^string

image recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#image_record

A record which describes and identifies an image, e.g. an image from the mouse atlas

belongs to: database entry type^c
has facts: unique identifier^dp "MO_691"^^string

imprinting designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#imprinting_design

An experiment design type where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared.

belongs to: biological property^c
has facts: unique identifier^dp "MO_914"^^string

in mediumⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#in_medium

Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment).

belongs to: delivery method^c
has facts: unique identifier^dp "MO_733"^^string

in situ oligo featuresⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#in_situ_oligo_features

The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)

belongs to: technology type^c
has facts: unique identifier^dp "MO_514"^^string

in vitro designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#in_vitro_design

An experiment done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_347"^^string

in vivo designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#in_vivo_design

An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_454"^^string

inconclusiveⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#inconclusive

a result which can not be interpreted as positive or negative

belongs to: result^c
has facts: unique identifier^dp "MO_744"^^string

incubateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#incubate

The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_965"^^string

individualⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#individual

A descriptor for FactorValue where BioSources are compared.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_639"^^string

individual chromosomal abnormalityⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#IndividualChromosomalAbnormality

has facts: deprecation replacement term^op individual chromosomal abnormality; deprecation old parent^op individual genetic characteristics
is also defined as: class

individual genetic characteristicⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#individual_genetic_characteristic

A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_722"^^string

individual genetic characteristics designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#individual_genetic_characteristics_design

An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared.

belongs to: biological property^c
has facts: unique identifier^dp "MO_527"^^string

induced mutationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#induced_mutation

The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.

belongs to: genetic modification^c
has facts: unique identifier^dp "MO_564"^^string

infectⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#infect

The organism (or organism part) has been exposed to a virus or pathogen.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.3.0"^^string; unique identifier^dp "MO_616"^^string; deprecation reason^dp "replaced_term"^^string; deprecation old parent^op complex action; deprecation old parent^op experimental protocol type; was replaced by^op inoculate; replaced with term^op inoculate; has reason for deprecation^op replaced term; deprecated from version^op version 1.3.0

injury designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#injury_design

An injury experiment design type is where the response of an organism(s) to injury or damage is studied.

belongs to: perturbational design^c
has facts: unique identifier^dp "MO_726"^^string

innate behavior designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#innate_behavior_design

A design in which the innate behavior of the organism is examined, e.g. path finding in bees.

belongs to: biological property^c
has facts: unique identifier^dp "MO_355"^^string

inoculateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#inoculate

The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_559"^^string; synonym^dp "infect"^^string

institutionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#institution

A contact's affiliation, e.g. university, research institute or business.

belongs to: roles^c
has facts: unique identifier^dp "MO_601"^^string

integerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#integer

A value which is a whole number (e.g. 10).

belongs to: data type^c
has facts: unique identifier^dp "MO_435"^^string

intergenicⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#intergenic

sequence from the region between genes

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_463"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

intramuscular injectionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#intramuscular_injection

Delivery method for a compound or drug where the substance is administered via an injection into the muscle.

belongs to: delivery method^c
has facts: unique identifier^dp "MO_617"^^string

intraperitoneal injectionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#intraperitoneal_injection

A delivery method for compound or drug whereby the substance is administered via the peritoneum.

belongs to: delivery method^c
has facts: unique identifier^dp "MO_473"^^string

intravenousⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#intravenous

delivery method whereby a compound or drug is administered via a vein

belongs to: delivery method^c
has facts: unique identifier^dp "MO_432"^^string

intronⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#intron

sequence spliced out from a transcript

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_709"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

investigatorⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#investigator

Person who contributed to the study.

belongs to: roles^c
has facts: unique identifier^dp "MO_769"^^string

irradiateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#irradiate

treatment of a biomaterial with radiation e.g. electromagnetic radiation

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_770"^^string

irregular shapeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#irregular_shape

The perimeter of the spotted DNA on the slide is irregular.

belongs to: defect type^c
has facts: unique identifier^dp "MO_669"^^string

is contaminatedⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#is_contaminated

The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination.

belongs to: warning type^c
has facts: unique identifier^dp "MO_489"^^string

is expressed designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#is_expressed_design

A design aimed at identifying genes expressed in biomaterials of interest.

belongs to: biological property^c
has facts: unique identifier^dp "MO_487"^^string

iterative mean log centeringⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#iterative_mean_log_centering

A method of re-scaling ratio data by iteratively subtracting the mean log base 2 ratio from each log2(ratio). This adjusts the mean log2(ratio) to zero. In each subsequent iteration, outliers are removed based on user-specified criteria, the mean log(2) ratio is recalculated based on the remaining data, and the entire data set is rescaled again. This continues until the mean log(2) ratio converges.

belongs to: normalization description type^c
has facts: unique identifier^dp "MO_957"^^string

j a x mouse strainsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#JAX_mouse_strains

Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.

belongs to: strain or line database^c
has facts: unique identifier^dp "MO_369"^^string; has human readable u r i^dp "http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml"^^string

j p e gⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#JPEG

Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss.

belongs to: image format^c
has facts: unique identifier^dp "MO_746"^^string

jackknife pearson correlationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#jackknife_Pearson_correlation

The jackknife Pearson correlation is the lowest Pearson correlation between two data series where one pair of values in the data series are omitted.

belongs to: node value type^c
has facts: unique identifier^dp "MO_784"^^string

journal articleⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#journal_article

A article published in a print or online journal having an ISSN.

belongs to: publication type^c
has facts: unique identifier^dp "MO_430"^^string

kⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#K

Kelvin, unit of temperature

belongs to: temperature unit^c
has facts: unique identifier^dp "MO_614"^^string

kat per lⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#kat_per_L

katal per liter, catalytic-activity concentration unit

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_869"^^string

kgⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#kg

kilogram, 1000 grams, unit of mass

belongs to: mass unit^c
has facts: unique identifier^dp "MO_846"^^string

kg per m2ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#kg_per_m2

The mass of an object in kilograms divided by the surface area in meters squared. Also known as the Body Mass Index (when applied to a person) which is a measure of leaness/obesity. Exact synonym:kg/m2

belongs to: other unit^c
has facts: unique identifier^dp "MO_658"^^string; synonym^dp "kg/m2"^^string

lⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#L

liter, unit of volume

belongs to: volume unit^c
has facts: unique identifier^dp "MO_444"^^string

l o i n cⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#LOINC

Database resource for universal identifiers for laboratory and other clinical observations

belongs to: test type database^c
has facts: unique identifier^dp "MO_731"^^string; has machine readable u r i^dp "http://www.loinc.org/download"^^string

labelingⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#labeling

The procedure of labeling a biosample.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_471"^^string

laser ablation markⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#laser_ablation_mark

mark made on slide using a laser which is used as a point of reference for orientation (fiducial)

belongs to: fiducial type^c
has facts: unique identifier^dp "MO_910"^^string

light durationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#light_duration

The length of the light period that a sample is subjected to. Exact synonym:photoperiod

belongs to: environmental factor category^c
has facts: unique identifier^dp "MO_604"^^string; synonym^dp "photoperiod"^^string

light intensityⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#light_intensity

The amount of light actually striking the surface of samples which are being assayed. It has a unit association as well, usually uEinstein /m2 /min or uEinstein /m2/s.

belongs to: environmental factor category^c
has facts: unique identifier^dp "MO_517"^^string

linear amplificationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#linear_amplification

Amplification of nucleic acid sequence by making many copies off the same template. An example is the use of the T7 promoter for amplification by transcribing many RNA copies. non exact synonym: Eberwine procedure

belongs to: complex action^c; experimental protocol type^c
has facts: synonym^dp "Eberwine procedure"^^string; unique identifier^dp "MO_997"^^string

linear regression normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#linear_regression_normalization

A method to re-scale paired-assay data from one data set relative to the other, based on regression of the values in the one set to those in the other, where the latter utilizes either all values in the data set, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). The slope of the regression line is used to re-scale all the values in the data set being normalized. This single parameter method assumes that there is a linear relationship between the data sets. A similar approach could be employed to re-scale data from a standalone assay to another standalone (baseline) assay.

belongs to: normalization description type^c
has facts: unique identifier^dp "MO_823"^^string

linear scaleⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#linear_scale

The scale is a standard base 10, non logarithmic scale.

belongs to: scale^c
has facts: unique identifier^dp "MO_751"^^string

linlog normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#linlog_normalization

A transformation method in which low intensities are linearly scaled while high intensities are logarithmically scaled. The transition point is determined by minimizing the absolute deviation of the variance of log ratios.

belongs to: normalization description type^c
has facts: unique identifier^dp "MO_956"^^string; has reason for deprecation^op replaced term; deprecated from version^op version 1.2.0

linlog transformationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#linlog_transformation

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_845"^^string

liquidⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#liquid

media type, usually some sort of broth

belongs to: media^c
has facts: unique identifier^dp "MO_715"^^string

liquid handlerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#liquid_handler

Hardware for automated liquid transfer and handling.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_868"^^string

liquid handler softwareⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#liquid_handler_software

Software used to control automated liquid handler.

belongs to: software type^c
has facts: unique identifier^dp "MO_761"^^string

list of booleansⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_booleans

An ordered, finite set of booleans.

belongs to: data type^c
has facts: unique identifier^dp "MO_712"^^string

list of floatsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_floats

An ordered, finite set of floats.

belongs to: data type^c
has facts: unique identifier^dp "MO_760"^^string

list of integersⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_integers

An ordered, finite set of integers.

belongs to: data type^c
has facts: unique identifier^dp "MO_891"^^string

list of negative floatsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_negative_floats

An ordered, finite set of negative floats.

belongs to: data type^c
has facts: unique identifier^dp "MO_851"^^string

list of negative integersⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_negative_integers

An ordered, finite set of negative integers.

belongs to: data type^c
has facts: unique identifier^dp "MO_900"^^string

list of nonnegative floatsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_nonnegative_floats

An ordered, finite set of nonnegative floats.

belongs to: data type^c
has facts: unique identifier^dp "MO_360"^^string

list of nonnegative integersⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_nonnegative_integers

An ordered, finite set of nonnegative integers.

belongs to: data type^c
has facts: unique identifier^dp "MO_973"^^string

list of nonpositive floatsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_nonpositive_floats

An ordered, finite set of nonpositive floats.

belongs to: data type^c
has facts: unique identifier^dp "MO_1000"^^string

list of nonpositive integersⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_nonpositive_integers

An ordered, finite set of nonpositive integers.

belongs to: data type^c
has facts: unique identifier^dp "MO_804"^^string

list of positive floatsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_positive_floats

An ordered, finite set of positive floats.

belongs to: data type^c
has facts: unique identifier^dp "MO_777"^^string

list of positive integersⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_positive_integers

An ordered, finite set of positive integers.

belongs to: data type^c
has facts: unique identifier^dp "MO_873"^^string

list of stringsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#list_of_strings

An ordered, finite set of strings.

belongs to: data type^c
has facts: unique identifier^dp "MO_800"^^string

loess global normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#loess_global_normalization

Application of a normalization of type loess_normalization where the same normalization curve is used for all points in the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_443"^^string

loess group normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#loess_group_normalization

Application of a normalization of type loess_normalization where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_377"^^string

loess normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#loess_normalization

A method of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.

belongs to: normalization description type^c
has facts: unique identifier^dp "MO_428"^^string

loess scaled group normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#loess_scaled_group_normalization

Application of a scale adjustment following loess_group_normalization, to render the group variances similar.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_521"^^string

log base 10ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#log_base_10

The values presented are logarithm, base 10.

belongs to: scale^c
has facts: unique identifier^dp "MO_735"^^string

log base 2ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#log_base_2

The values presented are logarithm, base 2.

belongs to: scale^c
has facts: unique identifier^dp "MO_647"^^string

log base eⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#log_base_e

The values presented are logarithm, base e.

belongs to: scale^c
has facts: unique identifier^dp "MO_554"^^string

log ratioⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#log_ratio

Logarithmic transformation of ratio data.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_896"^^string

long oligoⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#long_oligo

An element that is an oligonucleotide of at least 50 nucleotides in length.

belongs to: design element^c
has facts: unique identifier^dp "MO_598"^^string

loop designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#loop_design

A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design

belongs to: methodological design^c
has facts: unique identifier^dp "MO_912"^^string; synonym^dp "circular design"^^string

low intensity filterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#low_intensity_filter

A transformation method that involves removal of low intensity values in a data set. For microarrays and gels the threshold for exclusion is usually based on some estimation of local or global background intensity; for mass spectrometry and NMR, it is usually based on the signal-to-noise ratio in the spectrum.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.3.0"^^string; unique identifier^dp "MO_706"^^string; deprecation reason^dp "replaced_term"^^string; deprecation old parent^op data transformation protocol type; was replaced by^op flag filter; replaced with term^op flag filter; has reason for deprecation^op replaced term; deprecated from version^op version 1.3.0

lowess global normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#lowess_global_normalization

Application of a normalization of type lowess_normalization where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_692"^^string

lowess group normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#lowess_group_normalization

Application of a normalization of type lowess_normalization where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_861"^^string

lowess normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#lowess_normalization

belongs to: normalization description type^c
has facts: unique identifier^dp "MO_720"^^string

lowess scaled group normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#lowess_scaled_group_normalization

Application of a scale adjustment following lowess_group_normalization, to render the group variances similar.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_410"^^string

lumenⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#lumen

The unit of total light output from a light source.

belongs to: light unit^c
has facts: unique identifier^dp "MO_603"^^string

luxⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#lux

A metric unit equal to one lumen per square meter. This unit is the modern equivalent of foot-candles where one footcandle is 10.76 lux.

belongs to: light unit^c
has facts: unique identifier^dp "MO_573"^^string

mⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#M

Mole per liter or molarity, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_936"^^string

mⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#m

meter, distance unit

belongs to: distance unit^c
has facts: unique identifier^dp "MO_367"^^string

m a d stageⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MAD_stage

database entry from mouse anatomical dictionary for developmental stage term

belongs to: developmental stage database^c; organism part database^c; targeted cell type database^c
has facts: unique identifier^dp "MO_693"^^string; has human readable u r i^dp "http://www.informatics.jax.org/mgihome/GXD/AD/"^^string

m a s4 average differenceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MAS4_average_difference

A quantitative measure of the relative abundance of a transcript. Used in the MAS4.0 Affymetrix software to obtain an averaged signal intensity from a group of related Features. This involves calculation of the overall sum of perfect match minus mismatch pairs divided by the number of pairs.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_782"^^string

m a s5 signalⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MAS5_signal

A quantitative measure of the relative abundance of a transcript. Used in the MAS5.0 Affymetrix software to obtain a smoothed signal intensity from a group of related Features.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_653"^^string

m a s5 signal log ratioⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MAS5_signal_log_ratio

The difference in expression level for a transcript between data from two arrays, expressed as the log2ratio. A signal log ratio of 1 is the same as a Fold Change of 2.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_938"^^string

m b e iⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MBEI

Multiarray-Based Expression Index (MBEI). A quantitative measure of the relative abundance of a transcript. MBEI is used in the dChip software to obtain a signal intensity from a group of related Features on an Affymetrix array.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_756"^^string

m e s hⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MESH

database entry from MESH, medical subject headings vocabulary resource

belongs to: disease state database^c
has facts: unique identifier^dp "MO_580"^^string; has human readable u r i^dp "http://www.nlm.nih.gov/mesh/filelist.html"^^string

m l per lⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mL_per_L

milliliters per liter, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_801"^^string

m mⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mM

milimolar, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_509"^^string

m osm per kg h2 oⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mOsm_per_kg_H2O

osmolality per kilogram of water, concentration of the solute per unit of solvent

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_661"^^string

m r n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mRNA

sequence of a processed transcript capable of directing protein synthesis

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_803"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op theoretical bio sequence type; deprecation old parent^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

m t b databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MTB_Database

Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors.

belongs to: disease state database^c
has facts: unique identifier^dp "MO_942"^^string; has human readable u r i^dp "http://tumor.informatics.jax.org"^^string

maleⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#male

individual whose sex organs contain only male gametes

belongs to: sex^c
has facts: unique identifier^dp "MO_652"^^string

mammalian phenotype ontologyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Mammalian_Phenotype_Ontology

A community effort to provide standard terms for annotating phenotypic data.

belongs to: observation database^c
has facts: unique identifier^dp "MO_704"^^string; has human readable u r i^dp "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:0000001"^^string

manhattan distanceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#manhattan_distance

The "Manhattan distance" is the shortest path between two points in a block format, e.g. the length of the path along Manthattan city streets.

belongs to: node value type^c
has facts: unique identifier^dp "MO_567"^^string

mating type aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mating_type_a

Mating type of S. cerevisiae.

belongs to: sex^c
has facts: unique identifier^dp "MO_659"^^string

mating type alphaⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mating_type_alpha

Mating type of S. cerevisiae.

belongs to: sex^c
has facts: unique identifier^dp "MO_637"^^string

mating type h minusⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mating_type_h_minus

Mating type of S.pombe.

belongs to: sex^c
has facts: unique identifier^dp "MO_407"^^string

mating type h plusⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mating_type_h_plus

Mating type of S.pombe.

belongs to: sex^c
has facts: unique identifier^dp "MO_855"^^string

mean and coefficient of variationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mean_and_coefficient_of_variation

the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_425"^^string

mean and confidence indicatorsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mean_and_confidence_indicators

the mean and associated confidence values resulting from combining the data from 2 or more sets of BioAssayData. Confidence indicators include, but are not limited to: confidence interval, standard deviation, coefficient of variation, and p-value.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_702"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op derived bio assay type; deprecation old parent^op derived bio assay type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

mean and p valuesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mean_and_p_values

the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_943"^^string

mean and standard deviationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mean_and_standard_deviation

the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_445"^^string

mean and varianceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mean_and_variance

the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_458"^^string

mean log centeringⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mean_log_centering

A method of normalizing log ratio data by subtraction of the mean log ratios computed across all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins).

belongs to: normalization description type^c
has facts: unique identifier^dp "MO_398"^^string

mean log normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mean_log_normalization

Application of a normalization of type mean_log_centering.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_657"^^string

mediaⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#media

The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil)

belongs to: environmental factor category^c
has facts: unique identifier^dp "MO_545"^^string

median log centeringⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#median_log_centering

A method of normalizing log ratio data by subtraction of the median log ratios computed across all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins).

belongs to: normalization description type^c
has facts: unique identifier^dp "MO_811"^^string

median log normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#median_log_normalization

Application of a normalization of type median_log_centering.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_931"^^string

merged termⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#merged_term

the term has been subsumed into a more general term

belongs to: deprecation reason^c
has facts: unique identifier^dp "MO_1025"^^string

metastatic siteⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#metastatic_site

the organism part in which additional tumors are identified remote from the primary site

belongs to: cancer site^c
has facts: unique identifier^dp "MO_806"^^string

mgⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mg

milligram, mass unit

belongs to: mass unit^c
has facts: unique identifier^dp "MO_949"^^string

mg per kg per dayⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mg_per_kg_per_day

milligram per kilogram per day

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_353"^^string

mg per mlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mg_per_ml

milligrams per milliliter, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_522"^^string

microarray experiment recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#microarray_experiment_record

A record which describes and identifies a microarray experiment e.g. GEO

belongs to: database entry type^c
has facts: unique identifier^dp "MO_346"^^string

microeinstein per minute and square meterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#microeinstein_per_minute_and_square_meter

Microeinstein per minute and square meter (µE m-2 min-1 or uEinstein m-2 min-1). One einstein is one mole or 6.02x10e23 (avogadro constant) photons. It is commonly used as a unit for photosynthetically active radiation (PAR), however the einstein is not an SI unit. Therefore, microEinsteins per m2 per second is identical to micromoles per m2 per second (SI unit for light irradiance). i.e. (1000 µE m-2 s-1 = 1000 µmol m-2 s-1).

belongs to: light unit^c
has facts: unique identifier^dp "MO_526"^^string

microeinstein per second and square meterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#microeinstein_per_second_and_square_meter

Microeinstein per second and square meter (µE m-2 s-1 or uEinstein m-2 s-1). One einstein is one mole or 6.02x10e23 (Avogadro constant) photons. It is commonly used as a unit for photosynthetically active radiation (PAR), however the einstein is not an SI unit. Therefore, microEinsteins per m2 per second is identical to micromoles per m2 per second (SI unit for light irradiance). i.e. (1000 µE m-2 s-1 = 1000 µmol m-2 s-1).

belongs to: light unit^c
has facts: unique identifier^dp "MO_584"^^string

micromole per second and square meterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#micromole_per_second_and_square_meter

Number of photons in a certain waveband incident per unit time (s) on a unit area (m2) divided by the Avogadro constant (6.022 x 10e23 mol-1). It is used commonly to describe photosynthetically active radiation (PAR) in the 400-700 nm waveband.

belongs to: other unit^c
has facts: unique identifier^dp "MO_848"^^string

minutesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#minutes

60 seconds, unit of time

belongs to: time unit^c
has facts: unique identifier^dp "MO_877"^^string; synonym^dp "m"^^string

missing feature or zoneⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#missing_feature_or_zone

The source DNA was not printed for a Feature or Zone on the slide, possibly due to lack of sample, broken or clogged spotting pin.

belongs to: defect type^c
has facts: unique identifier^dp "MO_405"^^string

mix by inversionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mix_by_inversion

Mix through the process of inverting.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_700"^^string

mix by pipetteⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mix_by_pipette

Mix by drawing up and down with a pipette.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_479"^^string

mix by vortexⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mix_by_vortex

Mix through the use of a vortexer.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_880"^^string

mix generalⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mix_general

The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_944"^^string

mixed design element group typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mixed_design_element_group_type

a design element group consisting of multiple types

belongs to: design element group type^c
has facts: unique identifier^dp "MO_528"^^string

mixed sexⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mixed_sex

A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites.

belongs to: sex^c
has facts: unique identifier^dp "MO_436"^^string

mlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ml

milliliter, volume unit

belongs to: volume unit^c
has facts: unique identifier^dp "MO_488"^^string

ml per kgⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ml_per_kg

milliliter per kilogram

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_403"^^string

mmⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mm

millimeter, unit of distance

belongs to: distance unit^c
has facts: unique identifier^dp "MO_648"^^string

molⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mol

mole, unit of quantity

belongs to: quantity unit^c
has facts: unique identifier^dp "MO_998"^^string

molecular mixtureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#molecular_mixture

an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins

belongs to: material type^c
has facts: unique identifier^dp "MO_889"^^string

moleculesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#molecules

number of molecules, quantity unit

belongs to: quantity unit^c
has facts: unique identifier^dp "MO_707"^^string

monosomyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#monosomy

Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.9"^^string; unique identifier^dp "MO_424"^^string; deprecation reason^dp "replaced_term"^^string; deprecation old parent^op chromosomal aberration classification; replaced with term^op oligosomy; was replaced by^op oligosomy; has reason for deprecation^op replaced term; deprecated from version^op version 1.1.9

monthsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#months

Unit of time corresponding to approx. one cycle of the moon's phases.

belongs to: time unit^c
has facts: unique identifier^dp "MO_631"^^string

motherⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mother

A female parent.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_387"^^string

moving averageⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#moving_average

A type of data transformation in which an average, usually the mean, is calculated across values within a sliding window. e.g. The moving average of signal intensity, or array CGH, data may be used in normalization.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_681"^^string

msⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ms

millisecond, time unit

belongs to: time unit^c
has facts: unique identifier^dp "MO_920"^^string

mt d n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#mtDNA

sequence from the mitochondrial genome

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.3.1.1"^^string; unique identifier^dp "MO_581"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type

multiple testing correctionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#multiple_testing_correction

Multiple testing correction uses individual p-values derived from multiple statistical tests to control either the family-wise error rate or the false discovery rate.

belongs to: higher level analysis protocol type^c
has facts: unique identifier^dp "MO_561"^^string

n a s cⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NASC

The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.

belongs to: strain or line database^c
has facts: unique identifier^dp "MO_379"^^string; has human readable u r i^dp "http://arabidopsis.info/catalogue.html"^^string

n c b i taxonomyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCBI_taxonomy

identifier for a taxon provided by the NCBI taxonomy database

belongs to: organism database^c; strain or line database^c
has facts: unique identifier^dp "MO_773"^^string; has human readable u r i^dp "http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/"^^string

n c i cell type databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_cell_type_database

a controlled vocabulary of cell types

belongs to: cell type database^c
has facts: unique identifier^dp "MO_687"^^string; has human readable u r i^dp "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=12596"^^string

n c i compound databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_compound_database

a controlled vocabulary for compounds

belongs to: compound database^c
has facts: unique identifier^dp "MO_376"^^string; has human readable u r i^dp "http://nciterm.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C1908"^^string

n c i disease staging databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_disease_staging_database

a controlled vocabulary for disease stages

belongs to: disease staging database^c
has facts: unique identifier^dp "MO_422"^^string; has human readable u r i^dp "http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28108"^^string

n c i disease state databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_disease_state_database

a controlled vocabulary for disease states

belongs to: disease state database^c
has facts: unique identifier^dp "MO_790"^^string; has human readable u r i^dp "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C7057"^^string

n c i geographic location databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_geographic_location_database

a controlled vocabulary for geographic locations

belongs to: geographic location database^c
has facts: unique identifier^dp "MO_630"^^string; has human readable u r i^dp "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16632"^^string

n c i histology databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_histology_database

a controlled vocabulary for histology

belongs to: histology database^c
has facts: unique identifier^dp "MO_537"^^string; has human readable u r i^dp "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C4741"^^string

n c i organism part databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_organism_part_database

a controlled vocabulary of organism parts

belongs to: organism part database^c
has facts: unique identifier^dp "MO_690"^^string; has human readable u r i^dp "http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C13007"^^string

n c i strain or line databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_strain_or_line_database

a controlled vocabulary for strains or lines

belongs to: strain or line database^c
has facts: unique identifier^dp "MO_397"^^string; has human readable u r i^dp "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16403"^^string

n c i targeted cell type databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_targeted_cell_type_database

a controlled vocabulary of targeted cell types

belongs to: targeted cell type database^c
has facts: unique identifier^dp "MO_351"^^string; has human readable u r i^dp "http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12596"^^string

n c i thesaurusⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_Thesaurus

A description logic namespace that contains controlled terminology used at NCI.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.7"^^string; unique identifier^dp "MO_456"^^string; has human readable u r i^dp "http://nciterms.nci.nih.gov"^^string; deprecation reason^dp "split_term"^^string; deprecation old parent^op cell line database; deprecation old parent^op clinical treatment database; deprecation old parent^op compound database; deprecation old parent^op disease state database; deprecation old parent^op geographic location database; split to term^op n c i cell type database; split to term^op n c i compound database; split to term^op n c i disease state database; split to term^op n c i geographic location database; split to term^op n c i organism part database; split to term^op n c i strain or line database; split to term^op n c i targeted cell type database; split to term^op n c i tumor grading database; deprecation old parent^op organism part database; deprecation old parent^op strain or line database; deprecation old parent^op targeted cell type database; deprecation old parent^op tumor grading database; has reason for deprecation^op split term; deprecated from version^op version 1.1.7

n c i tumor grading databaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#NCI_tumor_grading_database

a controlled vocabulary of tumor grading terms

belongs to: tumor grading database^c
has facts: unique identifier^dp "MO_819"^^string; has human readable u r i^dp "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28076"^^string

negativeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#negative

false or no

belongs to: result^c
has facts: unique identifier^dp "MO_802"^^string

negative floatⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#negative_float

A float that is < 0.

belongs to: data type^c
has facts: unique identifier^dp "MO_728"^^string

negative integerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#negative_integer

An integer < 0.

belongs to: data type^c
has facts: unique identifier^dp "MO_864"^^string

ngⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ng

nanogram, a mass unit

belongs to: mass unit^c
has facts: unique identifier^dp "MO_796"^^string

nitrocelluloseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nitrocellulose

The array is made on a nitrocellulose filter.

belongs to: substrate type^c
has facts: unique identifier^dp "MO_455"^^string

nlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nl

nanoliter unit of volume

belongs to: volume unit^c
has facts: unique identifier^dp "MO_754"^^string

nmⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nm

nanometer distance unit

belongs to: distance unit^c
has facts: unique identifier^dp "MO_862"^^string

nmolⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nmol

nanomoles, quantity unit

belongs to: quantity unit^c
has facts: unique identifier^dp "MO_743"^^string

noⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#no

false

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.7"^^string; unique identifier^dp "MO_556"^^string; deprecation reason^dp "deleted_term"^^string; has reason for deprecation^op deleted term; deprecated from version^op version 1.1.7

non targeted transgenic variation designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#non-targeted_transgenic_variation_design

The modification of an organism due to the presence of DNA from another individual, e.g. of a different strain, species or breed. These do not include targeted transgenics such as knock-ins and knock-outs.

belongs to: perturbational design^c
has facts: unique identifier^dp "MO_775"^^string

nonnegative floatⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nonnegative_float

A float greater than or equal to 0.

belongs to: data type^c
has facts: unique identifier^dp "MO_386"^^string

nonnegative integerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nonnegative_integer

An integer >= 0.

belongs to: data type^c
has facts: unique identifier^dp "MO_390"^^string

nonpositive floatⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nonpositive_float

A float less than or equal to zero.

belongs to: data type^c
has facts: unique identifier^dp "MO_656"^^string

nonpositive integerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nonpositive_integer

An integer less than or equal to zero.

belongs to: data type^c
has facts: unique identifier^dp "MO_623"^^string

normalization testing designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#normalization_testing_design

A normalization testing experiment design tests different normalization procedures.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_729"^^string

normalized intensitiesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#normalized_intensities

Results of normalization, by some method, of a bioassay data set such as; intensities from one or both channels of a microarray-based assay; orthologous spot sets on 2D gels; or repeat measurements of the same metabolite in replicate cell cultures.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_994"^^string

normalized ratiosⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#normalized_ratios

Results obtained by either taking the pair wise ratios of two bioassay data sets and then normalizing, or normalizing each bioassay data set and then taking ratios.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_664"^^string

not extractⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#not_extract

The BioSample at any stage other than immediately before labeling.

belongs to: bio sample type^c
has facts: unique identifier^dp "MO_894"^^string

not sequence verifiedⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#not_sequence_verified

The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter.

belongs to: warning type^c
has facts: unique identifier^dp "MO_970"^^string

not uniformⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#not_uniform

The source DNA for a Feature was not uniformly deposited.

belongs to: defect type^c
has facts: unique identifier^dp "MO_906"^^string

nuclear r n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nuclear_RNA

RNA obtained from the nucleus.

belongs to: material type^c
has facts: unique identifier^dp "MO_679"^^string

nucleic acid extractionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nucleic_acid_extraction

The procedure of extracting nucleic acid from the biomaterial.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_607"^^string

nucleic acid primary sequence recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nucleic_acid_primary_sequence_record

A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank

belongs to: database entry type^c
has facts: unique identifier^dp "MO_757"^^string

number per dayⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#number_per_day

number of items or events per day

belongs to: other unit^c
has facts: unique identifier^dp "MO_670"^^string

nutrientsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nutrients

The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).

belongs to: environmental factor category^c
has facts: unique identifier^dp "MO_867"^^string

nylonⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nylon

The array is made on a nylon membrane.

belongs to: substrate type^c
has facts: unique identifier^dp "MO_492"^^string

o r fⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ORF

sequence which represents an open reading frame, a series of codon triplets deduced from a DNA sequence, that contain a start and a stop codon.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_413"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

oligo synthesizerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#oligo_synthesizer

Hardware for synthesizing oligos.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_930"^^string

oligosomyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#oligosomy

A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement.

belongs to: chromosomal aberration classification^c
has facts: unique identifier^dp "MO_1028"^^string

online resourceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#online_resource

A publication type which is available online and which is not an online journal article, e.g. a web site or service.

belongs to: publication type^c
has facts: unique identifier^dp "MO_991"^^string

ontology recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ontology_record

A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD

belongs to: database entry type^c
has facts: unique identifier^dp "MO_529"^^string

open g a l e nⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#openGALEN

OpenGALEN Human Anatomy - open source database of approx. ten thousand human anatomy concepts together with extensive semantic relationships between them including part-of, connects, branch-of, serves, laterality. Also includes some human physiological processes together with functional relationships between these and the anatomy concepts.

belongs to: organism part database^c
has facts: unique identifier^dp "MO_613"^^string; has human readable u r i^dp "http://www.opengalen.org/open/crm/crm-anatomy.html"^^string

operating systemⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#operating_system

Software upon which other software runs.

belongs to: software type^c
has facts: unique identifier^dp "MO_847"^^string

operator variation designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#operator_variation_design

An operator variation experiment design type assesses the operator performance and relation to data consistency and quality.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_519"^^string

operonⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#operon

sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_759"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

operon identification designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#operon_identification_design

An operon identification experiment type is designed to identify locations and members of operons in a genome.

belongs to: bio molecular annotation^c
has facts: unique identifier^dp "MO_772"^^string

optimization designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#optimization_design

An optimization experiment design type is where different protocols or protocol parameters are compared.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_934"^^string

oral gavageⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#oral_gavage

delivery method for drug or compound whereby the drug is administered via the mouth

belongs to: delivery method^c
has facts: unique identifier^dp "MO_975"^^string

organellar d n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organellar_DNA

DNA from organelles such as the mitochondria or chloroplast.

belongs to: material type^c
has facts: unique identifier^dp "MO_645"^^string

organellar r n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organellar_RNA

RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus.

belongs to: material type^c
has facts: unique identifier^dp "MO_574"^^string

organismⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism

one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_508"^^string

organism partⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism_part

The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).

belongs to: bio material characteristic category^c; material type^c
has facts: unique identifier^dp "MO_954"^^string

organism part comparison designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism_part_comparison_design

An organism part comparison experiment design type compares tissues, regions, organs within or between organisms

belongs to: biological property^c
has facts: unique identifier^dp "MO_953"^^string

organism statusⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism_status

The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_871"^^string

organism status designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism_status_design

A design that compares samples from live and dead organisms.

belongs to: biological property^c
has facts: unique identifier^dp "MO_841"^^string

p a cⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PAC

sequence from a P1 artificial chromosome

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_909"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

p c rⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PCR

Polymerase chain reaction. An element generated using this procedure.

belongs to: design element^c
has facts: unique identifier^dp "MO_915"^^string

p c r ampliconⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PCR_amplicon

BioSequence generated by means of polymerase chain reaction

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_450"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

p c r amplificationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PCR_amplification

Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_358"^^string

p c r failⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PCR_fail

PCR where no products of any kind appear in gel-separated reaction products.

belongs to: fail type^c
has facts: unique identifier^dp "MO_667"^^string

p c r primerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PCR_primer

single oligo used for polymerase chain reaction direction unspecified

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_651"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

p c r primer forwardⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PCR_primer_forward

single stranded oligo used for polymerase chain reaction

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_381"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op physical bio sequence type; deprecation replacement term^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

p c r primer reverseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PCR_primer_reverse

single stranded oligo used for polymerase chain reaction

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_640"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op physical bio sequence type; deprecation replacement term^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

p c r questionableⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PCR_questionable

PCR with multiple bands, or smear, in gel-separated reaction products

belongs to: fail type^c
has facts: unique identifier^dp "MO_620"^^string

p hⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pH

potential of hydrogen

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_814"^^string

p mⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pM

picomolar, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_628"^^string

p n gⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#PNG

Portable Network Graphic, a lossless image data format.

belongs to: image format^c
has facts: unique identifier^dp "MO_1001"^^string

paraffin sampleⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#paraffin_sample

A biomaterial obtained embedded in paraffin (wax).

belongs to: bio source type^c
has facts: unique identifier^dp "MO_990"^^string

pathbaseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Pathbase

database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice

belongs to: histology database^c
has facts: unique identifier^dp "MO_972"^^string; has human readable u r i^dp "http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php"^^string

pathogenicity designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pathogenicity_design

A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.

belongs to: perturbational design^c
has facts: unique identifier^dp "MO_807"^^string

pathway recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pathway_record

a record which identifies and describes biological pathways, e.g. a KEGG record

belongs to: database entry type^c
has facts: unique identifier^dp "MO_780"^^string

pearson correlationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Pearson_correlation

The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations.

belongs to: node value type^c
has facts: unique identifier^dp "MO_632"^^string

pearson correlation coefficientⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pearson_correlation_coefficient

The Pearson's correlation coefficient between two variables. Its values can range between -1.00 to +1.00. The closer the absolute value of the Pearson correlation coefficient is to 0, the smaller the linear relationship between the two variables. A Pearson correlation coefficient with absolute value 1 indicates perfect linear relationship.

belongs to: node value type^c
has facts: unique identifier^dp "MO_558"^^string

pedigree recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pedigree_record

A record which describes and identifies a pedigree or lineage for a strain, line, individual or cell whose lineage traceable e.g. a wormbase cell lineage record, or a pedigree record for a mouse

belongs to: database entry type^c
has facts: unique identifier^dp "MO_969"^^string

peer review quality controlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#peer_review_quality_control

An experiment which has a peer reviewed publication attached.

belongs to: quality control description type^c
has facts: unique identifier^dp "MO_365"^^string

percent confluenceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#percent_confluence

A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_378"^^string

percent purityⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#percent_purity

A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy.

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_482"^^string

percent vol per volⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#percent_vol_per_vol

percentage volume per volume, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_916"^^string

percent weight per volⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#percent_weight_per_vol

percent weight per volume, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_420"^^string

percent weight per weightⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#percent_weight_per_weight

percent weight per weight, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_474"^^string

pfu per mlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pfu_per_ml

the number of plaque forming units per ml

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_768"^^string

pgⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pg

picogram, mass unit

belongs to: mass unit^c
has facts: unique identifier^dp "MO_363"^^string

phylogeny recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#phylogeny_record

A record which describes and identifies the relationship between species and is computationally determined and based on sequences e.g. Treebase record

belongs to: database entry type^c
has facts: unique identifier^dp "MO_662"^^string

physical characteristicsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#physical_characteristics

A descriptor for FactorValue where PhysicalCharacteristics are compared.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_863"^^string

physiological process designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#physiological_process_design

Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. This includes those processes that exhibit an endogenous periodicity independently of any daily variation in the environment such as circadian rhythm or aging.

belongs to: biological property^c
has facts: unique identifier^dp "MO_1029"^^string

plⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pl

picoliter, volume unit

belongs to: volume unit^c
has facts: unique identifier^dp "MO_905"^^string

placeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#place

The procedure of putting a physical object in a container/physical space.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_470"^^string

plantingⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#planting

The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing.

belongs to: initial time point^c
has facts: unique identifier^dp "MO_495"^^string

plasmidⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#plasmid

sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_439"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op physical bio sequence type; deprecation replacement term^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

pmolⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pmol

picomoles, quantity unit

belongs to: quantity unit^c
has facts: unique identifier^dp "MO_688"^^string

poly a r n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#polyA_RNA

RNA which has been obtained by selection for polyA tracts. Exact synonym: polyA+_RNA Non-exact synonym: mRNA

belongs to: material type^c
has facts: unique identifier^dp "MO_600"^^string; synonym^dp "mRNA"^^string; synonym^dp "polyA+_RNA"^^string

polylysineⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#polylysine

a surface coating for immobilization with the polypeptide, polylysine

belongs to: surface type^c
has facts: unique identifier^dp "MO_569"^^string

polypeptideⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#polypeptide

sequence of a protein, a linear amino acid polymer

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_530"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type; deprecation replacement term^op theoretical bio sequence type; deprecation old parent^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

polyploidⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#polyploid

Describes a cell, nucleus or organism with three or more copies of each chromosome.

belongs to: ploidy^c
has facts: unique identifier^dp "MO_394"^^string

polysomyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#polysomy

A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement.

belongs to: chromosomal aberration classification^c
has facts: unique identifier^dp "MO_1030"^^string

poolⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pool

The process of combining two or more BioMaterials. Exact synonym: combine

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_779"^^string; synonym^dp "combine"^^string

population densityⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#population_density

The concentration range of the organism.

belongs to: environmental factor category^c
has facts: unique identifier^dp "MO_650"^^string

positiveⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#positive

true or yes

belongs to: result^c
has facts: unique identifier^dp "MO_429"^^string

positive floatⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#positive_float

A float > 0.

belongs to: data type^c
has facts: unique identifier^dp "MO_501"^^string

positive integerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#positive_integer

An integer > 0.

belongs to: data type^c
has facts: unique identifier^dp "MO_629"^^string

postmortemⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#postmortem

biomaterial removed after the death of the organism

belongs to: organism status^c
has facts: unique identifier^dp "MO_416"^^string

predicted geneⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#predicted_gene

gene sequence which has been computationally predicted

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.3.1.1"^^string; unique identifier^dp "MO_838"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type

premortemⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#premortem

sample which has been removed prior to the death of an organism

belongs to: organism status^c
has facts: unique identifier^dp "MO_705"^^string

preservationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#preservation

The type of protocol used to preserve (including storage or keep in stasis) the biomaterial.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_415"^^string

primary protein structure recordⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#primary_protein_structure_record

A record which describes and identifies an experimentally derived protein structure e.g. MSD

belongs to: database entry type^c
has facts: unique identifier^dp "MO_785"^^string

primary siteⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#primary_site

the organism part in which the tumor originated

belongs to: cancer site^c
has facts: unique identifier^dp "MO_408"^^string

promoterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#promoter

genomic sequence 5' to a gene where the transcription initiation complex forms.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_911"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op theoretical bio sequence type; deprecation old parent^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

proteinⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#protein

Polymer of amino acids.

belongs to: material type^c; polymer type^c
has facts: unique identifier^dp "MO_683"^^string

purifyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#purify

The action of enriching a BioMaterial (organism, cell, nucleic acid etc) or Compound e.g. for FACS for positive selection or RNA cleanup the Action or ProtocolType is purify (see fractionate).

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_406"^^string

quality control testing designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#quality_control_testing_design

A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance

belongs to: methodological design^c
has facts: unique identifier^dp "MO_981"^^string

quantile normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#quantile_normalization

A method of normalizing a set of MeasuredBioAssayData aimed at rendering the distribution of intensities for each assay in the set the same, by forcing the values of quantiles to be equal across assays.

belongs to: normalization description type^c
has facts: unique identifier^dp "MO_951"^^string

quantile normalization protocol typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#quantile_normalization_protocol_type

Application of a normalization of type quantile_normalization.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_457"^^string

rⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#R

Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg.

belongs to: radiation unit^c
has facts: unique identifier^dp "MO_725"^^string

r m aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#RMA

Robust Multiarray Average. A quantitative measure of the relative abundance of a transcript. RMA is a summary measure of related perfect match Features on an Affymetrix array. The values are background-adjusted, normalized and log-transformed values.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_987"^^string

r n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#RNA

Ribonucleic acid.

belongs to: polymer type^c
has facts: unique identifier^dp "MO_594"^^string

r n a stability designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#RNA_stability_design

A RNA stability experiment design type examines the stability and/or decay of RNA transcripts.

belongs to: bio molecular annotation^c
has facts: unique identifier^dp "MO_553"^^string

r r n a geneⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#rRNA_gene

sequence from gene coding for ribosomal RNA exact synonym: ribosomal RNA gene

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_955"^^string; deprecation reason^dp "deleted_term"^^string; synonym^dp "ribosomal RNA gene"^^string; deprecation replacement term^op theoretical bio sequence type; deprecation old parent^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

radⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Rad

Radiation absorbed dose. Unit of energy absorbed per unit mass as a result of exposure to radiation. 1 rad = Absorption of 100 ergs per gram of material = 0.01Gy.

belongs to: radiation unit^c
has facts: unique identifier^dp "MO_585"^^string

ratioⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ratio

Result of data reduction involving computation of the quotient of a pair of numerical values, such as signal intensities obtained from the hybridization of two or more labeled extracts to one or more microarrays; volumes of matched spots from comparative 2D gel electrophoresis of two or more labeled extracts; or comparative profiling of a particular metabolite in health and disease by NMR.

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_597"^^string

ratio statistics normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ratio_statistics_normalization

A method to re-scale paired-assay data from one data set relative to the other, based on an iterative regression method of calculating single parameter linear normalization factors. This method allows calculation of the mean, standard deviation and confidence interval limits for the distribution of measured ratio values.

belongs to: normalization description type^c
has facts: unique identifier^dp "MO_349"^^string

real time p c r quality controlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#real_time_PCR_quality_control

A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes.

belongs to: quality control description type^c
has facts: unique identifier^dp "MO_434"^^string

rectangular featureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#rectangular_feature

The shape of the feature on the array is rectangular.

belongs to: feature shape^c
has facts: unique identifier^dp "MO_897"^^string

reference designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#reference_design

A reference experiment design type is where all samples are compared to a common reference.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_699"^^string

relativeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#relative

a measurement where the value is dependent on another measurement

belongs to: measurement type^c
has facts: unique identifier^dp "MO_396"^^string

relative humidityⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#relative_humidity

The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding.

belongs to: environmental factor category^c
has facts: unique identifier^dp "MO_453"^^string

remⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Rem

Roentgen Equivalent Man. Unit of dose equivalent, i.e., the measure of potential biological damage caused by exposure and absorption of radiation. Rem = absorbed dose (rad) x quality factor (Q). Q is unique to the type of incident radiation.

belongs to: radiation unit^c
has facts: unique identifier^dp "MO_908"^^string

removeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#remove

The procedure of extracting/taking out a part of a reaction/contents of a container.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_713"^^string

replaced termⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#replaced_term

The term name was changed to one more appropriate to the intent of the definition.

belongs to: deprecation reason^c
has facts: unique identifier^dp "MO_1026"^^string

replicate analysisⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#replicate_analysis

A transformation method in which replicate intensity or ratio data sets are combined. Analysis of the mean and standard deviation values for replicate data points can be used to identify and potentially exclude low quality data.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_433"^^string

replicate designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#replicate_design

A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_885"^^string

resuspendⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#resuspend

The procedure in which solid material is dispensed or dissolved in a liquid.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_466"^^string

reverseⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#reverse

the reverse strand exact synonym: -

belongs to: strand type^c
has facts: synonym^dp "-"^^string; unique identifier^dp "MO_402"^^string

reverse transcriptionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#reverse_transcription

Generation of a DNA strand from an RNA strand using reverse transcriptase.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_480"^^string

reverse transcription p c r quality controlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#reverse_transcription_PCR_quality_control

A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes.

belongs to: quality control description type^c
has facts: unique identifier^dp "MO_986"^^string

sacrificeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sacrifice

The procedure of euthanizing an organism.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_602"^^string

sampling time pointⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sampling_time_point

<pre>The time point that a sample was taken. Not to be used where the sample is part of a time course. SamplingTimePoint is not related to age. An instance could be summer, a date, a time, or a range value</pre>

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_866"^^string

secondsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#seconds

time unit

belongs to: time unit^c
has facts: unique identifier^dp "MO_391"^^string

secreted protein identification designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#secreted_protein_identification_design

A secreted protein identification design type identifies transcripts associated with a secretory pathway during translation and is used to infer which proteins are secreted or membrane bound.

belongs to: bio molecular annotation^c
has facts: unique identifier^dp "MO_694"^^string

seed dormancyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#seed_dormancy

preservation type whereby the seed is maintained in a dormant state

belongs to: preservation type^c
has facts: unique identifier^dp "MO_666"^^string

self vs self designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#self_vs_self_design

A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_490"^^string

semisolidⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#semisolid

semisolid media type

belongs to: media^c
has facts: unique identifier^dp "MO_635"^^string

sequence ontologyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SequenceOntology

The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence.

belongs to: sequence ontology database^c
has facts: unique identifier^dp "MO_724"^^string; has machine readable u r i^dp "http://song.sourceforge.net/"^^string

set temperatureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#set_temperature

An action where the temperature is specified.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_393"^^string

sexⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sex

A descriptor for FactorValue where Sex is compared.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_680"^^string

sex designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sex_design

A sex experiment design type assays differences associated with an organism's sex, gender or mating type.

belongs to: biological property^c
has facts: unique identifier^dp "MO_575"^^string

short oligoⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#short_oligo

An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes).

belongs to: design element^c
has facts: unique identifier^dp "MO_749"^^string

signalⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#signal

A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software).

belongs to: derived bio assay type^c
has facts: unique identifier^dp "MO_534"^^string

signal log ratioⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#signal_log_ratio

The change in expression level for a transcript between a baseline and an experiment array. This change is expressed as the log2 ratio. A signal log ratio of 1 is the same as a Fold Change of 2.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.7"^^string; unique identifier^dp "MO_941"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op derived bio assay type; deprecation replacement term^op derived bio assay type; has reason for deprecation^op deleted term; deprecated from version^op version 1.1.7

siliconⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#silicon

the array is made on silicon

belongs to: substrate type^c
has facts: unique identifier^dp "MO_382"^^string

single strandedⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#single_stranded

a nucleic acid consisting of a single polynucleotide chain.

belongs to: strand type^c
has facts: unique identifier^dp "MO_576"^^string

sisterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sister

A female having the same genetic parents as another, or one genetic parent in common with another.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_723"^^string

slice analysisⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#slice_analysis

A method of analyzing the significant expression level of a Feature by calculating the intensity-dependent Z distribution value for the logarithm of the intensity ratios from the two channels.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_531"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op normalization description type; deprecation replacement term^op normalization description type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

sn r n a geneⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#snRNA_gene

sequence from gene coding for small nuclear RNA exact synonym: small nuclear RNA gene

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_961"^^string; deprecation old parent^op "deleted_term"^^string; deprecation reason^dp "deleted_term"^^string; synonym^dp "small nuclear RNA gene"^^string; deprecation replacement term^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

software manufacturerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#software_manufacturer

Person or organization that manufactured the software.

belongs to: roles^c
has facts: unique identifier^dp "MO_475"^^string

software variation designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#software_variation_design

A software variation design type compares different types of software for performance, accuracy, precision and reproducibility.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_643"^^string

soilⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#soil

soil, growth media for plants and other soil living organisms

belongs to: media^c
has facts: unique identifier^dp "MO_821"^^string

sonⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#son

The male offspring of the patient or individual under study.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_465"^^string

sonicatorⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sonicator

An instrument for sonicating biomaterials.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_477"^^string

sowingⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sowing

the process of placing a seed or spore in some media with the intention to invoke germination.

belongs to: initial time point^c
has facts: unique identifier^dp "MO_748"^^string

spearmans rank correlationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Spearmans_rank_correlation

Computed as the ordinary Pearson correlation coefficient between two groups of rankings.

belongs to: node value type^c
has facts: unique identifier^dp "MO_552"^^string

species designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#species_design

A species experiment design type assays differences between distinct species.

belongs to: biological property^c
has facts: unique identifier^dp "MO_675"^^string

species specific design element group typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#species_specific_design_element_group_type

A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species.

belongs to: design element group type^c
has facts: unique identifier^dp "MO_395"^^string

specified biomaterial actionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#specified_biomaterial_action

Conceptual action for specified protocol applied in treatment.

belongs to: atomic action^c; complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_968"^^string

spectrophotometerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#spectrophotometer

Hardware for measuring light at different wavelengths.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_716"^^string; synonym^dp "thermocycler"^^string

spike quality controlⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#spike_quality_control

An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes.

belongs to: quality control description type^c
has facts: unique identifier^dp "MO_937"^^string

spinⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#spin

The procedure of applying a centrifugal force to a physical object. Exact synonym: centrifuge

belongs to: atomic action^c
has facts: unique identifier^dp "MO_879"^^string; synonym^dp "centrifuge"^^string

splitⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#split

The procedure of separating a BioMaterial into two or more BioMaterials of similar composition e.g. aliquoting a sample. The BioMaterial may be a BioSource (e.g., a tissue) or a BioSample (e.g. RNA extracted from a BioSource). Non exact Synonym: sample

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_835"^^string; synonym^dp "sample"^^string

split termⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#split_term

the term has been decomposed into more specific terms

belongs to: deprecation reason^c
has facts: unique identifier^dp "MO_1027"^^string

spotted antibody featuresⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#spotted_antibody_features

TechnologyType of FeatureGroup where antibodies are spotted directly.

belongs to: technology type^c
has facts: unique identifier^dp "MO_483"^^string

spotted colony featuresⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#spotted_colony_features

TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.

belongs to: technology type^c
has facts: unique identifier^dp "MO_618"^^string

spotted ds d n a featuresⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#spotted_ds_DNA_features

A descriptor for the TechnologyType for a group of features where double stranded DNA is spotted on the array e.g. a PCR of a cDNA clone.

belongs to: technology type^c
has facts: unique identifier^dp "MO_499"^^string

spotted protein featuresⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#spotted_protein_features

TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly.

belongs to: technology type^c
has facts: unique identifier^dp "MO_996"^^string

spotted ss oligo featuresⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#spotted_ss_oligo_features

The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.

belongs to: technology type^c
has facts: unique identifier^dp "MO_579"^^string

spotted ss p c r amplicon featuresⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#spotted_ss_PCR_amplicon_features

A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array.

belongs to: technology type^c
has facts: unique identifier^dp "MO_921"^^string

square featureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#square_feature

The shape of the feature on the array is square.

belongs to: feature shape^c
has facts: unique identifier^dp "MO_817"^^string

ss oligoⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ss_oligo

sequence of a single stranded synthesized oligonucleotide

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_570"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op physical bio sequence type; deprecation replacement term^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

starvationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#starvation

Depriving an organism of food or nutrients

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_370"^^string

stimulated design typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#stimulated_design_type

A design in which a behavior is invoked by a variable controlled by the experimenter - e.g. administration of a drug that effects aggressivity.

belongs to: perturbational design^c
has facts: unique identifier^dp "MO_958"^^string

stimulus or stress designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#stimulus_or_stress_design

A stimulus or stress experiment design type is where the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.

belongs to: perturbational design^c
has facts: unique identifier^dp "MO_568"^^string

storeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#store

The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity, for the purposes of keeping it in the same state.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_442"^^string

strain or lineⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#strain_or_line

A descriptor of FactorValue where comparisons of strains or lines are made.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_859"^^string

strain or line designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#strain_or_line_design

A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.

belongs to: biological property^c
has facts: unique identifier^dp "MO_462"^^string

string datatypeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#string_datatype

The values are a sequence of one or more characters.

belongs to: data type^c
has facts: unique identifier^dp "MO_352"^^string

subcutaneousⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#subcutaneous

Delivery method whereby a drug or compound is administered under the skin of the organism.

belongs to: delivery method^c
has facts: unique identifier^dp "MO_960"^^string

submitterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#submitter

Person who is the primary contact for data submitted to a database.

belongs to: roles^c
has facts: unique identifier^dp "MO_882"^^string

synthetic d n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#synthetic_DNA

DNA which is generated by chemical or enzymatic (non cellular) means. non-exact synonym: cDNA

belongs to: material type^c
has facts: unique identifier^dp "MO_577"^^string; synonym^dp "cDNA"^^string

synthetic r n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#synthetic_RNA

RNA which is generated by chemical or enzymatic (non cellular) means. E.g. T7 promotor generated RNA. Non-exact synonym: cRNA, complementary RNA aRNA, amplified RNA

belongs to: material type^c
has facts: unique identifier^dp "MO_543"^^string; synonym^dp "aRNA"^^string; synonym^dp "amplified RNA"^^string; synonym^dp "cRNA"^^string; synonym^dp "complementary RNA"^^string

t a i rⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TAIR

The Arabidopsis Information Resource.

belongs to: cell type database^c; strain or line database^c
has facts: unique identifier^dp "MO_660"^^string; has human readable u r i^dp "http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype"^^string

t a i r arabidopsis anatomy ontologyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TAIR_arabidopsis_anatomy_ontology

A structured controlled vocabulary for the anatomy of Arabidopsis.

belongs to: organism part database^c
has facts: unique identifier^dp "MO_809"^^string; has machine readable u r i^dp "http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/Arabidopsis/Attic/arabidopsis_anatomy.ontology"^^string

t a i r arabidopsis development ontologyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TAIR_arabidopsis_development_ontology

An ontology of stages of growth and development of the model plant Arabidopsis thaliana.

belongs to: developmental stage database^c
has facts: unique identifier^dp "MO_919"^^string; has machine readable u r i^dp "http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/developmental/plant_development/Arabidopsis/temporal.tair?rev=1.21&view=markup"^^string

t d m sⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TDMS

Toxicology Data Management System, a database resource for systems, organs, pathology, etc.

belongs to: disease state database^c; histology database^c; organism part database^c; test type database^c
has facts: unique identifier^dp "MO_718"^^string; has human readable u r i^dp "http://hazel.niehs.nih.gov/user_spt/pct_terms.htm"^^string

t i f fⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#TIFF

Tag Image File Format (TIFF) is a common format to describe and store raster image data from scanners and other imaging devices. TIFFs may contain one or more channels and the data may be compressed using a lossless compression algorithm.

belongs to: image format^c
has facts: unique identifier^dp "MO_638"^^string

t r n a geneⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#tRNA_gene

sequence from a gene coding for transfer RNA exact synonym: transfer RNA gene

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_850"^^string; deprecation reason^dp "deleted_term"^^string; synonym^dp "transfer RNA gene"^^string; deprecation replacement term^op theoretical bio sequence type; deprecation old parent^op theoretical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

tau rank correlationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#tau_rank_correlation

a nonparametric measure of the agreement between two rankings

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.7"^^string; unique identifier^dp "MO_673"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op node value type; deprecation old parent^op node value type; has reason for deprecation^op deleted term; deprecated from version^op version 1.1.7

technical replicateⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#technical_replicate

A replicate where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment.

belongs to: quality control description type^c; replicate description type^c
has facts: unique identifier^dp "MO_641"^^string

temperatureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#temperature

Temperature associated with a particular environment.

belongs to: environmental factor category^c
has facts: unique identifier^dp "MO_791"^^string

thermal cyclerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#thermal_cycler

An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR. Exact Synonym: thermocycler

belongs to: hardware type^c
has facts: unique identifier^dp "MO_854"^^string

tiling path designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#tiling_path_design

An experiment in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using arrays containing oligonucleotides that are either overlapping or spaced at regular intervals.

belongs to: bio molecular annotation^c
has facts: unique identifier^dp "MO_507"^^string

time series designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#time_series_design

Groups of assays that are related as part of a time series.

belongs to: methodological design^c
has facts: unique identifier^dp "MO_887"^^string

timepointⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#timepoint

Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point.

belongs to: complex action^c
has facts: unique identifier^dp "MO_738"^^string

total intensity normalizationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#total_intensity_normalization

A method of re-scaling intensity data from one channel relative to another based on the ratio of the sums of the fluorescent intensities from each channel for all Features: N = sum(Ri) / sum(Gi) . The ratio is used to re-scale the intensities in one channel for each Feature. This is a single parameter linear normalization method.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_441"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op normalization description type; deprecation replacement term^op normalization description type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

total intensity normalization pairedⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#total_intensity_normalization_paired

A method to normalize paired-assay data that uses as a normalization coefficient the sum of intensity values from one assay divided by the sum of intensities from the other, where those sums are taken over all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). This normalization coefficient is used to rescale the intensity data in one data set relative to the other. Note that a normalization method that employs the average intensity rather than the sum (of all data points, or an appropriate subset) falls into this category as well.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_686"^^string

total intensity normalization singleⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#total_intensity_normalization_single

A normalization method that uses as a coefficient the sum of all intensities in the data set, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). The intensities are normalized through division by such a coefficient (and possible subsequent multiplication by a target constant). Note that a normalization method that employs the average intensity rather than the sum (of all data points, or an appropriate subset) falls into this category as well.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_472"^^string

total r n aⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#total_RNA

Total cellular and nuclear RNA.

belongs to: material type^c
has facts: unique identifier^dp "MO_373"^^string

transcriptⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#transcript

sequence that represents the product of an RNA polymerase engaged in transcription

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.3.1.1"^^string; unique identifier^dp "MO_827"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op theoretical bio sequence type; deprecation replacement term^op theoretical bio sequence type

transcript identification designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#transcript_identification_design

A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome.

belongs to: bio molecular annotation^c; technological design^c
has facts: unique identifier^dp "MO_533"^^string; synonym^dp "expression profiling"^^string; synonym^dp "expression_profiling"^^string; synonym^dp "gene expression"^^string; synonym^dp "gene_expression"^^string; synonym^dp "transcription profiling"^^string; synonym^dp "transcription_profiling"^^string

transfectⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#transfect

The process of bringing about genetic alteration of any cell or organism by a variety of means including recombinant DNA technology, viruses, chemical mutagens, and X-rays.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_849"^^string

transfectionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#transfection

Introduction of genetic material into an organism often in the form of a plasmid.

belongs to: genetic modification^c
has facts: unique identifier^dp "MO_366"^^string

translational bias designⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#translational_bias_design

A translational bias is an experiment design which characterizes the association of transcripts and translation machinery.

belongs to: bio molecular annotation^c
has facts: unique identifier^dp "MO_939"^^string

trisomyⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#trisomy

The possession of a third chromosome of any one type in an otherwise diploid cell.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.9"^^string; unique identifier^dp "MO_494"^^string; deprecation reason^dp "replaced_term"^^string; deprecation old parent^op chromosomal aberration classification; was replaced by^op polysomy; replaced with term^op polysomy; has reason for deprecation^op replaced term; deprecated from version^op version 1.1.9

tumor gradingⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#tumor_grading

A descriptor used in cancer biology to describe abnormalities of tumor cells.

belongs to: bio material characteristic category^c
has facts: unique identifier^dp "MO_843"^^string

u mⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#uM

Micromole per liter or micromolar, concentration unit

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_740"^^string

u m l sⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#UMLS

Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH.

belongs to: disease state database^c
has facts: unique identifier^dp "MO_947"^^string; has human readable u r i^dp "http://www.nlm.nih.gov/research/umls/"^^string

u per lⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#U_per_L

units per liter

belongs to: concentration unit^c
has facts: unique identifier^dp "MO_875"^^string

u per weekⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#U_per_week

units per week, e.g. the number of units of alcohol consumed over a period of 7 days

belongs to: other unit^c
has facts: unique identifier^dp "MO_388"^^string

ugⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ug

microgram, unit of mass

belongs to: mass unit^c
has facts: unique identifier^dp "MO_438"^^string

ulⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ul

microliter, unit of volume

belongs to: volume unit^c
has facts: unique identifier^dp "MO_926"^^string

umⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#um

micrometer, unit of distance

belongs to: distance unit^c
has facts: unique identifier^dp "MO_421"^^string

umolⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#umol

micromoles, quantity unit

belongs to: quantity unit^c
has facts: unique identifier^dp "MO_752"^^string

uncentered pearson correlationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#uncentered_Pearson_correlation

The uncentered Pearson correlation is defined as the Pearson correlation for two data series where the mean of each data series is assumed to be zero.

belongs to: node value type^c
has facts: unique identifier^dp "MO_974"^^string

uncleⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#uncle

The brother of one's father or mother.

belongs to: family relationship^c
has facts: unique identifier^dp "MO_950"^^string

unknown basis featureⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_basis_feature

Sequence feature whose derivation is unknown.

belongs to: seq feature basis^c
has facts: unique identifier^dp "MO_525"^^string

unknown experiment design typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_experiment_design_type

ExperimentDesignType of unknown type.

belongs to: bio molecular annotation^c; biological property^c; epidemiological design^c; methodological design^c; perturbational design^c
has facts: unique identifier^dp "MO_634"^^string

unknown protocol typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_protocol_type

ProtocolType of unknown type.

belongs to: experimental protocol type^c
has facts: unique identifier^dp "MO_460"^^string

unknown sequenceⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_sequence

BioSequence of unknown type

belongs to: physical bio sequence type^c; theoretical bio sequence type^c
has facts: unique identifier^dp "MO_535"^^string

unknown sexⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_sex

organism(s) whose sex is unknown

belongs to: sex^c
has facts: unique identifier^dp "MO_999"^^string

unknown substrate typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type

SubstrateType of unknown type.

belongs to: substrate type^c
has facts: unique identifier^dp "MO_484"^^string

unknown surface typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_surface_type

A SurfaceType of unknown type.

belongs to: surface type^c
has facts: unique identifier^dp "MO_359"^^string

unscaledⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unscaled

The values are unordered and have no scale.

belongs to: scale^c
has facts: unique identifier^dp "MO_542"^^string

urineⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#urine

The fluid and dissolved substances excreted by the kidney.

belongs to: bio source type^c
has facts: unique identifier^dp "MO_399"^^string

usⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#us

microsecond, unit of time

belongs to: time unit^c
has facts: unique identifier^dp "MO_795"^^string

vacuum dryerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#vacuum_dryer

An instrument designed to remove excess liquid by vacuum and heating.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_696"^^string

vectorⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#vector

Sequence from a vector, DNA of any transmissible agent e.g. plasmid or virus into which a segment of foreign DNA can be spliced, does not include insert sequence. These terms should be used when other terms such as plasmid, YAC, BAC are used.

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_551"^^string; deprecation reason^dp "deleted_term"^^string; deprecation replacement term^op physical bio sequence type; deprecation old parent^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

version 1.1.7ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#version_1.1.7

Version of the MGED Ontology.

belongs to: m g e d ontology version^c
has facts: unique identifier^dp "MO_1031"^^string

version 1.1.8ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#version_1.1.8

Version of the MGED Ontology.

belongs to: m g e d ontology version^c
has facts: unique identifier^dp "MO_469"^^string

version 1.1.9ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#version_1.1.9

Version of the MGEDOntology.

belongs to: m g e d ontology version^c
has facts: unique identifier^dp "MO_1032"^^string

version 1.2.0ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#version_1.2.0

Version of the MGEDOntology.

belongs to: m g e d ontology version^c
has facts: unique identifier^dp "MO_1033"^^string

version 1.3.0ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#version_1.3.0

Version of the MGEDOntology.

belongs to: m g e d ontology version^c
has facts: unique identifier^dp "MO_440"^^string

version 1.3.1ⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#version_1.3.1

Version of the MGED Ontology.

belongs to: m g e d ontology version^c
has facts: unique identifier^dp "MO_1034"^^string

virusⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#virus

one or more DNA or RNA based non cellular infective agent, including bacteriophage

belongs to: material type^c
has facts: unique identifier^dp "MO_372"^^string

vortexerⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#vortexer

An instrument that mixes by rapid oscillation.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_983"^^string

waitⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#wait

Allow time to pass. It's measurement should be a unit of time.

belongs to: atomic action^c
has facts: unique identifier^dp "MO_988"^^string

washⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#wash

The process of applying a solvent (e.g. water) or a solution (e.g. SSC/SDS) to a BioMaterial or an array to remove impurities or unwanted compounds.

belongs to: complex action^c; experimental protocol type^c
has facts: unique identifier^dp "MO_596"^^string

wash stationⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#wash_station

An instrument designed to mechanically wash or stain arrays.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_626"^^string

waterⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#water

Water consumed by or enveloping the organism that the biosource is derived from.

belongs to: environmental factor category^c
has facts: unique identifier^dp "MO_380"^^string

waterbathⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#waterbath

A device for controlling temperature by immersion in water.

belongs to: hardware type^c
has facts: unique identifier^dp "MO_541"^^string

web r e n iⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#WebRENI

database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions

belongs to: disease state database^c
has facts: unique identifier^dp "MO_737"^^string; has human readable u r i^dp "http://www.item.fraunhofer.de/reni/index/htm"^^string

weeksⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#weeks

7 days, unit of time

belongs to: time unit^c
has facts: unique identifier^dp "MO_842"^^string

whole organismⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#whole_organism

one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria

belongs to: material type^c
has facts: unique identifier^dp "MO_566"^^string

wild typeⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#wild_type

The genotype or phenotype that is found in nature or in standard laboratory stocks for a given organism. For a single locus, the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.

belongs to: allele^c; genotype^c
has facts: unique identifier^dp "MO_605"^^string

within bioassay data set functionⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#within_bioassay_data_set_function

A function applied to subsets of values from the same Measured/Derived bioassay data set.

belongs to: data transformation protocol type^c
has facts: unique identifier^dp "MO_668"^^string

x timesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#x_times

multiple of stock solution concentration, concentration unit

belongs to: concentration unit other^c
has facts: unique identifier^dp "MO_496"^^string

y a cⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#YAC

sequence from yeast artificial chromosome

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.2.0"^^string; unique identifier^dp "MO_794"^^string; deprecation reason^dp "deleted_term"^^string; deprecation old parent^op physical bio sequence type; deprecation replacement term^op physical bio sequence type; has reason for deprecation^op deleted term; deprecated from version^op version 1.2.0

yearsⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#years

365 days, time unit

belongs to: time unit^c
has facts: unique identifier^dp "MO_948"^^string

yesⁿⁱ back to ToC or Named Individual ToC

IRI: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#yes

true

belongs to: deprecated terms^c
has facts: deprecation in version^dp "1.1.7"^^string; unique identifier^dp "MO_540"^^string; deprecation reason^dp "deleted_term"^^string; has reason for deprecation^op deleted term; deprecated from version^op version 1.1.7

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.

The MGED Ontology

Table of Content

Introduction

Classes

actionc back to ToC or Class ToC

agec back to ToC or Class ToC

allelec back to ToC or Class ToC

array design packagec back to ToC or Class ToC

array groupc back to ToC or Class ToC

array packagec back to ToC or Class ToC

atmospherec back to ToC or Class ToC

atomic actionc back to ToC or Class ToC

audit and security packagec back to ToC or Class ToC

barrier facilityc back to ToC or Class ToC

beddingc back to ToC or Class ToC

bibliographic referencec back to ToC or Class ToC

bio assayc back to ToC or Class ToC

bio assay datac back to ToC or Class ToC

bio assay data clusterc back to ToC or Class ToC

bio assay data packagec back to ToC or Class ToC

bio assay packagec back to ToC or Class ToC

bio materialc back to ToC or Class ToC

bio material characteristic categoryc back to ToC or Class ToC

bio material characteristicsc back to ToC or Class ToC

bio material packagec back to ToC or Class ToC

bio material purityc back to ToC or Class ToC

bio molecular annotationc back to ToC or Class ToC

bio samplec back to ToC or Class ToC

bio sample typec back to ToC or Class ToC

bio sequencec back to ToC or Class ToC

bio sequence packagec back to ToC or Class ToC

bio sequence typec back to ToC or Class ToC

bio sourcec back to ToC or Class ToC

bio source providerc back to ToC or Class ToC

bio source typec back to ToC or Class ToC

biological factor categoryc back to ToC or Class ToC

biological propertyc back to ToC or Class ToC

biometricsc back to ToC or Class ToC

cancer sitec back to ToC or Class ToC

cell linec back to ToC or Class ToC

cell line databasec back to ToC or Class ToC

cell typec back to ToC or Class ToC

cell type databasec back to ToC or Class ToC

cellular componentc back to ToC or Class ToC

cellular component databasec back to ToC or Class ToC

chromosomal aberrationc back to ToC or Class ToC

chromosomal aberration classificationc back to ToC or Class ToC

clinical historyc back to ToC or Class ToC

clinical treatmentc back to ToC or Class ToC

clinical treatment databasec back to ToC or Class ToC

complex actionc back to ToC or Class ToC

compoundc back to ToC or Class ToC

compound databasec back to ToC or Class ToC

concentration unitc back to ToC or Class ToC

concentration unit otherc back to ToC or Class ToC

contactc back to ToC or Class ToC

control typec back to ToC or Class ToC

cultivarc back to ToC or Class ToC

data transformation protocol typec back to ToC or Class ToC

data typec back to ToC or Class ToC

databasec back to ToC or Class ToC

database entry typec back to ToC or Class ToC

defect typec back to ToC or Class ToC

delivery methodc back to ToC or Class ToC

deprecated termsc back to ToC or Class ToC

deprecation reasonc back to ToC or Class ToC

derived bio assayc back to ToC or Class ToC

derived bio assay typec back to ToC or Class ToC

description packagec back to ToC or Class ToC

design elementc back to ToC or Class ToC

design element groupc back to ToC or Class ToC

design element group typec back to ToC or Class ToC

design element packagec back to ToC or Class ToC

developmental stagec back to ToC or Class ToC

developmental stage databasec back to ToC or Class ToC

disease locationc back to ToC or Class ToC

disease stagingc back to ToC or Class ToC

disease staging databasec back to ToC or Class ToC

disease statec back to ToC or Class ToC

disease state databasec back to ToC or Class ToC

action^c back to ToC or Class ToC

age^c back to ToC or Class ToC

allele^c back to ToC or Class ToC

array design package^c back to ToC or Class ToC

array group^c back to ToC or Class ToC

array package^c back to ToC or Class ToC

atmosphere^c back to ToC or Class ToC

atomic action^c back to ToC or Class ToC

audit and security package^c back to ToC or Class ToC

barrier facility^c back to ToC or Class ToC

bedding^c back to ToC or Class ToC

bibliographic reference^c back to ToC or Class ToC

bio assay^c back to ToC or Class ToC

bio assay data^c back to ToC or Class ToC

bio assay data cluster^c back to ToC or Class ToC

bio assay data package^c back to ToC or Class ToC

bio assay package^c back to ToC or Class ToC

bio material^c back to ToC or Class ToC

bio material characteristic category^c back to ToC or Class ToC

bio material characteristics^c back to ToC or Class ToC

bio material package^c back to ToC or Class ToC

bio material purity^c back to ToC or Class ToC

bio molecular annotation^c back to ToC or Class ToC

bio sample^c back to ToC or Class ToC

bio sample type^c back to ToC or Class ToC

bio sequence^c back to ToC or Class ToC

bio sequence package^c back to ToC or Class ToC

bio sequence type^c back to ToC or Class ToC

bio source^c back to ToC or Class ToC

bio source provider^c back to ToC or Class ToC

bio source type^c back to ToC or Class ToC

biological factor category^c back to ToC or Class ToC

biological property^c back to ToC or Class ToC

biometrics^c back to ToC or Class ToC

cancer site^c back to ToC or Class ToC

cell line^c back to ToC or Class ToC

cell line database^c back to ToC or Class ToC

cell type^c back to ToC or Class ToC

cell type database^c back to ToC or Class ToC

cellular component^c back to ToC or Class ToC

cellular component database^c back to ToC or Class ToC

chromosomal aberration^c back to ToC or Class ToC

chromosomal aberration classification^c back to ToC or Class ToC

clinical history^c back to ToC or Class ToC

clinical treatment^c back to ToC or Class ToC

clinical treatment database^c back to ToC or Class ToC

complex action^c back to ToC or Class ToC

compound^c back to ToC or Class ToC

compound database^c back to ToC or Class ToC

concentration unit^c back to ToC or Class ToC

concentration unit other^c back to ToC or Class ToC

contact^c back to ToC or Class ToC

control type^c back to ToC or Class ToC

cultivar^c back to ToC or Class ToC

data transformation protocol type^c back to ToC or Class ToC

data type^c back to ToC or Class ToC

database^c back to ToC or Class ToC

database entry type^c back to ToC or Class ToC

defect type^c back to ToC or Class ToC

delivery method^c back to ToC or Class ToC

deprecated terms^c back to ToC or Class ToC

deprecation reason^c back to ToC or Class ToC

derived bio assay^c back to ToC or Class ToC

derived bio assay type^c back to ToC or Class ToC

description package^c back to ToC or Class ToC

design element^c back to ToC or Class ToC

design element group^c back to ToC or Class ToC

design element group type^c back to ToC or Class ToC

design element package^c back to ToC or Class ToC

developmental stage^c back to ToC or Class ToC

developmental stage database^c back to ToC or Class ToC

disease location^c back to ToC or Class ToC

disease staging^c back to ToC or Class ToC

disease staging database^c back to ToC or Class ToC

disease state^c back to ToC or Class ToC

disease state database^c back to ToC or Class ToC

distance unit^c back to ToC or Class ToC

distance unit other^c back to ToC or Class ToC

ecotype^c back to ToC or Class ToC

environmental factor category^c back to ToC or Class ToC