format-version: 1.2 idspace: BIRN_ImagePhenotype http://ccdb.ucsd.edu/SAO/DPO/1.0/ImagePhenotype.owl "" idspace: BIRN_PDPO http://ccdb.ucsd.edu/PDPhenotypeOntology/1.0# "" idspace: BIRN_PDStage http://ccdb.ucsd.edu/PDStageOntology/1.0/ "" idspace: BIRN_SA http://ccdb.ucsd.edu/smart_atlas_ontology/sa.owl# "" idspace: NDPO http://ccdb.ucsd.edu/SAO/Disease/1.0/NDPO.owl# "" idspace: PKB http://ccdb.ucsd.edu/PKB/1.0/PKB.owl# "" idspace: SAO_HumanDPO http://ccdb.ucsd.edu/SAO/HumanDPO.owl# "" idspace: bfo http://www.ifomis.org/bfo/1.1# "" idspace: biopax1 http://www.biopax.org/release/biopax-level1.owl# "" idspace: birnlex_anatomy http://purl.org/nbirn/birnlex/ontology/BIRNLex-Anatomy.owl# "" idspace: birnlex_disease http://purl.org/nbirn/birnlex/ontology/BIRNLex-Disease.owl# "" idspace: birnlex_tax http://purl.org/nbirn/birnlex/ontology/BIRNLex-OrganismalTaxonomy.owl# "" idspace: dc http://purl.org/dc/elements/1.1/ "" idspace: eor http://dublincore.org/2000/03/13/eor# "" idspace: galen http://www.co-ode.org/ontologies/galen# "" idspace: mged http://mged.sourceforge.net/ontologies/MGEDOntology.owl# "" idspace: oban http://www.berkeleybop.org/ontologies/oban/alpha# "" idspace: obd http://www.bioontology.org/obd/obd-ontology# "" idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# "" idspace: owl http://www.w3.org/2002/07/owl# "" idspace: propreo http://lsdis.cs.uga.edu/projects/glycomics/propreo# "" idspace: rdf http://www.w3.org/1999/02/22-rdf-syntax-ns# "" idspace: rdfs http://www.w3.org/2000/01/rdf-schema# "" idspace: reactome http://www.reactome.org/biopax# "" idspace: sao http://ccdb.ucsd.edu/SAO/1.2# "" idspace: serql http://www.openrdf.org/schema/serql# "" idspace: snap http://www.ifomis.org/bfo/1.1/snap# "" idspace: span http://www.ifomis.org/bfo/1.1/span# "" idspace: swrl http://www.w3.org/2003/11/swrl# "" idspace: xsd http://www.w3.org/2001/XMLSchema# "" [Term] id: mged:Action namespace: comment: Procedures used during treatment. is_a: mged:BioMaterialPackage is_a: mged:BiologicalFactorCategory property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_193" xsd:string [Term] id: mged:Age namespace: comment: 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). is_a: mged:BioMaterialCharacteristics relationship: mged:has_initial_time_point mged:InitialTimePoint relationship: mged:has_maximum_measurement mged:Measurement relationship: mged:has_measurement mged:Measurement property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_178" xsd:string [Term] id: mged:Allele namespace: comment: 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. is_a: mged:IndividualGeneticCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_58" xsd:string [Term] id: mged:ArrayDesignPackage namespace: comment: MAGE package that describes the array layout and design. The array may be physical or virtual. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_33" xsd:string [Term] id: mged:ArrayGroup namespace: comment: An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays. is_a: mged:ArrayPackage relationship: mged:has_fiducials mged:Fiducial relationship: mged:has_type mged:SubstrateType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_34" xsd:string [Term] id: mged:ArrayPackage namespace: comment: MAGE package for describing the process by which arrays were manufactured. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_107" xsd:string [Term] id: mged:Atmosphere namespace: comment: The atmospheric conditions used to culture or grow an organism. is_a: mged:GrowthCondition relationship: mged:has_atmospheric_component mged:Compound property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_219" xsd:string [Term] id: mged:AtomicAction namespace: comment: An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add is_a: mged:Action property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_68" xsd:string [Term] id: mged:AuditAndSecurityPackage namespace: comment: MAGE package for contacts including organizations and people. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_172" xsd:string [Term] id: mged:BarrierFacility namespace: comment: Rating of containment system for the protection of organisms from infectious agents. is_a: mged:GrowthCondition property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_97" xsd:string [Term] id: mged:Bedding namespace: comment: Refers to the bedding material present in an animals housing. is_a: mged:EnvironmentalHistory property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_154" xsd:string [Term] id: mged:BibliographicReference namespace: comment: A bibliographic reference is a published citation in a journal, book, other format e.g. web resource is_a: mged:DescriptionPackage relationship: mged:has_URI mged:URI relationship: mged:has_authors xsd:string relationship: mged:has_editor xsd:string relationship: mged:has_issue xsd:string relationship: mged:has_pages xsd:string relationship: mged:has_publication xsd:string relationship: mged:has_publisher xsd:string relationship: mged:has_title xsd:string relationship: mged:has_type mged:PublicationType relationship: mged:has_volume xsd:string relationship: mged:has_year xsd:date property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_201" xsd:string [Term] id: mged:BioAssay namespace: comment: A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays. is_a: mged:BioAssayPackage property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_56" xsd:string [Term] id: mged:BioAssayData namespace: comment: BioAssayData refers to the data files including images generated from one or more BioAssays. is_a: mged:BioAssayDataPackage property_value: mged:unique_identifier "MO_40" xsd:string [Term] id: mged:BioAssayDataCluster namespace: comment: A grouping of bioassay data that has been organized by one or more mathematical functions into nodes. is_a: mged:HigherLevelAnalysisPackage relationship: mged:has_nodes mged:Node property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_116" xsd:string [Term] id: mged:BioAssayDataPackage namespace: comment: MAGE package for BioAssayData. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_186" xsd:string [Term] id: mged:BioAssayPackage namespace: comment: MAGE package for bioassay. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_0" xsd:string [Term] id: mged:BioMaterial namespace: comment: Description of the processing state of the biomaterial for use in the microarray hybridization. is_a: mged:BioMaterialPackage relationship: mged:has_biomaterial_characteristics mged:BioMaterialCharacteristics relationship: mged:has_type mged:MaterialType property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_226" xsd:string [Term] id: mged:BioMaterialCharacteristicCategory namespace: comment: General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue. is_a: mged:BiologicalFactorCategory property_value: mged:unique_identifier "MO_100" xsd:string [Term] id: mged:BioMaterialCharacteristics namespace: comment: Properties of the biomaterial before treated in any manner for the purposes of the experiment. is_a: mged:BioMaterialPackage is_a: mged:BiologicalFactorCategory property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_5" xsd:string [Term] id: mged:BioMaterialPackage namespace: comment: Description of the source of the nucleic acid used to generate labeled material for the microarray experiment. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_182" xsd:string [Term] id: mged:BioMaterialPurity namespace: comment: A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_20" xsd:string [Term] id: mged:BioMolecularAnnotation namespace: comment: 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. is_a: mged:ExperimentDesignType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_213" xsd:string [Term] id: mged:BioSample namespace: comment: The BioSource after any treatment. is_a: mged:BioMaterial relationship: mged:has_been_treated mged:Treatment relationship: mged:has_type mged:BioSampleType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_93" xsd:string [Term] id: mged:BioSampleType namespace: comment: Used to tell when the BioSample is an extract or not. is_a: mged:BioMaterialPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_161" xsd:string [Term] id: mged:BioSequence namespace: comment: A representation of a DNA, RNA, or protein sequence. is_a: mged:BioSequencePackage relationship: mged:has_species mged:Organism relationship: mged:has_type mged:BioSequenceType relationship: mged:has_type mged:PolymerType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_163" xsd:string [Term] id: mged:BioSequencePackage namespace: comment: MAGE package for biological sequences (biosequence). is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_191" xsd:string [Term] id: mged:BioSequenceType namespace: comment: 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). is_a: mged:BioSequencePackage property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_152" xsd:string [Term] id: mged:BioSource namespace: comment: The BioSource is the original source material before any treatment events. is_a: mged:BioMaterial property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_77" xsd:string [Term] id: mged:BioSourceProvider namespace: comment: The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial. is_a: mged:BioMaterialCharacteristics relationship: mged:has_donor mged:Organization relationship: mged:has_owner mged:Person property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_230" xsd:string [Term] id: mged:BioSourceType namespace: comment: 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. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_95" xsd:string [Term] id: mged:BiologicalFactorCategory namespace: comment: Factors that relate to properties of the biomaterial, its treatment, or \n its growth. is_a: mged:ExperimentalFactorCategory property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_190" xsd:string [Term] id: mged:BiologicalProperty namespace: comment: A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined. is_a: mged:ExperimentDesignType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_224" xsd:string [Term] id: mged:Biometrics namespace: comment: Physical properties of the BioMaterial e. g. mass or height is_a: mged:BioMaterialCharacteristics relationship: mged:has_cubic_volume mged:Measurement relationship: mged:has_diameter mged:Measurement relationship: mged:has_height mged:Measurement relationship: mged:has_individual mged:Individual relationship: mged:has_length mged:Measurement relationship: mged:has_mass mged:Measurement relationship: mged:has_organism_part mged:OrganismPart property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_129" xsd:string [Term] id: mged:CancerSite namespace: comment: class to hold instances used as the filler for the property has_cancer_site is_a: mged:MGEDCoreOntology property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_26" xsd:string [Term] id: mged:CellLine namespace: comment: The identifier for the established culture of a metazoan cell if one was used as a biomaterial.\n is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:CellLineDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_49" xsd:string [Term] id: mged:CellLineDatabase namespace: comment: Database of cell line information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_145" xsd:string [Term] id: mged:CellType namespace: comment: 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. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:CellTypeDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_135" xsd:string [Term] id: mged:CellTypeDatabase namespace: comment: Database of cell type information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_141" xsd:string [Term] id: mged:CellularComponent namespace: comment: 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). is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:CellularComponentDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_1020" xsd:string [Term] id: mged:CellularComponentDatabase namespace: comment: A resource for terms to describe cellular components, e.g. GO Cellular Component ontology. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_1021" xsd:string [Term] id: mged:ChromosomalAberration namespace: comment: 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. is_a: mged:DeprecatedTerms relationship: mged:has_chromosomal_aberration_classification mged:ChromosomalAberrationClassification property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:deprecation_old_restriction "some|has_chromosomal_aberration_classification|ChromosomalAberrationClassification" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_78" xsd:string [Term] id: mged:ChromosomalAberrationClassification namespace: comment: 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. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_6" xsd:string [Term] id: mged:ClinicalHistory namespace: comment: The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment. is_a: mged:EnvironmentalHistory relationship: mged:has_clinical_finding mged:TestResult relationship: mged:has_clinical_record mged:OntologyEntry relationship: mged:has_clinical_treatment mged:ClinicalTreatment relationship: mged:has_prior_disease_state mged:DiseaseState relationship: mged:has_test_type mged:TestType property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_189" xsd:string [Term] id: mged:ClinicalTreatment namespace: comment: The current clinical treatment(s) of the patient from which the biosource is derived. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:ClinicalTreatmentDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_69" xsd:string [Term] id: mged:ClinicalTreatmentDatabase namespace: comment: Database of clinical treatment information is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_114" xsd:string [Term] id: mged:ComplexAction namespace: comment: Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification. is_a: mged:Action property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_90" xsd:string [Term] id: mged:Compound namespace: comment: A drug, solvent, chemical, etc., with a property that can be measured such as concentration. is_a: mged:BiologicalFactorCategory is_a: mged:OntologyEntry relationship: mged:has_database mged:CompoundDatabase relationship: mged:has_measurement mged:Compound relationship: mged:is_solvent xsd:boolean property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_70" xsd:string [Term] id: mged:CompoundDatabase namespace: comment: Database of compound information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_151" xsd:string [Term] id: mged:ConcentrationUnit namespace: comment: Units used for concentration measurements. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_61" xsd:string [Term] id: mged:ConcentrationUnitOther namespace: comment: Concentration units not specified in MAGE. is_a: mged:ConcentrationUnit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_86" xsd:string [Term] id: mged:Contact namespace: comment: Organizations or individuals that may be contacted. is_a: mged:AuditAndSecurityPackage relationship: mged:has_URI mged:URI relationship: mged:has_address xsd:string relationship: mged:has_email xsd:string relationship: mged:has_fax xsd:string relationship: mged:has_phone xsd:string relationship: mged:has_toll_free_phone xsd:string relationship: mged:has_type mged:Roles property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_147" xsd:string [Term] id: mged:ControlType namespace: comment: Controlled terms for descriptors for the type of control design element. is_a: mged:DesignElementPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_50" xsd:string [Term] id: mged:Cultivar namespace: comment: a plant variety obtained in agriculture in horticulture is_a: mged:StrainOrLine relationship: mged:has_database mged:StrainOrLineDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_124" xsd:string [Term] id: mged:DataTransformationProtocolType namespace: comment: The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays. is_a: mged:ProtocolType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_165" xsd:string [Term] id: mged:DataType namespace: comment: Primitive data types found in computing languages such as float, boolean, etc. is_a: mged:MGEDCoreOntology property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_125" xsd:string [Term] id: mged:Database namespace: comment: Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records. is_a: mged:DescriptionPackage relationship: mged:has_URI mged:URI relationship: mged:has_version xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_118" xsd:string [Term] id: mged:DatabaseEntryType namespace: comment: Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD). is_a: mged:DescriptionPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_157" xsd:string [Term] id: mged:DefectType namespace: comment: Defects associated with features or zones such as those that are missing or moved. is_a: mged:ArrayPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_16" xsd:string [Term] id: mged:DeliveryMethod namespace: comment: Method used to deliver a compound for treatment. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_223" xsd:string [Term] id: mged:DeprecatedTerms namespace: comment: Class to hold deprecated instances and classes. is_a: mged:MGEDCoreOntology relationship: mged:has_reason_for_deprecation mged:DeprecationReason property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_206" xsd:string [Term] id: mged:DeprecationReason namespace: comment: class to hold instances used as the filler for the property has_reason_for_deprecation is_a: mged:MGEDCoreOntology property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_94" xsd:string [Term] id: mged:DerivedBioAssay namespace: comment: A BioAssay that is created by the transformation of measured or derived BioAssays. is_a: mged:BioAssay relationship: mged:has_type mged:DerivedBioAssayType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_209" xsd:string [Term] id: mged:DerivedBioAssayType namespace: comment: 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. is_a: mged:BioAssayPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_111" xsd:string [Term] id: mged:DescriptionPackage namespace: comment: MAGE package for description of annotations and references to annotations. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_167" xsd:string [Term] id: mged:DesignElement namespace: comment: Design elements are reporters, features, and composite elements as defined by MAGE. is_a: mged:DesignElementPackage relationship: mged:has_type mged:ControlType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_173" xsd:string [Term] id: mged:DesignElementGroup namespace: comment: A DesignElementGroup holds information on Features, Reporters, or CompositeSequences. is_a: mged:ArrayDesignPackage relationship: mged:has_species mged:Organism relationship: mged:has_type mged:DesignElementGroupType property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_128" xsd:string [Term] id: mged:DesignElementGroupType namespace: comment: Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence. is_a: mged:ArrayDesignPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_14" xsd:string [Term] id: mged:DesignElementPackage namespace: comment: The MAGE package for describing the elements located on the array. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_15" xsd:string [Term] id: mged:DevelopmentalStage namespace: comment: The developmental stage of the organism's life cycle during which the biomaterial was extracted. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:DevelopmentalStageDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_120" xsd:string [Term] id: mged:DevelopmentalStageDatabase namespace: comment: Database of developmental stage information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_215" xsd:string [Term] id: mged:DiseaseLocation namespace: comment: Anatomical location(s) of disease. is_a: mged:OrganismPart relationship: mged:has_cancer_site mged:CancerSite property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_37" xsd:string [Term] id: mged:DiseaseStaging namespace: comment: The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:DiseaseStagingDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_133" xsd:string [Term] id: mged:DiseaseStagingDatabase namespace: comment: Database of disease staging information is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_225" xsd:string [Term] id: mged:DiseaseState namespace: comment: 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. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:DiseaseStateDatabase relationship: mged:has_disease_location mged:DiseaseLocation relationship: mged:has_disease_staging mged:DiseaseStaging property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_126" xsd:string [Term] id: mged:DiseaseStateDatabase namespace: comment: Database of disease state information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_181" xsd:string [Term] id: mged:DistanceUnit namespace: comment: Units used for distance measurements. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_4" xsd:string [Term] id: mged:DistanceUnitOther namespace: comment: Distance units not specified in MAGE. is_a: mged:DistanceUnit property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_143" xsd:string [Term] id: mged:Ecotype namespace: comment: a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler is_a: mged:StrainOrLine relationship: mged:has_database mged:StrainOrLineDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_71" xsd:string [Term] id: mged:EnvironmentalFactorCategory namespace: comment: Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth. is_a: mged:ExperimentalFactorCategory property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_117" xsd:string [Term] id: mged:EnvironmentalHistory namespace: comment: A description of the conditions the organism has been exposed to that are not one of the variables under study. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_55" xsd:string [Term] id: mged:EnvironmentalStress namespace: comment: 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 is_a: mged:MGEDExtendedOntology relationship: mged:has_measurement mged:Measurement property_value: mged:unique_identifier "MO_227" xsd:string [Term] id: mged:EpidemiologicalDesign namespace: comment: An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history. is_a: mged:ExperimentDesignType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_142" xsd:string [Term] id: mged:Experiment namespace: comment: 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. is_a: mged:ExperimentPackage relationship: mged:has_bioassay_data mged:BioAssayData relationship: mged:has_bioassays mged:BioAssay relationship: mged:has_citation mged:BibliographicReference relationship: mged:has_experiment_design mged:ExperimentDesign relationship: mged:has_providers mged:Contact property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_112" xsd:string [Term] id: mged:ExperimentDesign namespace: comment: 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. is_a: mged:ExperimentPackage relationship: mged:has_MAGE_description mged:NormalizationDescription relationship: mged:has_MAGE_description mged:QualityControlDescription relationship: mged:has_MAGE_description mged:ReplicateDescription relationship: mged:has_bioassays mged:BioAssay relationship: mged:has_description xsd:string relationship: mged:has_experiment_design_type mged:ExperimentDesignType relationship: mged:has_experiment_factors mged:ExperimentalFactor property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_170" xsd:string [Term] id: mged:ExperimentDesignType namespace: comment: The ExperimentDesignType is the high level description for studies such as \"time series\", \"dose response\", etc. is_a: mged:ExperimentPackage property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_158" xsd:string [Term] id: mged:ExperimentPackage namespace: comment: The descriptions associated with the Experiment package of MAGE is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_31" xsd:string [Term] id: mged:ExperimentalFactor namespace: comment: The factors in the study that are experimental parameters or regarded as influencing the experimental results. is_a: mged:ExperimentPackage relationship: mged:has_category mged:BiologicalFactorCategory relationship: mged:has_category mged:MethodologicalFactorCategory relationship: mged:has_factor_value mged:FactorValue property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_10" xsd:string [Term] id: mged:ExperimentalFactorCategory namespace: comment: A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML. is_a: mged:ExperimentPackage property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_205" xsd:string [Term] id: mged:ExperimentalProtocolType namespace: comment: All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment. is_a: mged:ProtocolType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_75" xsd:string [Term] id: mged:FactorValue namespace: comment: The value of an ExperimentFactor. is_a: mged:ExperimentPackage relationship: mged:has_factor_value_ontology_entry mged:ExperimentalFactorCategory relationship: mged:has_measurement mged:Measurement relationship: mged:has_property_set mged:FactorValueDependency relationship: mged:has_property_set mged:FactorValueSet property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_203" xsd:string [Term] id: mged:FactorValueDependency namespace: comment: 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. is_a: mged:DeprecatedTerms is_a: mged:ExperimentPackage relationship: mged:has_value xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: mged:deprecation_old_restriction "some|has_value|string" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_148" xsd:string [Term] id: mged:FactorValueSet namespace: comment: 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. is_a: mged:DeprecatedTerms is_a: mged:ExperimentPackage relationship: mged:has_value xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: mged:deprecation_old_restriction "some|has_value|string" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_217" xsd:string [Term] id: mged:FailType namespace: comment: Controlled terms for descriptors of failures (as in PCR) associated with reporters. is_a: mged:DesignElementPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_98" xsd:string [Term] id: mged:FamilyHistory namespace: comment: Relevant aspects of genetic preconditions or family member's clinical history. is_a: mged:EnvironmentalHistory relationship: mged:has_family_member mged:FamilyMember property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_59" xsd:string [Term] id: mged:FamilyMember namespace: comment: Member of the biosource's family. is_a: mged:BioMaterialPackage relationship: mged:has_clinical_record mged:OntologyEntry relationship: mged:has_disease_state mged:DiseaseState relationship: mged:has_family_relationship mged:FamilyRelationship relationship: mged:has_individual_genetic_characteristics mged:IndividualGeneticCharacteristics property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_188" xsd:string [Term] id: mged:FamilyRelationship namespace: comment: A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother. is_a: mged:BioMaterialPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_36" xsd:string [Term] id: mged:FeatureDefect namespace: comment: A technical manufacturer described defect for features. is_a: mged:ArrayPackage relationship: mged:has_type mged:DefectType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_138" xsd:string [Term] id: mged:FeatureGroup namespace: comment: Technology-based grouping of features representing individual locations on the array. is_a: mged:DesignElementGroup relationship: mged:has_feature_shape mged:FeatureShape relationship: mged:has_type mged:TechnologyType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_54" xsd:string [Term] id: mged:FeatureShape namespace: comment: The expected shape of the feature on the array. is_a: mged:ArrayDesignPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_8" xsd:string [Term] id: mged:Fiducial namespace: comment: A marking on the surface of the array that can be used to identify the origin of the array. is_a: mged:ArrayPackage relationship: mged:has_type mged:FiducialType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_136" xsd:string [Term] id: mged:FiducialType namespace: comment: A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark. is_a: mged:ArrayPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_17" xsd:string [Term] id: mged:Generation namespace: comment: 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. is_a: mged:EnvironmentalHistory property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_43" xsd:string [Term] id: mged:GeneticMaterial namespace: comment: 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. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_137" xsd:string [Term] id: mged:GeneticModification namespace: comment: 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. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_122" xsd:string [Term] id: mged:Genotype namespace: comment: 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\neither prior to or during the experiment. is_a: mged:IndividualGeneticCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_51" xsd:string [Term] id: mged:GeographicLocation namespace: comment: A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference. is_a: mged:EnvironmentalHistory is_a: mged:OntologyEntry relationship: mged:has_database mged:GeographicLocationDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_132" xsd:string [Term] id: mged:GeographicLocationDatabase namespace: comment: Database of geographic locations. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_35" xsd:string [Term] id: mged:GrowthCondition namespace: comment: 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. is_a: mged:EnvironmentalHistory relationship: mged:has_maximum_measurement mged:Measurement relationship: mged:has_measurement mged:Measurement relationship: mged:has_value xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_183" xsd:string [Term] id: mged:Haplotype namespace: comment: The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed. is_a: mged:IndividualGeneticCharacteristics property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_146" xsd:string [Term] id: mged:Hardware namespace: comment: The machine or instrument used. is_a: mged:ProtocolPackage relationship: mged:has_make xsd:string relationship: mged:has_manufacturer mged:Contact relationship: mged:has_model xsd:string relationship: mged:has_software mged:Software relationship: mged:has_type mged:HardwareType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_134" xsd:string [Term] id: mged:HardwareType namespace: comment: Controlled terms for descriptors of types of hardware. is_a: mged:ProtocolPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_113" xsd:string [Term] id: mged:HardwareVariation namespace: comment: The effects of different hardware, types of hardware, or models of hardware on experimental results are studied. is_a: mged:MethodologicalFactorCategory property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_81" xsd:string [Term] id: mged:HigherLevelAnalysisPackage namespace: comment: MAGE package for HigherLevelAnalysis is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_228" xsd:string [Term] id: mged:HigherLevelAnalysisProtocolType namespace: comment: A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging). is_a: mged:ProtocolType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_47" xsd:string [Term] id: mged:Histology namespace: comment: Microscopic morphology of tissues. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:HistologyDatabase relationship: mged:has_organism_part mged:OrganismPart relationship: mged:has_performer mged:Contact property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_194" xsd:string [Term] id: mged:HistologyDatabase namespace: comment: Database of histology information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_175" xsd:string [Term] id: mged:HistoryFactor namespace: comment: 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). is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_82" xsd:string [Term] id: mged:Host namespace: comment: Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells). is_a: mged:EnvironmentalHistory relationship: mged:has_host mged:Organism relationship: mged:has_host_part mged:OrganismPart property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_101" xsd:string [Term] id: mged:Humidity namespace: comment: The humidity that the biosource is exposed to. is_a: mged:GrowthCondition property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_29" xsd:string [Term] id: mged:Image namespace: is_a: mged:DescriptionPackage relationship: mged:has_URI mged:URI relationship: mged:has_database mged:Database relationship: mged:has_image_format mged:ImageFormat property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_22" xsd:string [Term] id: mged:ImageFormat namespace: comment: Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.) is_a: mged:BioAssayPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_211" xsd:string [Term] id: mged:Individual namespace: comment: Identifier or name of the individual organism from which the biomaterial was derived. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_169" xsd:string [Term] id: mged:IndividualChromosomalAbnormality namespace: comment: 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. is_a: mged:DeprecatedTerms is_a: mged:IndividualGeneticCharacteristics property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_185" xsd:string [Term] id: mged:IndividualGeneticCharacteristics namespace: comment: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. is_a: mged:BioMaterialCharacteristics relationship: mged:has_value xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_66" xsd:string [Term] id: mged:InitialTimePoint namespace: comment: The point from which measurements of age were taken. is_a: mged:BioMaterialPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_80" xsd:string [Term] id: mged:LabelCompound namespace: comment: Compounds that are used for labeling extracts. is_a: mged:Compound property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_13" xsd:string [Term] id: mged:LabeledExtract namespace: comment: The BioSample after labeling for detection of the nucleic acids. is_a: mged:BioMaterial relationship: mged:has_been_treated mged:Treatment relationship: mged:has_compound mged:LabelCompound property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_221" xsd:string [Term] id: mged:Light namespace: comment: The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. is_a: mged:GrowthCondition property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_60" xsd:string [Term] id: mged:LightUnit namespace: comment: Units for measuring the intensity of light. is_a: mged:OtherUnit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_119" xsd:string [Term] id: mged:MGEDCoreOntology namespace: comment: An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents. is_a: mged:MGEDOntology relationship: mged:has_ID xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_57" xsd:string [Term] id: mged:MGEDExtendedOntology namespace: comment: 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 is_a: mged:MGEDOntology property_value: mged:unique_identifier "MO_196" xsd:string [Term] id: mged:MGEDOntology namespace: comment: 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. relationship: mged:is_user_defined mged:BibliographicReference relationship: mged:is_user_defined mged:Contact property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_174" xsd:string [Term] id: mged:MGEDOntologyVersion namespace: comment: The version of the MGED Ontology. is_a: mged:MGEDCoreOntology property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_115" xsd:string [Term] id: mged:MassUnit namespace: comment: Units used for mass measurements. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_149" xsd:string [Term] id: mged:MassUnitOther namespace: comment: Mass units not specified in MAGE. is_a: mged:MassUnit property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_11" xsd:string [Term] id: mged:MaterialType namespace: comment: 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. is_a: mged:BioMaterialPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_32" xsd:string [Term] id: mged:Measurement namespace: comment: Measured values and units. is_a: mged:MeasurementPackage relationship: mged:has_measurement_type mged:MeasurementType relationship: mged:has_units mged:Unit relationship: mged:has_value xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_144" xsd:string [Term] id: mged:MeasurementPackage namespace: comment: MAGE package for measurement. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_89" xsd:string [Term] id: mged:MeasurementType namespace: comment: class to hold instances used as the filler for the property has_measurement_type is_a: mged:MGEDCoreOntology property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_72" xsd:string [Term] id: mged:Media namespace: comment: The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) . is_a: mged:GrowthCondition property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_19" xsd:string [Term] id: mged:MethodologicalDesign namespace: comment: A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop. is_a: mged:ExperimentDesignType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_2" xsd:string [Term] id: mged:MethodologicalFactorCategory namespace: comment: 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. is_a: mged:ExperimentalFactorCategory property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_85" xsd:string [Term] id: mged:Node namespace: comment: A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes. is_a: mged:HigherLevelAnalysisPackage relationship: mged:has_node_value mged:NodeValue property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_73" xsd:string [Term] id: mged:NodeValue namespace: comment: Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm. is_a: mged:HigherLevelAnalysisPackage relationship: mged:has_node_value_type mged:NodeValueType relationship: mged:has_scale mged:Scale relationship: mged:has_type mged:DataType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_104" xsd:string [Term] id: mged:NodeValueType namespace: comment: Controlled set of terms for describing the type of values (e.g., Euclidean distance). is_a: mged:HigherLevelAnalysisPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_160" xsd:string [Term] id: mged:NormalizationDescription namespace: comment: NormalizationDescription provides details of the normalization strategy for the experiment. is_a: mged:ExperimentPackage relationship: mged:has_type mged:NormalizationDescriptionType property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_131" xsd:string [Term] id: mged:NormalizationDescriptionType namespace: comment: Controlled descriptors for the normalization strategy used for the experiment. is_a: mged:ExperimentPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_27" xsd:string [Term] id: mged:Nutrients namespace: comment: The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). is_a: mged:GrowthCondition relationship: mged:has_nutrient_component mged:Compound property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_127" xsd:string [Term] id: mged:Observation namespace: comment: Observation will record the macroscopic examination of the biomaterial. is_a: mged:BioMaterialCharacteristics relationship: mged:has_database mged:ObservationDatabase relationship: mged:has_performer mged:Contact property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_53" xsd:string [Term] id: mged:ObservationDatabase namespace: comment: Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_91" xsd:string [Term] id: mged:OntologyEntry namespace: comment: External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology. is_a: mged:DescriptionPackage relationship: mged:has_accession xsd:string relationship: mged:has_accession_version xsd:string relationship: mged:has_database mged:Database relationship: mged:has_database_entry_type mged:DatabaseEntryType relationship: mged:has_description xsd:string relationship: mged:has_value xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_87" xsd:string [Term] id: mged:OperatorVariation namespace: comment: The effects of different investigators, laboratories, or organizations on experimental results are studied. is_a: mged:MethodologicalFactorCategory property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_38" xsd:string [Term] id: mged:Organism namespace: comment: The genus and species (and subspecies) of the organism from which the biomaterial is derived from. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:OrganismDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_229" xsd:string [Term] id: mged:OrganismDatabase namespace: comment: Database of taxonomic information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_64" xsd:string [Term] id: mged:OrganismPart namespace: comment: 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). is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:OrganismPartDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_1" xsd:string [Term] id: mged:OrganismPartDatabase namespace: comment: Database of organism part information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_200" xsd:string [Term] id: mged:OrganismStatus namespace: comment: The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_84" xsd:string [Term] id: mged:Organization namespace: comment: The organization (e.g. company, hospital) to contact to obtain or purchase something. is_a: mged:Contact relationship: mged:has_name xsd:string relationship: mged:has_parent_organization mged:Organization property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_177" xsd:string [Term] id: mged:OtherUnit namespace: comment: Other units are those types not specified in MAGE such as lumens, radioactivity, etc. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_199" xsd:string [Term] id: mged:Parameter namespace: comment: A parameter is a variable within a protocol. is_a: mged:ProtocolPackage relationship: mged:has_type mged:DataType relationship: mged:has_units mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_110" xsd:string [Term] id: mged:PathogenTest namespace: comment: Tests and results for pathogens infecting organism from which the biosource is derived is_a: mged:EnvironmentalHistory relationship: mged:has_result mged:Result relationship: mged:was_tested_for mged:Organism property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_184" xsd:string [Term] id: mged:Person namespace: comment: The individual to contact regarding something provided such as a biomaterial. is_a: mged:Contact relationship: mged:has_affiliation mged:Organization relationship: mged:has_first_name xsd:string relationship: mged:has_last_name xsd:string relationship: mged:has_mid_initials xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_24" xsd:string [Term] id: mged:PerturbationalDesign namespace: comment: A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification is_a: mged:ExperimentDesignType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_106" xsd:string [Term] id: mged:Phenotype namespace: comment: 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. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:PhenotypeDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_192" xsd:string [Term] id: mged:PhenotypeDatabase namespace: comment: Database of phenotype information is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_39" xsd:string [Term] id: mged:PhysicalArrayDesign namespace: comment: Descriptions pertaining to the array. is_a: mged:ArrayDesignPackage relationship: mged:has_type mged:SurfaceType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_212" xsd:string [Term] id: mged:PhysicalBioAssay namespace: comment: A physical bioassay is the combination of arrays and biomaterials as in a hybridization. is_a: mged:BioAssay relationship: mged:has_image_format mged:ImageFormat property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_99" xsd:string [Term] id: mged:PhysicalBioSequenceType namespace: comment: A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC. is_a: mged:BioSequenceType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_92" xsd:string [Term] id: mged:Ploidy namespace: comment: The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc. is_a: mged:IndividualGeneticCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_220" xsd:string [Term] id: mged:PolymerType namespace: comment: Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence. is_a: mged:BioSequencePackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_102" xsd:string [Term] id: mged:PopulationDensity namespace: comment: The concentration range of the organism. is_a: mged:GrowthCondition property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_46" xsd:string [Term] id: mged:Preservation namespace: comment: Method and type of preserving the organism or biosource (i.e. keeping it in stasis). is_a: mged:MGEDExtendedOntology relationship: mged:has_protocol mged:Protocol relationship: mged:has_type mged:PreservationType property_value: mged:unique_identifier "MO_176" xsd:string [Term] id: mged:PreservationType namespace: comment: The type of method used to preserve (keep in stasis) the organism or biosource. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_195" xsd:string [Term] id: mged:Protocol namespace: comment: Documentation of the set of steps taken in a procedure. is_a: mged:ProtocolPackage relationship: mged:has_URI mged:URI relationship: mged:has_citation mged:BibliographicReference relationship: mged:has_description xsd:string relationship: mged:has_hardware mged:Hardware relationship: mged:has_software mged:Software relationship: mged:has_text xsd:string relationship: mged:has_title xsd:string relationship: mged:has_type mged:ProtocolType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_214" xsd:string [Term] id: mged:ProtocolPackage namespace: comment: The MAGE package for protocols. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_63" xsd:string [Term] id: mged:ProtocolParameterType namespace: comment: Descriptors for protocol parameter types, e.g. compound concentration, media type. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_164" xsd:string [Term] id: mged:ProtocolType namespace: comment: A controlled set of terms to provide a descriptor for the type of protocol. is_a: mged:MethodologicalFactorCategory is_a: mged:ProtocolPackage property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_150" xsd:string [Term] id: mged:ProtocolVariation namespace: comment: The effects of different protocols or changes in protocols on experimental results are studied. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_140" xsd:string [Term] id: mged:PublicationType namespace: comment: Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.). is_a: mged:DescriptionPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_208" xsd:string [Term] id: mged:QualityControlDescription namespace: comment: QualityControlDescription provides details of the quality control aspects of the experiment. is_a: mged:ExperimentPackage relationship: mged:has_type mged:QualityControlDescriptionType property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_88" xsd:string [Term] id: mged:QualityControlDescriptionType namespace: comment: Controlled descriptors for the quality control strategy for an experiment. is_a: mged:ExperimentPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_121" xsd:string [Term] id: mged:QuantitationType namespace: comment: The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix. is_a: mged:QuantitationTypePackage relationship: mged:has_scale mged:Scale relationship: mged:has_type mged:DataType property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_67" xsd:string [Term] id: mged:QuantitationTypePackage namespace: comment: The MAGE package for defining classes for quantitation. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_130" xsd:string [Term] id: mged:QuantityUnit namespace: comment: Units used for quantity measurements. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_210" xsd:string [Term] id: mged:QuantityUnitOther namespace: comment: Quantity units not specified in MAGE. is_a: mged:QuantityUnit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_156" xsd:string [Term] id: mged:RadiationUnit namespace: comment: Units for measuring decay of a radioactive isotope over time. is_a: mged:OtherUnit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_204" xsd:string [Term] id: mged:ReplicateDescription namespace: comment: ReplicateDescription provides details about the type of replication used in the experiment. is_a: mged:ExperimentPackage relationship: mged:has_type mged:ReplicateDescriptionType property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_162" xsd:string [Term] id: mged:ReplicateDescriptionType namespace: comment: Controlled descriptors for the type of replication. is_a: mged:ExperimentPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_52" xsd:string [Term] id: mged:Reporter namespace: comment: Description of the material placed on a feature (spot). is_a: mged:DesignElement relationship: mged:has_type mged:FailType relationship: mged:has_type mged:WarningType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_74" xsd:string [Term] id: mged:Result namespace: comment: class to hold instances used as the filler for the property has_result is_a: mged:MGEDCoreOntology property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_65" xsd:string [Term] id: mged:Roles namespace: comment: Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider. is_a: mged:AuditAndSecurityPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_180" xsd:string [Term] id: mged:SamplingTimePoint namespace: comment: A descriptor of the time point that a sample was taken. Not to be used \n where the sample is part of a time course. SamplingTimePoint is not \n related to age. An instance could be summer, a date, a time, or a range \n value. is_a: mged:EnvironmentalHistory property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_139" xsd:string [Term] id: mged:Scale namespace: comment: The scale (linear, log10, ln, etc) used to represent the value. is_a: mged:MGEDCoreOntology property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_108" xsd:string [Term] id: mged:SeqFeatureBasis namespace: comment: Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.) is_a: mged:BioSequencePackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_207" xsd:string [Term] id: mged:SequenceOntologyBioSequenceType namespace: comment: Descriptors of biosequence based on the Sequence Ontology (SO) project. is_a: mged:OntologyEntry is_a: mged:PhysicalBioSequenceType is_a: mged:TheoreticalBioSequenceType relationship: mged:has_database mged:SequenceOntologyDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_25" xsd:string [Term] id: mged:SequenceOntologyDatabase namespace: comment: Database for sequence annotation information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_83" xsd:string [Term] id: mged:Serotype namespace: comment: An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_159" xsd:string [Term] id: mged:Sex namespace: comment: 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. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_168" xsd:string [Term] id: mged:Software namespace: comment: The software application used. is_a: mged:ProtocolPackage relationship: mged:has_hardware mged:Hardware relationship: mged:has_manufacturer mged:Contact relationship: mged:has_software mged:Software relationship: mged:has_type mged:SoftwareType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_109" xsd:string [Term] id: mged:SoftwareType namespace: comment: Controlled terms that provide descriptors for the type of software. is_a: mged:ProtocolPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_202" xsd:string [Term] id: mged:SoftwareVariation namespace: comment: The effects of different software, software packages, or software versions on experimental results are studied. is_a: mged:MethodologicalFactorCategory property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_222" xsd:string [Term] id: mged:SomaticModification namespace: comment: The organism has had non-genetic parts removed, added, or rearranged. is_a: mged:MGEDExtendedOntology relationship: mged:has_part_modified mged:OrganismPart property_value: mged:unique_identifier "MO_44" xsd:string [Term] id: mged:StrainOrLine namespace: comment: 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. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:StrainOrLineDatabase relationship: mged:has_species mged:Organism property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_9" xsd:string [Term] id: mged:StrainOrLineDatabase namespace: comment: Database of strain, line, cultivar or ecotype information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_30" xsd:string [Term] id: mged:StrandType namespace: comment: A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_7" xsd:string [Term] id: mged:SubstrateType namespace: comment: Controlled terms for descriptors of types of array substrates. is_a: mged:ArrayPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_79" xsd:string [Term] id: mged:SurfaceType namespace: comment: Controlled terms for descriptors for coating of the substrate. is_a: mged:ArrayDesignPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_198" xsd:string [Term] id: mged:TargetedCellType namespace: comment: 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. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_123" xsd:string [Term] id: mged:TargetedCellTypeDatabase namespace: comment: Database of targeted cell type information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_45" xsd:string [Term] id: mged:TechnologicalDesign namespace: comment: The purpose(s) for which the array is used within an experiment, e.g. to \n assess the transcriptome, the genomic content, or to identify \n transcription factor binding sites. is_a: mged:ExperimentDesignType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_21" xsd:string [Term] id: mged:TechnologyType namespace: comment: The technology type or platform of the reporters on the array. is_a: mged:ArrayDesignPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_18" xsd:string [Term] id: mged:Temperature namespace: comment: The temperature that a biosource is exposed to. is_a: mged:GrowthCondition property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_171" xsd:string [Term] id: mged:TemperatureUnit namespace: comment: Units used for temperature measurements. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_48" xsd:string [Term] id: mged:Test namespace: comment: An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry. is_a: mged:BioMaterialCharacteristics relationship: mged:has_performer mged:Contact relationship: mged:has_test_result mged:TestResult relationship: mged:has_test_type mged:TestType property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_197" xsd:string [Term] id: mged:TestResult namespace: comment: TestResult is the recorded value of the test outcome. is_a: mged:BioMaterialCharacteristics relationship: mged:has_measurement mged:Measurement property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_96" xsd:string [Term] id: mged:TestType namespace: comment: Descriptor of the Test performed e.g. Leukocyte count is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:TestTypeDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_218" xsd:string [Term] id: mged:TestTypeDatabase namespace: comment: Database of codes for clinical findings. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_76" xsd:string [Term] id: mged:TheoreticalBioSequenceType namespace: comment: A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron. is_a: mged:BioSequenceType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_42" xsd:string [Term] id: mged:TimeUnit namespace: comment: Units used for time measurements. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_166" xsd:string [Term] id: mged:TimeUnitOther namespace: comment: Time units not specified in MAGE. is_a: mged:TimeUnit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_103" xsd:string [Term] id: mged:Transformation namespace: comment: The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data. is_a: mged:BioAssayDataPackage relationship: mged:has_protocol mged:Protocol property_value: mged:unique_identifier "MO_216" xsd:string [Term] id: mged:Treatment namespace: comment: A treatment is the process or action by which a biomaterial is created from an input biomaterial. is_a: mged:BioMaterialPackage relationship: mged:has_action mged:Action relationship: mged:has_order xsd:int relationship: mged:has_protocol mged:Protocol property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_23" xsd:string [Term] id: mged:TumorGrading namespace: comment: A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:TumorGradingDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_28" xsd:string [Term] id: mged:TumorGradingDatabase namespace: comment: Database of tumor grading information is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_187" xsd:string [Term] id: mged:URI namespace: comment: Uniform Resource Identifier is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_12" xsd:string [Term] id: mged:Unit namespace: comment: Units of measure. is_a: mged:MeasurementPackage property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_3" xsd:string [Term] id: mged:User namespace: comment: User is a way to id a person in a database is_a: mged:MGEDExtendedOntology relationship: mged:has_ID xsd:string property_value: mged:unique_identifier "MO_62" xsd:string [Term] id: mged:VolumeUnit namespace: comment: Units used for volume measurements. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_179" xsd:string [Term] id: mged:VolumeUnitOther namespace: comment: Volume units not specified in MAGE. is_a: mged:VolumeUnit property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_155" xsd:string [Term] id: mged:WarningType namespace: comment: Controlled terms for descriptors of the warnings associated with reporters. is_a: mged:DesignElementPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_41" xsd:string [Term] id: mged:Water namespace: comment: Water consumed by or enveloping the organism that the biosource is derived from. is_a: mged:GrowthCondition relationship: mged:has_additive mged:Compound relationship: mged:has_treatment mged:Protocol property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_153" xsd:string [Term] id: mged:ZoneDefect namespace: comment: A technical manufactured described defect for zones. is_a: mged:ArrayPackage relationship: mged:has_type mged:DefectType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_105" xsd:string [Instance] id: mged:A instance_of: mged:DistanceUnit comment: Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer property_value: mged:unique_identifier "MO_515" xsd:string [Instance] id: mged:ATCC_Cultures instance_of: mged:CellLineDatabase instance_of: mged:StrainOrLineDatabase comment: database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses property_value: mged:has_human_readable_URI "http://www.atcc.org/Cultures/Products.cfm" xsd:string property_value: mged:unique_identifier "MO_979" xsd:string [Instance] id: mged:Adult_Mouse_Anatomy instance_of: mged:OrganismPartDatabase comment: This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28). property_value: mged:unique_identifier "MO_992" xsd:string property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology?rev=1.1&view=markup" xsd:string [Instance] id: mged:Affymetrix_DAT instance_of: mged:ImageFormat comment: A proprietary image data format that is lossless and containing one channel of data. property_value: mged:unique_identifier "MO_786" xsd:string [Instance] id: mged:Affymetrix_average_difference instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_649" xsd:string [Instance] id: mged:BAC instance_of: mged:DeprecatedTerms comment: sequence from a bacterial artificial chromosome\nexact synonym: bacterial artificial chromosome relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:synonym "bacterial artificial chromosome" xsd:string property_value: mged:unique_identifier "MO_985" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:CABRI_Bacteria_and_Archaea_Strains instance_of: mged:StrainOrLineDatabase comment: 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. property_value: mged:unique_identifier "MO_1008" xsd:string property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/bact/all_A.htm" xsd:string [Instance] id: mged:CABRI_Filamentous_Fungi_Strains instance_of: mged:StrainOrLineDatabase comment: 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. property_value: mged:unique_identifier "MO_1009" xsd:string property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/fun/all_A.htm" xsd:string [Instance] id: mged:CABRI_HLA_typed_B_Cell_lines instance_of: mged:CellLineDatabase comment: 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\n and Information) initiative (see http://www.cabri.org/ ). Detailed \ndescriptions can be reached from the list and cell lines of interest can be requested. property_value: mged:unique_identifier "MO_1005" xsd:string property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/cells/hla.htm" xsd:string [Instance] id: mged:CABRI_Human_and_Animal_Cell_lines instance_of: mged:CellLineDatabase comment: Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc. property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/cells/all.htm" xsd:string property_value: mged:unique_identifier "MO_536" xsd:string [Instance] id: mged:CABRI_Hybridomas instance_of: mged:CellLineDatabase comment: 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. property_value: mged:unique_identifier "MO_1006" xsd:string property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/cells/hybrid.htm" xsd:string [Instance] id: mged:CABRI_Yeasts_Strains instance_of: mged:StrainOrLineDatabase comment: 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. property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/yeast/all_A.htm" xsd:string property_value: mged:unique_identifier "MO_1010" xsd:string [Instance] id: mged:CBIL_CV instance_of: mged:CellTypeDatabase instance_of: mged:OrganismPartDatabase instance_of: mged:TargetedCellTypeDatabase comment: a controlled vocabulary provided by CBIL property_value: mged:has_human_readable_URI "http://www.cbil.upenn.edu/anatomy.php3" xsd:string property_value: mged:unique_identifier "MO_886" xsd:string [Instance] id: mged:CLDB_Human_and_Animal_Cell_Line instance_of: mged:CellLineDatabase comment: 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. property_value: mged:unique_identifier "MO_1007" xsd:string property_value: mged:has_human_readable_URI "" xsd:string [Instance] id: mged:CellML instance_of: mged:OrganismPartDatabase comment: Ontology describing anatomical and physiological relationships. property_value: mged:unique_identifier "MO_967" xsd:string property_value: mged:has_human_readable_URI "http://portal.bioengineering.elyt.ods.org/ontology/" xsd:string [Instance] id: mged:ChEBI instance_of: mged:CompoundDatabase comment: 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. property_value: mged:unique_identifier "MO_857" xsd:string property_value: mged:has_human_readable_URI "http://www.ebi.ac.uk/chebi" xsd:string [Instance] id: mged:ChemID instance_of: mged:CompoundDatabase comment: Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds. property_value: mged:has_human_readable_URI "http://chem.sis.nlm.nih.gov/chemidplus" xsd:string property_value: mged:unique_identifier "MO_426" xsd:string [Instance] id: mged:Ci instance_of: mged:RadiationUnit comment: 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). property_value: mged:unique_identifier "MO_642" xsd:string [Instance] id: mged:Cy3 instance_of: mged:LabelCompound comment: fluorophore used for labeling/detection purposes property_value: mged:unique_identifier "MO_739" xsd:string [Instance] id: mged:Cy5 instance_of: mged:LabelCompound comment: fluorophore used for labeling/detection purposes property_value: mged:unique_identifier "MO_646" xsd:string [Instance] id: mged:DNA instance_of: mged:MaterialType instance_of: mged:PolymerType comment: Deoxyribonucleic acid. property_value: mged:unique_identifier "MO_945" xsd:string [Instance] id: mged:DNA_sequencer instance_of: mged:HardwareType comment: An instrument that produces DNA sequences. property_value: mged:unique_identifier "MO_676" xsd:string [Instance] id: mged:EMAP instance_of: mged:DevelopmentalStageDatabase comment: The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth. property_value: mged:unique_identifier "MO_357" xsd:string property_value: mged:has_human_readable_URI "http://genex.hgu.mrc.ac.uk" xsd:string [Instance] id: mged:EST instance_of: mged:DeprecatedTerms comment: Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences. relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_412" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:Euclidean_distance instance_of: mged:NodeValueType comment: 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). property_value: mged:unique_identifier "MO_932" xsd:string [Instance] id: mged:F instance_of: mged:Sex comment: mating type indicating the presence of F plasmid in a bacterial cell property_value: mged:unique_identifier "MO_717" xsd:string [Instance] id: mged:FMA instance_of: mged:OrganismPartDatabase comment: 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. property_value: mged:has_human_readable_URI "http://sig.biostr.wahington.edu/projects/fm/" xsd:string property_value: mged:unique_identifier "MO_468" xsd:string [Instance] id: mged:F_minus instance_of: mged:Sex comment: mating type indicating the absence of F plasmid in a bacterial cell\n property_value: mged:unique_identifier "MO_682" xsd:string [Instance] id: mged:FlyBase_developmental_stage_database instance_of: mged:DevelopmentalStageDatabase comment: uri for FlyBase developmental stage terms property_value: mged:unique_identifier "MO_865" xsd:string property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/viewcvs.py/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.ontology?content-type=text/plain&rev=1.1" xsd:string [Instance] id: mged:FlyBase_organism_part_database instance_of: mged:OrganismPartDatabase comment: curated database containing information on Drosophila genes, alleles etc property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/" xsd:string property_value: mged:unique_identifier "MO_504" xsd:string [Instance] id: mged:GIF instance_of: mged:ImageFormat comment: Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss. property_value: mged:unique_identifier "MO_963" xsd:string [Instance] id: mged:GRAMENE instance_of: mged:StrainOrLineDatabase comment: A Comparative Mapping Resource for Grains. property_value: mged:unique_identifier "MO_678" xsd:string property_value: mged:has_human_readable_URI "http://www.gramene.org/" xsd:string [Instance] id: mged:GeneOntology instance_of: mged:CellularComponentDatabase comment: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. property_value: mged:has_machine_readable_URI "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo" xsd:string property_value: mged:unique_identifier "MO_1022" xsd:string [Instance] id: mged:HUMAT instance_of: mged:DevelopmentalStageDatabase comment: Ontology of human developmental anatomy for Carnegie stages 1-20. property_value: mged:has_machine_readable_URI "http://obo.sourceforge.net/list.shtml" xsd:string property_value: mged:unique_identifier "MO_844" xsd:string [Instance] id: mged:Hfr instance_of: mged:DeprecatedTerms comment: High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome relationship: mged:deprecated_from_version mged:version_1.1.7 relationship: mged:deprecation_old_parent mged:Sex relationship: mged:deprecation_replacement_term mged:Sex relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_419" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string [Instance] id: mged:ICD-9-CM instance_of: mged:DiseaseStateDatabase comment: Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001. property_value: mged:unique_identifier "MO_654" xsd:string property_value: mged:has_machine_readable_URI "ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2002" xsd:string [Instance] id: mged:IU instance_of: mged:QuantityUnit comment: 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. property_value: mged:synonym "International unit" xsd:string property_value: mged:synonym "UI" xsd:string property_value: mged:unique_identifier "MO_1011" xsd:string [Instance] id: mged:IUPAC_Clinical_Chemistry_Guidelines instance_of: mged:TestTypeDatabase comment: A resource of vocabularies for describing clinical tests, e.g. blood chemistry. property_value: mged:has_human_readable_URI "http://www.iupac.org/publications/pac/2000/205/205olesen.html" xsd:string property_value: mged:unique_identifier "MO_593" xsd:string [Instance] id: mged:JAX_mouse_strains instance_of: mged:StrainOrLineDatabase comment: Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature. property_value: mged:has_human_readable_URI "http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml" xsd:string property_value: mged:unique_identifier "MO_369" xsd:string [Instance] id: mged:JPEG instance_of: mged:ImageFormat comment: Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss. property_value: mged:unique_identifier "MO_746" xsd:string [Instance] id: mged:K instance_of: mged:TemperatureUnit comment: Kelvin, unit of temperature property_value: mged:unique_identifier "MO_614" xsd:string [Instance] id: mged:L instance_of: mged:VolumeUnit comment: liter, unit of volume property_value: mged:unique_identifier "MO_444" xsd:string [Instance] id: mged:LOINC instance_of: mged:TestTypeDatabase comment: Database resource for universal identifiers for laboratory and other clinical observations property_value: mged:unique_identifier "MO_731" xsd:string property_value: mged:has_machine_readable_URI "http://www.loinc.org/download" xsd:string [Instance] id: mged:M instance_of: mged:ConcentrationUnit comment: Mole per liter or molarity, concentration unit property_value: mged:unique_identifier "MO_936" xsd:string [Instance] id: mged:MAD_stage instance_of: mged:DevelopmentalStageDatabase instance_of: mged:OrganismPartDatabase instance_of: mged:TargetedCellTypeDatabase comment: database entry from mouse anatomical dictionary for developmental stage term property_value: mged:has_human_readable_URI "http://www.informatics.jax.org/mgihome/GXD/AD/" xsd:string property_value: mged:unique_identifier "MO_693" xsd:string [Instance] id: mged:MAS4_average_difference instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_782" xsd:string [Instance] id: mged:MAS5_signal instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_653" xsd:string [Instance] id: mged:MAS5_signal_log_ratio instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_938" xsd:string [Instance] id: mged:MBEI instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_756" xsd:string [Instance] id: mged:MESH instance_of: mged:DiseaseStateDatabase comment: database entry from MESH, medical subject headings vocabulary resource property_value: mged:unique_identifier "MO_580" xsd:string property_value: mged:has_human_readable_URI "http://www.nlm.nih.gov/mesh/filelist.html" xsd:string [Instance] id: mged:MTB_Database instance_of: mged:DiseaseStateDatabase comment: Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors. property_value: mged:has_human_readable_URI "http://tumor.informatics.jax.org" xsd:string property_value: mged:unique_identifier "MO_942" xsd:string [Instance] id: mged:Mammalian_Phenotype_Ontology instance_of: mged:ObservationDatabase comment: A community effort to provide standard terms for annotating phenotypic data. property_value: mged:has_human_readable_URI "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:0000001" xsd:string property_value: mged:unique_identifier "MO_704" xsd:string [Instance] id: mged:NASC instance_of: mged:StrainOrLineDatabase comment: The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. property_value: mged:unique_identifier "MO_379" xsd:string property_value: mged:has_human_readable_URI "http://arabidopsis.info/catalogue.html" xsd:string [Instance] id: mged:NCBI_taxonomy instance_of: mged:OrganismDatabase instance_of: mged:StrainOrLineDatabase comment: identifier for a taxon provided by the NCBI taxonomy database property_value: mged:has_human_readable_URI "http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/" xsd:string property_value: mged:unique_identifier "MO_773" xsd:string [Instance] id: mged:NCI_Thesaurus instance_of: mged:DeprecatedTerms comment: A description logic namespace that contains controlled terminology used at NCI. relationship: mged:deprecated_from_version mged:version_1.1.7 relationship: mged:deprecation_old_parent mged:CellLineDatabase relationship: mged:deprecation_old_parent mged:ClinicalTreatmentDatabase relationship: mged:deprecation_old_parent mged:CompoundDatabase relationship: mged:deprecation_old_parent mged:DiseaseStateDatabase relationship: mged:deprecation_old_parent mged:GeographicLocationDatabase relationship: mged:deprecation_old_parent mged:OrganismPartDatabase relationship: mged:deprecation_old_parent mged:StrainOrLineDatabase relationship: mged:deprecation_old_parent mged:TargetedCellTypeDatabase relationship: mged:deprecation_old_parent mged:TumorGradingDatabase relationship: mged:has_reason_for_deprecation mged:split_term relationship: mged:split_to_term mged:NCI_cell_type_database relationship: mged:split_to_term mged:NCI_compound_database relationship: mged:split_to_term mged:NCI_disease_state_database relationship: mged:split_to_term mged:NCI_geographic_location_database relationship: mged:split_to_term mged:NCI_organism_part_database relationship: mged:split_to_term mged:NCI_strain_or_line_database relationship: mged:split_to_term mged:NCI_targeted_cell_type_database relationship: mged:split_to_term mged:NCI_tumor_grading_database property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:deprecation_reason "split_term" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov" xsd:string property_value: mged:unique_identifier "MO_456" xsd:string [Instance] id: mged:NCI_cell_type_database instance_of: mged:CellTypeDatabase comment: a controlled vocabulary of cell types property_value: mged:unique_identifier "MO_687" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=12596" xsd:string [Instance] id: mged:NCI_compound_database instance_of: mged:CompoundDatabase comment: a controlled vocabulary for compounds property_value: mged:unique_identifier "MO_376" xsd:string property_value: mged:has_human_readable_URI "http://nciterm.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C1908" xsd:string [Instance] id: mged:NCI_disease_staging_database instance_of: mged:DiseaseStagingDatabase comment: a controlled vocabulary for disease stages property_value: mged:unique_identifier "MO_422" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28108" xsd:string [Instance] id: mged:NCI_disease_state_database instance_of: mged:DiseaseStateDatabase comment: a controlled vocabulary for disease states property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C7057" xsd:string property_value: mged:unique_identifier "MO_790" xsd:string [Instance] id: mged:NCI_geographic_location_database instance_of: mged:GeographicLocationDatabase comment: a controlled vocabulary for geographic locations property_value: mged:unique_identifier "MO_630" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16632" xsd:string [Instance] id: mged:NCI_histology_database instance_of: mged:HistologyDatabase comment: a controlled vocabulary for histology property_value: mged:unique_identifier "MO_537" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C4741" xsd:string [Instance] id: mged:NCI_organism_part_database instance_of: mged:OrganismPartDatabase comment: a controlled vocabulary of organism parts property_value: mged:unique_identifier "MO_690" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C13007" xsd:string [Instance] id: mged:NCI_strain_or_line_database instance_of: mged:StrainOrLineDatabase comment: a controlled vocabulary for strains or lines property_value: mged:unique_identifier "MO_397" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16403" xsd:string [Instance] id: mged:NCI_targeted_cell_type_database instance_of: mged:TargetedCellTypeDatabase comment: a controlled vocabulary of targeted cell types property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12596" xsd:string property_value: mged:unique_identifier "MO_351" xsd:string [Instance] id: mged:NCI_tumor_grading_database instance_of: mged:TumorGradingDatabase comment: a controlled vocabulary of tumor grading terms property_value: mged:unique_identifier "MO_819" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28076" xsd:string [Instance] id: mged:ORF instance_of: mged:DeprecatedTerms comment: 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. relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_413" xsd:string [Instance] id: mged:PAC instance_of: mged:DeprecatedTerms comment: sequence from a P1 artificial chromosome relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_909" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:PCR instance_of: mged:DesignElement comment: Polymerase chain reaction. An element generated using this procedure. property_value: mged:unique_identifier "MO_915" xsd:string [Instance] id: mged:PCR_amplicon instance_of: mged:DeprecatedTerms comment: BioSequence generated by means of polymerase chain reaction relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_450" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:PCR_amplification instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle. property_value: mged:unique_identifier "MO_358" xsd:string [Instance] id: mged:PCR_fail instance_of: mged:FailType comment: PCR where no products of any kind appear in gel-separated reaction products. property_value: mged:unique_identifier "MO_667" xsd:string [Instance] id: mged:PCR_primer instance_of: mged:DeprecatedTerms comment: single oligo used for polymerase chain reaction direction unspecified relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_651" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:PCR_primer_forward instance_of: mged:DeprecatedTerms comment: single stranded oligo used for polymerase chain reaction relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_381" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:PCR_primer_reverse instance_of: mged:DeprecatedTerms comment: single stranded oligo used for polymerase chain reaction relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_640" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:PCR_questionable instance_of: mged:FailType comment: PCR with multiple bands, or smear, in gel-separated reaction products property_value: mged:unique_identifier "MO_620" xsd:string [Instance] id: mged:PNG instance_of: mged:ImageFormat comment: Portable Network Graphic, a lossless image data format. property_value: mged:unique_identifier "MO_1001" xsd:string [Instance] id: mged:Pathbase instance_of: mged:HistologyDatabase comment: database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice property_value: mged:unique_identifier "MO_972" xsd:string property_value: mged:has_human_readable_URI "http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php" xsd:string [Instance] id: mged:Pearson_correlation instance_of: mged:NodeValueType comment: The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations. property_value: mged:unique_identifier "MO_632" xsd:string [Instance] id: mged:R instance_of: mged:RadiationUnit comment: Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg. property_value: mged:unique_identifier "MO_725" xsd:string [Instance] id: mged:RMA instance_of: mged:DerivedBioAssayType comment: Robust Multiarray Average. A quantitative measure of the relative \n abundance of a transcript. RMA is a summary measure of related perfect \n match Features on an Affymetrix array. The values are background-adjusted, \n normalized and log-transformed values. property_value: mged:unique_identifier "MO_987" xsd:string [Instance] id: mged:RNA instance_of: mged:PolymerType comment: Ribonucleic acid. property_value: mged:unique_identifier "MO_594" xsd:string [Instance] id: mged:RNA_stability_design instance_of: mged:BioMolecularAnnotation comment: A RNA stability experiment design type examines the stability and/or decay of RNA transcripts. property_value: mged:unique_identifier "MO_553" xsd:string [Instance] id: mged:Rad instance_of: mged:RadiationUnit comment: 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. property_value: mged:unique_identifier "MO_585" xsd:string [Instance] id: mged:Rem instance_of: mged:RadiationUnit comment: 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. property_value: mged:unique_identifier "MO_908" xsd:string [Instance] id: mged:SequenceOntology instance_of: mged:SequenceOntologyDatabase comment: The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence. property_value: mged:has_machine_readable_URI "http://song.sourceforge.net/" xsd:string property_value: mged:unique_identifier "MO_724" xsd:string [Instance] id: mged:Spearmans_rank_correlation instance_of: mged:NodeValueType comment: Computed as the ordinary Pearson correlation coefficient between two groups of rankings. property_value: mged:unique_identifier "MO_552" xsd:string [Instance] id: mged:TAIR instance_of: mged:CellTypeDatabase instance_of: mged:StrainOrLineDatabase comment: The Arabidopsis Information Resource. property_value: mged:has_human_readable_URI "http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype" xsd:string property_value: mged:unique_identifier "MO_660" xsd:string [Instance] id: mged:TAIR_arabidopsis_anatomy_ontology instance_of: mged:OrganismPartDatabase comment: A structured controlled vocabulary for the anatomy of Arabidopsis. property_value: mged:unique_identifier "MO_809" xsd:string property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/Arabidopsis/Attic/arabidopsis_anatomy.ontology" xsd:string [Instance] id: mged:TAIR_arabidopsis_development_ontology instance_of: mged:DevelopmentalStageDatabase comment: An ontology of stages of growth and development of the model plant Arabidopsis thaliana. property_value: mged:unique_identifier "MO_919" xsd:string property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/developmental/plant_development/Arabidopsis/temporal.tair?rev=1.21&view=markup" xsd:string [Instance] id: mged:TDMS instance_of: mged:DiseaseStateDatabase instance_of: mged:HistologyDatabase instance_of: mged:OrganismPartDatabase instance_of: mged:TestTypeDatabase comment: Toxicology Data Management System, a database resource for systems, organs, pathology, etc. property_value: mged:has_human_readable_URI "http://hazel.niehs.nih.gov/user_spt/pct_terms.htm" xsd:string property_value: mged:unique_identifier "MO_718" xsd:string [Instance] id: mged:TIFF instance_of: mged:ImageFormat comment: 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. property_value: mged:unique_identifier "MO_638" xsd:string [Instance] id: mged:UMLS instance_of: mged:DiseaseStateDatabase comment: Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH. property_value: mged:has_human_readable_URI "http://www.nlm.nih.gov/research/umls/" xsd:string property_value: mged:unique_identifier "MO_947" xsd:string [Instance] id: mged:U_per_L instance_of: mged:ConcentrationUnit comment: units per liter property_value: mged:unique_identifier "MO_875" xsd:string [Instance] id: mged:U_per_week instance_of: mged:OtherUnit comment: units per week, e.g. the number of units of alcohol consumed over a period of 7 days property_value: mged:unique_identifier "MO_388" xsd:string [Instance] id: mged:WebRENI instance_of: mged:DiseaseStateDatabase comment: database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions property_value: mged:has_human_readable_URI "http://www.item.fraunhofer.de/reni/index/htm" xsd:string property_value: mged:unique_identifier "MO_737" xsd:string [Instance] id: mged:YAC instance_of: mged:DeprecatedTerms comment: sequence from yeast artificial chromosome relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_794" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:_32P instance_of: mged:LabelCompound comment: 32 P, radioactive isotope of phosphorus used for labeling/detection purposes property_value: mged:unique_identifier "MO_839" xsd:string [Instance] id: mged:_33P instance_of: mged:LabelCompound comment: 33 P, radioactive isotope of phosphorus, used for labeling/detection purposes. property_value: mged:unique_identifier "MO_427" xsd:string [Instance] id: mged:absolute instance_of: mged:MeasurementType comment: a measurement where the value is independent of other measurements property_value: mged:unique_identifier "MO_741" xsd:string [Instance] id: mged:acclimatization instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The action of stabilizing an organism prior to treatment property_value: mged:unique_identifier "MO_776" xsd:string [Instance] id: mged:acrossBioAssay_mean_and_coefficient_of_variation instance_of: mged:DerivedBioAssayType comment: The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data. property_value: mged:unique_identifier "MO_840" xsd:string [Instance] id: mged:acrossBioAssay_mean_and_p_values instance_of: mged:DerivedBioAssayType comment: The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data. property_value: mged:unique_identifier "MO_671" xsd:string [Instance] id: mged:acrossBioAssay_mean_and_standard_deviation instance_of: mged:DerivedBioAssayType comment: The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data. property_value: mged:unique_identifier "MO_946" xsd:string [Instance] id: mged:acrossBioAssay_mean_and_variance instance_of: mged:DerivedBioAssayType comment: The mean and variance values resulting from computationally combining 2 or more sets of bioassay data. property_value: mged:unique_identifier "MO_400" xsd:string [Instance] id: mged:across_bioassay_data_set_function instance_of: mged:DataTransformationProtocolType comment: 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. property_value: mged:unique_identifier "MO_606" xsd:string [Instance] id: mged:activity_units_per_ml instance_of: mged:OtherUnit comment: Units of defined biological activity, e.g. cytokine stimulation, per ml. relationship: mged:deprecated_from_version mged:version_1.3.1 relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_870" xsd:string [Instance] id: mged:ad_libitum instance_of: mged:DeliveryMethod comment: A delivery method for compounds/drugs where the compound or drug is freely available. property_value: mged:unique_identifier "MO_592" xsd:string [Instance] id: mged:add instance_of: mged:AtomicAction comment: The procedure of placing one physical object in the same container/physical space as another. property_value: mged:unique_identifier "MO_815" xsd:string [Instance] id: mged:agar instance_of: mged:Media comment: A type of solid media commonly used for growing organisms property_value: mged:unique_identifier "MO_935" xsd:string [Instance] id: mged:agar_stab instance_of: mged:BioSourceType comment: agar stab, a cell culture inoculated into agar for long term storage property_value: mged:unique_identifier "MO_971" xsd:string [Instance] id: mged:age instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for FactorValue where age is compared. property_value: mged:unique_identifier "MO_467" xsd:string [Instance] id: mged:alexa_350 instance_of: mged:LabelCompound comment: 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. \n property_value: mged:unique_identifier "MO_512" xsd:string [Instance] id: mged:alexa_430 instance_of: mged:LabelCompound comment: 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. \n property_value: mged:unique_identifier "MO_401" xsd:string [Instance] id: mged:alexa_488 instance_of: mged:LabelCompound comment: 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. property_value: mged:unique_identifier "MO_446" xsd:string [Instance] id: mged:alexa_532 instance_of: mged:LabelCompound comment: 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. \n property_value: mged:unique_identifier "MO_375" xsd:string [Instance] id: mged:alexa_546 instance_of: mged:LabelCompound comment: 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. \n property_value: mged:unique_identifier "MO_493" xsd:string [Instance] id: mged:alexa_568 instance_of: mged:LabelCompound comment: 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. \n property_value: mged:unique_identifier "MO_736" xsd:string [Instance] id: mged:alexa_594 instance_of: mged:LabelCompound comment: 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. \n property_value: mged:unique_identifier "MO_461" xsd:string [Instance] id: mged:alexa_633 instance_of: mged:LabelCompound comment: 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. \n property_value: mged:unique_identifier "MO_345" xsd:string [Instance] id: mged:alexa_660 instance_of: mged:LabelCompound comment: 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. \n property_value: mged:unique_identifier "MO_547" xsd:string [Instance] id: mged:alexa_680 instance_of: mged:LabelCompound comment: 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. \n property_value: mged:unique_identifier "MO_799" xsd:string [Instance] id: mged:all_pairs instance_of: mged:MethodologicalDesign comment: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. property_value: mged:unique_identifier "MO_565" xsd:string [Instance] id: mged:amino_acid_primary_sequence_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record property_value: mged:unique_identifier "MO_829" xsd:string [Instance] id: mged:aminosilane instance_of: mged:SurfaceType comment: a surface coating type for immobilization with the compound aminosilane property_value: mged:unique_identifier "MO_747" xsd:string [Instance] id: mged:amol instance_of: mged:QuantityUnit comment: attomole, quantity unit property_value: mged:unique_identifier "MO_977" xsd:string [Instance] id: mged:aneuploid instance_of: mged:Ploidy comment: Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n). property_value: mged:unique_identifier "MO_918" xsd:string [Instance] id: mged:antibody instance_of: mged:PhysicalBioSequenceType comment: glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen property_value: mged:unique_identifier "MO_833" xsd:string [Instance] id: mged:array_manufacture_software instance_of: mged:SoftwareType comment: Software to control an arrayer. property_value: mged:unique_identifier "MO_502" xsd:string [Instance] id: mged:array_manufacturer instance_of: mged:Roles comment: Person or organization that manufactured the array. property_value: mged:unique_identifier "MO_890" xsd:string [Instance] id: mged:array_manufacturing instance_of: mged:ExperimentalProtocolType comment: The process of physically creating the array. property_value: mged:unique_identifier "MO_818" xsd:string [Instance] id: mged:array_platform_variation_design instance_of: mged:MethodologicalDesign comment: An experiment in which the array platform is compared, e.g. Agilent versus \n Affy. property_value: mged:unique_identifier "MO_899" xsd:string [Instance] id: mged:array_scanner instance_of: mged:HardwareType comment: An instrument capable of acquiring images of arrays. property_value: mged:unique_identifier "MO_824" xsd:string [Instance] id: mged:arrayer instance_of: mged:HardwareType comment: An instrument capable of manufacturing arrays by spotting material. property_value: mged:unique_identifier "MO_697" xsd:string [Instance] id: mged:atmosphere instance_of: mged:EnvironmentalFactorCategory comment: The atmospheric conditions used to culture or grow an organism. property_value: mged:unique_identifier "MO_498" xsd:string [Instance] id: mged:aunt instance_of: mged:FamilyRelationship comment: The sister of one's father or mother. property_value: mged:unique_identifier "MO_354" xsd:string [Instance] id: mged:averaged_intensity instance_of: mged:DerivedBioAssayType comment: Results of data reduction involving computation of the average of multiple \n intensities of identical type. These could include identical Features, \n Reporters or CompositeSequences in different microarray hybridizations, \n matched replicate spots on 2D gels run from the same sample, or repeat \n measurements of the same metabolite in replicate cell cultures. property_value: mged:unique_identifier "MO_362" xsd:string [Instance] id: mged:barrier_facility instance_of: mged:EnvironmentalFactorCategory comment: The rating of containment system used to protect organisms from infectious agents. property_value: mged:unique_identifier "MO_511" xsd:string [Instance] id: mged:bedding instance_of: mged:DeprecatedTerms comment: The material (e.g. straw) that an animal sleeps on relationship: mged:deprecated_from_version mged:version_1.1.7 relationship: mged:deprecation_old_parent mged:BioMaterialCharacteristicCategory relationship: mged:deprecation_replacement_term mged:BioMaterialCharacteristicCategory relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_615" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string [Instance] id: mged:beginning_of_stage instance_of: mged:InitialTimePoint comment: time point that indicates the start of some developmental stage property_value: mged:unique_identifier "MO_608" xsd:string [Instance] id: mged:behavior_design instance_of: mged:DeprecatedTerms comment: 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. relationship: mged:deprecated_from_version mged:version_1.1.9 relationship: mged:deprecation_old_parent mged:BiologicalProperty relationship: mged:has_reason_for_deprecation mged:split_term relationship: mged:split_to_term mged:innate_behavior_design relationship: mged:split_to_term mged:stimulated_design_type property_value: mged:deprecation_reason "split_term" xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: mged:unique_identifier "MO_532" xsd:string [Instance] id: mged:behavioral_design_type instance_of: mged:DeprecatedTerms comment: 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\nexperimental behavioral stimulus such as sleep deprivation. relationship: mged:deprecated_from_version mged:version_1.1.9 relationship: mged:deprecation_old_parent mged:PerturbationalDesign relationship: mged:has_reason_for_deprecation mged:replaced_term relationship: mged:replaced_with_term mged:innate_behavior_design relationship: mged:was_replaced_by mged:innate_behavior_design property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: mged:unique_identifier "MO_766" xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string [Instance] id: mged:behavioral_stimulus instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.) property_value: mged:unique_identifier "MO_674" xsd:string [Instance] id: mged:bibliographic_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies a paper publication e.g. a medline record property_value: mged:unique_identifier "MO_923" xsd:string [Instance] id: mged:binding_site_identification_design instance_of: mged:BioMolecularAnnotation instance_of: mged:TechnologicalDesign comment: A binding site identification design type investigates protein binding sites on nucleic acids\nnon-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP property_value: mged:unique_identifier "MO_933" xsd:string property_value: mged:synonym "chromatin immunoprecipitation" xsd:string property_value: mged:synonym "chromatin IP" xsd:string property_value: mged:synonym "chromatin_immunoprecipitation" xsd:string property_value: mged:synonym "ChIP-chip" xsd:string [Instance] id: mged:bioassay_data_transformation_software instance_of: mged:SoftwareType comment: Software used to transform the Measured or DerivedBioAssay data e.g. normalization.\nNon-exact synonym: normalization software property_value: mged:unique_identifier "MO_672" xsd:string property_value: mged:synonym "normalization software" xsd:string [Instance] id: mged:bioassay_replicate_reduction instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_976" xsd:string [Instance] id: mged:biological_fluid_collection instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: 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. property_value: mged:unique_identifier "MO_685" xsd:string [Instance] id: mged:biological_replicate instance_of: mged:QualityControlDescriptionType instance_of: mged:ReplicateDescriptionType comment: A replicate that consists of independent biological replicates made from different individual BioSources. property_value: mged:unique_identifier "MO_952" xsd:string [Instance] id: mged:biological_resource_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list property_value: mged:unique_identifier "MO_989" xsd:string [Instance] id: mged:biomaterial_provider instance_of: mged:BioMaterialCharacteristicCategory instance_of: mged:Roles comment: Term used to describe a role or factor value for the person or organization that provides a BioMaterial. property_value: mged:unique_identifier "MO_591" xsd:string [Instance] id: mged:biopsy instance_of: mged:ComplexAction comment: The process of removing tissue from a living organism. property_value: mged:unique_identifier "MO_711" xsd:string [Instance] id: mged:biosequence_provider instance_of: mged:Roles comment: Provider of biosequences (clones, oligos etc) for deposition on the array. property_value: mged:unique_identifier "MO_881" xsd:string [Instance] id: mged:biotin instance_of: mged:LabelCompound comment: a compound used for labeling/detection purposes property_value: mged:unique_identifier "MO_793" xsd:string [Instance] id: mged:birth instance_of: mged:InitialTimePoint comment: the action of emergence and separation of offspring from the mother. property_value: mged:unique_identifier "MO_710" xsd:string [Instance] id: mged:blood instance_of: mged:DeprecatedTerms comment: A biomaterial obtained as fluid consisting of plasma, blood cells and platelets. relationship: mged:deprecated_from_version mged:version_1.1.9 relationship: mged:deprecation_old_parent mged:BioSourceType relationship: mged:deprecation_replacement_term mged:BioSourceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_409" xsd:string [Instance] id: mged:book instance_of: mged:PublicationType comment: A publication type which has an ISBN. property_value: mged:unique_identifier "MO_627" xsd:string [Instance] id: mged:boolean instance_of: mged:DataType comment: The values are either TRUE or FALSE, which can be expressed as 1 and 0. property_value: mged:unique_identifier "MO_826" xsd:string [Instance] id: mged:brother instance_of: mged:FamilyRelationship comment: A male having the same genetic parents as another, or one genetic parent in common with another. property_value: mged:unique_identifier "MO_655" xsd:string [Instance] id: mged:cDNA_clone instance_of: mged:DeprecatedTerms comment: sequence of complementary cDNA copy of an RNA molecule contained on a plasmid including the plasmid sequence, used when the entire clone is spotted\nnon-exact synonym: cDNA, complementary DNA relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:synonym "complementary DNA" xsd:string property_value: mged:synonym "cDNA" xsd:string property_value: mged:unique_identifier "MO_966" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:candela instance_of: mged:LightUnit comment: 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.\nExact synonym: candle power property_value: mged:unique_identifier "MO_572" xsd:string property_value: mged:synonym "candle power" xsd:string [Instance] id: mged:candelas_per_square_meter instance_of: mged:LightUnit comment: Unit of brightness or luminance. property_value: mged:unique_identifier "MO_813" xsd:string [Instance] id: mged:cc instance_of: mged:VolumeUnit comment: a cubic centimeter, volume unit property_value: mged:unique_identifier "MO_834" xsd:string [Instance] id: mged:cell instance_of: mged:MaterialType comment: One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms. property_value: mged:unique_identifier "MO_612" xsd:string [Instance] id: mged:cell_component_comparison_design instance_of: mged:BiologicalProperty comment: A design in which RNA from different cell components is examined. property_value: mged:unique_identifier "MO_1019" xsd:string [Instance] id: mged:cell_cycle_design instance_of: mged:BiologicalProperty comment: 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. property_value: mged:unique_identifier "MO_822" xsd:string [Instance] id: mged:cell_line instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for FactorValue where CellLine is compared. property_value: mged:unique_identifier "MO_562" xsd:string [Instance] id: mged:cell_lysate instance_of: mged:MaterialType comment: cell lysate, a collection of cells whose membranes have been disrupted property_value: mged:unique_identifier "MO_903" xsd:string [Instance] id: mged:cell_ontology instance_of: mged:CellTypeDatabase instance_of: mged:TargetedCellTypeDatabase comment: database of cell ontology terms property_value: mged:unique_identifier "MO_404" xsd:string property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/views.py/obo/obo/ontology/anatomy/cell_type/cell.ontology?rev=HEAD&content-type=text/vnd.viewcvs-markup" xsd:string [Instance] id: mged:cell_type instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for FactorValue where CellType is compared. property_value: mged:unique_identifier "MO_548" xsd:string [Instance] id: mged:cell_type_comparison_design instance_of: mged:BiologicalProperty comment: A cell type comparison design experiment design type compares cells of different type for example different cell lines. property_value: mged:unique_identifier "MO_764" xsd:string [Instance] id: mged:cells_per_ml instance_of: mged:ConcentrationUnitOther comment: the number of cells per ml property_value: mged:unique_identifier "MO_727" xsd:string [Instance] id: mged:cellular_modification_design instance_of: mged:PerturbationalDesign instance_of: mged:TechnologicalDesign comment: A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. property_value: mged:unique_identifier "MO_392" xsd:string property_value: mged:synonym "RNAi" xsd:string [Instance] id: mged:cellular_process_design instance_of: mged:BiologicalProperty comment: 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. property_value: mged:unique_identifier "MO_810" xsd:string [Instance] id: mged:centrifuge instance_of: mged:HardwareType comment: An instrument capable of applying centrifugal force to tubes or microtiter plates. property_value: mged:unique_identifier "MO_476" xsd:string [Instance] id: mged:cfu_per_ml instance_of: mged:ConcentrationUnitOther comment: the number of colony forming units per ml property_value: mged:unique_identifier "MO_788" xsd:string [Instance] id: mged:change_biomaterial_characteristics instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. \nNon exact synonym: change growth condition, change environment property_value: mged:synonym "change environment" xsd:string property_value: mged:synonym "change growth condition" xsd:string property_value: mged:unique_identifier "MO_383" xsd:string [Instance] id: mged:change_humidity instance_of: mged:AtomicAction comment: The action of changing the relative humidity, e.g. from 1% to 10%. property_value: mged:unique_identifier "MO_917" xsd:string [Instance] id: mged:change_light instance_of: mged:AtomicAction comment: Change in light intensity or wavelength. property_value: mged:unique_identifier "MO_549" xsd:string [Instance] id: mged:change_temperature instance_of: mged:AtomicAction comment: Change in temperature. property_value: mged:unique_identifier "MO_677" xsd:string [Instance] id: mged:chrome_border instance_of: mged:FiducialType comment: the chrome border on an Affymetrix type array which is used as a point of\nreference for orientation (fiducial) property_value: mged:unique_identifier "MO_491" xsd:string [Instance] id: mged:chromosomal_deletion instance_of: mged:ChromosomalAberrationClassification comment: The loss of a segment of the genetic material from a chromosome. property_value: mged:unique_identifier "MO_922" xsd:string [Instance] id: mged:chromosomal_duplication instance_of: mged:ChromosomalAberrationClassification comment: An irregularity in the number of chromosomes, usually in the form of a gain of genetic material. property_value: mged:unique_identifier "MO_1002" xsd:string [Instance] id: mged:chromosomal_insertion instance_of: mged:ChromosomalAberrationClassification comment: 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. property_value: mged:unique_identifier "MO_518" xsd:string [Instance] id: mged:chromosomal_inversion instance_of: mged:ChromosomalAberrationClassification comment: 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. property_value: mged:unique_identifier "MO_622" xsd:string [Instance] id: mged:chromosomal_substitution instance_of: mged:GeneticModification comment: 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. property_value: mged:unique_identifier "MO_995" xsd:string [Instance] id: mged:chromosomal_translocation instance_of: mged:ChromosomalAberrationClassification comment: 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. property_value: mged:unique_identifier "MO_368" xsd:string [Instance] id: mged:chromosome instance_of: mged:DeprecatedTerms comment: Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome. relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_578" xsd:string [Instance] id: mged:circadian_rhythm_design instance_of: mged:DeprecatedTerms comment: 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. relationship: mged:deprecated_from_version mged:version_1.1.7 relationship: mged:deprecation_old_parent mged:BiologicalProperty relationship: mged:has_reason_for_deprecation mged:replaced_term relationship: mged:replaced_with_term mged:physiological_process_design relationship: mged:was_replaced_by mged:physiological_process_design property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:unique_identifier "MO_539" xsd:string [Typedef] id: mged:class_role is_metadata_tag: true comment: This property is used to identify the type of class of the term. The value \"abstract\" indicates that the class is used for organizational purposes. The value \"instantiated\" indicates that the class contains Individuals that can be used as annotation terms. The value \"abstract\" indicates that the class is used to provide organization within the MGED Ontology. The value \"place_holder\" indicates that this class represents the location in the ontology where terms of this class would be located. property_value: mged:unique_identifier "MO_338" xsd:string [Typedef] id: mged:class_source is_metadata_tag: true comment: The property indicates the derivation of the class. A value of \"mage\" means that the class is derived from the MAGE-OM and the value \"ontology\" indicates that the class is derived from the ontology. This property is being added since the MGED Ontology was developed in such a way to include classes that exist in the MAGE-OM as well as classes that exist only in the MGED Ontology. property_value: mged:unique_identifier "MO_343" xsd:string [Instance] id: mged:clinical_history_design instance_of: mged:EpidemiologicalDesign comment: A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. property_value: mged:unique_identifier "MO_832" xsd:string [Instance] id: mged:clinical_information instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for FactorValue where ClinicalInformation is compared. property_value: mged:unique_identifier "MO_816" xsd:string [Instance] id: mged:clinical_record instance_of: mged:DatabaseEntryType comment: record which describes and identifies clinical information about an organism property_value: mged:unique_identifier "MO_852" xsd:string [Instance] id: mged:clinical_treatment instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for a clinical treatment for a patient. property_value: mged:unique_identifier "MO_384" xsd:string [Instance] id: mged:clone_of_unknown_source instance_of: mged:PhysicalBioSequenceType comment: Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown. property_value: mged:unique_identifier "MO_371" xsd:string [Instance] id: mged:clustered_data instance_of: mged:DerivedBioAssayType comment: Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance. property_value: mged:unique_identifier "MO_418" xsd:string [Instance] id: mged:clustering_software instance_of: mged:SoftwareType comment: Software used to cluster the data. property_value: mged:unique_identifier "MO_464" xsd:string [Instance] id: mged:cm instance_of: mged:DistanceUnit comment: centimeter, a unit of distance property_value: mged:unique_identifier "MO_837" xsd:string [Instance] id: mged:co-expression_design instance_of: mged:BioMolecularAnnotation comment: 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)\nnon-exact synonym: guilt by association property_value: mged:unique_identifier "MO_904" xsd:string property_value: mged:synonym "guilt by association" xsd:string [Instance] id: mged:coitus instance_of: mged:InitialTimePoint comment: the physical act of copulation that occurs during the process of sexual reproduction\nsynonyms: copulation, insemination property_value: mged:unique_identifier "MO_783" xsd:string property_value: mged:synonym "insemination" xsd:string property_value: mged:synonym "copulation" xsd:string [Instance] id: mged:collapsed_spot_replicate instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_789" xsd:string [Instance] id: mged:comparative_genome_hybridization_design instance_of: mged:BioMolecularAnnotation instance_of: mged:TechnologicalDesign comment: Experiment design type in which genomic content is studied using an array based assay. property_value: mged:unique_identifier "MO_856" xsd:string property_value: mged:synonym "array_CGH" xsd:string property_value: mged:synonym "array CGH" xsd:string property_value: mged:synonym "CGH" xsd:string [Instance] id: mged:compound_based_treatment instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: 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. property_value: mged:unique_identifier "MO_798" xsd:string [Instance] id: mged:compound_record instance_of: mged:DatabaseEntryType comment: a record which describes and identifies a compound e.g. drug record part of NCI thesaurus property_value: mged:unique_identifier "MO_546" xsd:string [Instance] id: mged:compound_treatment_design instance_of: mged:PerturbationalDesign comment: A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed. property_value: mged:unique_identifier "MO_555" xsd:string [Instance] id: mged:computational_feature instance_of: mged:SeqFeatureBasis comment: Computationally derived sequence feature. property_value: mged:unique_identifier "MO_411" xsd:string [Instance] id: mged:computed_amino_acid_sequence_feature_record instance_of: mged:DatabaseEntryType comment: a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM property_value: mged:unique_identifier "MO_797" xsd:string [Instance] id: mged:computed_nucleic_acid_sequence_feature_record instance_of: mged:DatabaseEntryType comment: A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record property_value: mged:unique_identifier "MO_774" xsd:string [Instance] id: mged:computed_protein_structure_record instance_of: mged:DatabaseEntryType comment: a record which describes and identifies a protein structure e.g. PDB property_value: mged:unique_identifier "MO_765" xsd:string [Instance] id: mged:computer instance_of: mged:HardwareType comment: A device capable of applying software. property_value: mged:unique_identifier "MO_510" xsd:string [Instance] id: mged:concentrate instance_of: mged:AtomicAction comment: Increasing the concentration of solutes in a solution or suspension. property_value: mged:unique_identifier "MO_883" xsd:string [Instance] id: mged:condition_specificity instance_of: mged:HigherLevelAnalysisProtocolType comment: 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. property_value: mged:unique_identifier "MO_417" xsd:string [Instance] id: mged:consensus_DNA instance_of: mged:DeprecatedTerms comment: DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.3.1.1" xsd:string property_value: mged:unique_identifier "MO_361" xsd:string [Instance] id: mged:consensus_mRNA instance_of: mged:DeprecatedTerms comment: mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input. relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:unique_identifier "MO_423" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.3.1.1" xsd:string [Instance] id: mged:consortium_member instance_of: mged:Roles comment: A member of a consortium of institutions. property_value: mged:unique_identifier "MO_778" xsd:string [Instance] id: mged:consultant instance_of: mged:Roles comment: 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. property_value: mged:unique_identifier "MO_984" xsd:string [Instance] id: mged:control_biosequence instance_of: mged:ControlType comment: 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. property_value: mged:unique_identifier "MO_940" xsd:string [Instance] id: mged:control_buffer instance_of: mged:ControlType comment: A Reporter where only buffer was deposited on the array property_value: mged:unique_identifier "MO_505" xsd:string [Instance] id: mged:control_design_element_group_type instance_of: mged:DesignElementGroupType comment: 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. property_value: mged:unique_identifier "MO_414" xsd:string [Instance] id: mged:control_empty instance_of: mged:ControlType comment: A Reporter where no material or buffer was deposited on the array property_value: mged:unique_identifier "MO_830" xsd:string [Instance] id: mged:control_genomic_DNA instance_of: mged:ControlType comment: A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA. property_value: mged:unique_identifier "MO_449" xsd:string [Instance] id: mged:control_hybridization_quality instance_of: mged:ControlType comment: 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). property_value: mged:unique_identifier "MO_385" xsd:string [Instance] id: mged:control_label instance_of: mged:ControlType comment: Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone.\n property_value: mged:unique_identifier "MO_708" xsd:string [Instance] id: mged:control_reporter_size instance_of: mged:ControlType comment: A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency. property_value: mged:unique_identifier "MO_431" xsd:string [Instance] id: mged:control_spike_calibration instance_of: mged:ControlType comment: 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. property_value: mged:unique_identifier "MO_364" xsd:string [Instance] id: mged:control_unknown_type instance_of: mged:ControlType comment: A Reporter indicated as being a control of unknown type. property_value: mged:unique_identifier "MO_925" xsd:string [Instance] id: mged:cosine_distance instance_of: mged:NodeValueType comment: 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. property_value: mged:unique_identifier "MO_550" xsd:string [Instance] id: mged:cosmid instance_of: mged:DeprecatedTerms comment: sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_888" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:count instance_of: mged:QuantityUnitOther comment: Unit for a simple count of things property_value: mged:unique_identifier "MO_500" xsd:string [Instance] id: mged:cpm instance_of: mged:RadiationUnit comment: counts per minute, unit of light emissions produced by ionizing radiation. property_value: mged:unique_identifier "MO_348" xsd:string [Instance] id: mged:ctDNA instance_of: mged:DeprecatedTerms comment: ctDNA: sequence from the chloroplast \nsynonym: chloroplast DNA relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:synonym "chloroplast DNA" xsd:string property_value: mged:unique_identifier "MO_586" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.3.1.1" xsd:string [Instance] id: mged:curated_amino_acid_sequence_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies an amino acid sequence which has been curated property_value: mged:unique_identifier "MO_451" xsd:string [Instance] id: mged:curated_gene_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies nucleic acid sequence which has been identified as a gene by a curator. e.g. Flybase gene record property_value: mged:unique_identifier "MO_913" xsd:string [Instance] id: mged:curated_nucleic_acid_sequence_feature_record instance_of: mged:DatabaseEntryType comment: A record which identifies a nucleic acid sequence feature(s) and which has been curated. property_value: mged:unique_identifier "MO_644" xsd:string [Instance] id: mged:curator instance_of: mged:Roles comment: person who checks the consistency of the data and MAGE-ML file property_value: mged:unique_identifier "MO_893" xsd:string [Instance] id: mged:cytoplasmic_RNA instance_of: mged:MaterialType comment: RNA obtained from the cytoplasm. property_value: mged:unique_identifier "MO_978" xsd:string [Instance] id: mged:data_analyst instance_of: mged:Roles comment: A contact who performs data analysis, e.g. statistician. property_value: mged:unique_identifier "MO_753" xsd:string [Instance] id: mged:data_coder instance_of: mged:Roles comment: person who prepares the MAGE-ML file property_value: mged:unique_identifier "MO_695" xsd:string [Instance] id: mged:date instance_of: mged:DataType comment: Time stated in terms of the day, month, and year. property_value: mged:unique_identifier "MO_587" xsd:string [Instance] id: mged:daughter instance_of: mged:FamilyRelationship comment: The female offspring of the patient or individual under study. property_value: mged:unique_identifier "MO_665" xsd:string [Instance] id: mged:days instance_of: mged:TimeUnit comment: 24 hours, time unit property_value: mged:synonym "d" xsd:string property_value: mged:unique_identifier "MO_513" xsd:string [Instance] id: mged:decontaminate instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma). property_value: mged:unique_identifier "MO_389" xsd:string [Instance] id: mged:degrees_C instance_of: mged:TemperatureUnit comment: degrees celsius, unit of temperature property_value: mged:unique_identifier "MO_980" xsd:string [Instance] id: mged:degrees_F instance_of: mged:TemperatureUnit comment: degrees Fahrenheit, unit of temperature property_value: mged:unique_identifier "MO_812" xsd:string [Instance] id: mged:deleted_term instance_of: mged:DeprecationReason comment: The term was deleted from the MGED CoreOntology. property_value: mged:unique_identifier "MO_1023" xsd:string [Typedef] id: mged:deprecated_from_version comment: property indicating the version of the MGED Ontology that the term was deprecated from property_value: mged:unique_identifier "MO_299" xsd:string [Typedef] id: mged:deprecation_in_version is_metadata_tag: true comment: The value of the property indicates what version of the ontology the term was deprecated from. property_value: mged:unique_identifier "MO_1014" xsd:string [Typedef] id: mged:deprecation_old_parent is_metadata_tag: true comment: The value indicates the parent of the term before the term was deprecated. property_value: mged:unique_identifier "MO_1016" xsd:string [Typedef] id: mged:deprecation_old_restriction is_metadata_tag: true comment: The value of the property indicates the restriction that was applied to the class at the time it was deprecated. The value is in the form of: some|property|filler, e.g. some|has_species|Organism. property_value: mged:unique_identifier "MO_1015" xsd:string [Typedef] id: mged:deprecation_reason is_metadata_tag: true comment: Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term. property_value: mged:unique_identifier "MO_1013" xsd:string [Typedef] id: mged:deprecation_replacement_term is_metadata_tag: true comment: The value of the property indicates the replacement term for the deprecated term. If the term is deprecated without replacement, the value of the property will be the same as the deprecated term itself. property_value: mged:unique_identifier "MO_1012" xsd:string [Instance] id: mged:development_or_differentiation_design instance_of: mged:BiologicalProperty comment: 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. property_value: mged:unique_identifier "MO_892" xsd:string [Instance] id: mged:developmental_stage instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for FactorValue where DevelopmentalStage is compared. property_value: mged:unique_identifier "MO_878" xsd:string [Instance] id: mged:diameter_aberration instance_of: mged:DefectType comment: The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter. property_value: mged:unique_identifier "MO_781" xsd:string [Instance] id: mged:differential_expression instance_of: mged:HigherLevelAnalysisProtocolType comment: An analysis aimed at identifying differentially expressed genes in two or more conditions. property_value: mged:unique_identifier "MO_874" xsd:string [Instance] id: mged:differential_expression_software instance_of: mged:SoftwareType comment: A software implementing a Higher Level Analysis protocol of type differential_expresssion. property_value: mged:unique_identifier "MO_350" xsd:string [Instance] id: mged:dilute instance_of: mged:AtomicAction comment: Decreasing the concentration of solutes in a solution or suspension. property_value: mged:unique_identifier "MO_962" xsd:string [Instance] id: mged:diploid instance_of: mged:Ploidy comment: Describes a cell, nucleus or an organism with two copies of each chromosome. property_value: mged:unique_identifier "MO_836" xsd:string [Instance] id: mged:disease_staging instance_of: mged:BioMaterialCharacteristicCategory comment: The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. property_value: mged:unique_identifier "MO_792" xsd:string [Instance] id: mged:disease_state instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for FactorValue where DiseaseState is compared. property_value: mged:unique_identifier "MO_787" xsd:string [Instance] id: mged:disease_state_design instance_of: mged:EpidemiologicalDesign instance_of: mged:PerturbationalDesign comment: 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. property_value: mged:unique_identifier "MO_902" xsd:string [Instance] id: mged:displaced_feature_or_zone instance_of: mged:DefectType comment: The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s). property_value: mged:unique_identifier "MO_959" xsd:string [Instance] id: mged:dissect instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The action of removing one or more organism parts. property_value: mged:unique_identifier "MO_374" xsd:string [Instance] id: mged:dl instance_of: mged:VolumeUnit comment: deciliter, unit of volume property_value: mged:unique_identifier "MO_624" xsd:string [Instance] id: mged:dose_response_design instance_of: mged:PerturbationalDesign comment: 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). property_value: mged:unique_identifier "MO_485" xsd:string [Instance] id: mged:double_stranded instance_of: mged:StrandType comment: 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. property_value: mged:unique_identifier "MO_828" xsd:string [Instance] id: mged:dpm instance_of: mged:RadiationUnit comment: disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument. property_value: mged:unique_identifier "MO_583" xsd:string [Instance] id: mged:ds_oligo instance_of: mged:DeprecatedTerms comment: a double stranded oligonucleotide relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_344" xsd:string [Instance] id: mged:dye_swap_design instance_of: mged:MethodologicalDesign comment: An experiment design type where the label orientations are reversed.\nexact synonym: flip dye, dye flip property_value: mged:unique_identifier "MO_858" xsd:string property_value: mged:synonym "dye flip" xsd:string property_value: mged:synonym "flip dye" xsd:string [Instance] id: mged:dye_swap_merge instance_of: mged:DataTransformationProtocolType comment: 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. property_value: mged:unique_identifier "MO_448" xsd:string [Instance] id: mged:dye_swap_quality_control instance_of: mged:QualityControlDescriptionType comment: Indicates that a dye swap was performed for some or all hybridizations within an experiment property_value: mged:unique_identifier "MO_524" xsd:string [Instance] id: mged:dye_swap_replicate instance_of: mged:ReplicateDescriptionType comment: 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. property_value: mged:unique_identifier "MO_901" xsd:string [Instance] id: mged:dye_swap_replicate_reduction instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_750" xsd:string [Instance] id: mged:eVOC instance_of: mged:CellTypeDatabase instance_of: mged:DevelopmentalStageDatabase instance_of: mged:DiseaseStateDatabase instance_of: mged:OrganismPartDatabase comment: Ontology of human terms that describe the sample source of human cDNA and SAGE libraries. property_value: mged:unique_identifier "MO_684" xsd:string property_value: mged:has_human_readable_URI "http://www.sanbi.ac.za/evoc/ontologies.html" xsd:string [Instance] id: mged:eclosion instance_of: mged:InitialTimePoint comment: Emergence of an adult insect from its pupa or cocoon. property_value: mged:unique_identifier "MO_876" xsd:string [Instance] id: mged:egg_laying instance_of: mged:InitialTimePoint comment: The point at which the egg(s) is laid by an organism. property_value: mged:unique_identifier "MO_767" xsd:string [Instance] id: mged:element_design instance_of: mged:ExperimentalProtocolType comment: protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design property_value: mged:unique_identifier "MO_523" xsd:string [Instance] id: mged:ellipsoid_feature instance_of: mged:FeatureShape comment: The shape of the feature on the array is circular or oval. property_value: mged:unique_identifier "MO_459" xsd:string [Instance] id: mged:environmental_history_design instance_of: mged:EnvironmentalHistory comment: 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. property_value: mged:unique_identifier "MO_698" xsd:string [Instance] id: mged:ex_vivo_design instance_of: mged:MethodologicalDesign comment: 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\ncell culture with an established cell line is an in vitro experiment. property_value: mged:unique_identifier "MO_808" xsd:string [Instance] id: mged:exemplar_mRNA instance_of: mged:DeprecatedTerms comment: An exemplar is a representative cDNA sequence for each gene. The exemplar\napproach is a method that usually involves some initial clustering into gene\ngroups and the subsequent selection of a representative from each gene\ngroup. relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_621" xsd:string property_value: mged:deprecation_in_version "1.3.1.1" xsd:string [Instance] id: mged:exon instance_of: mged:DeprecatedTerms comment: sequence which represents regions of a transcript that are joined to another exon during splicing relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_619" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:experimental_and_computational_feature instance_of: mged:SeqFeatureBasis comment: Sequence features derived by both computational and experimental methods. property_value: mged:unique_identifier "MO_516" xsd:string [Instance] id: mged:experimental_design_element_group_type instance_of: mged:DesignElementGroupType comment: A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial. property_value: mged:unique_identifier "MO_755" xsd:string [Instance] id: mged:experimental_feature instance_of: mged:SeqFeatureBasis comment: An experimentally defined sequence feature. property_value: mged:unique_identifier "MO_452" xsd:string [Instance] id: mged:extract instance_of: mged:BioSampleType comment: The BioSample immediately before labeling. property_value: mged:unique_identifier "MO_895" xsd:string [Instance] id: mged:fM instance_of: mged:ConcentrationUnit comment: femtomolar, concentration unit property_value: mged:unique_identifier "MO_898" xsd:string [Instance] id: mged:family_history_design instance_of: mged:EpidemiologicalDesign comment: A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied property_value: mged:unique_identifier "MO_544" xsd:string [Instance] id: mged:father instance_of: mged:FamilyRelationship comment: A male parent. property_value: mged:unique_identifier "MO_762" xsd:string [Instance] id: mged:feature_extraction instance_of: mged:ExperimentalProtocolType comment: The process of obtaining quantifiable values from the scanned image of the \n array. Exact synonyms: image analysis, image quantification property_value: mged:synonym "image analysis" xsd:string property_value: mged:synonym "image quantification" xsd:string property_value: mged:unique_identifier "MO_928" xsd:string [Instance] id: mged:feature_extraction_software instance_of: mged:SoftwareType comment: Software to create MeasuredBioAssayData from images.\nExact Synonym: image analysis software, image quantification software. property_value: mged:synonym "image quantification software" xsd:string property_value: mged:synonym "image analysis software" xsd:string property_value: mged:unique_identifier "MO_633" xsd:string [Instance] id: mged:feces instance_of: mged:DeprecatedTerms comment: A biosource obtained as fecal matter. relationship: mged:deprecated_from_version mged:version_1.1.9 relationship: mged:deprecation_old_parent mged:BioSourceType relationship: mged:deprecation_replacement_term mged:BioSourceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: mged:unique_identifier "MO_636" xsd:string [Instance] id: mged:feeding instance_of: mged:DeliveryMethod comment: Delivery method where a compound/drug is administered in food or water. property_value: mged:unique_identifier "MO_993" xsd:string [Instance] id: mged:female instance_of: mged:Sex comment: of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes. property_value: mged:unique_identifier "MO_506" xsd:string [Instance] id: mged:fertilization instance_of: mged:InitialTimePoint comment: The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO) property_value: mged:unique_identifier "MO_701" xsd:string [Instance] id: mged:fg instance_of: mged:MassUnit comment: femtogram, unit of mass property_value: mged:unique_identifier "MO_732" xsd:string [Instance] id: mged:filtered_data instance_of: mged:DerivedBioAssayType comment: Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold. property_value: mged:unique_identifier "MO_625" xsd:string [Instance] id: mged:fl instance_of: mged:VolumeUnit comment: femtoliter, unit of volume property_value: mged:unique_identifier "MO_721" xsd:string [Instance] id: mged:flag_filter instance_of: mged:DataTransformationProtocolType comment: transformation method that involves removal of values in a data set based \n on visual or computed flags (e.g. the GenePix feature_extraction software \n standard flags). This includes low-intensity filtering methods, where the \n flag indicates low intensity values in the data set (for microarrays and \n gels the threshold for exclusion is usually based on some estimation of \n local or global background intensity; for mass spectrometry and NMR, it is \n usually based on the signal-to-noise ratio in the spectrum). property_value: mged:unique_identifier "MO_1024" xsd:string [Instance] id: mged:flip-dye_consistency instance_of: mged:NormalizationDescriptionType comment: 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. relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:has_reason_for_deprecation mged:replaced_term relationship: mged:was_replaced_by mged:dye_swap_merge property_value: mged:unique_identifier "MO_907" xsd:string [Instance] id: mged:float instance_of: mged:DataType comment: A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34). property_value: mged:unique_identifier "MO_860" xsd:string [Instance] id: mged:fmol instance_of: mged:QuantityUnit comment: femtomole, unit of quantity property_value: mged:unique_identifier "MO_689" xsd:string [Instance] id: mged:forward instance_of: mged:StrandType comment: the forward strand\nexact synonym: + property_value: mged:synonym "+" xsd:string property_value: mged:unique_identifier "MO_820" xsd:string [Instance] id: mged:fractionate instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify). property_value: mged:unique_identifier "MO_872" xsd:string [Instance] id: mged:freeze_dried_sample instance_of: mged:BioSourceType comment: A biomaterial that has been lyophilized or dried by freezing under a vacuum. property_value: mged:unique_identifier "MO_589" xsd:string [Instance] id: mged:french_railway_distance instance_of: mged:NodeValueType comment: 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. property_value: mged:unique_identifier "MO_964" xsd:string [Instance] id: mged:fresh_sample instance_of: mged:BioSourceType comment: A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat. property_value: mged:unique_identifier "MO_730" xsd:string [Instance] id: mged:frozen_sample instance_of: mged:BioSourceType comment: A biomaterial obtained frozen property_value: mged:unique_identifier "MO_610" xsd:string [Instance] id: mged:frozen_storage instance_of: mged:PreservationType comment: Storage where the thing stored is stored below 0 degrees celsius. property_value: mged:unique_identifier "MO_481" xsd:string [Instance] id: mged:function_record instance_of: mged:DatabaseEntryType comment: a record which identifies and describes the function of a gene product, e.g. E.C. record property_value: mged:unique_identifier "MO_538" xsd:string [Instance] id: mged:funder instance_of: mged:Roles comment: Contact which provides funding for experiments. property_value: mged:unique_identifier "MO_520" xsd:string [Instance] id: mged:g instance_of: mged:MassUnit comment: gram, unit of mass property_value: mged:unique_identifier "MO_825" xsd:string [Instance] id: mged:g_per_L instance_of: mged:ConcentrationUnit comment: grams per liter, concentration unit property_value: mged:unique_identifier "MO_805" xsd:string [Instance] id: mged:gene instance_of: mged:DeprecatedTerms comment: 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 relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_503" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:gene_fragment instance_of: mged:DeprecatedTerms comment: sequence of part of a gene, which is missing one or both ends relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:unique_identifier "MO_853" xsd:string property_value: mged:deprecation_in_version "1.3.1.1" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:gene_knock_in instance_of: mged:GeneticModification comment: 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. property_value: mged:unique_identifier "MO_437" xsd:string [Instance] id: mged:gene_knock_out instance_of: mged:GeneticModification comment: 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. property_value: mged:unique_identifier "MO_771" xsd:string [Instance] id: mged:genetic_modification instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: An action whereby an organism(s) has had genetic material removed, added, or rearranged. property_value: mged:unique_identifier "MO_927" xsd:string [Instance] id: mged:genetic_modification_design instance_of: mged:PerturbationalDesign comment: A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out property_value: mged:unique_identifier "MO_447" xsd:string [Instance] id: mged:genetic_variation instance_of: mged:DeprecatedTerms comment: A descriptor for FactorValue where GeneticVariation is compared. relationship: mged:deprecated_from_version mged:version_1.1.8 relationship: mged:deprecation_old_parent mged:BioMaterialCharacteristicCategory relationship: mged:deprecation_replacement_term mged:BioMaterialCharacteristicCategory relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.1.8" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_557" xsd:string [Instance] id: mged:genomic_DNA instance_of: mged:MaterialType comment: high molecular weight DNA property_value: mged:unique_identifier "MO_599" xsd:string [Instance] id: mged:genomic_region_amplification instance_of: mged:ChromosomalAberrationClassification comment: increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification property_value: mged:unique_identifier "MO_609" xsd:string [Instance] id: mged:genotyping_design instance_of: mged:BioMolecularAnnotation comment: A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. property_value: mged:unique_identifier "MO_560" xsd:string [Instance] id: mged:germination instance_of: mged:InitialTimePoint comment: 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). property_value: mged:unique_identifier "MO_590" xsd:string [Instance] id: mged:glass instance_of: mged:SubstrateType comment: The array is made on a glass slide. property_value: mged:unique_identifier "MO_742" xsd:string [Instance] id: mged:gram_percent instance_of: mged:ConcentrationUnit comment: grams per deciliter, concentration unit property_value: mged:unique_identifier "MO_582" xsd:string [Instance] id: mged:granddaughter instance_of: mged:FamilyRelationship comment: A daughter of one's son or daughter. property_value: mged:unique_identifier "MO_703" xsd:string [Instance] id: mged:grandfather instance_of: mged:FamilyRelationship comment: The father of one's father or mother. property_value: mged:unique_identifier "MO_478" xsd:string [Instance] id: mged:grandmother instance_of: mged:FamilyRelationship comment: The mother of one's father or mother. property_value: mged:unique_identifier "MO_924" xsd:string [Instance] id: mged:grandson instance_of: mged:FamilyRelationship comment: A son of one's son or daughter. property_value: mged:unique_identifier "MO_831" xsd:string [Instance] id: mged:grow instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: A ComplexAction or ProtocolType describing growth of an organism or cell culture. property_value: mged:unique_identifier "MO_758" xsd:string [Instance] id: mged:growth_condition_design instance_of: mged:PerturbationalDesign comment: 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. property_value: mged:unique_identifier "MO_588" xsd:string [Instance] id: mged:half-life instance_of: mged:TimeUnitOther comment: 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. property_value: mged:unique_identifier "MO_595" xsd:string [Instance] id: mged:haploid instance_of: mged:Ploidy comment: Describes a cell, nucleus or an organism with one copy of each chromosome.\n property_value: mged:unique_identifier "MO_719" xsd:string [Instance] id: mged:hardware_manufacturer instance_of: mged:Roles comment: Person or organization that manufactured the hardware. property_value: mged:unique_identifier "MO_763" xsd:string [Instance] id: mged:hardware_variation_design instance_of: mged:MethodologicalDesign comment: A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision. property_value: mged:unique_identifier "MO_734" xsd:string [Instance] id: mged:harvest instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The process of harvesting cells from culture. property_value: mged:unique_identifier "MO_982" xsd:string [Typedef] id: mged:has_ID comment: property indicating that the class has an identifier property_value: mged:unique_identifier "MO_323" xsd:string [Typedef] id: mged:has_MAGE_description comment: property indicating that the class has an association to a MAGE description property_value: mged:unique_identifier "MO_260" xsd:string [Typedef] id: mged:has_URI comment: property indicating that the class has a URI property_value: mged:unique_identifier "MO_340" xsd:string [Typedef] id: mged:has_accession comment: property indicating that the class has an accession number property_value: mged:unique_identifier "MO_231" xsd:string [Typedef] id: mged:has_accession_version comment: property indicating that the class has an accession number version property_value: mged:unique_identifier "MO_339" xsd:string [Typedef] id: mged:has_action comment: property indicating that the class has an action property_value: mged:unique_identifier "MO_312" xsd:string [Typedef] id: mged:has_additive comment: property indicating that the class has an additive property_value: mged:unique_identifier "MO_314" xsd:string [Typedef] id: mged:has_address comment: property indicating that the class has an address property_value: mged:unique_identifier "MO_277" xsd:string [Typedef] id: mged:has_affiliation comment: property indicating that the class has an affiliation to an institution property_value: mged:unique_identifier "MO_309" xsd:string [Typedef] id: mged:has_atmospheric_component comment: property indicating that the class has an atmospheric component property_value: mged:unique_identifier "MO_259" xsd:string [Typedef] id: mged:has_authors comment: property indicating that the class has authors property_value: mged:unique_identifier "MO_318" xsd:string [Typedef] id: mged:has_been_treated comment: property indicating that the class has been treated property_value: mged:unique_identifier "MO_341" xsd:string [Typedef] id: mged:has_bioassay_data comment: property indicating that the class has bioassaydata property_value: mged:unique_identifier "MO_252" xsd:string [Typedef] id: mged:has_bioassays comment: property indicating that the class has bioassays property_value: mged:unique_identifier "MO_238" xsd:string [Typedef] id: mged:has_biomaterial_characteristics comment: property indicating that the class has biomaterial characteristics property_value: mged:unique_identifier "MO_272" xsd:string [Typedef] id: mged:has_biosource_type comment: property indicating that the class has a biosource type domain: mged:BioSourceProvider property_value: mged:unique_identifier "MO_315" xsd:string [Typedef] id: mged:has_cancer_site comment: property indicating that the class has a cancer site property_value: mged:unique_identifier "MO_248" xsd:string [Typedef] id: mged:has_category comment: property indicating that the class has a category property_value: mged:unique_identifier "MO_249" xsd:string [Typedef] id: mged:has_chromosomal_aberration_classification comment: property indicating that the class has a chromosomal aberration classification property_value: mged:unique_identifier "MO_253" xsd:string [Typedef] id: mged:has_citation comment: property indicating that the class has a citation property_value: mged:unique_identifier "MO_274" xsd:string [Typedef] id: mged:has_clinical_finding comment: property indicating that the class has a clinical finding property_value: mged:unique_identifier "MO_316" xsd:string [Typedef] id: mged:has_clinical_record comment: property indicating that the class has a clinical record property_value: mged:unique_identifier "MO_247" xsd:string [Typedef] id: mged:has_clinical_treatment comment: property indicating that the class has a clinical treatment property_value: mged:unique_identifier "MO_282" xsd:string [Typedef] id: mged:has_compound comment: property indicating that the class has a compound property_value: mged:unique_identifier "MO_302" xsd:string [Typedef] id: mged:has_cubic_volume comment: property indicating that the class contains a cubic volume measurement property_value: mged:unique_identifier "MO_245" xsd:string [Typedef] id: mged:has_database comment: property indicating that the class has a database property_value: mged:unique_identifier "MO_233" xsd:string [Typedef] id: mged:has_database_entry_type comment: property indicating that the class has a database entry type property_value: mged:unique_identifier "MO_240" xsd:string [Typedef] id: mged:has_description comment: property indicating that the class has a description property_value: mged:unique_identifier "MO_334" xsd:string [Typedef] id: mged:has_diameter comment: property indicating that the class has a diameter property_value: mged:unique_identifier "MO_301" xsd:string [Typedef] id: mged:has_disease_location comment: property indicating the location of the disease. property_value: mged:unique_identifier "MO_290" xsd:string [Typedef] id: mged:has_disease_staging comment: property indicating that the class has disease staging property_value: mged:unique_identifier "MO_275" xsd:string [Typedef] id: mged:has_disease_state comment: property indicating that the class has a disease state property_value: mged:unique_identifier "MO_305" xsd:string [Typedef] id: mged:has_donor comment: property indicating that the class has a donor property_value: mged:unique_identifier "MO_342" xsd:string [Typedef] id: mged:has_editor comment: property indicating that the class has an editor property_value: mged:unique_identifier "MO_256" xsd:string [Typedef] id: mged:has_email comment: property indicating that the class has an email address property_value: mged:unique_identifier "MO_293" xsd:string [Typedef] id: mged:has_experiment_design comment: property indicating that the class has an experiment design property_value: mged:unique_identifier "MO_291" xsd:string [Typedef] id: mged:has_experiment_design_type comment: property indicating that the class has an experiment design type property_value: mged:unique_identifier "MO_288" xsd:string [Typedef] id: mged:has_experiment_factors comment: property indicating that the class has experiment factors property_value: mged:unique_identifier "MO_328" xsd:string [Typedef] id: mged:has_factor_value comment: property indicating that the class has a factor value property_value: mged:unique_identifier "MO_236" xsd:string [Typedef] id: mged:has_factor_value_ontology_entry comment: property indicating that the class has an ontology entry property_value: mged:unique_identifier "MO_263" xsd:string [Typedef] id: mged:has_family_member comment: property indicating that the class has a family member property_value: mged:unique_identifier "MO_243" xsd:string [Typedef] id: mged:has_family_relationship comment: property indicating that the class has a family relationship property_value: mged:unique_identifier "MO_250" xsd:string [Typedef] id: mged:has_fax comment: property indicating that the class has a fax property_value: mged:unique_identifier "MO_289" xsd:string [Typedef] id: mged:has_feature_shape comment: property indicating that the class has a feature shape property_value: mged:unique_identifier "MO_268" xsd:string [Typedef] id: mged:has_fiducials comment: property indicating that the class has fiducials property_value: mged:unique_identifier "MO_267" xsd:string [Typedef] id: mged:has_first_name comment: property indicating that the class has a first name property_value: mged:unique_identifier "MO_258" xsd:string [Typedef] id: mged:has_hardware comment: property indicating that the class has hardware property_value: mged:unique_identifier "MO_286" xsd:string [Typedef] id: mged:has_height comment: property indicating that the class has a height property_value: mged:unique_identifier "MO_317" xsd:string [Typedef] id: mged:has_host comment: property indicating that the class has a host domain: mged:Host property_value: mged:unique_identifier "MO_313" xsd:string [Typedef] id: mged:has_host_part comment: property indicating that the class has a host part domain: mged:Host property_value: mged:unique_identifier "MO_283" xsd:string [Typedef] id: mged:has_human_readable_URI comment: property indicating that the contents found at this uri are human readable property_value: mged:unique_identifier "MO_330" xsd:string [Typedef] id: mged:has_image_format comment: property indicating that the class has an image format domain: mged:PhysicalBioAssay property_value: mged:unique_identifier "MO_234" xsd:string [Typedef] id: mged:has_individual comment: property indicating that the class has an individual property_value: mged:unique_identifier "MO_327" xsd:string [Typedef] id: mged:has_individual_genetic_characteristics comment: property indicating that the class has individual genetic characteristics property_value: mged:unique_identifier "MO_254" xsd:string [Typedef] id: mged:has_initial_time_point comment: property indicating that the class has an individual time point domain: mged:Age property_value: mged:unique_identifier "MO_292" xsd:string [Typedef] id: mged:has_issue comment: property indicating that the class has an issue domain: mged:BibliographicReference property_value: mged:unique_identifier "MO_294" xsd:string [Typedef] id: mged:has_laboratory_test comment: property indicating that the class has a laboratory test property_value: mged:unique_identifier "MO_281" xsd:string [Typedef] id: mged:has_last_name comment: property indicating that the class has a last name property_value: mged:unique_identifier "MO_255" xsd:string [Typedef] id: mged:has_length [Typedef] id: mged:has_machine_readable_URI comment: property indicating that the contents found at this uri are machine readable (i.e. in a standard format) property_value: mged:unique_identifier "MO_336" xsd:string [Typedef] id: mged:has_make comment: property indicating that the class has a make domain: mged:Hardware property_value: mged:unique_identifier "MO_271" xsd:string [Typedef] id: mged:has_manufacturer comment: property indicating that the class has a manufacturer property_value: mged:unique_identifier "MO_232" xsd:string [Typedef] id: mged:has_mass comment: property indicating that the class has a mass property_value: mged:unique_identifier "MO_280" xsd:string [Typedef] id: mged:has_maximum_measurement comment: property indicating that the class has a maximum measurement domain: mged:Age property_value: mged:unique_identifier "MO_297" xsd:string [Typedef] id: mged:has_measurement comment: property indicating that the class has a measurement property_value: mged:unique_identifier "MO_325" xsd:string [Typedef] id: mged:has_measurement_type comment: property indicating that the class has a measurement type domain: mged:Measurement property_value: mged:unique_identifier "MO_242" xsd:string [Typedef] id: mged:has_mid_initials comment: property indicating that the class has a middle initials property_value: mged:unique_identifier "MO_237" xsd:string [Typedef] id: mged:has_model comment: property indicating that the class has a model domain: mged:Hardware property_value: mged:unique_identifier "MO_270" xsd:string [Typedef] id: mged:has_name comment: property indicating that the class has a name property_value: mged:unique_identifier "MO_296" xsd:string [Typedef] id: mged:has_node_value comment: property indicating that the class has a node value property_value: mged:unique_identifier "MO_310" xsd:string [Typedef] id: mged:has_node_value_type comment: property indicating that the class has a node value type property_value: mged:unique_identifier "MO_264" xsd:string [Typedef] id: mged:has_nodes comment: property indicating that the class has a node property_value: mged:unique_identifier "MO_307" xsd:string [Typedef] id: mged:has_nutrient_component comment: property indicating that the class has a nutrient component property_value: mged:unique_identifier "MO_321" xsd:string [Typedef] id: mged:has_order comment: property indicating that the class has an order property_value: mged:unique_identifier "MO_335" xsd:string [Typedef] id: mged:has_organism_part comment: property indicating that the class has an organism part property_value: mged:unique_identifier "MO_285" xsd:string [Typedef] id: mged:has_owner comment: property indicating that the class has an owner property_value: mged:unique_identifier "MO_278" xsd:string [Typedef] id: mged:has_pages comment: property indicating that the class has pages domain: mged:BibliographicReference property_value: mged:unique_identifier "MO_246" xsd:string [Typedef] id: mged:has_parent_organization comment: property indicating that the class has a parent organization property_value: mged:unique_identifier "MO_257" xsd:string [Typedef] id: mged:has_part_modified comment: property indicating that the class has a modified part property_value: mged:unique_identifier "MO_241" xsd:string [Typedef] id: mged:has_performer comment: property indicating that the protocol has a performer or contact person property_value: mged:unique_identifier "MO_273" xsd:string [Typedef] id: mged:has_phone comment: property indicating that the class has a phone property_value: mged:unique_identifier "MO_235" xsd:string [Typedef] id: mged:has_prior_disease_state comment: property indicating that the class has a prior disease state property_value: mged:unique_identifier "MO_276" xsd:string [Typedef] id: mged:has_property_set comment: property indicating that the class has a property set property_value: mged:unique_identifier "MO_266" xsd:string [Typedef] id: mged:has_protocol comment: property indicating that the class has a protocol property_value: mged:unique_identifier "MO_300" xsd:string [Typedef] id: mged:has_providers comment: property indicating that the class has providers property_value: mged:unique_identifier "MO_303" xsd:string [Typedef] id: mged:has_publication comment: property indicating that the class has a publication property_value: mged:unique_identifier "MO_251" xsd:string [Typedef] id: mged:has_publisher comment: property indicating that the class has a publisher property_value: mged:unique_identifier "MO_295" xsd:string [Typedef] id: mged:has_reason_for_deprecation comment: property to indicate the reason for deprecating a term property_value: mged:unique_identifier "MO_306" xsd:string [Typedef] id: mged:has_result comment: property indicating the class has a result property_value: mged:unique_identifier "MO_324" xsd:string [Typedef] id: mged:has_scale comment: property indicating that the class has a scale property_value: mged:unique_identifier "MO_287" xsd:string [Typedef] id: mged:has_software comment: property indicating that the class has software property_value: mged:unique_identifier "MO_284" xsd:string [Typedef] id: mged:has_species comment: property indicating that the class has species property_value: mged:unique_identifier "MO_320" xsd:string [Typedef] id: mged:has_test_protocol comment: property indicating that the test has a test protocol property_value: mged:unique_identifier "MO_244" xsd:string [Typedef] id: mged:has_test_result comment: property indicating that the test has a test result property_value: mged:unique_identifier "MO_261" xsd:string [Typedef] id: mged:has_test_type comment: property indicating that the class has a clinical test property_value: mged:unique_identifier "MO_311" xsd:string [Typedef] id: mged:has_text comment: property indicating that the class has text property_value: mged:unique_identifier "MO_298" xsd:string [Typedef] id: mged:has_title comment: property indicating that the class has a title property_value: mged:unique_identifier "MO_337" xsd:string [Typedef] id: mged:has_toll_free_phone comment: property indicating that the class has a toll free phone property_value: mged:unique_identifier "MO_329" xsd:string [Typedef] id: mged:has_treatment comment: property indicating that the class has a treatment property_value: mged:unique_identifier "MO_262" xsd:string [Typedef] id: mged:has_type comment: property indicating that the class has a type property_value: mged:unique_identifier "MO_319" xsd:string [Typedef] id: mged:has_units comment: property indicating that the class has units property_value: mged:unique_identifier "MO_269" xsd:string [Typedef] id: mged:has_value comment: property indicating that the class has a value property_value: mged:unique_identifier "MO_326" xsd:string [Typedef] id: mged:has_version comment: property indicating that the class has a version property_value: mged:unique_identifier "MO_239" xsd:string [Typedef] id: mged:has_volume comment: property indicating that the class has a volume domain: mged:BibliographicReference property_value: mged:unique_identifier "MO_308" xsd:string [Typedef] id: mged:has_year comment: property indicating that the class has a year property_value: mged:unique_identifier "MO_322" xsd:string [Instance] id: mged:hatching instance_of: mged:InitialTimePoint comment: The point at which an organism emerges from an egg. property_value: mged:unique_identifier "MO_745" xsd:string [Instance] id: mged:heating_block instance_of: mged:HardwareType comment: A device for controlling temperature. property_value: mged:unique_identifier "MO_663" xsd:string [Instance] id: mged:heavy_background instance_of: mged:DefectType comment: The Zone is excluded due to smearing, streaking, or dense background in the Zone. property_value: mged:unique_identifier "MO_571" xsd:string [Instance] id: mged:hermaphrodite instance_of: mged:Sex comment: an organism with both male and female sexual organs in one individual\nsynonym: intersex property_value: mged:synonym "intersex" xsd:string property_value: mged:unique_identifier "MO_356" xsd:string [Instance] id: mged:histological_slide_preparation instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The action of preparing a slide for the microscopical examination of organism parts or cell types. property_value: mged:unique_identifier "MO_611" xsd:string [Instance] id: mged:homogenizer instance_of: mged:HardwareType comment: An instrument which fragments tissues or other biomaterials. property_value: mged:unique_identifier "MO_714" xsd:string [Instance] id: mged:hours instance_of: mged:TimeUnit comment: 60 minutes, time unit property_value: mged:synonym "h" xsd:string property_value: mged:unique_identifier "MO_486" xsd:string [Instance] id: mged:hybridization instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The process of incubating one or more labeled extracts with an array. property_value: mged:unique_identifier "MO_884" xsd:string [Instance] id: mged:hybridization_chamber instance_of: mged:HardwareType comment: A chamber in which the hybridization is performed which maintains constant conditions. property_value: mged:unique_identifier "MO_563" xsd:string [Instance] id: mged:hybridization_station instance_of: mged:HardwareType comment: An instrument which controls hybridization conditions, into which a hybridization chamber may fit. property_value: mged:unique_identifier "MO_497" xsd:string [Instance] id: mged:image_acquisition instance_of: mged:ExperimentalProtocolType comment: The process of generating an image from the array. property_value: mged:unique_identifier "MO_929" xsd:string [Instance] id: mged:image_acquisition_software instance_of: mged:SoftwareType comment: Software to control a scanner and manipulate and save images.\nExact synonym: scanning software property_value: mged:synonym "scanning software" xsd:string property_value: mged:unique_identifier "MO_1003" xsd:string [Instance] id: mged:image_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies an image, e.g. an image from the mouse atlas property_value: mged:unique_identifier "MO_691" xsd:string [Instance] id: mged:imprinting_design instance_of: mged:BiologicalProperty comment: 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. property_value: mged:unique_identifier "MO_914" xsd:string [Instance] id: mged:in_medium instance_of: mged:DeliveryMethod comment: Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment). property_value: mged:unique_identifier "MO_733" xsd:string [Instance] id: mged:in_situ_oligo_features instance_of: mged:TechnologyType comment: The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent) property_value: mged:unique_identifier "MO_514" xsd:string [Instance] id: mged:in_vitro_design instance_of: mged:MethodologicalDesign comment: An experiment done in a test tube or a culture dish, e.g. \nA bacterial invasion assay in an established cell culture. property_value: mged:unique_identifier "MO_347" xsd:string [Instance] id: mged:in_vivo_design instance_of: mged:MethodologicalDesign comment: An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. property_value: mged:unique_identifier "MO_454" xsd:string [Instance] id: mged:inconclusive instance_of: mged:Result comment: a result which can not be interpreted as positive or negative property_value: mged:unique_identifier "MO_744" xsd:string [Instance] id: mged:incubate instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product. property_value: mged:unique_identifier "MO_965" xsd:string [Instance] id: mged:individual instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for FactorValue where BioSources are compared. property_value: mged:unique_identifier "MO_639" xsd:string [Instance] id: mged:individual_genetic_characteristic instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for FactorValue where IndividualGeneticCharacteristic is compared. property_value: mged:unique_identifier "MO_722" xsd:string [Instance] id: mged:individual_genetic_characteristics_design instance_of: mged:BiologicalProperty comment: An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared. property_value: mged:unique_identifier "MO_527" xsd:string [Instance] id: mged:induced_mutation instance_of: mged:GeneticModification comment: The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation. property_value: mged:unique_identifier "MO_564" xsd:string [Instance] id: mged:infect instance_of: mged:DeprecatedTerms comment: The organism (or organism part) has been exposed to a virus or pathogen. relationship: mged:deprecated_from_version mged:version_1.3.0 relationship: mged:deprecation_old_parent mged:ComplexAction relationship: mged:deprecation_old_parent mged:ExperimentalProtocolType relationship: mged:has_reason_for_deprecation mged:replaced_term relationship: mged:replaced_with_term mged:inoculate relationship: mged:was_replaced_by mged:inoculate property_value: mged:deprecation_in_version "1.3.0" xsd:string property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: mged:unique_identifier "MO_616" xsd:string [Instance] id: mged:injury_design instance_of: mged:PerturbationalDesign comment: An injury experiment design type is where the response of an organism(s) to injury or damage is studied. property_value: mged:unique_identifier "MO_726" xsd:string [Instance] id: mged:innate_behavior_design instance_of: mged:BiologicalProperty comment: A design in which the innate behavior of the organism is examined, e.g. \n path finding in bees. property_value: mged:unique_identifier "MO_355" xsd:string [Instance] id: mged:inoculate instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism. property_value: mged:unique_identifier "MO_559" xsd:string property_value: mged:synonym "infect" xsd:string [Instance] id: mged:institution instance_of: mged:Roles comment: A contact's affiliation, e.g. university, research institute or business. property_value: mged:unique_identifier "MO_601" xsd:string [Instance] id: mged:integer instance_of: mged:DataType comment: A value which is a whole number (e.g. 10). property_value: mged:unique_identifier "MO_435" xsd:string [Instance] id: mged:intergenic instance_of: mged:DeprecatedTerms comment: sequence from the region between genes relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_463" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:intramuscular_injection instance_of: mged:DeliveryMethod comment: Delivery method for a compound or drug where the substance is administered via an injection into the muscle. property_value: mged:unique_identifier "MO_617" xsd:string [Instance] id: mged:intraperitoneal_injection instance_of: mged:DeliveryMethod comment: A delivery method for compound or drug whereby the substance is administered via the peritoneum. property_value: mged:unique_identifier "MO_473" xsd:string [Instance] id: mged:intravenous instance_of: mged:DeliveryMethod comment: delivery method whereby a compound or drug is administered via a vein property_value: mged:unique_identifier "MO_432" xsd:string [Instance] id: mged:intron instance_of: mged:DeprecatedTerms comment: sequence spliced out from a transcript relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_709" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:investigator instance_of: mged:Roles comment: Person who contributed to the study. property_value: mged:unique_identifier "MO_769" xsd:string [Instance] id: mged:irradiate instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: treatment of a biomaterial with radiation e.g. electromagnetic radiation property_value: mged:unique_identifier "MO_770" xsd:string [Instance] id: mged:irregular_shape instance_of: mged:DefectType comment: The perimeter of the spotted DNA on the slide is irregular. property_value: mged:unique_identifier "MO_669" xsd:string [Instance] id: mged:is_contaminated instance_of: mged:WarningType comment: The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination. property_value: mged:unique_identifier "MO_489" xsd:string [Instance] id: mged:is_expressed_design instance_of: mged:BiologicalProperty comment: A design aimed at identifying genes expressed in biomaterials of interest. property_value: mged:unique_identifier "MO_487" xsd:string [Typedef] id: mged:is_solvent comment: property indicating that the class is a solvent property_value: mged:unique_identifier "MO_332" xsd:string [Typedef] id: mged:is_user_defined comment: property indicating that the class is user defined property_value: mged:unique_identifier "MO_279" xsd:string [Instance] id: mged:iterative_mean_log_centering instance_of: mged:NormalizationDescriptionType comment: 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. property_value: mged:unique_identifier "MO_957" xsd:string [Instance] id: mged:jackknife_Pearson_correlation instance_of: mged:NodeValueType comment: The jackknife Pearson correlation is the lowest Pearson correlation between two data series where one pair of values in the data series are omitted. property_value: mged:unique_identifier "MO_784" xsd:string [Instance] id: mged:journal_article instance_of: mged:PublicationType comment: A article published in a print or online journal having an ISSN. property_value: mged:unique_identifier "MO_430" xsd:string [Instance] id: mged:kat_per_L instance_of: mged:ConcentrationUnitOther comment: katal per liter, catalytic-activity concentration unit property_value: mged:unique_identifier "MO_869" xsd:string [Instance] id: mged:kg instance_of: mged:MassUnit comment: kilogram, 1000 grams, unit of mass property_value: mged:unique_identifier "MO_846" xsd:string [Instance] id: mged:kg_per_m2 instance_of: mged:OtherUnit comment: 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 property_value: mged:unique_identifier "MO_658" xsd:string property_value: mged:synonym "kg/m2" xsd:string [Instance] id: mged:labeling instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The procedure of labeling a biosample. property_value: mged:unique_identifier "MO_471" xsd:string [Instance] id: mged:laser_ablation_mark instance_of: mged:FiducialType comment: mark made on slide using a laser which is used as a point of reference for orientation (fiducial) property_value: mged:unique_identifier "MO_910" xsd:string [Instance] id: mged:light_duration instance_of: mged:EnvironmentalFactorCategory comment: The length of the light period that a sample is subjected to.\nExact synonym:photoperiod property_value: mged:unique_identifier "MO_604" xsd:string property_value: mged:synonym "photoperiod" xsd:string [Instance] id: mged:light_intensity instance_of: mged:EnvironmentalFactorCategory comment: 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. property_value: mged:unique_identifier "MO_517" xsd:string [Instance] id: mged:linear_amplification instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: 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.\nnon exact synonym: Eberwine procedure property_value: mged:synonym "Eberwine procedure" xsd:string property_value: mged:unique_identifier "MO_997" xsd:string [Instance] id: mged:linear_regression_normalization instance_of: mged:NormalizationDescriptionType comment: 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. property_value: mged:unique_identifier "MO_823" xsd:string [Instance] id: mged:linear_scale instance_of: mged:Scale comment: The scale is a standard base 10, non logarithmic scale. property_value: mged:unique_identifier "MO_751" xsd:string [Instance] id: mged:linlog_normalization instance_of: mged:NormalizationDescriptionType comment: 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. relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:has_reason_for_deprecation mged:replaced_term property_value: mged:unique_identifier "MO_956" xsd:string [Instance] id: mged:linlog_transformation instance_of: mged:DataTransformationProtocolType comment: 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. property_value: mged:unique_identifier "MO_845" xsd:string [Instance] id: mged:liquid instance_of: mged:Media comment: media type, usually some sort of broth property_value: mged:unique_identifier "MO_715" xsd:string [Instance] id: mged:liquid_handler instance_of: mged:HardwareType comment: Hardware for automated liquid transfer and handling. property_value: mged:unique_identifier "MO_868" xsd:string [Instance] id: mged:liquid_handler_software instance_of: mged:SoftwareType comment: Software used to control automated liquid handler. property_value: mged:unique_identifier "MO_761" xsd:string [Instance] id: mged:list_of_booleans instance_of: mged:DataType comment: An ordered, finite set of booleans. property_value: mged:unique_identifier "MO_712" xsd:string [Instance] id: mged:list_of_floats instance_of: mged:DataType comment: An ordered, finite set of floats. property_value: mged:unique_identifier "MO_760" xsd:string [Instance] id: mged:list_of_integers instance_of: mged:DataType comment: An ordered, finite set of integers. property_value: mged:unique_identifier "MO_891" xsd:string [Instance] id: mged:list_of_negative_floats instance_of: mged:DataType comment: An ordered, finite set of negative floats. property_value: mged:unique_identifier "MO_851" xsd:string [Instance] id: mged:list_of_negative_integers instance_of: mged:DataType comment: An ordered, finite set of negative integers. property_value: mged:unique_identifier "MO_900" xsd:string [Instance] id: mged:list_of_nonnegative_floats instance_of: mged:DataType comment: An ordered, finite set of nonnegative floats. property_value: mged:unique_identifier "MO_360" xsd:string [Instance] id: mged:list_of_nonnegative_integers instance_of: mged:DataType comment: An ordered, finite set of nonnegative integers. property_value: mged:unique_identifier "MO_973" xsd:string [Instance] id: mged:list_of_nonpositive_floats instance_of: mged:DataType comment: An ordered, finite set of nonpositive floats. property_value: mged:unique_identifier "MO_1000" xsd:string [Instance] id: mged:list_of_nonpositive_integers instance_of: mged:DataType comment: An ordered, finite set of nonpositive integers. property_value: mged:unique_identifier "MO_804" xsd:string [Instance] id: mged:list_of_positive_floats instance_of: mged:DataType comment: An ordered, finite set of positive floats. property_value: mged:unique_identifier "MO_777" xsd:string [Instance] id: mged:list_of_positive_integers instance_of: mged:DataType comment: An ordered, finite set of positive integers. property_value: mged:unique_identifier "MO_873" xsd:string [Instance] id: mged:list_of_strings instance_of: mged:DataType comment: An ordered, finite set of strings. property_value: mged:unique_identifier "MO_800" xsd:string [Instance] id: mged:loess_global_normalization instance_of: mged:DataTransformationProtocolType comment: 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. property_value: mged:unique_identifier "MO_443" xsd:string [Instance] id: mged:loess_group_normalization instance_of: mged:DataTransformationProtocolType comment: 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. property_value: mged:unique_identifier "MO_377" xsd:string [Instance] id: mged:loess_normalization instance_of: mged:NormalizationDescriptionType comment: 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 \nbe applied globally, or limited by one or more specified criteria. property_value: mged:unique_identifier "MO_428" xsd:string [Instance] id: mged:loess_scaled_group_normalization instance_of: mged:DataTransformationProtocolType comment: Application of a scale adjustment following loess_group_normalization, to render the group variances similar. property_value: mged:unique_identifier "MO_521" xsd:string [Instance] id: mged:log_base_10 instance_of: mged:Scale comment: The values presented are logarithm, base 10. property_value: mged:unique_identifier "MO_735" xsd:string [Instance] id: mged:log_base_2 instance_of: mged:Scale comment: The values presented are logarithm, base 2. property_value: mged:unique_identifier "MO_647" xsd:string [Instance] id: mged:log_base_e instance_of: mged:Scale comment: The values presented are logarithm, base e. property_value: mged:unique_identifier "MO_554" xsd:string [Instance] id: mged:log_ratio instance_of: mged:DerivedBioAssayType comment: Logarithmic transformation of ratio data. property_value: mged:unique_identifier "MO_896" xsd:string [Instance] id: mged:long_oligo instance_of: mged:DesignElement comment: An element that is an oligonucleotide of at least 50 nucleotides in length. property_value: mged:unique_identifier "MO_598" xsd:string [Instance] id: mged:loop_design instance_of: mged:MethodologicalDesign comment: A loop experiment design is where labeled extracts are compared in consecutive pairs.\nsynonym: circular design property_value: mged:synonym "circular design" xsd:string property_value: mged:unique_identifier "MO_912" xsd:string [Instance] id: mged:low_intensity_filter instance_of: mged:DeprecatedTerms comment: 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. relationship: mged:deprecated_from_version mged:version_1.3.0 relationship: mged:deprecation_old_parent mged:DataTransformationProtocolType relationship: mged:has_reason_for_deprecation mged:replaced_term relationship: mged:replaced_with_term mged:flag_filter relationship: mged:was_replaced_by mged:flag_filter property_value: mged:deprecation_in_version "1.3.0" xsd:string property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: mged:unique_identifier "MO_706" xsd:string [Instance] id: mged:lowess_global_normalization instance_of: mged:DataTransformationProtocolType comment: 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. property_value: mged:unique_identifier "MO_692" xsd:string [Instance] id: mged:lowess_group_normalization instance_of: mged:DataTransformationProtocolType comment: 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. property_value: mged:unique_identifier "MO_861" xsd:string [Instance] id: mged:lowess_normalization instance_of: mged:NormalizationDescriptionType comment: A method of normalizing ratio data by using a locally weighted polynomial \n regression (typically after a log transformation). The regression can be \n performed on log ratios resulting from the relation of two data sets \n versus the average log intensity data from the same two data sets or it \n can be performed on raw or log transformed values from one data set versus \n values from another. The goal could be to remove intensity-dependent \n dye-specific effects from the set of pair wise ratios. This method can be \n applied globally, or limited by one or more specified criteria. property_value: mged:unique_identifier "MO_720" xsd:string [Instance] id: mged:lowess_scaled_group_normalization instance_of: mged:DataTransformationProtocolType comment: Application of a scale adjustment following lowess_group_normalization, to render the group variances similar. property_value: mged:unique_identifier "MO_410" xsd:string [Instance] id: mged:lumen instance_of: mged:LightUnit comment: The unit of total light output from a light source. property_value: mged:unique_identifier "MO_603" xsd:string [Instance] id: mged:lux instance_of: mged:LightUnit comment: 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. property_value: mged:unique_identifier "MO_573" xsd:string [Instance] id: mged:m instance_of: mged:DistanceUnit comment: meter, distance unit property_value: mged:unique_identifier "MO_367" xsd:string [Instance] id: mged:mL_per_L instance_of: mged:ConcentrationUnit comment: milliliters per liter, concentration unit property_value: mged:unique_identifier "MO_801" xsd:string [Instance] id: mged:mM instance_of: mged:ConcentrationUnit comment: milimolar, concentration unit property_value: mged:unique_identifier "MO_509" xsd:string [Instance] id: mged:mOsm_per_kg_H2O instance_of: mged:ConcentrationUnitOther comment: osmolality per kilogram of water, concentration of the solute per unit of solvent property_value: mged:unique_identifier "MO_661" xsd:string [Instance] id: mged:mRNA instance_of: mged:DeprecatedTerms comment: sequence of a processed transcript capable of directing protein synthesis relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_803" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:male instance_of: mged:Sex comment: individual whose sex organs contain only male gametes property_value: mged:unique_identifier "MO_652" xsd:string [Instance] id: mged:manhattan_distance instance_of: mged:NodeValueType comment: 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. property_value: mged:unique_identifier "MO_567" xsd:string [Instance] id: mged:mating_type_a instance_of: mged:Sex comment: Mating type of S. cerevisiae. property_value: mged:unique_identifier "MO_659" xsd:string [Instance] id: mged:mating_type_alpha instance_of: mged:Sex comment: Mating type of S. cerevisiae. property_value: mged:unique_identifier "MO_637" xsd:string [Instance] id: mged:mating_type_h_minus instance_of: mged:Sex comment: Mating type of S.pombe. property_value: mged:unique_identifier "MO_407" xsd:string [Instance] id: mged:mating_type_h_plus instance_of: mged:Sex comment: Mating type of S.pombe. property_value: mged:unique_identifier "MO_855" xsd:string [Instance] id: mged:mean_and_coefficient_of_variation instance_of: mged:DerivedBioAssayType comment: the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData property_value: mged:unique_identifier "MO_425" xsd:string [Instance] id: mged:mean_and_confidence_indicators instance_of: mged:DeprecatedTerms comment: 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. relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:DerivedBioAssayType relationship: mged:deprecation_replacement_term mged:DerivedBioAssayType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_702" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:mean_and_p_values instance_of: mged:DerivedBioAssayType comment: the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData property_value: mged:unique_identifier "MO_943" xsd:string [Instance] id: mged:mean_and_standard_deviation instance_of: mged:DerivedBioAssayType comment: the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData property_value: mged:unique_identifier "MO_445" xsd:string [Instance] id: mged:mean_and_variance instance_of: mged:DerivedBioAssayType comment: the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData property_value: mged:unique_identifier "MO_458" xsd:string [Instance] id: mged:mean_log_centering instance_of: mged:NormalizationDescriptionType comment: 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). property_value: mged:unique_identifier "MO_398" xsd:string [Instance] id: mged:mean_log_normalization instance_of: mged:DataTransformationProtocolType comment: Application of a normalization of type mean_log_centering. property_value: mged:unique_identifier "MO_657" xsd:string [Instance] id: mged:media instance_of: mged:EnvironmentalFactorCategory comment: The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) property_value: mged:unique_identifier "MO_545" xsd:string [Instance] id: mged:median_log_centering instance_of: mged:NormalizationDescriptionType comment: 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). property_value: mged:unique_identifier "MO_811" xsd:string [Instance] id: mged:median_log_normalization instance_of: mged:DataTransformationProtocolType comment: Application of a normalization of type median_log_centering. property_value: mged:unique_identifier "MO_931" xsd:string [Instance] id: mged:merged_term instance_of: mged:DeprecationReason comment: the term has been subsumed into a more general term property_value: mged:unique_identifier "MO_1025" xsd:string [Instance] id: mged:metastatic_site instance_of: mged:CancerSite comment: the organism part in which additional tumors are identified remote from the primary site property_value: mged:unique_identifier "MO_806" xsd:string [Instance] id: mged:mg instance_of: mged:MassUnit comment: milligram, mass unit property_value: mged:unique_identifier "MO_949" xsd:string [Instance] id: mged:mg_per_kg_per_day instance_of: mged:ConcentrationUnitOther comment: milligram per kilogram per day property_value: mged:unique_identifier "MO_353" xsd:string [Instance] id: mged:mg_per_ml instance_of: mged:ConcentrationUnit comment: milligrams per milliliter, concentration unit property_value: mged:unique_identifier "MO_522" xsd:string [Instance] id: mged:microarray_experiment_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies a microarray experiment e.g. GEO property_value: mged:unique_identifier "MO_346" xsd:string [Instance] id: mged:microeinstein_per_minute_and_square_meter instance_of: mged:LightUnit comment: 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). property_value: mged:unique_identifier "MO_526" xsd:string [Instance] id: mged:microeinstein_per_second_and_square_meter instance_of: mged:LightUnit comment: 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). property_value: mged:unique_identifier "MO_584" xsd:string [Instance] id: mged:micromole_per_second_and_square_meter instance_of: mged:OtherUnit comment: 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. property_value: mged:unique_identifier "MO_848" xsd:string [Instance] id: mged:minutes instance_of: mged:TimeUnit comment: 60 seconds, unit of time property_value: mged:synonym "m" xsd:string property_value: mged:unique_identifier "MO_877" xsd:string [Instance] id: mged:missing_feature_or_zone instance_of: mged:DefectType comment: 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. property_value: mged:unique_identifier "MO_405" xsd:string [Instance] id: mged:mix_by_inversion instance_of: mged:AtomicAction comment: Mix through the process of inverting. property_value: mged:unique_identifier "MO_700" xsd:string [Instance] id: mged:mix_by_pipette instance_of: mged:AtomicAction comment: Mix by drawing up and down with a pipette. property_value: mged:unique_identifier "MO_479" xsd:string [Instance] id: mged:mix_by_vortex instance_of: mged:AtomicAction comment: Mix through the use of a vortexer. property_value: mged:unique_identifier "MO_880" xsd:string [Instance] id: mged:mix_general instance_of: mged:AtomicAction comment: The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas. property_value: mged:unique_identifier "MO_944" xsd:string [Instance] id: mged:mixed_design_element_group_type instance_of: mged:DesignElementGroupType comment: a design element group consisting of multiple types property_value: mged:unique_identifier "MO_528" xsd:string [Instance] id: mged:mixed_sex instance_of: mged:Sex comment: A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites. property_value: mged:unique_identifier "MO_436" xsd:string [Instance] id: mged:ml instance_of: mged:VolumeUnit comment: milliliter, volume unit property_value: mged:unique_identifier "MO_488" xsd:string [Instance] id: mged:ml_per_kg instance_of: mged:ConcentrationUnitOther comment: milliliter per kilogram property_value: mged:unique_identifier "MO_403" xsd:string [Instance] id: mged:mm instance_of: mged:DistanceUnit comment: millimeter, unit of distance property_value: mged:unique_identifier "MO_648" xsd:string [Instance] id: mged:mol instance_of: mged:QuantityUnit comment: mole, unit of quantity property_value: mged:unique_identifier "MO_998" xsd:string [Instance] id: mged:molecular_mixture instance_of: mged:MaterialType comment: an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins property_value: mged:unique_identifier "MO_889" xsd:string [Instance] id: mged:molecules instance_of: mged:QuantityUnit comment: number of molecules, quantity unit property_value: mged:unique_identifier "MO_707" xsd:string [Instance] id: mged:monosomy instance_of: mged:DeprecatedTerms comment: Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1. relationship: mged:deprecated_from_version mged:version_1.1.9 relationship: mged:deprecation_old_parent mged:ChromosomalAberrationClassification relationship: mged:has_reason_for_deprecation mged:replaced_term relationship: mged:replaced_with_term mged:oligosomy relationship: mged:was_replaced_by mged:oligosomy property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: mged:unique_identifier "MO_424" xsd:string [Instance] id: mged:months instance_of: mged:TimeUnit comment: Unit of time corresponding to approx. one cycle of the moon's phases. property_value: mged:unique_identifier "MO_631" xsd:string [Instance] id: mged:mother instance_of: mged:FamilyRelationship comment: A female parent. property_value: mged:unique_identifier "MO_387" xsd:string [Instance] id: mged:moving_average instance_of: mged:DataTransformationProtocolType comment: 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. property_value: mged:unique_identifier "MO_681" xsd:string [Instance] id: mged:ms instance_of: mged:TimeUnit comment: millisecond, time unit property_value: mged:unique_identifier "MO_920" xsd:string [Instance] id: mged:mtDNA instance_of: mged:DeprecatedTerms comment: sequence from the mitochondrial genome relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:unique_identifier "MO_581" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.3.1.1" xsd:string [Instance] id: mged:multiple_testing_correction instance_of: mged:HigherLevelAnalysisProtocolType comment: 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. property_value: mged:unique_identifier "MO_561" xsd:string [Instance] id: mged:negative instance_of: mged:Result comment: false or no property_value: mged:unique_identifier "MO_802" xsd:string [Instance] id: mged:negative_float instance_of: mged:DataType comment: A float that is < 0. property_value: mged:unique_identifier "MO_728" xsd:string [Instance] id: mged:negative_integer instance_of: mged:DataType comment: An integer < 0. property_value: mged:unique_identifier "MO_864" xsd:string [Instance] id: mged:ng instance_of: mged:MassUnit comment: nanogram, a mass unit property_value: mged:unique_identifier "MO_796" xsd:string [Instance] id: mged:nitrocellulose instance_of: mged:SubstrateType comment: The array is made on a nitrocellulose filter. property_value: mged:unique_identifier "MO_455" xsd:string [Instance] id: mged:nl instance_of: mged:VolumeUnit comment: nanoliter unit of volume property_value: mged:unique_identifier "MO_754" xsd:string [Instance] id: mged:nm instance_of: mged:DistanceUnit comment: nanometer distance unit property_value: mged:unique_identifier "MO_862" xsd:string [Instance] id: mged:nmol instance_of: mged:QuantityUnit comment: nanomoles, quantity unit property_value: mged:unique_identifier "MO_743" xsd:string [Instance] id: mged:no instance_of: mged:DeprecatedTerms comment: false relationship: mged:deprecated_from_version mged:version_1.1.7 relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:unique_identifier "MO_556" xsd:string [Instance] id: mged:non-targeted_transgenic_variation_design instance_of: mged:PerturbationalDesign comment: 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. property_value: mged:unique_identifier "MO_775" xsd:string [Instance] id: mged:nonnegative_float instance_of: mged:DataType comment: A float greater than or equal to 0. property_value: mged:unique_identifier "MO_386" xsd:string [Instance] id: mged:nonnegative_integer instance_of: mged:DataType comment: An integer >= 0. property_value: mged:unique_identifier "MO_390" xsd:string [Instance] id: mged:nonpositive_float instance_of: mged:DataType comment: A float less than or equal to zero. property_value: mged:unique_identifier "MO_656" xsd:string [Instance] id: mged:nonpositive_integer instance_of: mged:DataType comment: An integer less than or equal to zero. property_value: mged:unique_identifier "MO_623" xsd:string [Instance] id: mged:normalization_testing_design instance_of: mged:MethodologicalDesign comment: A normalization testing experiment design tests different normalization procedures. property_value: mged:unique_identifier "MO_729" xsd:string [Instance] id: mged:normalized_intensities instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_994" xsd:string [Instance] id: mged:normalized_ratios instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_664" xsd:string [Instance] id: mged:not_extract instance_of: mged:BioSampleType comment: The BioSample at any stage other than immediately before labeling. property_value: mged:unique_identifier "MO_894" xsd:string [Instance] id: mged:not_sequence_verified instance_of: mged:WarningType comment: The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter. property_value: mged:unique_identifier "MO_970" xsd:string [Instance] id: mged:not_uniform instance_of: mged:DefectType comment: The source DNA for a Feature was not uniformly deposited. property_value: mged:unique_identifier "MO_906" xsd:string [Instance] id: mged:nuclear_RNA instance_of: mged:MaterialType comment: RNA obtained from the nucleus. property_value: mged:unique_identifier "MO_679" xsd:string [Instance] id: mged:nucleic_acid_extraction instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The procedure of extracting nucleic acid from the biomaterial. property_value: mged:unique_identifier "MO_607" xsd:string [Instance] id: mged:nucleic_acid_primary_sequence_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank property_value: mged:unique_identifier "MO_757" xsd:string [Instance] id: mged:number_per_day instance_of: mged:OtherUnit comment: number of items or events per day property_value: mged:unique_identifier "MO_670" xsd:string [Instance] id: mged:nutrients instance_of: mged:EnvironmentalFactorCategory comment: The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). property_value: mged:unique_identifier "MO_867" xsd:string [Instance] id: mged:nylon instance_of: mged:SubstrateType comment: The array is made on a nylon membrane. property_value: mged:unique_identifier "MO_492" xsd:string [Instance] id: mged:oligo_synthesizer instance_of: mged:HardwareType comment: Hardware for synthesizing oligos. property_value: mged:unique_identifier "MO_930" xsd:string [Instance] id: mged:oligosomy instance_of: mged:ChromosomalAberrationClassification comment: A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement. property_value: mged:unique_identifier "MO_1028" xsd:string [Instance] id: mged:online_resource instance_of: mged:PublicationType comment: A publication type which is available online and which is not an online journal article, e.g. a web site or service. property_value: mged:unique_identifier "MO_991" xsd:string [Instance] id: mged:ontology_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD property_value: mged:unique_identifier "MO_529" xsd:string [Instance] id: mged:openGALEN instance_of: mged:OrganismPartDatabase comment: OpenGALEN Human Anatomy - open source database of approx. ten thousand\nhuman 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. property_value: mged:unique_identifier "MO_613" xsd:string property_value: mged:has_human_readable_URI "http://www.opengalen.org/open/crm/crm-anatomy.html" xsd:string [Instance] id: mged:operating_system instance_of: mged:SoftwareType comment: Software upon which other software runs. property_value: mged:unique_identifier "MO_847" xsd:string [Instance] id: mged:operator_variation_design instance_of: mged:MethodologicalDesign comment: An operator variation experiment design type assesses the operator performance and relation to data consistency and quality. property_value: mged:unique_identifier "MO_519" xsd:string [Instance] id: mged:operon instance_of: mged:DeprecatedTerms comment: sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_759" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:operon_identification_design instance_of: mged:BioMolecularAnnotation comment: An operon identification experiment type is designed to identify locations and members of operons in a genome. property_value: mged:unique_identifier "MO_772" xsd:string [Instance] id: mged:optimization_design instance_of: mged:MethodologicalDesign comment: An optimization experiment design type is where different protocols or protocol parameters are compared. property_value: mged:unique_identifier "MO_934" xsd:string [Instance] id: mged:oral_gavage instance_of: mged:DeliveryMethod comment: delivery method for drug or compound whereby the drug is administered via the mouth property_value: mged:unique_identifier "MO_975" xsd:string [Instance] id: mged:organellar_DNA instance_of: mged:MaterialType comment: DNA from organelles such as the mitochondria or chloroplast. property_value: mged:unique_identifier "MO_645" xsd:string [Instance] id: mged:organellar_RNA instance_of: mged:MaterialType comment: RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus. property_value: mged:unique_identifier "MO_574" xsd:string [Instance] id: mged:organism instance_of: mged:BioMaterialCharacteristicCategory comment: one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria property_value: mged:unique_identifier "MO_508" xsd:string [Instance] id: mged:organism_part instance_of: mged:BioMaterialCharacteristicCategory instance_of: mged:MaterialType comment: 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). property_value: mged:unique_identifier "MO_954" xsd:string [Instance] id: mged:organism_part_comparison_design instance_of: mged:BiologicalProperty comment: An organism part comparison experiment design type compares tissues, regions, organs within or between organisms property_value: mged:unique_identifier "MO_953" xsd:string [Instance] id: mged:organism_status instance_of: mged:BioMaterialCharacteristicCategory comment: The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. property_value: mged:unique_identifier "MO_871" xsd:string [Instance] id: mged:organism_status_design instance_of: mged:BiologicalProperty comment: A design that compares samples from live and dead organisms. property_value: mged:unique_identifier "MO_841" xsd:string [Instance] id: mged:pH instance_of: mged:ConcentrationUnitOther comment: potential of hydrogen property_value: mged:unique_identifier "MO_814" xsd:string [Instance] id: mged:pM instance_of: mged:ConcentrationUnit comment: picomolar, concentration unit property_value: mged:unique_identifier "MO_628" xsd:string [Instance] id: mged:paraffin_sample instance_of: mged:BioSourceType comment: A biomaterial obtained embedded in paraffin (wax). property_value: mged:unique_identifier "MO_990" xsd:string [Instance] id: mged:pathogenicity_design instance_of: mged:PerturbationalDesign comment: 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. property_value: mged:unique_identifier "MO_807" xsd:string [Instance] id: mged:pathway_record instance_of: mged:DatabaseEntryType comment: a record which identifies and describes biological pathways, e.g. a KEGG record property_value: mged:unique_identifier "MO_780" xsd:string [Instance] id: mged:pearson_correlation_coefficient instance_of: mged:NodeValueType comment: 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. property_value: mged:unique_identifier "MO_558" xsd:string [Instance] id: mged:pedigree_record instance_of: mged:DatabaseEntryType comment: 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 property_value: mged:unique_identifier "MO_969" xsd:string [Instance] id: mged:peer_review_quality_control instance_of: mged:QualityControlDescriptionType comment: An experiment which has a peer reviewed publication attached. property_value: mged:unique_identifier "MO_365" xsd:string [Instance] id: mged:percent_confluence instance_of: mged:ConcentrationUnitOther comment: A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.\n property_value: mged:unique_identifier "MO_378" xsd:string [Instance] id: mged:percent_purity instance_of: mged:ConcentrationUnitOther comment: A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy. property_value: mged:unique_identifier "MO_482" xsd:string [Instance] id: mged:percent_vol_per_vol instance_of: mged:ConcentrationUnit comment: percentage volume per volume, concentration unit property_value: mged:unique_identifier "MO_916" xsd:string [Instance] id: mged:percent_weight_per_vol instance_of: mged:ConcentrationUnit comment: percent weight per volume, concentration unit property_value: mged:unique_identifier "MO_420" xsd:string [Instance] id: mged:percent_weight_per_weight instance_of: mged:ConcentrationUnit comment: percent weight per weight, concentration unit property_value: mged:unique_identifier "MO_474" xsd:string [Instance] id: mged:pfu_per_ml instance_of: mged:ConcentrationUnitOther comment: the number of plaque forming units per ml property_value: mged:unique_identifier "MO_768" xsd:string [Instance] id: mged:pg instance_of: mged:MassUnit comment: picogram, mass unit property_value: mged:unique_identifier "MO_363" xsd:string [Instance] id: mged:phylogeny_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies the relationship between species and is\ncomputationally determined and based on sequences e.g. Treebase record property_value: mged:unique_identifier "MO_662" xsd:string [Instance] id: mged:physical_characteristics instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for FactorValue where PhysicalCharacteristics are compared. property_value: mged:unique_identifier "MO_863" xsd:string [Instance] id: mged:physiological_process_design instance_of: mged:BiologicalProperty comment: Those processes specifically pertinent to the functioning of integrated \n living units: cells, tissues, organs, and organisms. This includes those \n processes that exhibit an endogenous periodicity independently of any \n daily variation in the environment such as circadian rhythm or aging. property_value: mged:unique_identifier "MO_1029" xsd:string [Instance] id: mged:pl instance_of: mged:VolumeUnit comment: picoliter, volume unit property_value: mged:unique_identifier "MO_905" xsd:string [Instance] id: mged:place instance_of: mged:AtomicAction comment: The procedure of putting a physical object in a container/physical space. property_value: mged:unique_identifier "MO_470" xsd:string [Instance] id: mged:planting instance_of: mged:InitialTimePoint comment: The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing. property_value: mged:unique_identifier "MO_495" xsd:string [Instance] id: mged:plasmid instance_of: mged:DeprecatedTerms comment: sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_439" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:pmol instance_of: mged:QuantityUnit comment: picomoles, quantity unit property_value: mged:unique_identifier "MO_688" xsd:string [Instance] id: mged:polyA_RNA instance_of: mged:MaterialType comment: RNA which has been obtained by selection for polyA tracts. \nExact synonym: polyA+_RNA\nNon-exact synonym: mRNA property_value: mged:unique_identifier "MO_600" xsd:string property_value: mged:synonym "mRNA" xsd:string property_value: mged:synonym "polyA+_RNA" xsd:string [Instance] id: mged:polylysine instance_of: mged:SurfaceType comment: a surface coating for immobilization with the polypeptide, polylysine property_value: mged:unique_identifier "MO_569" xsd:string [Instance] id: mged:polypeptide instance_of: mged:DeprecatedTerms comment: sequence of a protein, a linear amino acid polymer relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_530" xsd:string [Instance] id: mged:polyploid instance_of: mged:Ploidy comment: Describes a cell, nucleus or organism with three or more copies of each chromosome. property_value: mged:unique_identifier "MO_394" xsd:string [Instance] id: mged:polysomy instance_of: mged:ChromosomalAberrationClassification comment: A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement. property_value: mged:unique_identifier "MO_1030" xsd:string [Instance] id: mged:pool instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The process of combining two or more BioMaterials. \nExact synonym: combine property_value: mged:unique_identifier "MO_779" xsd:string property_value: mged:synonym "combine" xsd:string [Instance] id: mged:population_density instance_of: mged:EnvironmentalFactorCategory comment: The concentration range of the organism. property_value: mged:unique_identifier "MO_650" xsd:string [Instance] id: mged:positive instance_of: mged:Result comment: true or yes property_value: mged:unique_identifier "MO_429" xsd:string [Instance] id: mged:positive_float instance_of: mged:DataType comment: A float > 0. property_value: mged:unique_identifier "MO_501" xsd:string [Instance] id: mged:positive_integer instance_of: mged:DataType comment: An integer > 0. property_value: mged:unique_identifier "MO_629" xsd:string [Instance] id: mged:postmortem instance_of: mged:OrganismStatus comment: biomaterial removed after the death of the organism property_value: mged:unique_identifier "MO_416" xsd:string [Instance] id: mged:predicted_gene instance_of: mged:DeprecatedTerms comment: gene sequence which has been computationally predicted relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:deprecation_in_version "1.3.1.1" xsd:string property_value: mged:unique_identifier "MO_838" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:premortem instance_of: mged:OrganismStatus comment: sample which has been removed prior to the death of an organism property_value: mged:unique_identifier "MO_705" xsd:string [Instance] id: mged:preservation instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The type of protocol used to preserve (including storage or keep in stasis) the biomaterial. property_value: mged:unique_identifier "MO_415" xsd:string [Instance] id: mged:primary_protein_structure_record instance_of: mged:DatabaseEntryType comment: A record which describes and identifies an experimentally derived protein structure e.g. MSD property_value: mged:unique_identifier "MO_785" xsd:string [Instance] id: mged:primary_site instance_of: mged:CancerSite comment: the organism part in which the tumor originated property_value: mged:unique_identifier "MO_408" xsd:string [Instance] id: mged:promoter instance_of: mged:DeprecatedTerms comment: genomic sequence 5' to a gene where the transcription initiation complex forms. relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_911" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:protein instance_of: mged:MaterialType instance_of: mged:PolymerType comment: Polymer of amino acids. property_value: mged:unique_identifier "MO_683" xsd:string [Instance] id: mged:purify instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: 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). property_value: mged:unique_identifier "MO_406" xsd:string [Instance] id: mged:quality_control_testing_design instance_of: mged:MethodologicalDesign comment: A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance property_value: mged:unique_identifier "MO_981" xsd:string [Instance] id: mged:quantile_normalization instance_of: mged:NormalizationDescriptionType comment: 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. property_value: mged:unique_identifier "MO_951" xsd:string [Instance] id: mged:quantile_normalization_protocol_type instance_of: mged:DataTransformationProtocolType comment: Application of a normalization of type quantile_normalization. property_value: mged:unique_identifier "MO_457" xsd:string [Instance] id: mged:rRNA_gene instance_of: mged:DeprecatedTerms comment: sequence from gene coding for ribosomal RNA\nexact synonym: ribosomal RNA gene relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:synonym "ribosomal RNA gene" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_955" xsd:string [Instance] id: mged:ratio instance_of: mged:DerivedBioAssayType comment: 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. property_value: mged:unique_identifier "MO_597" xsd:string [Instance] id: mged:ratio_statistics_normalization instance_of: mged:NormalizationDescriptionType comment: 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. property_value: mged:unique_identifier "MO_349" xsd:string [Instance] id: mged:real_time_PCR_quality_control instance_of: mged:QualityControlDescriptionType comment: A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes. property_value: mged:unique_identifier "MO_434" xsd:string [Instance] id: mged:rectangular_feature instance_of: mged:FeatureShape comment: The shape of the feature on the array is rectangular. property_value: mged:unique_identifier "MO_897" xsd:string [Instance] id: mged:reference_design instance_of: mged:MethodologicalDesign comment: A reference experiment design type is where all samples are compared to a common reference. property_value: mged:unique_identifier "MO_699" xsd:string [Instance] id: mged:relative instance_of: mged:MeasurementType comment: a measurement where the value is dependent on another measurement property_value: mged:unique_identifier "MO_396" xsd:string [Instance] id: mged:relative_humidity instance_of: mged:EnvironmentalFactorCategory comment: The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding. property_value: mged:unique_identifier "MO_453" xsd:string [Instance] id: mged:remove instance_of: mged:AtomicAction comment: The procedure of extracting/taking out a part of a reaction/contents of a container. property_value: mged:unique_identifier "MO_713" xsd:string [Instance] id: mged:replaced_term instance_of: mged:DeprecationReason comment: The term name was changed to one more appropriate to the intent of the definition. property_value: mged:unique_identifier "MO_1026" xsd:string [Typedef] id: mged:replaced_with_term is_metadata_tag: true comment: The value of the property indicates the replacement term. property_value: mged:unique_identifier "MO_1018" xsd:string [Instance] id: mged:replicate_analysis instance_of: mged:DataTransformationProtocolType comment: 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. property_value: mged:unique_identifier "MO_433" xsd:string [Instance] id: mged:replicate_design instance_of: mged:MethodologicalDesign comment: 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. property_value: mged:unique_identifier "MO_885" xsd:string [Instance] id: mged:resuspend instance_of: mged:AtomicAction comment: The procedure in which solid material is dispensed or dissolved in a liquid. property_value: mged:unique_identifier "MO_466" xsd:string [Instance] id: mged:reverse instance_of: mged:StrandType comment: the reverse strand\nexact synonym: - property_value: mged:synonym "-" xsd:string property_value: mged:unique_identifier "MO_402" xsd:string [Instance] id: mged:reverse_transcription instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: Generation of a DNA strand from an RNA strand using reverse transcriptase. property_value: mged:unique_identifier "MO_480" xsd:string [Instance] id: mged:reverse_transcription_PCR_quality_control instance_of: mged:QualityControlDescriptionType comment: A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes. property_value: mged:unique_identifier "MO_986" xsd:string [Instance] id: mged:sacrifice instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: The procedure of euthanizing an organism. property_value: mged:unique_identifier "MO_602" xsd:string [Instance] id: mged:sampling_time_point instance_of: mged:BioMaterialCharacteristicCategory comment: 
The time point that a sample was taken. Not to be used where the sample is part of a time\ncourse. SamplingTimePoint is not related to age. An instance could be summer, a date, a time, or a range value
property_value: mged:unique_identifier "MO_866" xsd:string [Instance] id: mged:seconds instance_of: mged:TimeUnit comment: time unit property_value: mged:unique_identifier "MO_391" xsd:string [Instance] id: mged:secreted_protein_identification_design instance_of: mged:BioMolecularAnnotation comment: 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. property_value: mged:unique_identifier "MO_694" xsd:string [Instance] id: mged:seed_dormancy instance_of: mged:PreservationType comment: preservation type whereby the seed is maintained in a dormant state property_value: mged:unique_identifier "MO_666" xsd:string [Instance] id: mged:self_vs_self_design instance_of: mged:MethodologicalDesign comment: A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared. property_value: mged:unique_identifier "MO_490" xsd:string [Instance] id: mged:semisolid instance_of: mged:Media comment: semisolid media type property_value: mged:unique_identifier "MO_635" xsd:string [Instance] id: mged:set_temperature instance_of: mged:AtomicAction comment: An action where the temperature is specified. property_value: mged:unique_identifier "MO_393" xsd:string [Instance] id: mged:sex instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor for FactorValue where Sex is compared. property_value: mged:unique_identifier "MO_680" xsd:string [Instance] id: mged:sex_design instance_of: mged:BiologicalProperty comment: A sex experiment design type assays differences associated with an organism's sex, gender or mating type. property_value: mged:unique_identifier "MO_575" xsd:string [Instance] id: mged:short_oligo instance_of: mged:DesignElement comment: An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes). property_value: mged:unique_identifier "MO_749" xsd:string [Instance] id: mged:signal instance_of: mged:DerivedBioAssayType comment: A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software). property_value: mged:unique_identifier "MO_534" xsd:string [Instance] id: mged:signal_log_ratio instance_of: mged:DeprecatedTerms comment: 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 \nratio of 1 is the same as a Fold Change of 2. relationship: mged:deprecated_from_version mged:version_1.1.7 relationship: mged:deprecation_old_parent mged:DerivedBioAssayType relationship: mged:deprecation_replacement_term mged:DerivedBioAssayType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_941" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:silicon instance_of: mged:SubstrateType comment: the array is made on silicon property_value: mged:unique_identifier "MO_382" xsd:string [Instance] id: mged:single_stranded instance_of: mged:StrandType comment: a nucleic acid consisting of a single polynucleotide chain. property_value: mged:unique_identifier "MO_576" xsd:string [Instance] id: mged:sister instance_of: mged:FamilyRelationship comment: A female having the same genetic parents as another, or one genetic parent in common with another. property_value: mged:unique_identifier "MO_723" xsd:string [Instance] id: mged:slice_analysis instance_of: mged:DeprecatedTerms comment: 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. relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:NormalizationDescriptionType relationship: mged:deprecation_replacement_term mged:NormalizationDescriptionType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_531" xsd:string [Instance] id: mged:snRNA_gene instance_of: mged:DeprecatedTerms comment: sequence from gene coding for small nuclear RNA\nexact synonym: small nuclear RNA gene relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:synonym "small nuclear RNA gene" xsd:string property_value: mged:unique_identifier "MO_961" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_old_parent "deleted_term" xsd:string [Instance] id: mged:software_manufacturer instance_of: mged:Roles comment: Person or organization that manufactured the software. property_value: mged:unique_identifier "MO_475" xsd:string [Instance] id: mged:software_variation_design instance_of: mged:MethodologicalDesign comment: A software variation design type compares different types of software for performance, accuracy, precision and reproducibility. property_value: mged:unique_identifier "MO_643" xsd:string [Instance] id: mged:soil instance_of: mged:Media comment: soil, growth media for plants and other soil living organisms property_value: mged:unique_identifier "MO_821" xsd:string [Instance] id: mged:son instance_of: mged:FamilyRelationship comment: The male offspring of the patient or individual under study. property_value: mged:unique_identifier "MO_465" xsd:string [Instance] id: mged:sonicator instance_of: mged:HardwareType comment: An instrument for sonicating biomaterials. property_value: mged:unique_identifier "MO_477" xsd:string [Instance] id: mged:sowing instance_of: mged:InitialTimePoint comment: the process of placing a seed or spore in some media with the intention to invoke germination. property_value: mged:unique_identifier "MO_748" xsd:string [Instance] id: mged:species_design instance_of: mged:BiologicalProperty comment: A species experiment design type assays differences between distinct species. property_value: mged:unique_identifier "MO_675" xsd:string [Instance] id: mged:species_specific_design_element_group_type instance_of: mged:DesignElementGroupType comment: A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species. property_value: mged:unique_identifier "MO_395" xsd:string [Instance] id: mged:specified_biomaterial_action instance_of: mged:AtomicAction instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: Conceptual action for specified protocol applied in treatment. property_value: mged:unique_identifier "MO_968" xsd:string [Instance] id: mged:spectrophotometer instance_of: mged:HardwareType comment: Hardware for measuring light at different wavelengths. property_value: mged:synonym "thermocycler" xsd:string property_value: mged:unique_identifier "MO_716" xsd:string [Instance] id: mged:spike_quality_control instance_of: mged:QualityControlDescriptionType comment: An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes. property_value: mged:unique_identifier "MO_937" xsd:string [Instance] id: mged:spin instance_of: mged:AtomicAction comment: The procedure of applying a centrifugal force to a physical object.\nExact synonym: centrifuge property_value: mged:synonym "centrifuge" xsd:string property_value: mged:unique_identifier "MO_879" xsd:string [Instance] id: mged:split instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: 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).\nNon exact Synonym: sample property_value: mged:unique_identifier "MO_835" xsd:string property_value: mged:synonym "sample" xsd:string [Instance] id: mged:split_term instance_of: mged:DeprecationReason comment: the term has been decomposed into more specific terms property_value: mged:unique_identifier "MO_1027" xsd:string [Typedef] id: mged:split_to_term is_metadata_tag: true comment: The value of the property indicates a replacement term since the term was split. property_value: mged:unique_identifier "MO_1017" xsd:string [Instance] id: mged:spotted_antibody_features instance_of: mged:TechnologyType comment: TechnologyType of FeatureGroup where antibodies are spotted directly. property_value: mged:unique_identifier "MO_483" xsd:string [Instance] id: mged:spotted_colony_features instance_of: mged:TechnologyType comment: TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly. property_value: mged:unique_identifier "MO_618" xsd:string [Instance] id: mged:spotted_ds_DNA_features instance_of: mged:TechnologyType comment: 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. property_value: mged:unique_identifier "MO_499" xsd:string [Instance] id: mged:spotted_protein_features instance_of: mged:TechnologyType comment: TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly. property_value: mged:unique_identifier "MO_996" xsd:string [Instance] id: mged:spotted_ss_PCR_amplicon_features instance_of: mged:TechnologyType comment: A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array. property_value: mged:unique_identifier "MO_921" xsd:string [Instance] id: mged:spotted_ss_oligo_features instance_of: mged:TechnologyType comment: The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate. property_value: mged:unique_identifier "MO_579" xsd:string [Instance] id: mged:square_feature instance_of: mged:FeatureShape comment: The shape of the feature on the array is square. property_value: mged:unique_identifier "MO_817" xsd:string [Instance] id: mged:ss_oligo instance_of: mged:DeprecatedTerms comment: sequence of a single stranded synthesized oligonucleotide relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_570" xsd:string [Instance] id: mged:starvation instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: Depriving an organism of food or nutrients property_value: mged:unique_identifier "MO_370" xsd:string [Instance] id: mged:stimulated_design_type instance_of: mged:PerturbationalDesign comment: A design in which a behavior is invoked by a variable controlled by the experimenter - e.g. administration of a drug that effects aggressivity. property_value: mged:unique_identifier "MO_958" xsd:string [Instance] id: mged:stimulus_or_stress_design instance_of: mged:PerturbationalDesign comment: 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. property_value: mged:unique_identifier "MO_568" xsd:string [Instance] id: mged:store instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: 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. property_value: mged:unique_identifier "MO_442" xsd:string [Instance] id: mged:strain_or_line instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor of FactorValue where comparisons of strains or lines are made. property_value: mged:unique_identifier "MO_859" xsd:string [Instance] id: mged:strain_or_line_design instance_of: mged:BiologicalProperty comment: A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. property_value: mged:unique_identifier "MO_462" xsd:string [Instance] id: mged:string_datatype instance_of: mged:DataType comment: The values are a sequence of one or more characters. property_value: mged:unique_identifier "MO_352" xsd:string [Instance] id: mged:subcutaneous instance_of: mged:DeliveryMethod comment: Delivery method whereby a drug or compound is administered under the skin of the organism. property_value: mged:unique_identifier "MO_960" xsd:string [Instance] id: mged:submitter instance_of: mged:Roles comment: Person who is the primary contact for data submitted to a database. property_value: mged:unique_identifier "MO_882" xsd:string [Typedef] id: mged:synonym is_metadata_tag: true comment: This property is used to indicate additional terms that have the same meaning as the term that the property is applied to. The terms that have the same meaning as the term that this property is applied to will be the value of the property. property_value: mged:unique_identifier "MO_333" xsd:string [Instance] id: mged:synthetic_DNA instance_of: mged:MaterialType comment: DNA which is generated by chemical or enzymatic (non cellular) means.\nnon-exact synonym: cDNA property_value: mged:unique_identifier "MO_577" xsd:string property_value: mged:synonym "cDNA" xsd:string [Instance] id: mged:synthetic_RNA instance_of: mged:MaterialType comment: RNA which is generated by chemical or enzymatic (non cellular) means. E.g. T7 promotor generated RNA.\nNon-exact synonym:\ncRNA, complementary RNA\naRNA, amplified RNA property_value: mged:synonym "complementary RNA" xsd:string property_value: mged:synonym "cRNA" xsd:string property_value: mged:synonym "aRNA" xsd:string property_value: mged:synonym "amplified RNA" xsd:string property_value: mged:unique_identifier "MO_543" xsd:string [Instance] id: mged:tRNA_gene instance_of: mged:DeprecatedTerms comment: sequence from a gene coding for transfer RNA\nexact synonym: transfer RNA gene relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_850" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:synonym "transfer RNA gene" xsd:string [Instance] id: mged:tau_rank_correlation instance_of: mged:DeprecatedTerms comment: a nonparametric measure of the agreement between two rankings relationship: mged:deprecated_from_version mged:version_1.1.7 relationship: mged:deprecation_old_parent mged:NodeValueType relationship: mged:deprecation_replacement_term mged:NodeValueType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_673" xsd:string [Instance] id: mged:technical_replicate instance_of: mged:QualityControlDescriptionType instance_of: mged:ReplicateDescriptionType comment: 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. property_value: mged:unique_identifier "MO_641" xsd:string [Instance] id: mged:temperature instance_of: mged:EnvironmentalFactorCategory comment: Temperature associated with a particular environment. property_value: mged:unique_identifier "MO_791" xsd:string [Instance] id: mged:thermal_cycler instance_of: mged:HardwareType comment: An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR.\nExact Synonym: thermocycler property_value: mged:unique_identifier "MO_854" xsd:string [Instance] id: mged:tiling_path_design instance_of: mged:BioMolecularAnnotation comment: 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. property_value: mged:unique_identifier "MO_507" xsd:string [Instance] id: mged:time_series_design instance_of: mged:MethodologicalDesign comment: Groups of assays that are related as part of a time series. property_value: mged:unique_identifier "MO_887" xsd:string [Instance] id: mged:timepoint instance_of: mged:ComplexAction comment: Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. property_value: mged:unique_identifier "MO_738" xsd:string [Instance] id: mged:total_RNA instance_of: mged:MaterialType comment: Total cellular and nuclear RNA. property_value: mged:unique_identifier "MO_373" xsd:string [Instance] id: mged:total_intensity_normalization instance_of: mged:DeprecatedTerms comment: 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. relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:NormalizationDescriptionType relationship: mged:deprecation_replacement_term mged:NormalizationDescriptionType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_441" xsd:string [Instance] id: mged:total_intensity_normalization_paired instance_of: mged:DataTransformationProtocolType comment: 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. property_value: mged:unique_identifier "MO_686" xsd:string [Instance] id: mged:total_intensity_normalization_single instance_of: mged:DataTransformationProtocolType comment: 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\nemploys the average intensity rather than the sum (of all data points, or an appropriate subset) falls into this category as well. property_value: mged:unique_identifier "MO_472" xsd:string [Instance] id: mged:transcript instance_of: mged:DeprecatedTerms comment: sequence that represents the product of an RNA polymerase engaged in transcription relationship: mged:deprecation_old_parent mged:TheoreticalBioSequenceType relationship: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:unique_identifier "MO_827" xsd:string property_value: mged:deprecation_in_version "1.3.1.1" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:transcript_identification_design instance_of: mged:BioMolecularAnnotation instance_of: mged:TechnologicalDesign comment: A transcript identification design type characterizes the length and \n position of transcripts and allows identification of all forms of \n transcripts in the genome. property_value: mged:unique_identifier "MO_533" xsd:string property_value: mged:synonym "transcription_profiling" xsd:string property_value: mged:synonym "gene expression" xsd:string property_value: mged:synonym "expression_profiling" xsd:string property_value: mged:synonym "gene_expression" xsd:string property_value: mged:synonym "transcription profiling" xsd:string property_value: mged:synonym "expression profiling" xsd:string [Instance] id: mged:transfect instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: 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. property_value: mged:unique_identifier "MO_849" xsd:string [Instance] id: mged:transfection instance_of: mged:GeneticModification comment: Introduction of genetic material into an organism often in the form of a plasmid. property_value: mged:unique_identifier "MO_366" xsd:string [Instance] id: mged:translational_bias_design instance_of: mged:BioMolecularAnnotation comment: A translational bias is an experiment design which characterizes the association of transcripts and translation machinery. property_value: mged:unique_identifier "MO_939" xsd:string [Instance] id: mged:trisomy instance_of: mged:DeprecatedTerms comment: The possession of a third chromosome of any one type in an otherwise diploid cell. relationship: mged:deprecated_from_version mged:version_1.1.9 relationship: mged:deprecation_old_parent mged:ChromosomalAberrationClassification relationship: mged:has_reason_for_deprecation mged:replaced_term relationship: mged:replaced_with_term mged:polysomy relationship: mged:was_replaced_by mged:polysomy property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: mged:unique_identifier "MO_494" xsd:string property_value: mged:deprecation_reason "replaced_term" xsd:string [Instance] id: mged:tumor_grading instance_of: mged:BioMaterialCharacteristicCategory comment: A descriptor used in cancer biology to describe abnormalities of tumor cells. property_value: mged:unique_identifier "MO_843" xsd:string [Instance] id: mged:uM instance_of: mged:ConcentrationUnit comment: Micromole per liter or micromolar, concentration unit property_value: mged:unique_identifier "MO_740" xsd:string [Instance] id: mged:ug instance_of: mged:MassUnit comment: microgram, unit of mass property_value: mged:unique_identifier "MO_438" xsd:string [Instance] id: mged:ul instance_of: mged:VolumeUnit comment: microliter, unit of volume property_value: mged:unique_identifier "MO_926" xsd:string [Instance] id: mged:um instance_of: mged:DistanceUnit comment: micrometer, unit of distance property_value: mged:unique_identifier "MO_421" xsd:string [Instance] id: mged:umol instance_of: mged:QuantityUnit comment: micromoles, quantity unit property_value: mged:unique_identifier "MO_752" xsd:string [Instance] id: mged:uncentered_Pearson_correlation instance_of: mged:NodeValueType comment: 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. property_value: mged:unique_identifier "MO_974" xsd:string [Instance] id: mged:uncle instance_of: mged:FamilyRelationship comment: The brother of one's father or mother. property_value: mged:unique_identifier "MO_950" xsd:string [Typedef] id: mged:unique_identifier is_metadata_tag: true comment: A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123. property_value: mged:unique_identifier "MO_331" xsd:string [Instance] id: mged:unknown_basis_feature instance_of: mged:SeqFeatureBasis comment: Sequence feature whose derivation is unknown. property_value: mged:unique_identifier "MO_525" xsd:string [Instance] id: mged:unknown_experiment_design_type instance_of: mged:BioMolecularAnnotation instance_of: mged:BiologicalProperty instance_of: mged:EpidemiologicalDesign instance_of: mged:MethodologicalDesign instance_of: mged:PerturbationalDesign comment: ExperimentDesignType of unknown type. property_value: mged:unique_identifier "MO_634" xsd:string [Instance] id: mged:unknown_protocol_type instance_of: mged:ExperimentalProtocolType comment: ProtocolType of unknown type. property_value: mged:unique_identifier "MO_460" xsd:string [Instance] id: mged:unknown_sequence instance_of: mged:PhysicalBioSequenceType instance_of: mged:TheoreticalBioSequenceType comment: BioSequence of unknown type property_value: mged:unique_identifier "MO_535" xsd:string [Instance] id: mged:unknown_sex instance_of: mged:Sex comment: organism(s) whose sex is unknown property_value: mged:unique_identifier "MO_999" xsd:string [Instance] id: mged:unknown_substrate_type instance_of: mged:SubstrateType comment: SubstrateType of unknown type. property_value: mged:unique_identifier "MO_484" xsd:string [Instance] id: mged:unknown_surface_type instance_of: mged:SurfaceType comment: A SurfaceType of unknown type. property_value: mged:unique_identifier "MO_359" xsd:string [Instance] id: mged:unscaled instance_of: mged:Scale comment: The values are unordered and have no scale. property_value: mged:unique_identifier "MO_542" xsd:string [Instance] id: mged:urine instance_of: mged:BioSourceType comment: The fluid and dissolved substances excreted by the kidney. property_value: mged:unique_identifier "MO_399" xsd:string [Instance] id: mged:us instance_of: mged:TimeUnit comment: microsecond, unit of time property_value: mged:unique_identifier "MO_795" xsd:string [Instance] id: mged:vacuum_dryer instance_of: mged:HardwareType comment: An instrument designed to remove excess liquid by vacuum and heating. property_value: mged:unique_identifier "MO_696" xsd:string [Instance] id: mged:vector instance_of: mged:DeprecatedTerms comment: 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. relationship: mged:deprecated_from_version mged:version_1.2.0 relationship: mged:deprecation_old_parent mged:PhysicalBioSequenceType relationship: mged:deprecation_replacement_term mged:PhysicalBioSequenceType relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_551" xsd:string [Instance] id: mged:version_1.1.7 instance_of: mged:MGEDOntologyVersion comment: Version of the MGED Ontology. property_value: mged:unique_identifier "MO_1031" xsd:string [Instance] id: mged:version_1.1.8 instance_of: mged:MGEDOntologyVersion comment: Version of the MGED Ontology. property_value: mged:unique_identifier "MO_469" xsd:string [Instance] id: mged:version_1.1.9 instance_of: mged:MGEDOntologyVersion comment: Version of the MGEDOntology. property_value: mged:unique_identifier "MO_1032" xsd:string [Instance] id: mged:version_1.2.0 instance_of: mged:MGEDOntologyVersion comment: Version of the MGEDOntology. property_value: mged:unique_identifier "MO_1033" xsd:string [Instance] id: mged:version_1.3.0 instance_of: mged:MGEDOntologyVersion comment: Version of the MGEDOntology. property_value: mged:unique_identifier "MO_440" xsd:string [Instance] id: mged:version_1.3.1 instance_of: mged:MGEDOntologyVersion comment: Version of the MGED Ontology. property_value: mged:unique_identifier "MO_1034" xsd:string [Instance] id: mged:virus instance_of: mged:MaterialType comment: one or more DNA or RNA based non cellular infective agent, including bacteriophage property_value: mged:unique_identifier "MO_372" xsd:string [Instance] id: mged:vortexer instance_of: mged:HardwareType comment: An instrument that mixes by rapid oscillation. property_value: mged:unique_identifier "MO_983" xsd:string [Instance] id: mged:wait instance_of: mged:AtomicAction comment: Allow time to pass. It's measurement should be a unit of time. property_value: mged:unique_identifier "MO_988" xsd:string [Typedef] id: mged:was_replaced_by comment: instance property to indicate what the term was replaced by property_value: mged:unique_identifier "MO_304" xsd:string [Typedef] id: mged:was_tested_for comment: property indicating that the class was tested for property_value: mged:unique_identifier "MO_265" xsd:string [Instance] id: mged:wash instance_of: mged:ComplexAction instance_of: mged:ExperimentalProtocolType comment: 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. property_value: mged:unique_identifier "MO_596" xsd:string [Instance] id: mged:wash_station instance_of: mged:HardwareType comment: An instrument designed to mechanically wash or stain arrays. property_value: mged:unique_identifier "MO_626" xsd:string [Instance] id: mged:water instance_of: mged:EnvironmentalFactorCategory comment: Water consumed by or enveloping the organism that the biosource is derived from. property_value: mged:unique_identifier "MO_380" xsd:string [Instance] id: mged:waterbath instance_of: mged:HardwareType comment: A device for controlling temperature by immersion in water. property_value: mged:unique_identifier "MO_541" xsd:string [Instance] id: mged:weeks instance_of: mged:TimeUnit comment: 7 days, unit of time property_value: mged:unique_identifier "MO_842" xsd:string [Instance] id: mged:whole_organism instance_of: mged:MaterialType comment: one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria property_value: mged:unique_identifier "MO_566" xsd:string [Instance] id: mged:wild_type instance_of: mged:Allele instance_of: mged:Genotype comment: 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. property_value: mged:unique_identifier "MO_605" xsd:string [Instance] id: mged:within_bioassay_data_set_function instance_of: mged:DataTransformationProtocolType comment: A function applied to subsets of values from the same Measured/Derived bioassay data set. property_value: mged:unique_identifier "MO_668" xsd:string [Instance] id: mged:x_times instance_of: mged:ConcentrationUnitOther comment: multiple of stock solution concentration, concentration unit property_value: mged:unique_identifier "MO_496" xsd:string [Instance] id: mged:years instance_of: mged:TimeUnit comment: 365 days, time unit property_value: mged:unique_identifier "MO_948" xsd:string [Instance] id: mged:yes instance_of: mged:DeprecatedTerms comment: true relationship: mged:deprecated_from_version mged:version_1.1.7 relationship: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_540" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string