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"The MGED Ontology"

Ontology Container Information

Title:"The MGED Ontology" Classes:233
Creator:Chris Stoeckert, Helen Parkinson, Trish Whetzel, Paul Spellman, Catherine A. Ball, Joseph White, John Matese, Liju Fan, Gilberto Fragoso, Mervi Heiskanen, Susanna Sansone, Helen Causton, Laurence Game, Chris Taylor Properties:143
Subject:An ontology for microarray experiments in support of MAGE v.1. Individuals:681
Description:Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1 Axioms:0
Date:Feb. 9, 2007
Version:"1.3.1.1"

Note that this page now reflects the latest version 1.3.1.1. The previous verion (1.2.0) displayed is still available as an OWL file (see link below)

Deprecated Biosequence terms

Several of the MO BioSequence Terms have been deprecated as they map directly to the Sequence Ontology terms. A mapping file for the MO to SO terms is available.

Notes and edits to MO 1.3

Notes files for changes in MO version 1.3.0 and MO version 1.3.1.

Notes and edits to MO 1.2

A notes file containing edits, bug fixes, and additions is provided to document changes.

Notes and edits to MO 1.1.7/8/9

A notes file containing edits, bug fixes, and additions is provided to document changes.

Ontology terms under review

A tracker on sourceforge has been set up for new terms.

Mapping between MO and other Ontologies

MO terms mapped to the OBI/OBO foundry ontologies terms

Several of the MO Terms mapped to the ontology for Biomedical Investigation. A mapping file for the MO to OBI/OBO terms is available for review.
A list of the MO Terms mapped to OBO foundry ontologies (including PATO, SO, and UO) terms. A mapping file for the MO to OBO terms is available for review.

MO terms mapped to the Experimental Factor Ontology (EFO) terms

Total 189 of the MO Terms mapped to the EFO terms. Most of these terms are imported to EFO from MO. A mapping file can be viewed here.

Alternate views of the MGED Ontology

The MGED Ontology can be viewed by BioPortal

A static view of the class hierarchy can be found here.

The classes and individuals in the MGED Ontology can be viewed in the Excel format.


Files

OWL
http://mged.sourceforge.net/ontologies/MGEDOntology.owl
OWL (previous version 1.3.0.1)
http://mged.sourceforge.net/ontologies/MGEDOntology.1.3.0.1.owl
OWL (previous version 1.2.0)
http://mged.sourceforge.net/ontologies/MGEDOntology.1.2.0.owl
OWL (previous version 1.1.9)
http://mged.sourceforge.net/ontologies/MGEDOntology.1.1.9.owl
Please note that this file is not an exact match of MOv1.1.9 in DAML as a couple additional terms have been added.
DAML
http://mged.sourceforge.net/ontologies/MGEDOntology.daml
DAML (previous version 1.1.9)
http://mged.sourceforge.net/ontologies/MGEDOntology.1.1.9.daml
DAML (previous version 1.1.8)
http://mged.sourceforge.net/ontologies/MGEDOntology.1.1.8.daml
RDFS
The RDFS file was found to be missing things and has been retired until a complete copy of the daml version is generated.

Classes

Action Age Allele ArrayDesignPackage ArrayGroup ArrayPackage Atmosphere AtomicAction AuditAndSecurityPackage BarrierFacility Bedding BibliographicReference BioAssay BioAssayData BioAssayDataCluster BioAssayDataPackage BioAssayPackage BioMaterial BioMaterialCharacteristicCategory BioMaterialCharacteristics BioMaterialPackage BioMaterialPurity BioMolecularAnnotation BioSample BioSampleType BioSequence BioSequencePackage BioSequenceType BioSource BioSourceProvider BioSourceType BiologicalFactorCategory BiologicalProperty Biometrics CancerSite CellLine CellLineDatabase CellType CellTypeDatabase CellularComponent CellularComponentDatabase ChromosomalAberration ChromosomalAberrationClassification ClinicalHistory ClinicalTreatment ClinicalTreatmentDatabase ComplexAction Compound CompoundDatabase ConcentrationUnit ConcentrationUnitOther Contact ControlType Cultivar DataTransformationProtocolType DataType Database DatabaseEntryType DefectType DeliveryMethod DeprecatedTerms DeprecationReason DerivedBioAssay DerivedBioAssayType DescriptionPackage DesignElement DesignElementGroup DesignElementGroupType DesignElementPackage DevelopmentalStage DevelopmentalStageDatabase DiseaseLocation DiseaseStaging DiseaseStagingDatabase DiseaseState DiseaseStateDatabase DistanceUnit DistanceUnitOther Ecotype EnvironmentalFactorCategory EnvironmentalHistory EnvironmentalStress EpidemiologicalDesign Experiment ExperimentDesign ExperimentDesignType ExperimentPackage ExperimentalFactor ExperimentalFactorCategory ExperimentalProtocolType FactorValue FactorValueDependency FactorValueSet FailType FamilyHistory FamilyMember FamilyRelationship FeatureDefect FeatureGroup FeatureShape Fiducial FiducialType Generation GeneticMaterial GeneticModification Genotype GeographicLocation GeographicLocationDatabase GrowthCondition Haplotype Hardware HardwareType HardwareVariation HigherLevelAnalysisPackage HigherLevelAnalysisProtocolType Histology HistologyDatabase HistoryFactor Host Humidity Image ImageFormat Individual IndividualChromosomalAbnormality IndividualGeneticCharacteristics InitialTimePoint LabelCompound LabeledExtract Light LightUnit MGEDCoreOntology MGEDExtendedOntology MGEDOntology MGEDOntologyVersion MassUnit MassUnitOther MaterialType Measurement MeasurementPackage MeasurementType Media MethodologicalDesign MethodologicalFactorCategory Node NodeValue NodeValueType NormalizationDescription NormalizationDescriptionType Nutrients Observation ObservationDatabase OntologyEntry OperatorVariation Organism OrganismDatabase OrganismPart OrganismPartDatabase OrganismStatus Organization OtherUnit Parameter PathogenTest Person PerturbationalDesign Phenotype PhenotypeDatabase PhysicalArrayDesign PhysicalBioAssay PhysicalBioSequenceType Ploidy PolymerType PopulationDensity Preservation PreservationType Protocol ProtocolPackage ProtocolParameterType ProtocolType ProtocolVariation PublicationType QualityControlDescription QualityControlDescriptionType QuantitationType QuantitationTypePackage QuantityUnit QuantityUnitOther RadiationUnit ReplicateDescription ReplicateDescriptionType Reporter Result Roles SamplingTimePoint Scale SeqFeatureBasis SequenceOntologyBioSequenceType SequenceOntologyDatabase Serotype Sex Software SoftwareType SoftwareVariation SomaticModification StrainOrLine StrainOrLineDatabase StrandType SubstrateType SurfaceType TargetedCellType TargetedCellTypeDatabase TechnologicalDesign TechnologyType Temperature TemperatureUnit Test TestResult TestType TestTypeDatabase TheoreticalBioSequenceType TimeUnit TimeUnitOther Transformation Treatment TumorGrading TumorGradingDatabase URI Unit User VolumeUnit VolumeUnitOther WarningType Water ZoneDefect

Properties

class_role class_source dc:contributor dc:coverage dc:creator dc:date dc:description dc:format dc:identifier dc:language dc:publisher dc:relation dc:rights dc:source dc:subject dc:title dc:type deprecated_from_version deprecation_in_version deprecation_old_parent deprecation_old_restriction deprecation_reason deprecation_replacement_term has_ID has_MAGE_description has_URI has_accession has_accession_version has_action has_additive has_address has_affiliation has_atmospheric_component has_authors has_been_treated has_bioassay_data has_bioassays has_biomaterial_characteristics has_biosource_type has_cancer_site has_category has_chromosomal_aberration_classification has_citation has_clinical_finding has_clinical_record has_clinical_treatment has_compound has_cubic_volume has_database has_database_entry_type has_description has_diameter has_disease_location has_disease_staging has_disease_state has_donor has_editor has_email has_experiment_design has_experiment_design_type has_experiment_factors has_factor_value has_factor_value_ontology_entry has_family_member has_family_relationship has_fax has_feature_shape has_fiducials has_first_name has_hardware has_height has_host has_host_part has_human_readable_URI has_image_format has_individual has_individual_genetic_characteristics has_initial_time_point has_issue has_laboratory_test has_last_name has_length has_machine_readable_URI has_make has_manufacturer has_mass has_maximum_measurement has_measurement has_measurement_type has_mid_initials has_model has_name has_node_value has_node_value_type has_nodes has_nutrient_component has_order has_organism_part has_owner has_pages has_parent_organization has_part_modified has_performer has_phone has_prior_disease_state has_property_set has_protocol has_providers has_publication has_publisher has_reason_for_deprecation has_result has_scale has_software has_species has_test_protocol has_test_result has_test_type has_text has_title has_toll_free_phone has_treatment has_type has_units has_value has_version has_volume has_year is_solvent is_user_defined protege:abstract protege:allowedParent protege:defaultLanguage protege:excludedTest protege:probeClass protege:readOnly protege:subclassesDisjoint protege:todoPrefix protege:todoProperty protege:usedLanguage replaced_with_term split_to_term synonym unique_identifier was_replaced_by was_tested_for xsp:base xsp:fractionDigits xsp:length xsp:maxExclusive xsp:maxInclusive xsp:maxLength xsp:minExclusive xsp:minInclusive xsp:minLength xsp:pattern xsp:totalDigits

Individuals

A ATCC_Cultures Adult_Mouse_Anatomy Affymetrix_DAT Affymetrix_average_difference BAC CABRI_Bacteria_and_Archaea_Strains CABRI_Filamentous_Fungi_Strains CABRI_HLA_typed_B_Cell_lines CABRI_Human_and_Animal_Cell_lines CABRI_Hybridomas CABRI_Yeasts_Strains CBIL_CV CLDB_Human_and_Animal_Cell_Line CellML ChEBI ChemID Ci Cy3 Cy5 DNA DNA_sequencer EMAP EST Euclidean_distance F FMA F_minus FlyBase_developmental_stage_database FlyBase_organism_part_database GIF GRAMENE GeneOntology HUMAT Hfr ICD-9-CM IU IUPAC_Clinical_Chemistry_Guidelines JAX_mouse_strains JPEG K L LOINC M MAD_stage MAS4_average_difference MAS5_signal MAS5_signal_log_ratio MBEI MESH MTB_Database Mammalian_Phenotype_Ontology NASC NCBI_taxonomy NCI_Thesaurus NCI_cell_type_database NCI_compound_database NCI_disease_staging_database NCI_disease_state_database NCI_geographic_location_database NCI_histology_database NCI_organism_part_database NCI_strain_or_line_database NCI_targeted_cell_type_database NCI_tumor_grading_database ORF PAC PCR PCR_amplicon PCR_amplification PCR_fail PCR_primer PCR_primer_forward PCR_primer_reverse PCR_questionable PNG Pathbase Pearson_correlation R RMA RNA RNA_stability_design Rad Rem SequenceOntology Spearmans_rank_correlation TAIR TAIR_arabidopsis_anatomy_ontology TAIR_arabidopsis_development_ontology TDMS TIFF UMLS U_per_L U_per_week WebRENI YAC _32P _33P absolute acclimatization acrossBioAssay_mean_and_coefficient_of_variation acrossBioAssay_mean_and_p_values acrossBioAssay_mean_and_standard_deviation acrossBioAssay_mean_and_variance across_bioassay_data_set_function activity_units_per_ml ad_libitum add agar agar_stab age alexa_350 alexa_430 alexa_488 alexa_532 alexa_546 alexa_568 alexa_594 alexa_633 alexa_660 alexa_680 all_pairs amino_acid_primary_sequence_record aminosilane amol aneuploid antibody array_manufacture_software array_manufacturer array_manufacturing array_platform_variation_design array_scanner arrayer atmosphere aunt averaged_intensity barrier_facility bedding beginning_of_stage behavior_design behavioral_design_type behavioral_stimulus bibliographic_record binding_site_identification_design bioassay_data_transformation_software bioassay_replicate_reduction biological_fluid_collection biological_replicate biological_resource_record biomaterial_provider biopsy biosequence_provider biotin birth blood book boolean brother cDNA_clone candela candelas_per_square_meter cc cell cell_component_comparison_design cell_cycle_design cell_line cell_lysate cell_ontology cell_type cell_type_comparison_design cells_per_ml cellular_modification_design cellular_process_design centrifuge cfu_per_ml change_biomaterial_characteristics change_humidity change_light change_temperature chrome_border chromosomal_deletion chromosomal_duplication chromosomal_insertion chromosomal_inversion chromosomal_substitution chromosomal_translocation chromosome circadian_rhythm_design clinical_history_design clinical_information clinical_record clinical_treatment clone_of_unknown_source clustered_data clustering_software cm co-expression_design coitus collapsed_spot_replicate comparative_genome_hybridization_design compound_based_treatment compound_record compound_treatment_design computational_feature computed_amino_acid_sequence_feature_record computed_nucleic_acid_sequence_feature_record computed_protein_structure_record computer concentrate condition_specificity consensus_DNA consensus_mRNA consortium_member consultant control_biosequence control_buffer control_design_element_group_type control_empty control_genomic_DNA control_hybridization_quality control_label control_reporter_size control_spike_calibration control_unknown_type cosine_distance cosmid count cpm ctDNA curated_amino_acid_sequence_record curated_gene_record curated_nucleic_acid_sequence_feature_record curator cytoplasmic_RNA data_analyst data_coder date daughter days decontaminate degrees_C degrees_F deleted_term development_or_differentiation_design developmental_stage diameter_aberration differential_expression differential_expression_software dilute diploid disease_staging disease_state disease_state_design displaced_feature_or_zone dissect dl dose_response_design double_stranded dpm ds_oligo dye_swap_design dye_swap_merge dye_swap_quality_control dye_swap_replicate dye_swap_replicate_reduction eVOC eclosion egg_laying element_design ellipsoid_feature environmental_history_design ex_vivo_design exemplar_mRNA exon experimental_and_computational_feature experimental_design_element_group_type experimental_feature extract fM family_history_design father feature_extraction feature_extraction_software feces feeding female fertilization fg filtered_data fl flag_filter flip-dye_consistency float fmol forward fractionate freeze_dried_sample french_railway_distance fresh_sample frozen_sample frozen_storage function_record funder g g_per_L gene gene_fragment gene_knock_in gene_knock_out genetic_modification genetic_modification_design genetic_variation genomic_DNA genomic_region_amplification genotyping_design germination glass gram_percent granddaughter grandfather grandmother grandson grow growth_condition_design half-life haploid hardware_manufacturer hardware_variation_design harvest hatching heating_block heavy_background hermaphrodite histological_slide_preparation homogenizer hours hybridization hybridization_chamber hybridization_station image_acquisition image_acquisition_software image_record imprinting_design in_medium in_situ_oligo_features in_vitro_design in_vivo_design inconclusive incubate individual individual_genetic_characteristic individual_genetic_characteristics_design induced_mutation infect injury_design innate_behavior_design inoculate institution integer intergenic intramuscular_injection intraperitoneal_injection intravenous intron investigator irradiate irregular_shape is_contaminated is_expressed_design iterative_mean_log_centering jackknife_Pearson_correlation journal_article kat_per_L kg kg_per_m2 labeling laser_ablation_mark light_duration light_intensity linear_amplification linear_regression_normalization linear_scale linlog_normalization linlog_transformation liquid liquid_handler liquid_handler_software list_of_booleans list_of_floats list_of_integers list_of_negative_floats list_of_negative_integers list_of_nonnegative_floats list_of_nonnegative_integers list_of_nonpositive_floats list_of_nonpositive_integers list_of_positive_floats list_of_positive_integers list_of_strings loess_global_normalization loess_group_normalization loess_normalization loess_scaled_group_normalization log_base_10 log_base_2 log_base_e log_ratio long_oligo loop_design low_intensity_filter lowess_global_normalization lowess_group_normalization lowess_normalization lowess_scaled_group_normalization lumen lux m mL_per_L mM mOsm_per_kg_H2O mRNA male manhattan_distance mating_type_a mating_type_alpha mating_type_h_minus mating_type_h_plus mean_and_coefficient_of_variation mean_and_confidence_indicators mean_and_p_values mean_and_standard_deviation mean_and_variance mean_log_centering mean_log_normalization media median_log_centering median_log_normalization merged_term metastatic_site mg mg_per_kg_per_day mg_per_ml microarray_experiment_record microeinstein_per_minute_and_square_meter microeinstein_per_second_and_square_meter micromole_per_second_and_square_meter minutes missing_feature_or_zone mix_by_inversion mix_by_pipette mix_by_vortex mix_general mixed_design_element_group_type mixed_sex ml ml_per_kg mm mol molecular_mixture molecules monosomy months mother moving_average ms mtDNA multiple_testing_correction negative negative_float negative_integer ng nitrocellulose nl nm nmol no non-targeted_transgenic_variation_design nonnegative_float nonnegative_integer nonpositive_float nonpositive_integer normalization_testing_design normalized_intensities normalized_ratios not_extract not_sequence_verified not_uniform nuclear_RNA nucleic_acid_extraction nucleic_acid_primary_sequence_record number_per_day nutrients nylon oligo_synthesizer oligosomy online_resource ontology_record openGALEN operating_system operator_variation_design operon operon_identification_design optimization_design oral_gavage organellar_DNA organellar_RNA organism organism_part organism_part_comparison_design organism_status organism_status_design pH pM paraffin_sample pathogenicity_design pathway_record pearson_correlation_coefficient pedigree_record peer_review_quality_control percent_confluence percent_purity percent_vol_per_vol percent_weight_per_vol percent_weight_per_weight pfu_per_ml pg phylogeny_record physical_characteristics physiological_process_design pl place planting plasmid pmol polyA_RNA polylysine polypeptide polyploid polysomy pool population_density positive positive_float positive_integer postmortem predicted_gene premortem preservation primary_protein_structure_record primary_site promoter protein purify quality_control_testing_design quantile_normalization quantile_normalization_protocol_type rRNA_gene ratio ratio_statistics_normalization real_time_PCR_quality_control rectangular_feature reference_design relative relative_humidity remove replaced_term replicate_analysis replicate_design resuspend reverse reverse_transcription reverse_transcription_PCR_quality_control sacrifice sampling_time_point seconds secreted_protein_identification_design seed_dormancy self_vs_self_design semisolid set_temperature sex sex_design short_oligo signal signal_log_ratio silicon single_stranded sister slice_analysis snRNA_gene software_manufacturer software_variation_design soil son sonicator sowing species_design species_specific_design_element_group_type specified_biomaterial_action spectrophotometer spike_quality_control spin split split_term spotted_antibody_features spotted_colony_features spotted_ds_DNA_features spotted_protein_features spotted_ss_PCR_amplicon_features spotted_ss_oligo_features square_feature ss_oligo starvation stimulated_design_type stimulus_or_stress_design store strain_or_line strain_or_line_design string_datatype subcutaneous submitter synthetic_DNA synthetic_RNA tRNA_gene tau_rank_correlation technical_replicate temperature thermal_cycler tiling_path_design time_series_design timepoint total_RNA total_intensity_normalization total_intensity_normalization_paired total_intensity_normalization_single transcript transcript_identification_design transfect transfection translational_bias_design trisomy tumor_grading uM ug ul um umol uncentered_Pearson_correlation uncle unknown_basis_feature unknown_experiment_design_type unknown_protocol_type unknown_sequence unknown_sex unknown_substrate_type unknown_surface_type unscaled urine us vacuum_dryer vector version_1.1.7 version_1.1.8 version_1.1.9 version_1.2.0 version_1.3.0 version_1.3.1 virus vortexer wait wash wash_station water waterbath weeks whole_organism wild_type within_bioassay_data_set_function x_times years yes

class Action

definition:
Procedures used during treatment.

superclasses:
    BioMaterialPackage
    BiologicalFactorCategory
known subclasses:
    AtomicAction
    ComplexAction
properties:
    unique_identifier MO_193
    class_role abstract
    class_source ontology

class Age

definition:
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).

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_178
    class_role abstract
    class_source ontology
constraints:
    restriction: has_measurement has-class Measurement
    restriction: has_maximum_measurement has-class Measurement
    restriction: has_initial_time_point has-class InitialTimePoint

class Allele

definition:
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.

superclasses:
    IndividualGeneticCharacteristics
properties:
    unique_identifier MO_58
    class_role concrete
    class_source ontology
used in individuals:
    wild_type

class ArrayDesignPackage

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

superclasses:
    MGEDCoreOntology
known subclasses:
    DesignElementGroup
    DesignElementGroupType
    FeatureShape
    PhysicalArrayDesign
    SurfaceType
    TechnologyType
properties:
    unique_identifier MO_33
    class_role abstract
    class_source mage

class ArrayGroup

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

superclasses:
    ArrayPackage
properties:
    unique_identifier MO_34
    class_role concrete
    class_source mage
constraints:
    restriction: has_fiducials has-class Fiducial
    restriction: has_type has-class SubstrateType

class ArrayPackage

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

superclasses:
    MGEDCoreOntology
known subclasses:
    ArrayGroup
    DefectType
    FeatureDefect
    Fiducial
    FiducialType
    SubstrateType
    ZoneDefect
properties:
    unique_identifier MO_107
    class_role abstract
    class_source mage

class Atmosphere

definition:
The atmospheric conditions used to culture or grow an organism.

superclasses:
    GrowthCondition
properties:
    unique_identifier MO_219
    class_role abstract
    class_source ontology
constraints:
    restriction: has_atmospheric_component has-class Compound

class AtomicAction

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

superclasses:
    Action
properties:
    unique_identifier MO_68
    class_role concrete
    class_source ontology
used in individuals:
    add
    change_humidity
    change_light
    change_temperature
    concentrate
    dilute
    mix_by_inversion
    mix_by_pipette
    mix_by_vortex
    mix_general
    place
    remove
    resuspend
    set_temperature
    specified_biomaterial_action
    spin
    wait

class AuditAndSecurityPackage

definition:
MAGE package for contacts including organizations and people.

superclasses:
    MGEDCoreOntology
known subclasses:
    Contact
    Roles
properties:
    unique_identifier MO_172
    class_role abstract
    class_source mage

class BarrierFacility

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

superclasses:
    GrowthCondition
properties:
    unique_identifier MO_97
    class_role abstract
    class_source ontology

class Bedding

definition:
Refers to the bedding material present in an animals housing.

superclasses:
    EnvironmentalHistory
properties:
    unique_identifier MO_154
    class_role place_holder
    class_source ontology

class BibliographicReference

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

superclasses:
    DescriptionPackage
properties:
    unique_identifier MO_201
    class_role concrete
    class_source mage
constraints:
    restriction: has_pages has-class string
    restriction: has_issue has-class string
    restriction: has_editor has-class string
    restriction: has_URI has-class URI
    restriction: has_volume has-class string
    restriction: has_authors has-class string
    restriction: has_type has-class PublicationType
    restriction: has_year has-class date
    restriction: has_publication has-class string
    restriction: has_publisher has-class string
    restriction: has_title has-class string

class BioAssay

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

superclasses:
    BioAssayPackage
known subclasses:
    DerivedBioAssay
    PhysicalBioAssay
properties:
    unique_identifier MO_56
    class_role abstract
    class_source mage

class BioAssayData

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

superclasses:
    BioAssayDataPackage
properties:
    unique_identifier MO_40

class BioAssayDataCluster

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

superclasses:
    HigherLevelAnalysisPackage
properties:
    unique_identifier MO_116
    class_role concrete
    class_source mage
constraints:
    restriction: has_nodes has-class Node

class BioAssayDataPackage

definition:
MAGE package for BioAssayData.

superclasses:
    MGEDExtendedOntology
known subclasses:
    BioAssayData
    Transformation
properties:
    unique_identifier MO_186

class BioAssayPackage

definition:
MAGE package for bioassay.

superclasses:
    MGEDCoreOntology
known subclasses:
    BioAssay
    DerivedBioAssayType
    ImageFormat
properties:
    unique_identifier MO_0
    class_role abstract
    class_source mage

class BioMaterial

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

superclasses:
    BioMaterialPackage
known subclasses:
    BioSample
    BioSource
    LabeledExtract
properties:
    unique_identifier MO_226
    class_role abstract
    class_source mage
constraints:
    restriction: has_type has-class MaterialType
    restriction: has_biomaterial_characteristics has-class BioMaterialCharacteristics

class BioMaterialCharacteristicCategory

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

superclasses:
    BiologicalFactorCategory
properties:
    unique_identifier MO_100
used in individuals:
    age
    biomaterial_provider
    cell_line
    cell_type
    clinical_information
    clinical_treatment
    developmental_stage
    disease_staging
    disease_state
    individual
    individual_genetic_characteristic
    organism
    organism_part
    organism_status
    physical_characteristics
    sampling_time_point
    sex
    strain_or_line
    tumor_grading

class BioMaterialCharacteristics

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

superclasses:
    BioMaterialPackage
    BiologicalFactorCategory
known subclasses:
    Age
    BioMaterialPurity
    Biometrics
    BioSourceProvider
    BioSourceType
    CellLine
    CellType
    CellularComponent
    ChromosomalAberrationClassification
    ClinicalTreatment
    DevelopmentalStage
    DiseaseStaging
    DiseaseState
    EnvironmentalHistory
    GeneticModification
    Histology
    Individual
    IndividualGeneticCharacteristics
    Observation
    Organism
    OrganismPart
    OrganismStatus
    Phenotype
    Serotype
    Sex
    StrainOrLine
    TargetedCellType
    Test
    TestResult
    TestType
    TumorGrading
properties:
    unique_identifier MO_5
    class_role abstract
    class_source ontology

class BioMaterialPackage

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

superclasses:
    MGEDCoreOntology
known subclasses:
    Action
    BioMaterial
    BioMaterialCharacteristics
    BioSampleType
    FamilyMember
    FamilyRelationship
    InitialTimePoint
    MaterialType
    Treatment
properties:
    unique_identifier MO_182
    class_role abstract
    class_source mage

class BioMaterialPurity

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

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_20
    class_role abstract
    class_source ontology

class BioMolecularAnnotation

definition:
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.

superclasses:
    ExperimentDesignType
properties:
    unique_identifier MO_213
    class_role concrete
    class_source ontology
used in individuals:
    RNA_stability_design
    binding_site_identification_design
    co-expression_design
    comparative_genome_hybridization_design
    genotyping_design
    operon_identification_design
    secreted_protein_identification_design
    tiling_path_design
    transcript_identification_design
    translational_bias_design
    unknown_experiment_design_type

class BioSample

definition:
The BioSource after any treatment.

superclasses:
    BioMaterial
properties:
    unique_identifier MO_93
    class_role concrete
    class_source mage
constraints:
    restriction: has_type has-class BioSampleType
    restriction: has_been_treated has-class Treatment

class BioSampleType

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

superclasses:
    BioMaterialPackage
properties:
    unique_identifier MO_161
    class_role concrete
    class_source ontology
used in individuals:
    extract
    not_extract

class BioSequence

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

superclasses:
    BioSequencePackage
properties:
    unique_identifier MO_163
    class_role concrete
    class_source mage
constraints:
    restriction: has_species has-class Organism
    restriction: has_type has-class PolymerType
    restriction: has_type has-class BioSequenceType

class BioSequencePackage

definition:
MAGE package for biological sequences (biosequence).

superclasses:
    MGEDCoreOntology
known subclasses:
    BioSequence
    BioSequenceType
    PolymerType
    SeqFeatureBasis
properties:
    unique_identifier MO_191
    class_role abstract
    class_source mage

class BioSequenceType

definition:
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).

superclasses:
    BioSequencePackage
known subclasses:
    PhysicalBioSequenceType
    TheoreticalBioSequenceType
properties:
    unique_identifier MO_152
    class_role abstract
    class_source ontology

class BioSource

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

superclasses:
    BioMaterial
properties:
    unique_identifier MO_77
    class_role concrete
    class_source mage

class BioSourceProvider

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

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_230
    class_role abstract
    class_source ontology
constraints:
    restriction: has_owner has-class Person
    restriction: has_donor has-class Organization

class BioSourceType

definition:
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.

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_95
    class_role concrete
    class_source ontology
used in individuals:
    agar_stab
    freeze_dried_sample
    fresh_sample
    frozen_sample
    paraffin_sample
    urine

class BiologicalFactorCategory

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

superclasses:
    ExperimentalFactorCategory
known subclasses:
    Action
    BioMaterialCharacteristicCategory
    BioMaterialCharacteristics
    Compound
properties:
    unique_identifier MO_190
    class_role abstract
    class_source ontology

class BiologicalProperty

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

superclasses:
    ExperimentDesignType
properties:
    unique_identifier MO_224
    class_role concrete
    class_source ontology
used in individuals:
    cell_component_comparison_design
    cell_cycle_design
    cell_type_comparison_design
    cellular_process_design
    development_or_differentiation_design
    imprinting_design
    individual_genetic_characteristics_design
    innate_behavior_design
    is_expressed_design
    organism_part_comparison_design
    organism_status_design
    physiological_process_design
    sex_design
    species_design
    strain_or_line_design
    unknown_experiment_design_type

class Biometrics

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

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_129
    class_role abstract
    class_source ontology
constraints:
    restriction: has_cubic_volume has-class Measurement
    restriction: has_mass has-class Measurement
    restriction: has_diameter has-class Measurement
    restriction: has_length has-class Measurement
    restriction: has_height has-class Measurement
    restriction: has_individual has-class Individual
    restriction: has_organism_part has-class OrganismPart

class CancerSite

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

superclasses:
    MGEDCoreOntology
properties:
    unique_identifier MO_26
    class_role concrete
    class_source ontology
used in individuals:
    metastatic_site
    primary_site

class CellLine

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

superclasses:
    OntologyEntry
    BioMaterialCharacteristics
properties:
    unique_identifier MO_49
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class CellLineDatabase

class CellLineDatabase

definition:
Database of cell line information.

superclasses:
    Database
properties:
    unique_identifier MO_145
    class_role concrete
    class_source ontology
used in individuals:
    ATCC_Cultures
    CABRI_HLA_typed_B_Cell_lines
    CABRI_Human_and_Animal_Cell_lines
    CABRI_Hybridomas
    CLDB_Human_and_Animal_Cell_Line

class CellType

definition:
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.

superclasses:
    BioMaterialCharacteristics
    OntologyEntry
properties:
    unique_identifier MO_135
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class CellTypeDatabase

class CellTypeDatabase

definition:
Database of cell type information.

superclasses:
    Database
properties:
    unique_identifier MO_141
    class_role concrete
    class_source ontology
used in individuals:
    CBIL_CV
    NCI_cell_type_database
    TAIR
    cell_ontology
    eVOC

class CellularComponent

definition:
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).

superclasses:
    OntologyEntry
    BioMaterialCharacteristics
properties:
    unique_identifier MO_1020
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class CellularComponentDatabase

class CellularComponentDatabase

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

superclasses:
    Database
properties:
    unique_identifier MO_1021
    class_role concrete
    class_source ontology
used in individuals:
    GeneOntology

class ChromosomalAberration

definition:
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.

superclasses:
    DeprecatedTerms
properties:
    deprecation_old_restriction some|has_chromosomal_aberration_classification|ChromosomalAberrationClassification
    deprecation_in_version 1.1.7
    unique_identifier MO_78
    class_role abstract
    class_source ontology
    deprecation_reason deleted_term
    deprecation_replacement_term ChromosomalAberration
constraints:
    restriction: has_reason_for_deprecation has-class deleted_term
    restriction: has_chromosomal_aberration_classification has-class ChromosomalAberrationClassification
    restriction: deprecated_from_version has-class version_1.1.7

class ChromosomalAberrationClassification

definition:
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.

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_6
    class_role concrete
    class_source ontology
used in individuals:
    chromosomal_deletion
    chromosomal_duplication
    chromosomal_insertion
    chromosomal_inversion
    chromosomal_translocation
    genomic_region_amplification
    oligosomy
    polysomy

class ClinicalHistory

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

superclasses:
    EnvironmentalHistory
properties:
    unique_identifier MO_189
    class_role abstract
    class_source ontology
constraints:
    restriction: has_clinical_treatment has-class ClinicalTreatment
    restriction: has_clinical_record has-class OntologyEntry
    restriction: has_clinical_finding has-class TestResult
    restriction: has_prior_disease_state has-class DiseaseState
    restriction: has_test_type has-class TestType

class ClinicalTreatment

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

superclasses:
    BioMaterialCharacteristics
    OntologyEntry
properties:
    unique_identifier MO_69
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class ClinicalTreatmentDatabase

class ClinicalTreatmentDatabase

definition:
Database of clinical treatment information

superclasses:
    Database
properties:
    unique_identifier MO_114
    class_role concrete
    class_source ontology

class ComplexAction

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

superclasses:
    Action
properties:
    unique_identifier MO_90
    class_role concrete
    class_source ontology
used in individuals:
    PCR_amplification
    acclimatization
    behavioral_stimulus
    biological_fluid_collection
    biopsy
    change_biomaterial_characteristics
    compound_based_treatment
    decontaminate
    dissect
    fractionate
    genetic_modification
    grow
    harvest
    histological_slide_preparation
    hybridization
    incubate
    inoculate
    irradiate
    labeling
    linear_amplification
    nucleic_acid_extraction
    pool
    preservation
    purify
    reverse_transcription
    sacrifice
    specified_biomaterial_action
    split
    starvation
    store
    timepoint
    transfect
    wash

class Compound

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

superclasses:
    OntologyEntry
    BiologicalFactorCategory
known subclasses:
    LabelCompound
properties:
    unique_identifier MO_70
    class_role abstract
    class_source ontology
constraints:
    restriction: has_measurement has-class Compound
    restriction: is_solvent has-class boolean
    restriction: has_database has-class CompoundDatabase

class CompoundDatabase

definition:
Database of compound information.

superclasses:
    Database
properties:
    unique_identifier MO_151
    class_role concrete
    class_source ontology
used in individuals:
    ChEBI
    ChemID
    NCI_compound_database

class ConcentrationUnit

definition:
Units used for concentration measurements.

superclasses:
    Unit
known subclasses:
    ConcentrationUnitOther
properties:
    unique_identifier MO_61
    class_role concrete
    class_source ontology
used in individuals:
    M
    U_per_L
    fM
    g_per_L
    gram_percent
    mL_per_L
    mM
    mg_per_ml
    pM
    percent_vol_per_vol
    percent_weight_per_vol
    percent_weight_per_weight
    uM

class ConcentrationUnitOther

definition:
Concentration units not specified in MAGE.

superclasses:
    ConcentrationUnit
properties:
    unique_identifier MO_86
    class_role concrete
    class_source ontology
used in individuals:
    cells_per_ml
    cfu_per_ml
    kat_per_L
    mOsm_per_kg_H2O
    mg_per_kg_per_day
    ml_per_kg
    pH
    percent_confluence
    percent_purity
    pfu_per_ml
    x_times

class Contact

definition:
Organizations or individuals that may be contacted.

superclasses:
    AuditAndSecurityPackage
known subclasses:
    Organization
    Person
properties:
    unique_identifier MO_147
    class_role abstract
    class_source mage
constraints:
    restriction: has_address has-class string
    restriction: has_phone has-class string
    restriction: has_URI has-class URI
    restriction: has_email has-class string
    restriction: has_fax has-class string
    restriction: has_toll_free_phone has-class string
    restriction: has_type has-class Roles

class ControlType

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

superclasses:
    DesignElementPackage
properties:
    unique_identifier MO_50
    class_role concrete
    class_source ontology
used in individuals:
    control_biosequence
    control_buffer
    control_empty
    control_genomic_DNA
    control_hybridization_quality
    control_label
    control_reporter_size
    control_spike_calibration
    control_unknown_type

class Cultivar

definition:
a plant variety obtained in agriculture in horticulture

superclasses:
    StrainOrLine
properties:
    unique_identifier MO_124
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class StrainOrLineDatabase

class DataTransformationProtocolType

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

superclasses:
    ProtocolType
properties:
    unique_identifier MO_165
    class_role concrete
    class_source ontology
used in individuals:
    across_bioassay_data_set_function
    dye_swap_merge
    flag_filter
    linlog_transformation
    loess_global_normalization
    loess_group_normalization
    loess_scaled_group_normalization
    lowess_global_normalization
    lowess_group_normalization
    lowess_scaled_group_normalization
    mean_log_normalization
    median_log_normalization
    moving_average
    quantile_normalization_protocol_type
    replicate_analysis
    total_intensity_normalization_paired
    total_intensity_normalization_single
    within_bioassay_data_set_function

class DataType

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

superclasses:
    MGEDCoreOntology
properties:
    unique_identifier MO_125
    class_role concrete
    class_source ontology
used in individuals:
    boolean
    date
    float
    integer
    list_of_booleans
    list_of_floats
    list_of_integers
    list_of_negative_floats
    list_of_negative_integers
    list_of_nonnegative_floats
    list_of_nonnegative_integers
    list_of_nonpositive_floats
    list_of_nonpositive_integers
    list_of_positive_floats
    list_of_positive_integers
    list_of_strings
    negative_float
    negative_integer
    nonnegative_float
    nonnegative_integer
    nonpositive_float
    nonpositive_integer
    positive_float
    positive_integer
    string_datatype

class Database

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

superclasses:
    DescriptionPackage
known subclasses:
    CellLineDatabase
    CellTypeDatabase
    CellularComponentDatabase
    ClinicalTreatmentDatabase
    CompoundDatabase
    DevelopmentalStageDatabase
    DiseaseStagingDatabase
    DiseaseStateDatabase
    GeographicLocationDatabase
    HistologyDatabase
    ObservationDatabase
    OrganismDatabase
    OrganismPartDatabase
    PhenotypeDatabase
    SequenceOntologyDatabase
    StrainOrLineDatabase
    TargetedCellTypeDatabase
    TestTypeDatabase
    TumorGradingDatabase
properties:
    unique_identifier MO_118
    class_role abstract
    class_source ontology
constraints:
    restriction: has_version has-class string
    restriction: has_URI has-class URI

class DatabaseEntryType

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

superclasses:
    DescriptionPackage
properties:
    unique_identifier MO_157
    class_role concrete
    class_source ontology
used in individuals:
    amino_acid_primary_sequence_record
    bibliographic_record
    biological_resource_record
    clinical_record
    compound_record
    computed_amino_acid_sequence_feature_record
    computed_nucleic_acid_sequence_feature_record
    computed_protein_structure_record
    curated_amino_acid_sequence_record
    curated_gene_record
    curated_nucleic_acid_sequence_feature_record
    function_record
    image_record
    microarray_experiment_record
    nucleic_acid_primary_sequence_record
    ontology_record
    pathway_record
    pedigree_record
    phylogeny_record
    primary_protein_structure_record

class DefectType

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

superclasses:
    ArrayPackage
properties:
    unique_identifier MO_16
    class_role concrete
    class_source ontology
used in individuals:
    diameter_aberration
    displaced_feature_or_zone
    heavy_background
    irregular_shape
    missing_feature_or_zone
    not_uniform

class DeliveryMethod

definition:
Method used to deliver a compound for treatment.

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_223
used in individuals:
    ad_libitum
    feeding
    in_medium
    intramuscular_injection
    intraperitoneal_injection
    intravenous
    oral_gavage
    subcutaneous

class DeprecatedTerms

definition:
Class to hold deprecated instances and classes.

superclasses:
    MGEDCoreOntology
known subclasses:
    ChromosomalAberration
    FactorValueDependency
    FactorValueSet
    IndividualChromosomalAbnormality
properties:
    unique_identifier MO_206
    class_role concrete
    class_source ontology
constraints:
    restriction: has_reason_for_deprecation has-class DeprecationReason
used in individuals:
    BAC
    EST
    Hfr
    NCI_Thesaurus
    ORF
    PAC
    PCR_amplicon
    PCR_primer
    PCR_primer_forward
    PCR_primer_reverse
    YAC
    bedding
    behavior_design
    behavioral_design_type
    blood
    cDNA_clone
    chromosome
    circadian_rhythm_design
    consensus_DNA
    consensus_mRNA
    cosmid
    ctDNA
    ds_oligo
    exemplar_mRNA
    exon
    feces
    gene
    gene_fragment
    genetic_variation
    infect
    intergenic
    intron
    low_intensity_filter
    mRNA
    mean_and_confidence_indicators
    monosomy
    mtDNA
    no
    operon
    plasmid
    polypeptide
    predicted_gene
    promoter
    rRNA_gene
    signal_log_ratio
    slice_analysis
    snRNA_gene
    ss_oligo
    tRNA_gene
    tau_rank_correlation
    total_intensity_normalization
    transcript
    trisomy
    vector
    yes

class DeprecationReason

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

superclasses:
    MGEDCoreOntology
properties:
    unique_identifier MO_94
    class_role concrete
    class_source ontology
used in individuals:
    deleted_term
    merged_term
    replaced_term
    split_term

class DerivedBioAssay

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

superclasses:
    BioAssay
properties:
    unique_identifier MO_209
    class_role concrete
    class_source mage
constraints:
    restriction: has_type has-class DerivedBioAssayType

class DerivedBioAssayType

definition:
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.

superclasses:
    BioAssayPackage
properties:
    unique_identifier MO_111
    class_role concrete
    class_source ontology
used in individuals:
    Affymetrix_average_difference
    MAS4_average_difference
    MAS5_signal
    MAS5_signal_log_ratio
    MBEI
    RMA
    acrossBioAssay_mean_and_coefficient_of_variation
    acrossBioAssay_mean_and_p_values
    acrossBioAssay_mean_and_standard_deviation
    acrossBioAssay_mean_and_variance
    averaged_intensity
    bioassay_replicate_reduction
    clustered_data
    collapsed_spot_replicate
    dye_swap_replicate_reduction
    filtered_data
    log_ratio
    mean_and_coefficient_of_variation
    mean_and_p_values
    mean_and_standard_deviation
    mean_and_variance
    normalized_intensities
    normalized_ratios
    ratio
    signal

class DescriptionPackage

definition:
MAGE package for description of annotations and references to annotations.

superclasses:
    MGEDCoreOntology
known subclasses:
    BibliographicReference
    Database
    DatabaseEntryType
    Image
    OntologyEntry
    PublicationType
properties:
    unique_identifier MO_167
    class_role abstract
    class_source mage

class DesignElement

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

superclasses:
    DesignElementPackage
known subclasses:
    Reporter
properties:
    unique_identifier MO_173
    class_role concrete
    class_source ontology
constraints:
    restriction: has_type has-class ControlType
used in individuals:
    PCR
    long_oligo
    short_oligo

class DesignElementGroup

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

superclasses:
    ArrayDesignPackage
known subclasses:
    FeatureGroup
properties:
    unique_identifier MO_128
    class_role abstract
    class_source mage
constraints:
    restriction: has_species has-class Organism
    restriction: has_type has-class DesignElementGroupType

class DesignElementGroupType

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

superclasses:
    ArrayDesignPackage
properties:
    unique_identifier MO_14
    class_role concrete
    class_source ontology
used in individuals:
    control_design_element_group_type
    experimental_design_element_group_type
    mixed_design_element_group_type
    species_specific_design_element_group_type

class DesignElementPackage

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

superclasses:
    MGEDCoreOntology
known subclasses:
    ControlType
    DesignElement
    FailType
    WarningType
properties:
    unique_identifier MO_15
    class_role abstract
    class_source mage

class DevelopmentalStage

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

superclasses:
    OntologyEntry
    BioMaterialCharacteristics
properties:
    unique_identifier MO_120
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class DevelopmentalStageDatabase

class DevelopmentalStageDatabase

definition:
Database of developmental stage information.

superclasses:
    Database
properties:
    unique_identifier MO_215
    class_role concrete
    class_source ontology
used in individuals:
    EMAP
    FlyBase_developmental_stage_database
    HUMAT
    MAD_stage
    TAIR_arabidopsis_development_ontology
    eVOC

class DiseaseLocation

definition:
Anatomical location(s) of disease.

superclasses:
    OrganismPart
properties:
    unique_identifier MO_37
    class_role concrete
    class_source ontology
constraints:
    restriction: has_cancer_site has-class CancerSite

class DiseaseStaging

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

superclasses:
    BioMaterialCharacteristics
    OntologyEntry
properties:
    unique_identifier MO_133
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class DiseaseStagingDatabase

class DiseaseStagingDatabase

definition:
Database of disease staging information

superclasses:
    Database
properties:
    unique_identifier MO_225
    class_role concrete
    class_source ontology
used in individuals:
    NCI_disease_staging_database

class DiseaseState

definition:
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.

superclasses:
    OntologyEntry
    BioMaterialCharacteristics
properties:
    unique_identifier MO_126
    class_role abstract
    class_source ontology
constraints:
    restriction: has_disease_location has-class DiseaseLocation
    restriction: has_disease_staging has-class DiseaseStaging
    restriction: has_database has-class DiseaseStateDatabase

class DiseaseStateDatabase

definition:
Database of disease state information.

superclasses:
    Database
properties:
    unique_identifier MO_181
    class_role concrete
    class_source ontology
used in individuals:
    ICD-9-CM
    MESH
    MTB_Database
    NCI_disease_state_database
    TDMS
    UMLS
    WebRENI
    eVOC

class DistanceUnit

definition:
Units used for distance measurements.

superclasses:
    Unit
known subclasses:
    DistanceUnitOther
properties:
    unique_identifier MO_4
    class_role concrete
    class_source ontology
used in individuals:
    A
    cm
    m
    mm
    nm
    um

class DistanceUnitOther

definition:
Distance units not specified in MAGE.

superclasses:
    DistanceUnit
properties:
    unique_identifier MO_143
    class_role place_holder
    class_source ontology

class Ecotype

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

superclasses:
    StrainOrLine
properties:
    unique_identifier MO_71
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class StrainOrLineDatabase

class EnvironmentalFactorCategory

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

superclasses:
    ExperimentalFactorCategory
properties:
    unique_identifier MO_117
    class_role concrete
    class_source ontology
used in individuals:
    atmosphere
    barrier_facility
    light_duration
    light_intensity
    media
    nutrients
    population_density
    relative_humidity
    temperature
    water

class EnvironmentalHistory

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

superclasses:
    BioMaterialCharacteristics
known subclasses:
    Bedding
    ClinicalHistory
    FamilyHistory
    Generation
    GeographicLocation
    GrowthCondition
    Host
    PathogenTest
    SamplingTimePoint
properties:
    unique_identifier MO_55
    class_role abstract
    class_source ontology
used in individuals:
    environmental_history_design

class EnvironmentalStress

definition:
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

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_227
constraints:
    restriction: has_measurement has-class Measurement

class EpidemiologicalDesign

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

superclasses:
    ExperimentDesignType
properties:
    unique_identifier MO_142
    class_role concrete
    class_source ontology
used in individuals:
    clinical_history_design
    disease_state_design
    family_history_design
    unknown_experiment_design_type

class Experiment

definition:
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.

superclasses:
    ExperimentPackage
properties:
    unique_identifier MO_112
    class_role concrete
    class_source mage
constraints:
    restriction: has_experiment_design has-class ExperimentDesign
    restriction: has_citation has-class BibliographicReference
    restriction: has_bioassays has-class BioAssay
    restriction: has_providers has-class Contact
    restriction: has_bioassay_data has-class BioAssayData

class ExperimentDesign

definition:
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.

superclasses:
    ExperimentPackage
properties:
    unique_identifier MO_170
    class_role concrete
    class_source mage
constraints:
    restriction: has_MAGE_description has-class ReplicateDescription
    restriction: has_MAGE_description has-class QualityControlDescription
    restriction: has_bioassays has-class BioAssay
    restriction: has_experiment_factors has-class ExperimentalFactor
    restriction: has_MAGE_description has-class NormalizationDescription
    restriction: has_experiment_design_type has-class ExperimentDesignType
    restriction: has_description has-class string

class ExperimentDesignType

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

superclasses:
    ExperimentPackage
known subclasses:
    BiologicalProperty
    BioMolecularAnnotation
    EpidemiologicalDesign
    MethodologicalDesign
    PerturbationalDesign
    TechnologicalDesign
properties:
    unique_identifier MO_158
    class_role abstract
    class_source ontology

class ExperimentPackage

definition:
The descriptions associated with the Experiment package of MAGE

superclasses:
    MGEDCoreOntology
known subclasses:
    Experiment
    ExperimentalFactor
    ExperimentalFactorCategory
    ExperimentDesign
    ExperimentDesignType
    FactorValue
    FactorValueDependency
    FactorValueSet
    NormalizationDescription
    NormalizationDescriptionType
    QualityControlDescription
    QualityControlDescriptionType
    ReplicateDescription
    ReplicateDescriptionType
properties:
    unique_identifier MO_31
    class_role abstract
    class_source mage

class ExperimentalFactor

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

superclasses:
    ExperimentPackage
properties:
    unique_identifier MO_10
    class_role concrete
    class_source mage
constraints:
    restriction: has_category has-class BiologicalFactorCategory
    restriction: has_category has-class MethodologicalFactorCategory
    restriction: has_factor_value has-class FactorValue

class ExperimentalFactorCategory

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

superclasses:
    ExperimentPackage
known subclasses:
    BiologicalFactorCategory
    EnvironmentalFactorCategory
    MethodologicalFactorCategory
properties:
    unique_identifier MO_205
    class_role abstract
    class_source ontology

class ExperimentalProtocolType

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

superclasses:
    ProtocolType
properties:
    unique_identifier MO_75
    class_role concrete
    class_source ontology
used in individuals:
    PCR_amplification
    acclimatization
    array_manufacturing
    behavioral_stimulus
    biological_fluid_collection
    change_biomaterial_characteristics
    compound_based_treatment
    decontaminate
    dissect
    element_design
    feature_extraction
    fractionate
    genetic_modification
    grow
    harvest
    histological_slide_preparation
    hybridization
    image_acquisition
    incubate
    inoculate
    irradiate
    labeling
    linear_amplification
    nucleic_acid_extraction
    pool
    preservation
    purify
    reverse_transcription
    sacrifice
    specified_biomaterial_action
    split
    starvation
    store
    transfect
    unknown_protocol_type
    wash

class FactorValue

definition:
The value of an ExperimentFactor.

superclasses:
    ExperimentPackage
properties:
    unique_identifier MO_203
    class_role concrete
    class_source mage
constraints:
    restriction: has_measurement has-class Measurement
    restriction: has_property_set has-class FactorValueSet
    restriction: has_property_set has-class FactorValueDependency
    restriction: has_factor_value_ontology_entry has-class ExperimentalFactorCategory

class FactorValueDependency

definition:
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.

superclasses:
    DeprecatedTerms
    ExperimentPackage
properties:
    deprecation_old_restriction some|has_value|string
    deprecation_in_version 1.1.9
    unique_identifier MO_148
    class_role place_holder
    class_source ontology
    deprecation_reason deleted_term
    deprecation_old_parent ExperimentPackage
constraints:
    restriction: has_value has-class string
    restriction: deprecated_from_version has-class version_1.1.9
    restriction: has_reason_for_deprecation has-class deleted_term

class FactorValueSet

definition:
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.

superclasses:
    DeprecatedTerms
    ExperimentPackage
properties:
    deprecation_old_restriction some|has_value|string
    deprecation_in_version 1.1.9
    unique_identifier MO_217
    class_role place_holder
    class_source ontology
    deprecation_reason deleted_term
    deprecation_replacement_term FactorValueSet
    deprecation_old_parent ExperimentPackage
constraints:
    restriction: has_reason_for_deprecation has-class deleted_term
    restriction: deprecated_from_version has-class version_1.1.9
    restriction: has_value has-class string

class FailType

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

superclasses:
    DesignElementPackage
properties:
    unique_identifier MO_98
    class_role concrete
    class_source ontology
used in individuals:
    PCR_fail
    PCR_questionable

class FamilyHistory

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

superclasses:
    EnvironmentalHistory
properties:
    unique_identifier MO_59
    class_role abstract
    class_source ontology
constraints:
    restriction: has_family_member has-class FamilyMember

class FamilyMember

definition:
Member of the biosource's family.

superclasses:
    BioMaterialPackage
properties:
    unique_identifier MO_188
    class_role abstract
    class_source ontology
constraints:
    restriction: has_disease_state has-class DiseaseState
    restriction: has_individual_genetic_characteristics has-class IndividualGeneticCharacteristics
    restriction: has_clinical_record has-class OntologyEntry
    restriction: has_family_relationship has-class FamilyRelationship

class FamilyRelationship

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

superclasses:
    BioMaterialPackage
properties:
    unique_identifier MO_36
    class_role concrete
    class_source ontology
used in individuals:
    aunt
    brother
    daughter
    father
    granddaughter
    grandfather
    grandmother
    grandson
    mother
    sister
    son
    uncle

class FeatureDefect

definition:
A technical manufacturer described defect for features.

superclasses:
    ArrayPackage
properties:
    unique_identifier MO_138
    class_role concrete
    class_source mage
constraints:
    restriction: has_type has-class DefectType

class FeatureGroup

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

superclasses:
    DesignElementGroup
properties:
    unique_identifier MO_54
    class_role concrete
    class_source mage
constraints:
    restriction: has_feature_shape has-class FeatureShape
    restriction: has_type has-class TechnologyType

class FeatureShape

definition:
The expected shape of the feature on the array.

superclasses:
    ArrayDesignPackage
properties:
    unique_identifier MO_8
    class_role concrete
    class_source ontology
used in individuals:
    ellipsoid_feature
    rectangular_feature
    square_feature

class Fiducial

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

superclasses:
    ArrayPackage
properties:
    unique_identifier MO_136
    class_role concrete
    class_source mage
constraints:
    restriction: has_type has-class FiducialType

class FiducialType

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

superclasses:
    ArrayPackage
properties:
    unique_identifier MO_17
    class_role concrete
    class_source ontology
used in individuals:
    chrome_border
    laser_ablation_mark

class Generation

definition:
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.

superclasses:
    EnvironmentalHistory
properties:
    unique_identifier MO_43
    class_role place_holder
    class_source ontology

class GeneticMaterial

definition:
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.

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_137

class GeneticModification

definition:
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.

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_122
    class_role concrete
    class_source ontology
used in individuals:
    chromosomal_substitution
    gene_knock_in
    gene_knock_out
    induced_mutation
    transfection

class Genotype

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

superclasses:
    IndividualGeneticCharacteristics
properties:
    unique_identifier MO_51
    class_role concrete
    class_source ontology
used in individuals:
    wild_type

class GeographicLocation

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

superclasses:
    OntologyEntry
    EnvironmentalHistory
properties:
    unique_identifier MO_132
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class GeographicLocationDatabase

class GeographicLocationDatabase

definition:
Database of geographic locations.

superclasses:
    Database
properties:
    unique_identifier MO_35
    class_role concrete
    class_source ontology
used in individuals:
    NCI_geographic_location_database

class GrowthCondition

definition:
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.

superclasses:
    EnvironmentalHistory
known subclasses:
    Atmosphere
    BarrierFacility
    Humidity
    Light
    Media
    Nutrients
    PopulationDensity
    Temperature
    Water
properties:
    unique_identifier MO_183
    class_role abstract
    class_source ontology
constraints:
    restriction: has_maximum_measurement has-class Measurement
    restriction: has_value has-class string
    restriction: has_measurement has-class Measurement

class Haplotype

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

superclasses:
    IndividualGeneticCharacteristics
properties:
    unique_identifier MO_146
    class_role place_holder
    class_source ontology

class Hardware

definition:
The machine or instrument used.

superclasses:
    ProtocolPackage
properties:
    unique_identifier MO_134
    class_role concrete
    class_source mage
constraints:
    restriction: has_type has-class HardwareType
    restriction: has_software has-class Software
    restriction: has_model has-class string
    restriction: has_make has-class string
    restriction: has_manufacturer has-class Contact

class HardwareType

definition:
Controlled terms for descriptors of types of hardware.

superclasses:
    ProtocolPackage
properties:
    unique_identifier MO_113
    class_role concrete
    class_source ontology
used in individuals:
    DNA_sequencer
    array_scanner
    arrayer
    centrifuge
    computer
    heating_block
    homogenizer
    hybridization_chamber
    hybridization_station
    liquid_handler
    oligo_synthesizer
    sonicator
    spectrophotometer
    thermal_cycler
    vacuum_dryer
    vortexer
    wash_station
    waterbath

class HardwareVariation

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

superclasses:
    MethodologicalFactorCategory
properties:
    unique_identifier MO_81
    class_role place_holder
    class_source ontology

class HigherLevelAnalysisPackage

definition:
MAGE package for HigherLevelAnalysis

superclasses:
    MGEDCoreOntology
known subclasses:
    BioAssayDataCluster
    Node
    NodeValue
    NodeValueType
properties:
    unique_identifier MO_228
    class_role abstract
    class_source mage

class HigherLevelAnalysisProtocolType

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

superclasses:
    ProtocolType
properties:
    unique_identifier MO_47
    class_role concrete
    class_source ontology
used in individuals:
    condition_specificity
    differential_expression
    multiple_testing_correction

class Histology

definition:
Microscopic morphology of tissues.

superclasses:
    OntologyEntry
    BioMaterialCharacteristics
properties:
    unique_identifier MO_194
    class_role abstract
    class_source ontology
constraints:
    restriction: has_performer has-class Contact
    restriction: has_organism_part has-class OrganismPart
    restriction: has_database has-class HistologyDatabase

class HistologyDatabase

definition:
Database of histology information.

superclasses:
    Database
properties:
    unique_identifier MO_175
    class_role concrete
    class_source ontology
used in individuals:
    NCI_histology_database
    Pathbase
    TDMS

class HistoryFactor

definition:
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).

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_82

class Host

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

superclasses:
    EnvironmentalHistory
properties:
    unique_identifier MO_101
    class_role abstract
    class_source ontology
constraints:
    restriction: has_host_part has-class OrganismPart
    restriction: has_host has-class Organism

class Humidity

definition:
The humidity that the biosource is exposed to.

superclasses:
    GrowthCondition
properties:
    unique_identifier MO_29
    class_role abstract
    class_source ontology

class Image

superclasses:
    DescriptionPackage
properties:
    unique_identifier MO_22
    class_role concrete
    class_source mage
constraints:
    restriction: has_URI has-class URI
    restriction: has_image_format has-class ImageFormat
    restriction: has_database has-class Database

class ImageFormat

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

superclasses:
    BioAssayPackage
properties:
    unique_identifier MO_211
    class_role concrete
    class_source ontology
used in individuals:
    Affymetrix_DAT
    GIF
    JPEG
    PNG
    TIFF

class Individual

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

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_169
    class_role place_holder
    class_source ontology

class IndividualChromosomalAbnormality

definition:
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.

superclasses:
    DeprecatedTerms
    IndividualGeneticCharacteristics
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_185
    class_role place_holder
    class_source ontology
    deprecation_reason deleted_term
    deprecation_replacement_term IndividualChromosomalAbnormality
    deprecation_old_parent IndividualGeneticCharacteristics
constraints:
    restriction: deprecated_from_version has-class version_1.2.0
    restriction: has_reason_for_deprecation has-class deleted_term

class IndividualGeneticCharacteristics

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

superclasses:
    BioMaterialCharacteristics
known subclasses:
    Allele
    Genotype
    Haplotype
    IndividualChromosomalAbnormality
    Ploidy
properties:
    unique_identifier MO_66
    class_role abstract
    class_source ontology
constraints:
    restriction: has_value has-class string

class InitialTimePoint

definition:
The point from which measurements of age were taken.

superclasses:
    BioMaterialPackage
properties:
    unique_identifier MO_80
    class_role concrete
    class_source ontology
used in individuals:
    beginning_of_stage
    birth
    coitus
    eclosion
    egg_laying
    fertilization
    germination
    hatching
    planting
    sowing

class LabelCompound

definition:
Compounds that are used for labeling extracts.

superclasses:
    Compound
properties:
    unique_identifier MO_13
    class_role concrete
    class_source ontology
used in individuals:
    Cy3
    Cy5
    _32P
    _33P
    alexa_350
    alexa_430
    alexa_488
    alexa_532
    alexa_546
    alexa_568
    alexa_594
    alexa_633
    alexa_660
    alexa_680
    biotin

class LabeledExtract

definition:
The BioSample after labeling for detection of the nucleic acids.

superclasses:
    BioMaterial
properties:
    unique_identifier MO_221
    class_role concrete
    class_source mage
constraints:
    restriction: has_compound has-class LabelCompound
    restriction: has_been_treated has-class Treatment

class Light

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

superclasses:
    GrowthCondition
properties:
    unique_identifier MO_60
    class_role abstract
    class_source ontology

class LightUnit

definition:
Units for measuring the intensity of light.

superclasses:
    OtherUnit
properties:
    unique_identifier MO_119
    class_role concrete
    class_source ontology
used in individuals:
    candela
    candelas_per_square_meter
    lumen
    lux
    microeinstein_per_minute_and_square_meter
    microeinstein_per_second_and_square_meter

class MGEDCoreOntology

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

superclasses:
    MGEDOntology
known subclasses:
    ArrayDesignPackage
    ArrayPackage
    AuditAndSecurityPackage
    BioAssayPackage
    BioMaterialPackage
    BioSequencePackage
    CancerSite
    DataType
    DeprecatedTerms
    DeprecationReason
    DescriptionPackage
    DesignElementPackage
    ExperimentPackage
    HigherLevelAnalysisPackage
    MeasurementPackage
    MeasurementType
    MGEDOntologyVersion
    ProtocolPackage
    QuantitationTypePackage
    Result
    Scale
    URI
properties:
    unique_identifier MO_57
    class_role abstract
    class_source ontology
constraints:
    restriction: has_ID has-class string

class MGEDExtendedOntology

definition:
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

superclasses:
    MGEDOntology
known subclasses:
    BioAssayDataPackage
    DeliveryMethod
    EnvironmentalStress
    GeneticMaterial
    HistoryFactor
    Preservation
    PreservationType
    ProtocolParameterType
    ProtocolVariation
    SomaticModification
    StrandType
    User
properties:
    unique_identifier MO_196

class MGEDOntology

definition:
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.

superclasses:
    owl:Thing
known subclasses:
    MGEDCoreOntology
    MGEDExtendedOntology
properties:
    unique_identifier MO_174
    class_role abstract
    class_source ontology
constraints:
    restriction: is_user_defined has-class Contact
    restriction: is_user_defined has-class BibliographicReference

class MGEDOntologyVersion

definition:
The version of the MGED Ontology.

superclasses:
    MGEDCoreOntology
properties:
    unique_identifier MO_115
    class_role concrete
    class_source ontology
used in individuals:
    version_1.1.7
    version_1.1.8
    version_1.1.9
    version_1.2.0
    version_1.3.0
    version_1.3.1

class MassUnit

definition:
Units used for mass measurements.

superclasses:
    Unit
known subclasses:
    MassUnitOther
properties:
    unique_identifier MO_149
    class_role concrete
    class_source ontology
used in individuals:
    fg
    g
    kg
    mg
    ng
    pg
    ug

class MassUnitOther

definition:
Mass units not specified in MAGE.

superclasses:
    MassUnit
properties:
    unique_identifier MO_11
    class_role place_holder
    class_source ontology

class MaterialType

definition:
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.

superclasses:
    BioMaterialPackage
properties:
    unique_identifier MO_32
    class_role concrete
    class_source ontology
used in individuals:
    DNA
    cell
    cell_lysate
    cytoplasmic_RNA
    genomic_DNA
    molecular_mixture
    nuclear_RNA
    organellar_DNA
    organellar_RNA
    organism_part
    polyA_RNA
    protein
    synthetic_DNA
    synthetic_RNA
    total_RNA
    virus
    whole_organism

class Measurement

definition:
Measured values and units.

superclasses:
    MeasurementPackage
properties:
    unique_identifier MO_144
    class_role concrete
    class_source mage
constraints:
    restriction: has_value has-class string
    restriction: has_measurement_type has-class MeasurementType
    restriction: has_units has-class Unit

class MeasurementPackage

definition:
MAGE package for measurement.

superclasses:
    MGEDCoreOntology
known subclasses:
    Measurement
    Unit
properties:
    unique_identifier MO_89
    class_role abstract
    class_source mage

class MeasurementType

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

superclasses:
    MGEDCoreOntology
properties:
    unique_identifier MO_72
    class_role concrete
    class_source ontology
used in individuals:
    absolute
    relative

class Media

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

superclasses:
    GrowthCondition
properties:
    unique_identifier MO_19
    class_role concrete
    class_source ontology
used in individuals:
    agar
    liquid
    semisolid
    soil

class MethodologicalDesign

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

superclasses:
    ExperimentDesignType
properties:
    unique_identifier MO_2
    class_role concrete
    class_source ontology
used in individuals:
    all_pairs
    array_platform_variation_design
    dye_swap_design
    ex_vivo_design
    hardware_variation_design
    in_vitro_design
    in_vivo_design
    loop_design
    normalization_testing_design
    operator_variation_design
    optimization_design
    quality_control_testing_design
    reference_design
    replicate_design
    self_vs_self_design
    software_variation_design
    time_series_design
    unknown_experiment_design_type

class MethodologicalFactorCategory

definition:
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.

superclasses:
    ExperimentalFactorCategory
known subclasses:
    HardwareVariation
    OperatorVariation
    ProtocolType
    SoftwareVariation
properties:
    unique_identifier MO_85
    class_role abstract
    class_source ontology

class Node

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

superclasses:
    HigherLevelAnalysisPackage
properties:
    unique_identifier MO_73
    class_role concrete
    class_source mage
constraints:
    restriction: has_node_value has-class NodeValue

class NodeValue

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

superclasses:
    HigherLevelAnalysisPackage
properties:
    unique_identifier MO_104
    class_role concrete
    class_source mage
constraints:
    restriction: has_node_value_type has-class NodeValueType
    restriction: has_scale has-class Scale
    restriction: has_type has-class DataType

class NodeValueType

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

superclasses:
    HigherLevelAnalysisPackage
properties:
    unique_identifier MO_160
    class_role concrete
    class_source ontology
used in individuals:
    Euclidean_distance
    Pearson_correlation
    Spearmans_rank_correlation
    cosine_distance
    french_railway_distance
    jackknife_Pearson_correlation
    manhattan_distance
    pearson_correlation_coefficient
    uncentered_Pearson_correlation

class NormalizationDescription

definition:
NormalizationDescription provides details of the normalization strategy for the experiment.

superclasses:
    ExperimentPackage
properties:
    unique_identifier MO_131
    class_role abstract
    class_source ontology
constraints:
    restriction: has_type has-class NormalizationDescriptionType

class NormalizationDescriptionType

definition:
Controlled descriptors for the normalization strategy used for the experiment.

superclasses:
    ExperimentPackage
properties:
    unique_identifier MO_27
    class_role concrete
    class_source ontology
used in individuals:
    flip-dye_consistency
    iterative_mean_log_centering
    linear_regression_normalization
    linlog_normalization
    loess_normalization
    lowess_normalization
    mean_log_centering
    median_log_centering
    quantile_normalization
    ratio_statistics_normalization

class Nutrients

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

superclasses:
    GrowthCondition
properties:
    unique_identifier MO_127
    class_role abstract
    class_source ontology
constraints:
    restriction: has_nutrient_component has-class Compound

class Observation

definition:
Observation will record the macroscopic examination of the biomaterial.

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_53
    class_role abstract
    class_source ontology
constraints:
    restriction: has_performer has-class Contact
    restriction: has_database has-class ObservationDatabase

class ObservationDatabase

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

superclasses:
    Database
properties:
    unique_identifier MO_91
    class_role concrete
    class_source ontology
used in individuals:
    Mammalian_Phenotype_Ontology

class OntologyEntry

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

superclasses:
    DescriptionPackage
known subclasses:
    CellLine
    CellType
    CellularComponent
    ClinicalTreatment
    Compound
    DevelopmentalStage
    DiseaseStaging
    DiseaseState
    GeographicLocation
    Histology
    Organism
    OrganismPart
    Phenotype
    SequenceOntologyBioSequenceType
    StrainOrLine
    TargetedCellType
    TestType
    TumorGrading
properties:
    unique_identifier MO_87
    class_role abstract
    class_source ontology
constraints:
    restriction: has_value has-class string
    restriction: has_database has-class Database
    restriction: has_accession_version has-class string
    restriction: has_accession has-class string
    restriction: has_database_entry_type has-class DatabaseEntryType
    restriction: has_description has-class string

class OperatorVariation

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

superclasses:
    MethodologicalFactorCategory
properties:
    unique_identifier MO_38
    class_role place_holder
    class_source ontology

class Organism

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

superclasses:
    BioMaterialCharacteristics
    OntologyEntry
properties:
    unique_identifier MO_229
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class OrganismDatabase

class OrganismDatabase

definition:
Database of taxonomic information.

superclasses:
    Database
properties:
    unique_identifier MO_64
    class_role concrete
    class_source ontology
used in individuals:
    NCBI_taxonomy

class OrganismPart

definition:
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).

superclasses:
    BioMaterialCharacteristics
    OntologyEntry
known subclasses:
    DiseaseLocation
properties:
    unique_identifier MO_1
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class OrganismPartDatabase

class OrganismPartDatabase

definition:
Database of organism part information.

superclasses:
    Database
properties:
    unique_identifier MO_200
    class_role concrete
    class_source ontology
used in individuals:
    Adult_Mouse_Anatomy
    CBIL_CV
    CellML
    FMA
    FlyBase_organism_part_database
    MAD_stage
    NCI_organism_part_database
    TAIR_arabidopsis_anatomy_ontology
    TDMS
    eVOC
    openGALEN

class OrganismStatus

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

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_84
    class_role concrete
    class_source ontology
used in individuals:
    postmortem
    premortem

class Organization

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

superclasses:
    Contact
properties:
    unique_identifier MO_177
    class_role concrete
    class_source mage
constraints:
    restriction: has_name has-class string
    restriction: has_parent_organization has-class Organization

class OtherUnit

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

superclasses:
    Unit
known subclasses:
    LightUnit
    RadiationUnit
properties:
    unique_identifier MO_199
    class_role concrete
    class_source ontology
used in individuals:
    U_per_week
    activity_units_per_ml
    kg_per_m2
    micromole_per_second_and_square_meter
    number_per_day

class Parameter

definition:
A parameter is a variable within a protocol.

superclasses:
    ProtocolPackage
properties:
    unique_identifier MO_110
    class_role concrete
    class_source mage
constraints:
    restriction: has_units has-class Unit
    restriction: has_type has-class DataType

class PathogenTest

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

superclasses:
    EnvironmentalHistory
properties:
    unique_identifier MO_184
    class_role abstract
    class_source ontology
constraints:
    restriction: was_tested_for has-class Organism
    restriction: has_result has-class Result

class Person

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

superclasses:
    Contact
properties:
    unique_identifier MO_24
    class_role concrete
    class_source mage
constraints:
    restriction: has_first_name has-class string
    restriction: has_last_name has-class string
    restriction: has_affiliation has-class Organization
    restriction: has_mid_initials has-class string

class PerturbationalDesign

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

superclasses:
    ExperimentDesignType
properties:
    unique_identifier MO_106
    class_role concrete
    class_source ontology
used in individuals:
    cellular_modification_design
    compound_treatment_design
    disease_state_design
    dose_response_design
    genetic_modification_design
    growth_condition_design
    injury_design
    non-targeted_transgenic_variation_design
    pathogenicity_design
    stimulated_design_type
    stimulus_or_stress_design
    unknown_experiment_design_type

class Phenotype

definition:
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.

superclasses:
    OntologyEntry
    BioMaterialCharacteristics
properties:
    unique_identifier MO_192
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class PhenotypeDatabase

class PhenotypeDatabase

definition:
Database of phenotype information

superclasses:
    Database
properties:
    unique_identifier MO_39
    class_role concrete
    class_source ontology

class PhysicalArrayDesign

definition:
Descriptions pertaining to the array.

superclasses:
    ArrayDesignPackage
properties:
    unique_identifier MO_212
    class_role concrete
    class_source mage
constraints:
    restriction: has_type has-class SurfaceType

class PhysicalBioAssay

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

superclasses:
    BioAssay
properties:
    unique_identifier MO_99
    class_role concrete
    class_source mage
constraints:
    restriction: has_image_format has-class ImageFormat

class PhysicalBioSequenceType

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

superclasses:
    BioSequenceType
known subclasses:
    SequenceOntologyBioSequenceType
properties:
    unique_identifier MO_92
    class_role concrete
    class_source ontology
used in individuals:
    antibody
    clone_of_unknown_source
    unknown_sequence

class Ploidy

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

superclasses:
    IndividualGeneticCharacteristics
properties:
    unique_identifier MO_220
    class_role concrete
    class_source ontology
used in individuals:
    aneuploid
    diploid
    haploid
    polyploid

class PolymerType

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

superclasses:
    BioSequencePackage
properties:
    unique_identifier MO_102
    class_role concrete
    class_source ontology
used in individuals:
    DNA
    RNA
    protein

class PopulationDensity

definition:
The concentration range of the organism.

superclasses:
    GrowthCondition
properties:
    unique_identifier MO_46
    class_role abstract
    class_source ontology

class Preservation

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

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_176
constraints:
    restriction: has_protocol has-class Protocol
    restriction: has_type has-class PreservationType

class PreservationType

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

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_195
used in individuals:
    frozen_storage
    seed_dormancy

class Protocol

definition:
Documentation of the set of steps taken in a procedure.

superclasses:
    ProtocolPackage
properties:
    unique_identifier MO_214
    class_role concrete
    class_source mage
constraints:
    restriction: has_citation has-class BibliographicReference
    restriction: has_software has-class Software
    restriction: has_title has-class string
    restriction: has_description has-class string
    restriction: has_text has-class string
    restriction: has_hardware has-class Hardware
    restriction: has_type has-class ProtocolType
    restriction: has_URI has-class URI

class ProtocolPackage

definition:
The MAGE package for protocols.

superclasses:
    MGEDCoreOntology
known subclasses:
    Hardware
    HardwareType
    Parameter
    Protocol
    ProtocolType
    Software
    SoftwareType
properties:
    unique_identifier MO_63
    class_role abstract
    class_source mage

class ProtocolParameterType

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

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_164

class ProtocolType

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

superclasses:
    ProtocolPackage
    MethodologicalFactorCategory
known subclasses:
    DataTransformationProtocolType
    ExperimentalProtocolType
    HigherLevelAnalysisProtocolType
properties:
    unique_identifier MO_150
    class_role abstract
    class_source ontology

class ProtocolVariation

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

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_140

class PublicationType

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

superclasses:
    DescriptionPackage
properties:
    unique_identifier MO_208
    class_role concrete
    class_source ontology
used in individuals:
    book
    journal_article
    online_resource

class QualityControlDescription

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

superclasses:
    ExperimentPackage
properties:
    unique_identifier MO_88
    class_role abstract
    class_source ontology
constraints:
    restriction: has_type has-class QualityControlDescriptionType

class QualityControlDescriptionType

definition:
Controlled descriptors for the quality control strategy for an experiment.

superclasses:
    ExperimentPackage
properties:
    unique_identifier MO_121
    class_role concrete
    class_source ontology
used in individuals:
    biological_replicate
    dye_swap_quality_control
    peer_review_quality_control
    real_time_PCR_quality_control
    reverse_transcription_PCR_quality_control
    spike_quality_control
    technical_replicate

class QuantitationType

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

superclasses:
    QuantitationTypePackage
properties:
    unique_identifier MO_67
    class_role abstract
    class_source mage
constraints:
    restriction: has_scale has-class Scale
    restriction: has_type has-class DataType

class QuantitationTypePackage

definition:
The MAGE package for defining classes for quantitation.

superclasses:
    MGEDCoreOntology
known subclasses:
    QuantitationType
properties:
    unique_identifier MO_130
    class_role abstract
    class_source mage

class QuantityUnit

definition:
Units used for quantity measurements.

superclasses:
    Unit
known subclasses:
    QuantityUnitOther
properties:
    unique_identifier MO_210
    class_role concrete
    class_source ontology
used in individuals:
    IU
    amol
    fmol
    mol
    molecules
    nmol
    pmol
    umol

class QuantityUnitOther

definition:
Quantity units not specified in MAGE.

superclasses:
    QuantityUnit
properties:
    unique_identifier MO_156
    class_role concrete
    class_source ontology
used in individuals:
    count

class RadiationUnit

definition:
Units for measuring decay of a radioactive isotope over time.

superclasses:
    OtherUnit
properties:
    unique_identifier MO_204
    class_role concrete
    class_source ontology
used in individuals:
    Ci
    R
    Rad
    Rem
    cpm
    dpm

class ReplicateDescription

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

superclasses:
    ExperimentPackage
properties:
    unique_identifier MO_162
    class_role abstract
    class_source ontology
constraints:
    restriction: has_type has-class ReplicateDescriptionType

class ReplicateDescriptionType

definition:
Controlled descriptors for the type of replication.

superclasses:
    ExperimentPackage
properties:
    unique_identifier MO_52
    class_role concrete
    class_source ontology
used in individuals:
    biological_replicate
    dye_swap_replicate
    technical_replicate

class Reporter

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

superclasses:
    DesignElement
properties:
    unique_identifier MO_74
    class_role concrete
    class_source mage
constraints:
    restriction: has_type has-class WarningType
    restriction: has_type has-class FailType

class Result

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

superclasses:
    MGEDCoreOntology
properties:
    unique_identifier MO_65
    class_role concrete
    class_source ontology
used in individuals:
    inconclusive
    negative
    positive

class Roles

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

superclasses:
    AuditAndSecurityPackage
properties:
    unique_identifier MO_180
    class_role concrete
    class_source ontology
used in individuals:
    array_manufacturer
    biomaterial_provider
    biosequence_provider
    consortium_member
    consultant
    curator
    data_analyst
    data_coder
    funder
    hardware_manufacturer
    institution
    investigator
    software_manufacturer
    submitter

class SamplingTimePoint

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

superclasses:
    EnvironmentalHistory
properties:
    unique_identifier MO_139
    class_role abstract
    class_source ontology

class Scale

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

superclasses:
    MGEDCoreOntology
properties:
    unique_identifier MO_108
    class_role concrete
    class_source ontology
used in individuals:
    linear_scale
    log_base_10
    log_base_2
    log_base_e
    unscaled

class SeqFeatureBasis

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

superclasses:
    BioSequencePackage
properties:
    unique_identifier MO_207
    class_role concrete
    class_source ontology
used in individuals:
    computational_feature
    experimental_and_computational_feature
    experimental_feature
    unknown_basis_feature

class SequenceOntologyBioSequenceType

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

superclasses:
    OntologyEntry
    PhysicalBioSequenceType
    TheoreticalBioSequenceType
properties:
    unique_identifier MO_25
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class SequenceOntologyDatabase

class SequenceOntologyDatabase

definition:
Database for sequence annotation information.

superclasses:
    Database
properties:
    unique_identifier MO_83
    class_role concrete
    class_source ontology
used in individuals:
    SequenceOntology

class Serotype

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

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_159
    class_role place_holder
    class_source ontology

class Sex

definition:
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.

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_168
    class_role concrete
    class_source ontology
used in individuals:
    F
    F_minus
    female
    hermaphrodite
    male
    mating_type_a
    mating_type_alpha
    mating_type_h_minus
    mating_type_h_plus
    mixed_sex
    unknown_sex

class Software

definition:
The software application used.

superclasses:
    ProtocolPackage
properties:
    unique_identifier MO_109
    class_role concrete
    class_source mage
constraints:
    restriction: has_hardware has-class Hardware
    restriction: has_type has-class SoftwareType
    restriction: has_manufacturer has-class Contact
    restriction: has_software has-class Software

class SoftwareType

definition:
Controlled terms that provide descriptors for the type of software.

superclasses:
    ProtocolPackage
properties:
    unique_identifier MO_202
    class_role concrete
    class_source ontology
used in individuals:
    array_manufacture_software
    bioassay_data_transformation_software
    clustering_software
    differential_expression_software
    feature_extraction_software
    image_acquisition_software
    liquid_handler_software
    operating_system

class SoftwareVariation

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

superclasses:
    MethodologicalFactorCategory
properties:
    unique_identifier MO_222
    class_role place_holder
    class_source ontology

class SomaticModification

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

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_44
constraints:
    restriction: has_part_modified has-class OrganismPart

class StrainOrLine

definition:
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.

superclasses:
    OntologyEntry
    BioMaterialCharacteristics
known subclasses:
    Cultivar
    Ecotype
properties:
    unique_identifier MO_9
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class StrainOrLineDatabase
    restriction: has_species has-class Organism

class StrainOrLineDatabase

definition:
Database of strain, line, cultivar or ecotype information.

superclasses:
    Database
properties:
    unique_identifier MO_30
    class_role concrete
    class_source ontology
used in individuals:
    ATCC_Cultures
    CABRI_Bacteria_and_Archaea_Strains
    CABRI_Filamentous_Fungi_Strains
    CABRI_Yeasts_Strains
    GRAMENE
    JAX_mouse_strains
    NASC
    NCBI_taxonomy
    NCI_strain_or_line_database
    TAIR

class StrandType

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

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_7
used in individuals:
    double_stranded
    forward
    reverse
    single_stranded

class SubstrateType

definition:
Controlled terms for descriptors of types of array substrates.

superclasses:
    ArrayPackage
properties:
    unique_identifier MO_79
    class_role concrete
    class_source ontology
used in individuals:
    glass
    nitrocellulose
    nylon
    silicon
    unknown_substrate_type

class SurfaceType

definition:
Controlled terms for descriptors for coating of the substrate.

superclasses:
    ArrayDesignPackage
properties:
    unique_identifier MO_198
    class_role concrete
    class_source ontology
used in individuals:
    aminosilane
    polylysine
    unknown_surface_type

class TargetedCellType

definition:
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.

superclasses:
    OntologyEntry
    BioMaterialCharacteristics
properties:
    unique_identifier MO_123
    class_role abstract
    class_source ontology

class TargetedCellTypeDatabase

definition:
Database of targeted cell type information.

superclasses:
    Database
properties:
    unique_identifier MO_45
    class_role concrete
    class_source ontology
used in individuals:
    CBIL_CV
    MAD_stage
    NCI_targeted_cell_type_database
    cell_ontology

class TechnologicalDesign

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

superclasses:
    ExperimentDesignType
properties:
    unique_identifier MO_21
    class_role concrete
    class_source ontology
used in individuals:
    binding_site_identification_design
    cellular_modification_design
    comparative_genome_hybridization_design
    transcript_identification_design

class TechnologyType

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

superclasses:
    ArrayDesignPackage
properties:
    unique_identifier MO_18
    class_role concrete
    class_source ontology
used in individuals:
    in_situ_oligo_features
    spotted_antibody_features
    spotted_colony_features
    spotted_ds_DNA_features
    spotted_protein_features
    spotted_ss_PCR_amplicon_features
    spotted_ss_oligo_features

class Temperature

definition:
The temperature that a biosource is exposed to.

superclasses:
    GrowthCondition
properties:
    unique_identifier MO_171
    class_role abstract
    class_source ontology

class TemperatureUnit

definition:
Units used for temperature measurements.

superclasses:
    Unit
properties:
    unique_identifier MO_48
    class_role concrete
    class_source ontology
used in individuals:
    K
    degrees_C
    degrees_F

class Test

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

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_197
    class_role abstract
    class_source ontology
constraints:
    restriction: has_performer has-class Contact
    restriction: has_test_type has-class TestType
    restriction: has_test_result has-class TestResult

class TestResult

definition:
TestResult is the recorded value of the test outcome.

superclasses:
    BioMaterialCharacteristics
properties:
    unique_identifier MO_96
    class_role abstract
    class_source ontology
constraints:
    restriction: has_measurement has-class Measurement

class TestType

definition:
Descriptor of the Test performed e.g. Leukocyte count

superclasses:
    BioMaterialCharacteristics
    OntologyEntry
properties:
    unique_identifier MO_218
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class TestTypeDatabase

class TestTypeDatabase

definition:
Database of codes for clinical findings.

superclasses:
    Database
properties:
    unique_identifier MO_76
    class_role concrete
    class_source ontology
used in individuals:
    IUPAC_Clinical_Chemistry_Guidelines
    LOINC
    TDMS

class TheoreticalBioSequenceType

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

superclasses:
    BioSequenceType
known subclasses:
    SequenceOntologyBioSequenceType
properties:
    unique_identifier MO_42
    class_role concrete
    class_source ontology
used in individuals:
    unknown_sequence

class TimeUnit

definition:
Units used for time measurements.

superclasses:
    Unit
known subclasses:
    TimeUnitOther
properties:
    unique_identifier MO_166
    class_role concrete
    class_source ontology
used in individuals:
    days
    hours
    minutes
    months
    ms
    seconds
    us
    weeks
    years

class TimeUnitOther

definition:
Time units not specified in MAGE.

superclasses:
    TimeUnit
properties:
    unique_identifier MO_103
    class_role concrete
    class_source ontology
used in individuals:
    half-life

class Transformation

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

superclasses:
    BioAssayDataPackage
properties:
    unique_identifier MO_216
constraints:
    restriction: has_protocol has-class Protocol

class Treatment

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

superclasses:
    BioMaterialPackage
properties:
    unique_identifier MO_23
    class_role concrete
    class_source mage
constraints:
    restriction: has_action has-class Action
    restriction: has_order has-class int
    restriction: has_protocol has-class Protocol

class TumorGrading

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

superclasses:
    BioMaterialCharacteristics
    OntologyEntry
properties:
    unique_identifier MO_28
    class_role abstract
    class_source ontology
constraints:
    restriction: has_database has-class TumorGradingDatabase

class TumorGradingDatabase

definition:
Database of tumor grading information

superclasses:
    Database
properties:
    unique_identifier MO_187
    class_role concrete
    class_source ontology
used in individuals:
    NCI_tumor_grading_database

class URI

definition:
Uniform Resource Identifier

superclasses:
    MGEDCoreOntology
properties:
    unique_identifier MO_12
    class_role abstract
    class_source ontology

class Unit

definition:
Units of measure.

superclasses:
    MeasurementPackage
known subclasses:
    ConcentrationUnit
    DistanceUnit
    MassUnit
    OtherUnit
    QuantityUnit
    TemperatureUnit
    TimeUnit
    VolumeUnit
properties:
    unique_identifier MO_3
    class_role abstract
    class_source ontology

class User

definition:
User is a way to id a person in a database

superclasses:
    MGEDExtendedOntology
properties:
    unique_identifier MO_62
constraints:
    restriction: has_ID has-class string

class VolumeUnit

definition:
Units used for volume measurements.

superclasses:
    Unit
known subclasses:
    VolumeUnitOther
properties:
    unique_identifier MO_179
    class_role concrete
    class_source ontology
used in individuals:
    L
    cc
    dl
    fl
    ml
    nl
    pl
    ul

class VolumeUnitOther

definition:
Volume units not specified in MAGE.

superclasses:
    VolumeUnit
properties:
    unique_identifier MO_155
    class_role place_holder
    class_source ontology

class WarningType

definition:
Controlled terms for descriptors of the warnings associated with reporters.

superclasses:
    DesignElementPackage
properties:
    unique_identifier MO_41
    class_role concrete
    class_source ontology
used in individuals:
    is_contaminated
    not_sequence_verified

class Water

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

superclasses:
    GrowthCondition
properties:
    unique_identifier MO_153
    class_role abstract
    class_source ontology
constraints:
    restriction: has_treatment has-class Protocol
    restriction: has_additive has-class Compound

class ZoneDefect

definition:
A technical manufactured described defect for zones.

superclasses:
    ArrayPackage
properties:
    unique_identifier MO_105
    class_role concrete
    class_source mage
constraints:
    restriction: has_type has-class DefectType

property class_role


definition:
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.

range:
    owl:oneOf{"abstract" "place_holder" "concrete"}

property class_source


definition:
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.

range:
    owl:oneOf{"mage" "ontology"}

property dc:contributor


definition:
An entity responsible for making contributions to the content of the resource.


property dc:coverage


definition:
The extent or scope of the content of the resource.


property dc:creator


definition:
An entity primarily responsible for making the content of the resource.


property dc:date


definition:
A date associated with an event in the life cycle of the resource.


property dc:description


definition:
An account of the content of the resource.


property dc:format


definition:
The physical or digital manifestation of the resource.


property dc:identifier


definition:
An unambiguous reference to the resource within a given context.


property dc:language


definition:
A language of the intellectual content of the resource.


property dc:publisher


definition:
An entity responsible for making the resource available


property dc:relation


definition:
A reference to a related resource.


property dc:rights


definition:
Information about rights held in and over the resource.


property dc:source


definition:
A reference to a resource from which the present resource is derived.


property dc:subject


definition:
The topic of the content of the resource.


property dc:title


definition:
A name given to the resource.


property dc:type


definition:
The nature or genre of the content of the resource.


property deprecated_from_version


definition:
property indicating the version of the MGED Ontology that the term was deprecated from

used in classes:
    ChromosomalAberration
    FactorValueDependency
    FactorValueSet
    IndividualChromosomalAbnormality

property deprecation_in_version


definition:
The value of the property indicates what version of the ontology the term was deprecated from.

range:
    owl:oneOf{"1.1.7" "1.1.9" "1.2.0" "1.1.8" "1.3.0" "1.3.1.1"}

property deprecation_old_parent


definition:
The value indicates the parent of the term before the term was deprecated.


property deprecation_old_restriction


definition:
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 deprecation_reason


definition:
Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term.

range:
    owl:oneOf{"deleted_term" "split_term" "merged_term" "replaced_term"}

property deprecation_replacement_term


definition:
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 has_ID


definition:
property indicating that the class has an identifier

used in classes:
    MGEDCoreOntology
    User

property has_MAGE_description


definition:
property indicating that the class has an association to a MAGE description

used in classes:
    ExperimentDesign

property has_URI


definition:
property indicating that the class has a URI

used in classes:
    BibliographicReference
    Contact
    Database
    Image
    Protocol

property has_accession


definition:
property indicating that the class has an accession number

used in classes:
    OntologyEntry

property has_accession_version


definition:
property indicating that the class has an accession number version

used in classes:
    OntologyEntry

property has_action


definition:
property indicating that the class has an action

used in classes:
    Treatment

property has_additive


definition:
property indicating that the class has an additive

used in classes:
    Water

property has_address


definition:
property indicating that the class has an address

used in classes:
    Contact

property has_affiliation


definition:
property indicating that the class has an affiliation to an institution

used in classes:
    Person

property has_atmospheric_component


definition:
property indicating that the class has an atmospheric component

used in classes:
    Atmosphere

property has_authors


definition:
property indicating that the class has authors

used in classes:
    BibliographicReference

property has_been_treated


definition:
property indicating that the class has been treated

used in classes:
    BioSample
    LabeledExtract

property has_bioassay_data


definition:
property indicating that the class has bioassaydata

used in classes:
    Experiment

property has_bioassays


definition:
property indicating that the class has bioassays

used in classes:
    Experiment
    ExperimentDesign

property has_biomaterial_characteristics


definition:
property indicating that the class has biomaterial characteristics

used in classes:
    BioMaterial

property has_biosource_type


definition:
property indicating that the class has a biosource type

domain:
    BioSourceProvider

property has_cancer_site


definition:
property indicating that the class has a cancer site

used in classes:
    DiseaseLocation

property has_category


definition:
property indicating that the class has a category

used in classes:
    ExperimentalFactor

property has_chromosomal_aberration_classification


definition:
property indicating that the class has a chromosomal aberration classification

used in classes:
    ChromosomalAberration

property has_citation


definition:
property indicating that the class has a citation

used in classes:
    Experiment
    Protocol

property has_clinical_finding


definition:
property indicating that the class has a clinical finding

used in classes:
    ClinicalHistory

property has_clinical_record


definition:
property indicating that the class has a clinical record

used in classes:
    ClinicalHistory
    FamilyMember

property has_clinical_treatment


definition:
property indicating that the class has a clinical treatment

used in classes:
    ClinicalHistory

property has_compound


definition:
property indicating that the class has a compound

used in classes:
    LabeledExtract

property has_cubic_volume


definition:
property indicating that the class contains a cubic volume measurement

used in classes:
    Biometrics

property has_database


definition:
property indicating that the class has a database

used in classes:
    CellLine
    CellType
    CellularComponent
    ClinicalTreatment
    Compound
    Cultivar
    DevelopmentalStage
    DiseaseStaging
    DiseaseState
    Ecotype
    GeographicLocation
    Histology
    Image
    Observation
    OntologyEntry
    Organism
    OrganismPart
    Phenotype
    SequenceOntologyBioSequenceType
    StrainOrLine
    TestType
    TumorGrading

property has_database_entry_type


definition:
property indicating that the class has a database entry type

used in classes:
    OntologyEntry

property has_description


definition:
property indicating that the class has a description

used in classes:
    ExperimentDesign
    OntologyEntry
    Protocol

property has_diameter


definition:
property indicating that the class has a diameter

used in classes:
    Biometrics

property has_disease_location


definition:
property indicating the location of the disease.

used in classes:
    DiseaseState

property has_disease_staging


definition:
property indicating that the class has disease staging

used in classes:
    DiseaseState

property has_disease_state


definition:
property indicating that the class has a disease state

used in classes:
    FamilyMember

property has_donor


definition:
property indicating that the class has a donor

used in classes:
    BioSourceProvider

property has_editor


definition:
property indicating that the class has an editor

used in classes:
    BibliographicReference

property has_email


definition:
property indicating that the class has an email address

used in classes:
    Contact

property has_experiment_design


definition:
property indicating that the class has an experiment design

used in classes:
    Experiment

property has_experiment_design_type


definition:
property indicating that the class has an experiment design type

used in classes:
    ExperimentDesign

property has_experiment_factors


definition:
property indicating that the class has experiment factors

used in classes:
    ExperimentDesign

property has_factor_value


definition:
property indicating that the class has a factor value

used in classes:
    ExperimentalFactor

property has_factor_value_ontology_entry


definition:
property indicating that the class has an ontology entry

used in classes:
    FactorValue

property has_family_member


definition:
property indicating that the class has a family member

used in classes:
    FamilyHistory

property has_family_relationship


definition:
property indicating that the class has a family relationship

used in classes:
    FamilyMember

property has_fax


definition:
property indicating that the class has a fax

used in classes:
    Contact

property has_feature_shape


definition:
property indicating that the class has a feature shape

used in classes:
    FeatureGroup

property has_fiducials


definition:
property indicating that the class has fiducials

used in classes:
    ArrayGroup

property has_first_name


definition:
property indicating that the class has a first name

used in classes:
    Person

property has_hardware


definition:
property indicating that the class has hardware

used in classes:
    Protocol
    Software

property has_height


definition:
property indicating that the class has a height

used in classes:
    Biometrics

property has_host


definition:
property indicating that the class has a host

domain:
    Host
used in classes:
    Host

property has_host_part


definition:
property indicating that the class has a host part

domain:
    Host
used in classes:
    Host

property has_human_readable_URI


definition:
property indicating that the contents found at this uri are human readable


property has_image_format


definition:
property indicating that the class has an image format

domain:
    PhysicalBioAssay
used in classes:
    Image
    PhysicalBioAssay

property has_individual


definition:
property indicating that the class has an individual

used in classes:
    Biometrics

property has_individual_genetic_characteristics


definition:
property indicating that the class has individual genetic characteristics

used in classes:
    FamilyMember

property has_initial_time_point


definition:
property indicating that the class has an individual time point

domain:
    Age
used in classes:
    Age

property has_issue


definition:
property indicating that the class has an issue

domain:
    BibliographicReference
used in classes:
    BibliographicReference

property has_laboratory_test


definition:
property indicating that the class has a laboratory test


property has_last_name


definition:
property indicating that the class has a last name

used in classes:
    Person

property has_length


used in classes:
    Biometrics

property has_machine_readable_URI


definition:
property indicating that the contents found at this uri are machine readable (i.e. in a standard format)


property has_make


definition:
property indicating that the class has a make

domain:
    Hardware
used in classes:
    Hardware

property has_manufacturer


definition:
property indicating that the class has a manufacturer

used in classes:
    Hardware
    Software

property has_mass


definition:
property indicating that the class has a mass

used in classes:
    Biometrics

property has_maximum_measurement


definition:
property indicating that the class has a maximum measurement

domain:
    Age
used in classes:
    Age
    GrowthCondition

property has_measurement


definition:
property indicating that the class has a measurement

used in classes:
    Age
    Compound
    EnvironmentalStress
    FactorValue
    GrowthCondition
    TestResult

property has_measurement_type


definition:
property indicating that the class has a measurement type

domain:
    Measurement
used in classes:
    Measurement

property has_mid_initials


definition:
property indicating that the class has a middle initials

used in classes:
    Person

property has_model


definition:
property indicating that the class has a model

domain:
    Hardware
used in classes:
    Hardware

property has_name


definition:
property indicating that the class has a name

used in classes:
    Organization

property has_node_value


definition:
property indicating that the class has a node value

used in classes:
    Node

property has_node_value_type


definition:
property indicating that the class has a node value type

used in classes:
    NodeValue

property has_nodes


definition:
property indicating that the class has a node

used in classes:
    BioAssayDataCluster

property has_nutrient_component


definition:
property indicating that the class has a nutrient component

used in classes:
    Nutrients

property has_order


definition:
property indicating that the class has an order

used in classes:
    Treatment

property has_organism_part


definition:
property indicating that the class has an organism part

used in classes:
    Biometrics
    Histology

property has_owner


definition:
property indicating that the class has an owner

used in classes:
    BioSourceProvider

property has_pages


definition:
property indicating that the class has pages

domain:
    BibliographicReference
used in classes:
    BibliographicReference

property has_parent_organization


definition:
property indicating that the class has a parent organization

used in classes:
    Organization

property has_part_modified


definition:
property indicating that the class has a modified part

used in classes:
    SomaticModification

property has_performer


definition:
property indicating that the protocol has a performer or contact person

used in classes:
    Histology
    Observation
    Test

property has_phone


definition:
property indicating that the class has a phone

used in classes:
    Contact

property has_prior_disease_state


definition:
property indicating that the class has a prior disease state

used in classes:
    ClinicalHistory

property has_property_set


definition:
property indicating that the class has a property set

used in classes:
    FactorValue

property has_protocol


definition:
property indicating that the class has a protocol

used in classes:
    Preservation
    Transformation
    Treatment

property has_providers


definition:
property indicating that the class has providers

used in classes:
    Experiment

property has_publication


definition:
property indicating that the class has a publication

used in classes:
    BibliographicReference

property has_publisher


definition:
property indicating that the class has a publisher

used in classes:
    BibliographicReference

property has_reason_for_deprecation


definition:
property to indicate the reason for deprecating a term

used in classes:
    ChromosomalAberration
    DeprecatedTerms
    FactorValueDependency
    FactorValueSet
    IndividualChromosomalAbnormality

property has_result


definition:
property indicating the class has a result

used in classes:
    PathogenTest

property has_scale


definition:
property indicating that the class has a scale

used in classes:
    NodeValue
    QuantitationType

property has_software


definition:
property indicating that the class has software

used in classes:
    Hardware
    Protocol
    Software

property has_species


definition:
property indicating that the class has species

used in classes:
    BioSequence
    DesignElementGroup
    StrainOrLine

property has_test_protocol


definition:
property indicating that the test has a test protocol


property has_test_result


definition:
property indicating that the test has a test result

used in classes:
    Test

property has_test_type


definition:
property indicating that the class has a clinical test

used in classes:
    ClinicalHistory
    Test

property has_text


definition:
property indicating that the class has text

used in classes:
    Protocol

property has_title


definition:
property indicating that the class has a title

used in classes:
    BibliographicReference
    Protocol

property has_toll_free_phone


definition:
property indicating that the class has a toll free phone

used in classes:
    Contact

property has_treatment


definition:
property indicating that the class has a treatment

used in classes:
    Water

property has_type


definition:
property indicating that the class has a type

used in classes:
    ArrayGroup
    BibliographicReference
    BioMaterial
    BioSample
    BioSequence
    Contact
    DerivedBioAssay
    DesignElement
    DesignElementGroup
    FeatureDefect
    FeatureGroup
    Fiducial
    Hardware
    NodeValue
    NormalizationDescription
    Parameter
    PhysicalArrayDesign
    Preservation
    Protocol
    QualityControlDescription
    QuantitationType
    ReplicateDescription
    Reporter
    Software
    ZoneDefect

property has_units


definition:
property indicating that the class has units

used in classes:
    Measurement
    Parameter

property has_value


definition:
property indicating that the class has a value

used in classes:
    FactorValueDependency
    FactorValueSet
    GrowthCondition
    IndividualGeneticCharacteristics
    Measurement
    OntologyEntry

property has_version


definition:
property indicating that the class has a version

used in classes:
    Database

property has_volume


definition:
property indicating that the class has a volume

domain:
    BibliographicReference
used in classes:
    BibliographicReference

property has_year


definition:
property indicating that the class has a year

used in classes:
    BibliographicReference

property is_solvent


definition:
property indicating that the class is a solvent

used in classes:
    Compound

property is_user_defined


definition:
property indicating that the class is user defined

used in classes:
    MGEDOntology

property protege:abstract



property protege:allowedParent



property protege:defaultLanguage



property protege:excludedTest



property protege:probeClass



property protege:readOnly



property protege:subclassesDisjoint



property protege:todoPrefix



property protege:todoProperty



property protege:usedLanguage



property replaced_with_term


definition:
The value of the property indicates the replacement term.


property split_to_term


definition:
The value of the property indicates a replacement term since the term was split.


property synonym


definition:
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.

range:
    string

property unique_identifier


definition:
A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123.


property was_replaced_by


definition:
instance property to indicate what the term was replaced by


property was_tested_for


definition:
property indicating that the class was tested for

used in classes:
    PathogenTest

property xsp:base



property xsp:fractionDigits



property xsp:length



property xsp:maxExclusive



property xsp:maxInclusive



property xsp:maxLength



property xsp:minExclusive



property xsp:minInclusive



property xsp:minLength



property xsp:pattern



property xsp:totalDigits



individual A


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

instance of:
    DistanceUnit
properties:
    unique_identifier MO_515

individual ATCC_Cultures


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

instance of:
    CellLineDatabase
    StrainOrLineDatabase
properties:
    unique_identifier MO_979

individual Adult_Mouse_Anatomy


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

instance of:
    OrganismPartDatabase
properties:
    unique_identifier MO_992

individual Affymetrix_DAT


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

instance of:
    ImageFormat
properties:
    unique_identifier MO_786

individual Affymetrix_average_difference


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_649

individual BAC


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

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_985
    synonym bacterial artificial chromosome
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual CABRI_Bacteria_and_Archaea_Strains


definition:
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.

instance of:
    StrainOrLineDatabase
properties:
    unique_identifier MO_1008

individual CABRI_Filamentous_Fungi_Strains


definition:
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.

instance of:
    StrainOrLineDatabase
properties:
    unique_identifier MO_1009

individual CABRI_HLA_typed_B_Cell_lines


definition:
List of CABRI HLA typed B cell lines sorted by name. It includes 238 resources that are available from a European collection participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and cell lines of interest can be requested.

instance of:
    CellLineDatabase
properties:
    unique_identifier MO_1005

individual CABRI_Human_and_Animal_Cell_lines


definition:
Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc.

instance of:
    CellLineDatabase
properties:
    unique_identifier MO_536

individual CABRI_Hybridomas


definition:
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.

instance of:
    CellLineDatabase
properties:
    unique_identifier MO_1006

individual CABRI_Yeasts_Strains


definition:
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.

instance of:
    StrainOrLineDatabase
properties:
    unique_identifier MO_1010

individual CBIL_CV


definition:
a controlled vocabulary provided by CBIL

instance of:
    CellTypeDatabase
    OrganismPartDatabase
    TargetedCellTypeDatabase
properties:
    unique_identifier MO_886

individual CLDB_Human_and_Animal_Cell_Line


definition:
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.

instance of:
    CellLineDatabase
properties:
    unique_identifier MO_1007

individual CellML


definition:
Ontology describing anatomical and physiological relationships.

instance of:
    OrganismPartDatabase
properties:
    unique_identifier MO_967

individual ChEBI


definition:
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.

instance of:
    CompoundDatabase
properties:
    unique_identifier MO_857

individual ChemID


definition:
Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds.

instance of:
    CompoundDatabase
properties:
    unique_identifier MO_426

individual Ci


definition:
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).

instance of:
    RadiationUnit
properties:
    unique_identifier MO_642

individual Cy3


definition:
fluorophore used for labeling/detection purposes

instance of:
    LabelCompound
properties:
    unique_identifier MO_739

individual Cy5


definition:
fluorophore used for labeling/detection purposes

instance of:
    LabelCompound
properties:
    unique_identifier MO_646

individual DNA


definition:
Deoxyribonucleic acid.

instance of:
    MaterialType
    PolymerType
properties:
    unique_identifier MO_945

individual DNA_sequencer


definition:
An instrument that produces DNA sequences.

instance of:
    HardwareType
properties:
    unique_identifier MO_676

individual EMAP


definition:
The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth.

instance of:
    DevelopmentalStageDatabase
properties:
    unique_identifier MO_357

individual EST


definition:
Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_412
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual Euclidean_distance


definition:
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).

instance of:
    NodeValueType
properties:
    unique_identifier MO_932

individual F


definition:
mating type indicating the presence of F plasmid in a bacterial cell

instance of:
    Sex
properties:
    unique_identifier MO_717

individual FMA


definition:
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.

instance of:
    OrganismPartDatabase
properties:
    unique_identifier MO_468

individual F_minus


definition:
mating type indicating the absence of F plasmid in a bacterial cell

instance of:
    Sex
properties:
    unique_identifier MO_682

individual FlyBase_developmental_stage_database


definition:
uri for FlyBase developmental stage terms

instance of:
    DevelopmentalStageDatabase
properties:
    unique_identifier MO_865

individual FlyBase_organism_part_database


definition:
curated database containing information on Drosophila genes, alleles etc

instance of:
    OrganismPartDatabase
properties:
    unique_identifier MO_504

individual GIF


definition:
Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss.

instance of:
    ImageFormat
properties:
    unique_identifier MO_963

individual GRAMENE


definition:
A Comparative Mapping Resource for Grains.

instance of:
    StrainOrLineDatabase
properties:
    unique_identifier MO_678

individual GeneOntology


definition:
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.

instance of:
    CellularComponentDatabase
properties:
    unique_identifier MO_1022

individual HUMAT


definition:
Ontology of human developmental anatomy for Carnegie stages 1-20.

instance of:
    DevelopmentalStageDatabase
properties:
    unique_identifier MO_844

individual Hfr


definition:
High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.7
    unique_identifier MO_419
    deprecation_reason deleted_term
    deprecation_replacement_term Sex
    deprecation_old_parent Sex

individual ICD-9-CM


definition:
Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.

instance of:
    DiseaseStateDatabase
properties:
    unique_identifier MO_654

individual IU


definition:
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.

instance of:
    QuantityUnit
properties:
    unique_identifier MO_1011
    synonym International unitUI

individual IUPAC_Clinical_Chemistry_Guidelines


definition:
A resource of vocabularies for describing clinical tests, e.g. blood chemistry.

instance of:
    TestTypeDatabase
properties:
    unique_identifier MO_593

individual JAX_mouse_strains


definition:
Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.

instance of:
    StrainOrLineDatabase
properties:
    unique_identifier MO_369

individual JPEG


definition:
Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss.

instance of:
    ImageFormat
properties:
    unique_identifier MO_746

individual K


definition:
Kelvin, unit of temperature

instance of:
    TemperatureUnit
properties:
    unique_identifier MO_614

individual L


definition:
liter, unit of volume

instance of:
    VolumeUnit
properties:
    unique_identifier MO_444

individual LOINC


definition:
Database resource for universal identifiers for laboratory and other clinical observations

instance of:
    TestTypeDatabase
properties:
    unique_identifier MO_731

individual M


definition:
Mole per liter or molarity, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_936

individual MAD_stage


definition:
database entry from mouse anatomical dictionary for developmental stage term

instance of:
    DevelopmentalStageDatabase
    OrganismPartDatabase
    TargetedCellTypeDatabase
properties:
    unique_identifier MO_693

individual MAS4_average_difference


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_782

individual MAS5_signal


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_653

individual MAS5_signal_log_ratio


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_938

individual MBEI


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_756

individual MESH


definition:
database entry from MESH, medical subject headings vocabulary resource

instance of:
    DiseaseStateDatabase
properties:
    unique_identifier MO_580

individual MTB_Database


definition:
Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors.

instance of:
    DiseaseStateDatabase
properties:
    unique_identifier MO_942

individual Mammalian_Phenotype_Ontology


definition:
A community effort to provide standard terms for annotating phenotypic data.

instance of:
    ObservationDatabase
properties:
    unique_identifier MO_704

individual NASC


definition:
The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.

instance of:
    StrainOrLineDatabase
properties:
    unique_identifier MO_379

individual NCBI_taxonomy


definition:
identifier for a taxon provided by the NCBI taxonomy database

instance of:
    OrganismDatabase
    StrainOrLineDatabase
properties:
    unique_identifier MO_773

individual NCI_Thesaurus


definition:
A description logic namespace that contains controlled terminology used at NCI.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.7
    unique_identifier MO_456
    deprecation_reason split_term
    split_to_term NCI_cell_type_database NCI_disease_state_database NCI_strain_or_line_database NCI_geographic_location_database NCI_compound_database NCI_organism_part_database NCI_targeted_cell_type_database NCI_tumor_grading_database
    deprecation_old_parent StrainOrLineDatabase ClinicalTreatmentDatabase GeographicLocationDatabase TumorGradingDatabase CellLineDatabase TargetedCellTypeDatabase DiseaseStateDatabase CompoundDatabase OrganismPartDatabase

individual NCI_cell_type_database


definition:
a controlled vocabulary of cell types

instance of:
    CellTypeDatabase
properties:
    unique_identifier MO_687

individual NCI_compound_database


definition:
a controlled vocabulary for compounds

instance of:
    CompoundDatabase
properties:
    unique_identifier MO_376

individual NCI_disease_staging_database


definition:
a controlled vocabulary for disease stages

instance of:
    DiseaseStagingDatabase
properties:
    unique_identifier MO_422

individual NCI_disease_state_database


definition:
a controlled vocabulary for disease states

instance of:
    DiseaseStateDatabase
properties:
    unique_identifier MO_790

individual NCI_geographic_location_database


definition:
a controlled vocabulary for geographic locations

instance of:
    GeographicLocationDatabase
properties:
    unique_identifier MO_630

individual NCI_histology_database


definition:
a controlled vocabulary for histology

instance of:
    HistologyDatabase
properties:
    unique_identifier MO_537

individual NCI_organism_part_database


definition:
a controlled vocabulary of organism parts

instance of:
    OrganismPartDatabase
properties:
    unique_identifier MO_690

individual NCI_strain_or_line_database


definition:
a controlled vocabulary for strains or lines

instance of:
    StrainOrLineDatabase
properties:
    unique_identifier MO_397

individual NCI_targeted_cell_type_database


definition:
a controlled vocabulary of targeted cell types

instance of:
    TargetedCellTypeDatabase
properties:
    unique_identifier MO_351

individual NCI_tumor_grading_database


definition:
a controlled vocabulary of tumor grading terms

instance of:
    TumorGradingDatabase
properties:
    unique_identifier MO_819

individual ORF


definition:
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.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_413
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual PAC


definition:
sequence from a P1 artificial chromosome

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_909
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual PCR


definition:
Polymerase chain reaction. An element generated using this procedure.

instance of:
    DesignElement
properties:
    unique_identifier MO_915

individual PCR_amplicon


definition:
BioSequence generated by means of polymerase chain reaction

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_450
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual PCR_amplification


definition:
Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_358

individual PCR_fail


definition:
PCR where no products of any kind appear in gel-separated reaction products.

instance of:
    FailType
properties:
    unique_identifier MO_667

individual PCR_primer


definition:
single oligo used for polymerase chain reaction direction unspecified

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_651
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual PCR_primer_forward


definition:
single stranded oligo used for polymerase chain reaction

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_381
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual PCR_primer_reverse


definition:
single stranded oligo used for polymerase chain reaction

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_640
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual PCR_questionable


definition:
PCR with multiple bands, or smear, in gel-separated reaction products

instance of:
    FailType
properties:
    unique_identifier MO_620

individual PNG


definition:
Portable Network Graphic, a lossless image data format.

instance of:
    ImageFormat
properties:
    unique_identifier MO_1001

individual Pathbase


definition:
database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice

instance of:
    HistologyDatabase
properties:
    unique_identifier MO_972

individual Pearson_correlation


definition:
The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations.

instance of:
    NodeValueType
properties:
    unique_identifier MO_632

individual R


definition:
Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg.

instance of:
    RadiationUnit
properties:
    unique_identifier MO_725

individual RMA


definition:
Robust Multiarray Average. A quantitative measure of the relative abundance of a transcript. RMA is a summary measure of related perfect match Features on an Affymetrix array. The values are background-adjusted, normalized and log-transformed values.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_987

individual RNA


definition:
Ribonucleic acid.

instance of:
    PolymerType
properties:
    unique_identifier MO_594

individual RNA_stability_design


definition:
A RNA stability experiment design type examines the stability and/or decay of RNA transcripts.

instance of:
    BioMolecularAnnotation
properties:
    unique_identifier MO_553

individual Rad


definition:
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.

instance of:
    RadiationUnit
properties:
    unique_identifier MO_585

individual Rem


definition:
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.

instance of:
    RadiationUnit
properties:
    unique_identifier MO_908

individual SequenceOntology


definition:
The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence.

instance of:
    SequenceOntologyDatabase
properties:
    unique_identifier MO_724

individual Spearmans_rank_correlation


definition:
Computed as the ordinary Pearson correlation coefficient between two groups of rankings.

instance of:
    NodeValueType
properties:
    unique_identifier MO_552

individual TAIR


definition:
The Arabidopsis Information Resource.

instance of:
    CellTypeDatabase
    StrainOrLineDatabase
properties:
    unique_identifier MO_660

individual TAIR_arabidopsis_anatomy_ontology


definition:
A structured controlled vocabulary for the anatomy of Arabidopsis.

instance of:
    OrganismPartDatabase
properties:
    unique_identifier MO_809

individual TAIR_arabidopsis_development_ontology


definition:
An ontology of stages of growth and development of the model plant Arabidopsis thaliana.

instance of:
    DevelopmentalStageDatabase
properties:
    unique_identifier MO_919

individual TDMS


definition:
Toxicology Data Management System, a database resource for systems, organs, pathology, etc.

instance of:
    DiseaseStateDatabase
    HistologyDatabase
    OrganismPartDatabase
    TestTypeDatabase
properties:
    unique_identifier MO_718

individual TIFF


definition:
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.

instance of:
    ImageFormat
properties:
    unique_identifier MO_638

individual UMLS


definition:
Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH.

instance of:
    DiseaseStateDatabase
properties:
    unique_identifier MO_947

individual U_per_L


definition:
units per liter

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_875

individual U_per_week


definition:
units per week, e.g. the number of units of alcohol consumed over a period of 7 days

instance of:
    OtherUnit
properties:
    unique_identifier MO_388

individual WebRENI


definition:
database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions

instance of:
    DiseaseStateDatabase
properties:
    unique_identifier MO_737

individual YAC


definition:
sequence from yeast artificial chromosome

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_794
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual _32P


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

instance of:
    LabelCompound
properties:
    unique_identifier MO_839

individual _33P


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

instance of:
    LabelCompound
properties:
    unique_identifier MO_427

individual absolute


definition:
a measurement where the value is independent of other measurements

instance of:
    MeasurementType
properties:
    unique_identifier MO_741

individual acclimatization


definition:
The action of stabilizing an organism prior to treatment

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_776

individual acrossBioAssay_mean_and_coefficient_of_variation


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

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_840

individual acrossBioAssay_mean_and_p_values


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

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_671

individual acrossBioAssay_mean_and_standard_deviation


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

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_946

individual acrossBioAssay_mean_and_variance


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

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_400

individual across_bioassay_data_set_function


definition:
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.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_606

individual activity_units_per_ml


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

instance of:
    OtherUnit
properties:
    unique_identifier MO_870

individual ad_libitum


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

instance of:
    DeliveryMethod
properties:
    unique_identifier MO_592

individual add


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

instance of:
    AtomicAction
properties:
    unique_identifier MO_815

individual agar


definition:
A type of solid media commonly used for growing organisms

instance of:
    Media
properties:
    unique_identifier MO_935

individual agar_stab


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

instance of:
    BioSourceType
properties:
    unique_identifier MO_971

individual age


definition:
A descriptor for FactorValue where age is compared.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_467

individual alexa_350


definition:
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.

instance of:
    LabelCompound
properties:
    unique_identifier MO_512

individual alexa_430


definition:
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.

instance of:
    LabelCompound
properties:
    unique_identifier MO_401

individual alexa_488


definition:
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.

instance of:
    LabelCompound
properties:
    unique_identifier MO_446

individual alexa_532


definition:
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.

instance of:
    LabelCompound
properties:
    unique_identifier MO_375

individual alexa_546


definition:
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.

instance of:
    LabelCompound
properties:
    unique_identifier MO_493

individual alexa_568


definition:
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.

instance of:
    LabelCompound
properties:
    unique_identifier MO_736

individual alexa_594


definition:
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.

instance of:
    LabelCompound
properties:
    unique_identifier MO_461

individual alexa_633


definition:
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.

instance of:
    LabelCompound
properties:
    unique_identifier MO_345

individual alexa_660


definition:
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.

instance of:
    LabelCompound
properties:
    unique_identifier MO_547

individual alexa_680


definition:
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.

instance of:
    LabelCompound
properties:
    unique_identifier MO_799

individual all_pairs


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

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_565

individual amino_acid_primary_sequence_record


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

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_829

individual aminosilane


definition:
a surface coating type for immobilization with the compound aminosilane

instance of:
    SurfaceType
properties:
    unique_identifier MO_747

individual amol


definition:
attomole, quantity unit

instance of:
    QuantityUnit
properties:
    unique_identifier MO_977

individual aneuploid


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

instance of:
    Ploidy
properties:
    unique_identifier MO_918

individual antibody


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

instance of:
    PhysicalBioSequenceType
properties:
    unique_identifier MO_833

individual array_manufacture_software


definition:
Software to control an arrayer.

instance of:
    SoftwareType
properties:
    unique_identifier MO_502

individual array_manufacturer


definition:
Person or organization that manufactured the array.

instance of:
    Roles
properties:
    unique_identifier MO_890

individual array_manufacturing


definition:
The process of physically creating the array.

instance of:
    ExperimentalProtocolType
properties:
    unique_identifier MO_818

individual array_platform_variation_design


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

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_899

individual array_scanner


definition:
An instrument capable of acquiring images of arrays.

instance of:
    HardwareType
properties:
    unique_identifier MO_824

individual arrayer


definition:
An instrument capable of manufacturing arrays by spotting material.

instance of:
    HardwareType
properties:
    unique_identifier MO_697

individual atmosphere


definition:
The atmospheric conditions used to culture or grow an organism.

instance of:
    EnvironmentalFactorCategory
properties:
    unique_identifier MO_498

individual aunt


definition:
The sister of one's father or mother.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_354

individual averaged_intensity


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

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_362

individual barrier_facility


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

instance of:
    EnvironmentalFactorCategory
properties:
    unique_identifier MO_511

individual bedding


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

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.7
    unique_identifier MO_615
    deprecation_reason deleted_term
    deprecation_replacement_term BioMaterialCharacteristicCategory
    deprecation_old_parent BioMaterialCharacteristicCategory

individual beginning_of_stage


definition:
time point that indicates the start of some developmental stage

instance of:
    InitialTimePoint
properties:
    unique_identifier MO_608

individual behavior_design


definition:
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.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.9
    unique_identifier MO_532
    deprecation_reason split_term
    split_to_term stimulated_design_type innate_behavior_design
    deprecation_old_parent BiologicalProperty

individual behavioral_design_type


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

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.9
    unique_identifier MO_766
    deprecation_reason replaced_term
    replaced_with_term innate_behavior_design
    deprecation_old_parent PerturbationalDesign

individual behavioral_stimulus


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

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_674

individual bibliographic_record


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

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_923

individual binding_site_identification_design


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

instance of:
    BioMolecularAnnotation
    TechnologicalDesign
properties:
    unique_identifier MO_933
    synonym chromatin immunoprecipitationchromatin IPchromatin_immunoprecipitationChIP-chip

individual bioassay_data_transformation_software


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

instance of:
    SoftwareType
properties:
    unique_identifier MO_672
    synonym normalization software

individual bioassay_replicate_reduction


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_976

individual biological_fluid_collection


definition:
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.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_685

individual biological_replicate


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

instance of:
    QualityControlDescriptionType
    ReplicateDescriptionType
properties:
    unique_identifier MO_952

individual biological_resource_record


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

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_989

individual biomaterial_provider


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

instance of:
    BioMaterialCharacteristicCategory
    Roles
properties:
    unique_identifier MO_591

individual biopsy


definition:
The process of removing tissue from a living organism.

instance of:
    ComplexAction
properties:
    unique_identifier MO_711

individual biosequence_provider


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

instance of:
    Roles
properties:
    unique_identifier MO_881

individual biotin


definition:
a compound used for labeling/detection purposes

instance of:
    LabelCompound
properties:
    unique_identifier MO_793

individual birth


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

instance of:
    InitialTimePoint
properties:
    unique_identifier MO_710

individual blood


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

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.9
    unique_identifier MO_409
    deprecation_reason deleted_term
    deprecation_replacement_term BioSourceType
    deprecation_old_parent BioSourceType

individual book


definition:
A publication type which has an ISBN.

instance of:
    PublicationType
properties:
    unique_identifier MO_627

individual boolean


definition:
The values are either TRUE or FALSE, which can be expressed as 1 and 0.

instance of:
    DataType
properties:
    unique_identifier MO_826

individual brother


definition:
A male having the same genetic parents as another, or one genetic parent in common with another.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_655

individual cDNA_clone


definition:
sequence of complementary cDNA copy of an RNA molecule contained on a plasmid including the plasmid sequence, used when the entire clone is spotted non-exact synonym: cDNA, complementary DNA

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_966
    synonym complementary DNAcDNA
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual candela


definition:
One lumen per steradian. A steradian is a fraction of the surface area of a sphere that is equal to the square of the radius divided by the total surface area. This is approximately 8% of the total surface area. Exact synonym: candle power

instance of:
    LightUnit
properties:
    unique_identifier MO_572
    synonym candle power

individual candelas_per_square_meter


definition:
Unit of brightness or luminance.

instance of:
    LightUnit
properties:
    unique_identifier MO_813

individual cc


definition:
a cubic centimeter, volume unit

instance of:
    VolumeUnit
properties:
    unique_identifier MO_834

individual cell


definition:
One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms.

instance of:
    MaterialType
properties:
    unique_identifier MO_612

individual cell_component_comparison_design


definition:
A design in which RNA from different cell components is examined.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_1019

individual cell_cycle_design


definition:
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.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_822

individual cell_line


definition:
A descriptor for FactorValue where CellLine is compared.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_562

individual cell_lysate


definition:
cell lysate, a collection of cells whose membranes have been disrupted

instance of:
    MaterialType
properties:
    unique_identifier MO_903

individual cell_ontology


definition:
database of cell ontology terms

instance of:
    CellTypeDatabase
    TargetedCellTypeDatabase
properties:
    unique_identifier MO_404

individual cell_type


definition:
A descriptor for FactorValue where CellType is compared.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_548

individual cell_type_comparison_design


definition:
A cell type comparison design experiment design type compares cells of different type for example different cell lines.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_764

individual cells_per_ml


definition:
the number of cells per ml

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_727

individual cellular_modification_design


definition:
A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.

instance of:
    PerturbationalDesign
    TechnologicalDesign
properties:
    unique_identifier MO_392
    synonym RNAi

individual cellular_process_design


definition:
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.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_810

individual centrifuge


definition:
An instrument capable of applying centrifugal force to tubes or microtiter plates.

instance of:
    HardwareType
properties:
    unique_identifier MO_476

individual cfu_per_ml


definition:
the number of colony forming units per ml

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_788

individual change_biomaterial_characteristics


definition:
Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. Non exact synonym: change growth condition, change environment

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_383
    synonym change environmentchange growth condition

individual change_humidity


definition:
The action of changing the relative humidity, e.g. from 1% to 10%.

instance of:
    AtomicAction
properties:
    unique_identifier MO_917

individual change_light


definition:
Change in light intensity or wavelength.

instance of:
    AtomicAction
properties:
    unique_identifier MO_549

individual change_temperature


definition:
Change in temperature.

instance of:
    AtomicAction
properties:
    unique_identifier MO_677

individual chrome_border


definition:
the chrome border on an Affymetrix type array which is used as a point of reference for orientation (fiducial)

instance of:
    FiducialType
properties:
    unique_identifier MO_491

individual chromosomal_deletion


definition:
The loss of a segment of the genetic material from a chromosome.

instance of:
    ChromosomalAberrationClassification
properties:
    unique_identifier MO_922

individual chromosomal_duplication


definition:
An irregularity in the number of chromosomes, usually in the form of a gain of genetic material.

instance of:
    ChromosomalAberrationClassification
properties:
    unique_identifier MO_1002

individual chromosomal_insertion


definition:
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.

instance of:
    ChromosomalAberrationClassification
properties:
    unique_identifier MO_518

individual chromosomal_inversion


definition:
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.

instance of:
    ChromosomalAberrationClassification
properties:
    unique_identifier MO_622

individual chromosomal_substitution


definition:
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.

instance of:
    GeneticModification
properties:
    unique_identifier MO_995

individual chromosomal_translocation


definition:
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.

instance of:
    ChromosomalAberrationClassification
properties:
    unique_identifier MO_368

individual chromosome


definition:
Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_578
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType PhysicalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType PhysicalBioSequenceType

individual circadian_rhythm_design


definition:
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.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.7
    unique_identifier MO_539
    deprecation_reason replaced_term
    replaced_with_term physiological_process_design
    deprecation_old_parent BiologicalProperty

individual clinical_history_design


definition:
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.

instance of:
    EpidemiologicalDesign
properties:
    unique_identifier MO_832

individual clinical_information


definition:
A descriptor for FactorValue where ClinicalInformation is compared.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_816

individual clinical_record


definition:
record which describes and identifies clinical information about an organism

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_852

individual clinical_treatment


definition:
A descriptor for a clinical treatment for a patient.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_384

individual clone_of_unknown_source


definition:
Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown.

instance of:
    PhysicalBioSequenceType
properties:
    unique_identifier MO_371

individual clustered_data


definition:
Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_418

individual clustering_software


definition:
Software used to cluster the data.

instance of:
    SoftwareType
properties:
    unique_identifier MO_464

individual cm


definition:
centimeter, a unit of distance

instance of:
    DistanceUnit
properties:
    unique_identifier MO_837

individual co-expression_design


definition:
A co-expression experiment design type identifies genes which are coordinately expressed and are potentially used to infer a role in a biological process(es) non-exact synonym: guilt by association

instance of:
    BioMolecularAnnotation
properties:
    unique_identifier MO_904
    synonym guilt by association

individual coitus


definition:
the physical act of copulation that occurs during the process of sexual reproduction synonyms: copulation, insemination

instance of:
    InitialTimePoint
properties:
    unique_identifier MO_783
    synonym inseminationcopulation

individual collapsed_spot_replicate


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_789

individual comparative_genome_hybridization_design


definition:
Experiment design type in which genomic content is studied using an array based assay.

instance of:
    BioMolecularAnnotation
    TechnologicalDesign
properties:
    unique_identifier MO_856
    synonym array_CGHarray CGHCGH

individual compound_based_treatment


definition:
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.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_798

individual compound_record


definition:
a record which describes and identifies a compound e.g. drug record part of NCI thesaurus

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_546

individual compound_treatment_design


definition:
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.

instance of:
    PerturbationalDesign
properties:
    unique_identifier MO_555

individual computational_feature


definition:
Computationally derived sequence feature.

instance of:
    SeqFeatureBasis
properties:
    unique_identifier MO_411

individual computed_amino_acid_sequence_feature_record


definition:
a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_797

individual computed_nucleic_acid_sequence_feature_record


definition:
A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_774

individual computed_protein_structure_record


definition:
a record which describes and identifies a protein structure e.g. PDB

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_765

individual computer


definition:
A device capable of applying software.

instance of:
    HardwareType
properties:
    unique_identifier MO_510

individual concentrate


definition:
Increasing the concentration of solutes in a solution or suspension.

instance of:
    AtomicAction
properties:
    unique_identifier MO_883

individual condition_specificity


definition:
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.

instance of:
    HigherLevelAnalysisProtocolType
properties:
    unique_identifier MO_417

individual consensus_DNA


definition:
DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.3.1.1
    unique_identifier MO_361
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual consensus_mRNA


definition:
mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.3.1.1
    unique_identifier MO_423
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual consortium_member


definition:
A member of a consortium of institutions.

instance of:
    Roles
properties:
    unique_identifier MO_778

individual consultant


definition:
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.

instance of:
    Roles
properties:
    unique_identifier MO_984

individual control_biosequence


definition:
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.

instance of:
    ControlType
properties:
    unique_identifier MO_940

individual control_buffer


definition:
A Reporter where only buffer was deposited on the array

instance of:
    ControlType
properties:
    unique_identifier MO_505

individual control_design_element_group_type


definition:
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.

instance of:
    DesignElementGroupType
properties:
    unique_identifier MO_414

individual control_empty


definition:
A Reporter where no material or buffer was deposited on the array

instance of:
    ControlType
properties:
    unique_identifier MO_830

individual control_genomic_DNA


definition:
A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA.

instance of:
    ControlType
properties:
    unique_identifier MO_449

individual control_hybridization_quality


definition:
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).

instance of:
    ControlType
properties:
    unique_identifier MO_385

individual control_label


definition:
Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone.

instance of:
    ControlType
properties:
    unique_identifier MO_708

individual control_reporter_size


definition:
A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency.

instance of:
    ControlType
properties:
    unique_identifier MO_431

individual control_spike_calibration


definition:
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.

instance of:
    ControlType
properties:
    unique_identifier MO_364

individual control_unknown_type


definition:
A Reporter indicated as being a control of unknown type.

instance of:
    ControlType
properties:
    unique_identifier MO_925

individual cosine_distance


definition:
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.

instance of:
    NodeValueType
properties:
    unique_identifier MO_550

individual cosmid


definition:
sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_888
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual count


definition:
Unit for a simple count of things

instance of:
    QuantityUnitOther
properties:
    unique_identifier MO_500

individual cpm


definition:
counts per minute, unit of light emissions produced by ionizing radiation.

instance of:
    RadiationUnit
properties:
    unique_identifier MO_348

individual ctDNA


definition:
ctDNA: sequence from the chloroplast synonym: chloroplast DNA

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.3.1.1
    unique_identifier MO_586
    synonym chloroplast DNA
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual curated_amino_acid_sequence_record


definition:
A record which describes and identifies an amino acid sequence which has been curated

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_451

individual curated_gene_record


definition:
A record which describes and identifies nucleic acid sequence which has been identified as a gene by a curator. e.g. Flybase gene record

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_913

individual curated_nucleic_acid_sequence_feature_record


definition:
A record which identifies a nucleic acid sequence feature(s) and which has been curated.

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_644

individual curator


definition:
person who checks the consistency of the data and MAGE-ML file

instance of:
    Roles
properties:
    unique_identifier MO_893

individual cytoplasmic_RNA


definition:
RNA obtained from the cytoplasm.

instance of:
    MaterialType
properties:
    unique_identifier MO_978

individual data_analyst


definition:
A contact who performs data analysis, e.g. statistician.

instance of:
    Roles
properties:
    unique_identifier MO_753

individual data_coder


definition:
person who prepares the MAGE-ML file

instance of:
    Roles
properties:
    unique_identifier MO_695

individual date


definition:
Time stated in terms of the day, month, and year.

instance of:
    DataType
properties:
    unique_identifier MO_587

individual daughter


definition:
The female offspring of the patient or individual under study.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_665

individual days


definition:
24 hours, time unit

instance of:
    TimeUnit
properties:
    unique_identifier MO_513
    synonym d

individual decontaminate


definition:
Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma).

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_389

individual degrees_C


definition:
degrees celsius, unit of temperature

instance of:
    TemperatureUnit
properties:
    unique_identifier MO_980

individual degrees_F


definition:
degrees Fahrenheit, unit of temperature

instance of:
    TemperatureUnit
properties:
    unique_identifier MO_812

individual deleted_term


definition:
The term was deleted from the MGED CoreOntology.

used in classes:
    ChromosomalAberration
    FactorValueDependency
    FactorValueSet
    IndividualChromosomalAbnormality
instance of:
    DeprecationReason
properties:
    unique_identifier MO_1023

individual development_or_differentiation_design


definition:
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.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_892

individual developmental_stage


definition:
A descriptor for FactorValue where DevelopmentalStage is compared.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_878

individual diameter_aberration


definition:
The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.

instance of:
    DefectType
properties:
    unique_identifier MO_781

individual differential_expression


definition:
An analysis aimed at identifying differentially expressed genes in two or more conditions.

instance of:
    HigherLevelAnalysisProtocolType
properties:
    unique_identifier MO_874

individual differential_expression_software


definition:
A software implementing a Higher Level Analysis protocol of type differential_expresssion.

instance of:
    SoftwareType
properties:
    unique_identifier MO_350

individual dilute


definition:
Decreasing the concentration of solutes in a solution or suspension.

instance of:
    AtomicAction
properties:
    unique_identifier MO_962

individual diploid


definition:
Describes a cell, nucleus or an organism with two copies of each chromosome.

instance of:
    Ploidy
properties:
    unique_identifier MO_836

individual disease_staging


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

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_792

individual disease_state


definition:
A descriptor for FactorValue where DiseaseState is compared.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_787

individual disease_state_design


definition:
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.

instance of:
    EpidemiologicalDesign
    PerturbationalDesign
properties:
    unique_identifier MO_902

individual displaced_feature_or_zone


definition:
The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).

instance of:
    DefectType
properties:
    unique_identifier MO_959

individual dissect


definition:
The action of removing one or more organism parts.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_374

individual dl


definition:
deciliter, unit of volume

instance of:
    VolumeUnit
properties:
    unique_identifier MO_624

individual dose_response_design


definition:
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).

instance of:
    PerturbationalDesign
properties:
    unique_identifier MO_485

individual double_stranded


definition:
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.

instance of:
    StrandType
properties:
    unique_identifier MO_828

individual dpm


definition:
disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument.

instance of:
    RadiationUnit
properties:
    unique_identifier MO_583

individual ds_oligo


definition:
a double stranded oligonucleotide

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_344
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual dye_swap_design


definition:
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_858
    synonym dye flipflip dye

individual dye_swap_merge


definition:
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.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_448

individual dye_swap_quality_control


definition:
Indicates that a dye swap was performed for some or all hybridizations within an experiment

instance of:
    QualityControlDescriptionType
properties:
    unique_identifier MO_524

individual dye_swap_replicate


definition:
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.

instance of:
    ReplicateDescriptionType
properties:
    unique_identifier MO_901

individual dye_swap_replicate_reduction


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_750

individual eVOC


definition:
Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.

instance of:
    CellTypeDatabase
    DevelopmentalStageDatabase
    DiseaseStateDatabase
    OrganismPartDatabase
properties:
    unique_identifier MO_684

individual eclosion


definition:
Emergence of an adult insect from its pupa or cocoon.

instance of:
    InitialTimePoint
properties:
    unique_identifier MO_876

individual egg_laying


definition:
The point at which the egg(s) is laid by an organism.

instance of:
    InitialTimePoint
properties:
    unique_identifier MO_767

individual element_design


definition:
protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design

instance of:
    ExperimentalProtocolType
properties:
    unique_identifier MO_523

individual ellipsoid_feature


definition:
The shape of the feature on the array is circular or oval.

instance of:
    FeatureShape
properties:
    unique_identifier MO_459

individual environmental_history_design


definition:
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.

instance of:
    EnvironmentalHistory
properties:
    unique_identifier MO_698

individual ex_vivo_design


definition:
An experiment design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_808

individual exemplar_mRNA


definition:
An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.3.1.1
    unique_identifier MO_621
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual exon


definition:
sequence which represents regions of a transcript that are joined to another exon during splicing

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_619
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual experimental_and_computational_feature


definition:
Sequence features derived by both computational and experimental methods.

instance of:
    SeqFeatureBasis
properties:
    unique_identifier MO_516

individual experimental_design_element_group_type


definition:
A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial.

instance of:
    DesignElementGroupType
properties:
    unique_identifier MO_755

individual experimental_feature


definition:
An experimentally defined sequence feature.

instance of:
    SeqFeatureBasis
properties:
    unique_identifier MO_452

individual extract


definition:
The BioSample immediately before labeling.

instance of:
    BioSampleType
properties:
    unique_identifier MO_895

individual fM


definition:
femtomolar, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_898

individual family_history_design


definition:
A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied

instance of:
    EpidemiologicalDesign
properties:
    unique_identifier MO_544

individual father


definition:
A male parent.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_762

individual feature_extraction


definition:
The process of obtaining quantifiable values from the scanned image of the array. Exact synonyms: image analysis, image quantification

instance of:
    ExperimentalProtocolType
properties:
    unique_identifier MO_928
    synonym image analysisimage quantification

individual feature_extraction_software


definition:
Software to create MeasuredBioAssayData from images. Exact Synonym: image analysis software, image quantification software.

instance of:
    SoftwareType
properties:
    unique_identifier MO_633
    synonym image quantification softwareimage analysis software

individual feces


definition:
A biosource obtained as fecal matter.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.9
    unique_identifier MO_636
    deprecation_reason deleted_term
    deprecation_replacement_term BioSourceType
    deprecation_old_parent BioSourceType

individual feeding


definition:
Delivery method where a compound/drug is administered in food or water.

instance of:
    DeliveryMethod
properties:
    unique_identifier MO_993

individual female


definition:
of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes.

instance of:
    Sex
properties:
    unique_identifier MO_506

individual fertilization


definition:
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO)

instance of:
    InitialTimePoint
properties:
    unique_identifier MO_701

individual fg


definition:
femtogram, unit of mass

instance of:
    MassUnit
properties:
    unique_identifier MO_732

individual filtered_data


definition:
Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_625

individual fl


definition:
femtoliter, unit of volume

instance of:
    VolumeUnit
properties:
    unique_identifier MO_721

individual flag_filter


definition:
transformation method that involves removal of values in a data set based on visual or computed flags (e.g. the GenePix feature_extraction software standard flags). This includes low-intensity filtering methods, where the flag indicates low intensity values in the data set (for microarrays and gels the threshold for exclusion is usually based on some estimation of local or global background intensity; for mass spectrometry and NMR, it is usually based on the signal-to-noise ratio in the spectrum).

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_1024

individual flip-dye_consistency


definition:
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.

instance of:
    NormalizationDescriptionType
properties:
    unique_identifier MO_907

individual float


definition:
A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34).

instance of:
    DataType
properties:
    unique_identifier MO_860

individual fmol


definition:
femtomole, unit of quantity

instance of:
    QuantityUnit
properties:
    unique_identifier MO_689

individual forward


definition:
the forward strand exact synonym: +

instance of:
    StrandType
properties:
    unique_identifier MO_820
    synonym +

individual fractionate


definition:
The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify).

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_872

individual freeze_dried_sample


definition:
A biomaterial that has been lyophilized or dried by freezing under a vacuum.

instance of:
    BioSourceType
properties:
    unique_identifier MO_589

individual french_railway_distance


definition:
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.

instance of:
    NodeValueType
properties:
    unique_identifier MO_964

individual fresh_sample


definition:
A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat.

instance of:
    BioSourceType
properties:
    unique_identifier MO_730

individual frozen_sample


definition:
A biomaterial obtained frozen

instance of:
    BioSourceType
properties:
    unique_identifier MO_610

individual frozen_storage


definition:
Storage where the thing stored is stored below 0 degrees celsius.

instance of:
    PreservationType
properties:
    unique_identifier MO_481

individual function_record


definition:
a record which identifies and describes the function of a gene product, e.g. E.C. record

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_538

individual funder


definition:
Contact which provides funding for experiments.

instance of:
    Roles
properties:
    unique_identifier MO_520

individual g


definition:
gram, unit of mass

instance of:
    MassUnit
properties:
    unique_identifier MO_825

individual g_per_L


definition:
grams per liter, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_805

individual gene


definition:
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

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_503
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual gene_fragment


definition:
sequence of part of a gene, which is missing one or both ends

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.3.1.1
    unique_identifier MO_853
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual gene_knock_in


definition:
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.

instance of:
    GeneticModification
properties:
    unique_identifier MO_437

individual gene_knock_out


definition:
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.

instance of:
    GeneticModification
properties:
    unique_identifier MO_771

individual genetic_modification


definition:
An action whereby an organism(s) has had genetic material removed, added, or rearranged.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_927

individual genetic_modification_design


definition:
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out

instance of:
    PerturbationalDesign
properties:
    unique_identifier MO_447

individual genetic_variation


definition:
A descriptor for FactorValue where GeneticVariation is compared.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.8
    unique_identifier MO_557
    deprecation_reason deleted_term
    deprecation_replacement_term BioMaterialCharacteristicCategory
    deprecation_old_parent BioMaterialCharacteristicCategory

individual genomic_DNA


definition:
high molecular weight DNA

instance of:
    MaterialType
properties:
    unique_identifier MO_599

individual genomic_region_amplification


definition:
increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification

instance of:
    ChromosomalAberrationClassification
properties:
    unique_identifier MO_609

individual genotyping_design


definition:
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.

instance of:
    BioMolecularAnnotation
properties:
    unique_identifier MO_560

individual germination


definition:
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).

instance of:
    InitialTimePoint
properties:
    unique_identifier MO_590

individual glass


definition:
The array is made on a glass slide.

instance of:
    SubstrateType
properties:
    unique_identifier MO_742

individual gram_percent


definition:
grams per deciliter, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_582

individual granddaughter


definition:
A daughter of one's son or daughter.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_703

individual grandfather


definition:
The father of one's father or mother.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_478

individual grandmother


definition:
The mother of one's father or mother.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_924

individual grandson


definition:
A son of one's son or daughter.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_831

individual grow


definition:
A ComplexAction or ProtocolType describing growth of an organism or cell culture.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_758

individual growth_condition_design


definition:
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.

instance of:
    PerturbationalDesign
properties:
    unique_identifier MO_588

individual half-life


definition:
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.

instance of:
    TimeUnitOther
properties:
    unique_identifier MO_595

individual haploid


definition:
Describes a cell, nucleus or an organism with one copy of each chromosome.

instance of:
    Ploidy
properties:
    unique_identifier MO_719

individual hardware_manufacturer


definition:
Person or organization that manufactured the hardware.

instance of:
    Roles
properties:
    unique_identifier MO_763

individual hardware_variation_design


definition:
A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_734

individual harvest


definition:
The process of harvesting cells from culture.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_982

individual hatching


definition:
The point at which an organism emerges from an egg.

instance of:
    InitialTimePoint
properties:
    unique_identifier MO_745

individual heating_block


definition:
A device for controlling temperature.

instance of:
    HardwareType
properties:
    unique_identifier MO_663

individual heavy_background


definition:
The Zone is excluded due to smearing, streaking, or dense background in the Zone.

instance of:
    DefectType
properties:
    unique_identifier MO_571

individual hermaphrodite


definition:
an organism with both male and female sexual organs in one individual synonym: intersex

instance of:
    Sex
properties:
    unique_identifier MO_356
    synonym intersex

individual histological_slide_preparation


definition:
The action of preparing a slide for the microscopical examination of organism parts or cell types.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_611

individual homogenizer


definition:
An instrument which fragments tissues or other biomaterials.

instance of:
    HardwareType
properties:
    unique_identifier MO_714

individual hours


definition:
60 minutes, time unit

instance of:
    TimeUnit
properties:
    unique_identifier MO_486
    synonym h

individual hybridization


definition:
The process of incubating one or more labeled extracts with an array.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_884

individual hybridization_chamber


definition:
A chamber in which the hybridization is performed which maintains constant conditions.

instance of:
    HardwareType
properties:
    unique_identifier MO_563

individual hybridization_station


definition:
An instrument which controls hybridization conditions, into which a hybridization chamber may fit.

instance of:
    HardwareType
properties:
    unique_identifier MO_497

individual image_acquisition


definition:
The process of generating an image from the array.

instance of:
    ExperimentalProtocolType
properties:
    unique_identifier MO_929

individual image_acquisition_software


definition:
Software to control a scanner and manipulate and save images. Exact synonym: scanning software

instance of:
    SoftwareType
properties:
    unique_identifier MO_1003
    synonym scanning software

individual image_record


definition:
A record which describes and identifies an image, e.g. an image from the mouse atlas

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_691

individual imprinting_design


definition:
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.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_914

individual in_medium


definition:
Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment).

instance of:
    DeliveryMethod
properties:
    unique_identifier MO_733

individual in_situ_oligo_features


definition:
The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)

instance of:
    TechnologyType
properties:
    unique_identifier MO_514

individual in_vitro_design


definition:
An experiment done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_347

individual in_vivo_design


definition:
An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_454

individual inconclusive


definition:
a result which can not be interpreted as positive or negative

instance of:
    Result
properties:
    unique_identifier MO_744

individual incubate


definition:
The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_965

individual individual


definition:
A descriptor for FactorValue where BioSources are compared.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_639

individual individual_genetic_characteristic


definition:
A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_722

individual individual_genetic_characteristics_design


definition:
An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_527

individual induced_mutation


definition:
The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.

instance of:
    GeneticModification
properties:
    unique_identifier MO_564

individual infect


definition:
The organism (or organism part) has been exposed to a virus or pathogen.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.3.0
    unique_identifier MO_616
    deprecation_reason replaced_term
    replaced_with_term inoculate
    deprecation_old_parent ComplexAction ExperimentalProtocolType

individual injury_design


definition:
An injury experiment design type is where the response of an organism(s) to injury or damage is studied.

instance of:
    PerturbationalDesign
properties:
    unique_identifier MO_726

individual innate_behavior_design


definition:
A design in which the innate behavior of the organism is examined, e.g. path finding in bees.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_355

individual inoculate


definition:
The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_559
    synonym infect

individual institution


definition:
A contact's affiliation, e.g. university, research institute or business.

instance of:
    Roles
properties:
    unique_identifier MO_601

individual integer


definition:
A value which is a whole number (e.g. 10).

instance of:
    DataType
properties:
    unique_identifier MO_435

individual intergenic


definition:
sequence from the region between genes

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_463
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual intramuscular_injection


definition:
Delivery method for a compound or drug where the substance is administered via an injection into the muscle.

instance of:
    DeliveryMethod
properties:
    unique_identifier MO_617

individual intraperitoneal_injection


definition:
A delivery method for compound or drug whereby the substance is administered via the peritoneum.

instance of:
    DeliveryMethod
properties:
    unique_identifier MO_473

individual intravenous


definition:
delivery method whereby a compound or drug is administered via a vein

instance of:
    DeliveryMethod
properties:
    unique_identifier MO_432

individual intron


definition:
sequence spliced out from a transcript

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_709
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual investigator


definition:
Person who contributed to the study.

instance of:
    Roles
properties:
    unique_identifier MO_769

individual irradiate


definition:
treatment of a biomaterial with radiation e.g. electromagnetic radiation

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_770

individual irregular_shape


definition:
The perimeter of the spotted DNA on the slide is irregular.

instance of:
    DefectType
properties:
    unique_identifier MO_669

individual is_contaminated


definition:
The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination.

instance of:
    WarningType
properties:
    unique_identifier MO_489

individual is_expressed_design


definition:
A design aimed at identifying genes expressed in biomaterials of interest.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_487

individual iterative_mean_log_centering


definition:
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.

instance of:
    NormalizationDescriptionType
properties:
    unique_identifier MO_957

individual jackknife_Pearson_correlation


definition:
The jackknife Pearson correlation is the lowest Pearson correlation between two data series where one pair of values in the data series are omitted.

instance of:
    NodeValueType
properties:
    unique_identifier MO_784

individual journal_article


definition:
A article published in a print or online journal having an ISSN.

instance of:
    PublicationType
properties:
    unique_identifier MO_430

individual kat_per_L


definition:
katal per liter, catalytic-activity concentration unit

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_869

individual kg


definition:
kilogram, 1000 grams, unit of mass

instance of:
    MassUnit
properties:
    unique_identifier MO_846

individual kg_per_m2


definition:
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

instance of:
    OtherUnit
properties:
    unique_identifier MO_658
    synonym kg/m2

individual labeling


definition:
The procedure of labeling a biosample.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_471

individual laser_ablation_mark


definition:
mark made on slide using a laser which is used as a point of reference for orientation (fiducial)

instance of:
    FiducialType
properties:
    unique_identifier MO_910

individual light_duration


definition:
The length of the light period that a sample is subjected to. Exact synonym:photoperiod

instance of:
    EnvironmentalFactorCategory
properties:
    unique_identifier MO_604
    synonym photoperiod

individual light_intensity


definition:
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.

instance of:
    EnvironmentalFactorCategory
properties:
    unique_identifier MO_517

individual linear_amplification


definition:
Amplification of nucleic acid sequence by making many copies off the same template. An example is the use of the T7 promoter for amplification by transcribing many RNA copies. non exact synonym: Eberwine procedure

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_997
    synonym Eberwine procedure

individual linear_regression_normalization


definition:
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.

instance of:
    NormalizationDescriptionType
properties:
    unique_identifier MO_823

individual linear_scale


definition:
The scale is a standard base 10, non logarithmic scale.

instance of:
    Scale
properties:
    unique_identifier MO_751

individual linlog_normalization


definition:
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.

instance of:
    NormalizationDescriptionType
properties:
    unique_identifier MO_956

individual linlog_transformation


definition:
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.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_845

individual liquid


definition:
media type, usually some sort of broth

instance of:
    Media
properties:
    unique_identifier MO_715

individual liquid_handler


definition:
Hardware for automated liquid transfer and handling.

instance of:
    HardwareType
properties:
    unique_identifier MO_868

individual liquid_handler_software


definition:
Software used to control automated liquid handler.

instance of:
    SoftwareType
properties:
    unique_identifier MO_761

individual list_of_booleans


definition:
An ordered, finite set of booleans.

instance of:
    DataType
properties:
    unique_identifier MO_712

individual list_of_floats


definition:
An ordered, finite set of floats.

instance of:
    DataType
properties:
    unique_identifier MO_760

individual list_of_integers


definition:
An ordered, finite set of integers.

instance of:
    DataType
properties:
    unique_identifier MO_891

individual list_of_negative_floats


definition:
An ordered, finite set of negative floats.

instance of:
    DataType
properties:
    unique_identifier MO_851

individual list_of_negative_integers


definition:
An ordered, finite set of negative integers.

instance of:
    DataType
properties:
    unique_identifier MO_900

individual list_of_nonnegative_floats


definition:
An ordered, finite set of nonnegative floats.

instance of:
    DataType
properties:
    unique_identifier MO_360

individual list_of_nonnegative_integers


definition:
An ordered, finite set of nonnegative integers.

instance of:
    DataType
properties:
    unique_identifier MO_973

individual list_of_nonpositive_floats


definition:
An ordered, finite set of nonpositive floats.

instance of:
    DataType
properties:
    unique_identifier MO_1000

individual list_of_nonpositive_integers


definition:
An ordered, finite set of nonpositive integers.

instance of:
    DataType
properties:
    unique_identifier MO_804

individual list_of_positive_floats


definition:
An ordered, finite set of positive floats.

instance of:
    DataType
properties:
    unique_identifier MO_777

individual list_of_positive_integers


definition:
An ordered, finite set of positive integers.

instance of:
    DataType
properties:
    unique_identifier MO_873

individual list_of_strings


definition:
An ordered, finite set of strings.

instance of:
    DataType
properties:
    unique_identifier MO_800

individual loess_global_normalization


definition:
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.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_443

individual loess_group_normalization


definition:
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.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_377

individual loess_normalization


definition:
A method of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.

instance of:
    NormalizationDescriptionType
properties:
    unique_identifier MO_428

individual loess_scaled_group_normalization


definition:
Application of a scale adjustment following loess_group_normalization, to render the group variances similar.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_521

individual log_base_10


definition:
The values presented are logarithm, base 10.

instance of:
    Scale
properties:
    unique_identifier MO_735

individual log_base_2


definition:
The values presented are logarithm, base 2.

instance of:
    Scale
properties:
    unique_identifier MO_647

individual log_base_e


definition:
The values presented are logarithm, base e.

instance of:
    Scale
properties:
    unique_identifier MO_554

individual log_ratio


definition:
Logarithmic transformation of ratio data.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_896

individual long_oligo


definition:
An element that is an oligonucleotide of at least 50 nucleotides in length.

instance of:
    DesignElement
properties:
    unique_identifier MO_598

individual loop_design


definition:
A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_912
    synonym circular design

individual low_intensity_filter


definition:
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.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.3.0
    unique_identifier MO_706
    deprecation_reason replaced_term
    replaced_with_term flag_filter
    deprecation_old_parent DataTransformationProtocolType

individual lowess_global_normalization


definition:
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.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_692

individual lowess_group_normalization


definition:
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.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_861

individual lowess_normalization


definition:
A method of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.

instance of:
    NormalizationDescriptionType
properties:
    unique_identifier MO_720

individual lowess_scaled_group_normalization


definition:
Application of a scale adjustment following lowess_group_normalization, to render the group variances similar.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_410

individual lumen


definition:
The unit of total light output from a light source.

instance of:
    LightUnit
properties:
    unique_identifier MO_603

individual lux


definition:
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.

instance of:
    LightUnit
properties:
    unique_identifier MO_573

individual m


definition:
meter, distance unit

instance of:
    DistanceUnit
properties:
    unique_identifier MO_367

individual mL_per_L


definition:
milliliters per liter, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_801

individual mM


definition:
milimolar, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_509

individual mOsm_per_kg_H2O


definition:
osmolality per kilogram of water, concentration of the solute per unit of solvent

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_661

individual mRNA


definition:
sequence of a processed transcript capable of directing protein synthesis

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_803
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual male


definition:
individual whose sex organs contain only male gametes

instance of:
    Sex
properties:
    unique_identifier MO_652

individual manhattan_distance


definition:
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.

instance of:
    NodeValueType
properties:
    unique_identifier MO_567

individual mating_type_a


definition:
Mating type of S. cerevisiae.

instance of:
    Sex
properties:
    unique_identifier MO_659

individual mating_type_alpha


definition:
Mating type of S. cerevisiae.

instance of:
    Sex
properties:
    unique_identifier MO_637

individual mating_type_h_minus


definition:
Mating type of S.pombe.

instance of:
    Sex
properties:
    unique_identifier MO_407

individual mating_type_h_plus


definition:
Mating type of S.pombe.

instance of:
    Sex
properties:
    unique_identifier MO_855

individual mean_and_coefficient_of_variation


definition:
the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_425

individual mean_and_confidence_indicators


definition:
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.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_702
    deprecation_reason deleted_term
    deprecation_replacement_term DerivedBioAssayType
    deprecation_old_parent DerivedBioAssayType

individual mean_and_p_values


definition:
the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_943

individual mean_and_standard_deviation


definition:
the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_445

individual mean_and_variance


definition:
the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_458

individual mean_log_centering


definition:
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).

instance of:
    NormalizationDescriptionType
properties:
    unique_identifier MO_398

individual mean_log_normalization


definition:
Application of a normalization of type mean_log_centering.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_657

individual media


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

instance of:
    EnvironmentalFactorCategory
properties:
    unique_identifier MO_545

individual median_log_centering


definition:
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).

instance of:
    NormalizationDescriptionType
properties:
    unique_identifier MO_811

individual median_log_normalization


definition:
Application of a normalization of type median_log_centering.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_931

individual merged_term


definition:
the term has been subsumed into a more general term

instance of:
    DeprecationReason
properties:
    unique_identifier MO_1025

individual metastatic_site


definition:
the organism part in which additional tumors are identified remote from the primary site

instance of:
    CancerSite
properties:
    unique_identifier MO_806

individual mg


definition:
milligram, mass unit

instance of:
    MassUnit
properties:
    unique_identifier MO_949

individual mg_per_kg_per_day


definition:
milligram per kilogram per day

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_353

individual mg_per_ml


definition:
milligrams per milliliter, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_522

individual microarray_experiment_record


definition:
A record which describes and identifies a microarray experiment e.g. GEO

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_346

individual microeinstein_per_minute_and_square_meter


definition:
Microeinstein per minute and square meter (E 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 E m-2 s-1 = 1000 mol m-2 s-1).

instance of:
    LightUnit
properties:
    unique_identifier MO_526

individual microeinstein_per_second_and_square_meter


definition:
Microeinstein per second and square meter (E 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 E m-2 s-1 = 1000 mol m-2 s-1).

instance of:
    LightUnit
properties:
    unique_identifier MO_584

individual micromole_per_second_and_square_meter


definition:
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.

instance of:
    OtherUnit
properties:
    unique_identifier MO_848

individual minutes


definition:
60 seconds, unit of time

instance of:
    TimeUnit
properties:
    unique_identifier MO_877
    synonym m

individual missing_feature_or_zone


definition:
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.

instance of:
    DefectType
properties:
    unique_identifier MO_405

individual mix_by_inversion


definition:
Mix through the process of inverting.

instance of:
    AtomicAction
properties:
    unique_identifier MO_700

individual mix_by_pipette


definition:
Mix by drawing up and down with a pipette.

instance of:
    AtomicAction
properties:
    unique_identifier MO_479

individual mix_by_vortex


definition:
Mix through the use of a vortexer.

instance of:
    AtomicAction
properties:
    unique_identifier MO_880

individual mix_general


definition:
The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas.

instance of:
    AtomicAction
properties:
    unique_identifier MO_944

individual mixed_design_element_group_type


definition:
a design element group consisting of multiple types

instance of:
    DesignElementGroupType
properties:
    unique_identifier MO_528

individual mixed_sex


definition:
A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites.

instance of:
    Sex
properties:
    unique_identifier MO_436

individual ml


definition:
milliliter, volume unit

instance of:
    VolumeUnit
properties:
    unique_identifier MO_488

individual ml_per_kg


definition:
milliliter per kilogram

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_403

individual mm


definition:
millimeter, unit of distance

instance of:
    DistanceUnit
properties:
    unique_identifier MO_648

individual mol


definition:
mole, unit of quantity

instance of:
    QuantityUnit
properties:
    unique_identifier MO_998

individual molecular_mixture


definition:
an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins

instance of:
    MaterialType
properties:
    unique_identifier MO_889

individual molecules


definition:
number of molecules, quantity unit

instance of:
    QuantityUnit
properties:
    unique_identifier MO_707

individual monosomy


definition:
Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.9
    unique_identifier MO_424
    deprecation_reason replaced_term
    replaced_with_term oligosomy
    deprecation_old_parent ChromosomalAberrationClassification

individual months


definition:
Unit of time corresponding to approx. one cycle of the moon's phases.

instance of:
    TimeUnit
properties:
    unique_identifier MO_631

individual mother


definition:
A female parent.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_387

individual moving_average


definition:
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.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_681

individual ms


definition:
millisecond, time unit

instance of:
    TimeUnit
properties:
    unique_identifier MO_920

individual mtDNA


definition:
sequence from the mitochondrial genome

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.3.1.1
    unique_identifier MO_581
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual multiple_testing_correction


definition:
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.

instance of:
    HigherLevelAnalysisProtocolType
properties:
    unique_identifier MO_561

individual negative


definition:
false or no

instance of:
    Result
properties:
    unique_identifier MO_802

individual negative_float


definition:
A float that is < 0.

instance of:
    DataType
properties:
    unique_identifier MO_728

individual negative_integer


definition:
An integer < 0.

instance of:
    DataType
properties:
    unique_identifier MO_864

individual ng


definition:
nanogram, a mass unit

instance of:
    MassUnit
properties:
    unique_identifier MO_796

individual nitrocellulose


definition:
The array is made on a nitrocellulose filter.

instance of:
    SubstrateType
properties:
    unique_identifier MO_455

individual nl


definition:
nanoliter unit of volume

instance of:
    VolumeUnit
properties:
    unique_identifier MO_754

individual nm


definition:
nanometer distance unit

instance of:
    DistanceUnit
properties:
    unique_identifier MO_862

individual nmol


definition:
nanomoles, quantity unit

instance of:
    QuantityUnit
properties:
    unique_identifier MO_743

individual no


definition:
false

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.7
    unique_identifier MO_556
    deprecation_reason deleted_term

individual non-targeted_transgenic_variation_design


definition:
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.

instance of:
    PerturbationalDesign
properties:
    unique_identifier MO_775

individual nonnegative_float


definition:
A float greater than or equal to 0.

instance of:
    DataType
properties:
    unique_identifier MO_386

individual nonnegative_integer


definition:
An integer >= 0.

instance of:
    DataType
properties:
    unique_identifier MO_390

individual nonpositive_float


definition:
A float less than or equal to zero.

instance of:
    DataType
properties:
    unique_identifier MO_656

individual nonpositive_integer


definition:
An integer less than or equal to zero.

instance of:
    DataType
properties:
    unique_identifier MO_623

individual normalization_testing_design


definition:
A normalization testing experiment design tests different normalization procedures.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_729

individual normalized_intensities


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_994

individual normalized_ratios


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_664

individual not_extract


definition:
The BioSample at any stage other than immediately before labeling.

instance of:
    BioSampleType
properties:
    unique_identifier MO_894

individual not_sequence_verified


definition:
The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter.

instance of:
    WarningType
properties:
    unique_identifier MO_970

individual not_uniform


definition:
The source DNA for a Feature was not uniformly deposited.

instance of:
    DefectType
properties:
    unique_identifier MO_906

individual nuclear_RNA


definition:
RNA obtained from the nucleus.

instance of:
    MaterialType
properties:
    unique_identifier MO_679

individual nucleic_acid_extraction


definition:
The procedure of extracting nucleic acid from the biomaterial.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_607

individual nucleic_acid_primary_sequence_record


definition:
A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_757

individual number_per_day


definition:
number of items or events per day

instance of:
    OtherUnit
properties:
    unique_identifier MO_670

individual nutrients


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

instance of:
    EnvironmentalFactorCategory
properties:
    unique_identifier MO_867

individual nylon


definition:
The array is made on a nylon membrane.

instance of:
    SubstrateType
properties:
    unique_identifier MO_492

individual oligo_synthesizer


definition:
Hardware for synthesizing oligos.

instance of:
    HardwareType
properties:
    unique_identifier MO_930

individual oligosomy


definition:
A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement.

instance of:
    ChromosomalAberrationClassification
properties:
    unique_identifier MO_1028

individual online_resource


definition:
A publication type which is available online and which is not an online journal article, e.g. a web site or service.

instance of:
    PublicationType
properties:
    unique_identifier MO_991

individual ontology_record


definition:
A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_529

individual openGALEN


definition:
OpenGALEN Human Anatomy - open source database of approx. ten thousand human anatomy concepts together with extensive semantic relationships between them including part-of, connects, branch-of, serves, laterality. Also includes some human physiological processes together with functional relationships between these and the anatomy concepts.

instance of:
    OrganismPartDatabase
properties:
    unique_identifier MO_613

individual operating_system


definition:
Software upon which other software runs.

instance of:
    SoftwareType
properties:
    unique_identifier MO_847

individual operator_variation_design


definition:
An operator variation experiment design type assesses the operator performance and relation to data consistency and quality.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_519

individual operon


definition:
sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_759
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual operon_identification_design


definition:
An operon identification experiment type is designed to identify locations and members of operons in a genome.

instance of:
    BioMolecularAnnotation
properties:
    unique_identifier MO_772

individual optimization_design


definition:
An optimization experiment design type is where different protocols or protocol parameters are compared.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_934

individual oral_gavage


definition:
delivery method for drug or compound whereby the drug is administered via the mouth

instance of:
    DeliveryMethod
properties:
    unique_identifier MO_975

individual organellar_DNA


definition:
DNA from organelles such as the mitochondria or chloroplast.

instance of:
    MaterialType
properties:
    unique_identifier MO_645

individual organellar_RNA


definition:
RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus.

instance of:
    MaterialType
properties:
    unique_identifier MO_574

individual organism


definition:
one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_508

individual organism_part


definition:
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).

instance of:
    BioMaterialCharacteristicCategory
    MaterialType
properties:
    unique_identifier MO_954

individual organism_part_comparison_design


definition:
An organism part comparison experiment design type compares tissues, regions, organs within or between organisms

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_953

individual organism_status


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

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_871

individual organism_status_design


definition:
A design that compares samples from live and dead organisms.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_841

individual pH


definition:
potential of hydrogen

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_814

individual pM


definition:
picomolar, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_628

individual paraffin_sample


definition:
A biomaterial obtained embedded in paraffin (wax).

instance of:
    BioSourceType
properties:
    unique_identifier MO_990

individual pathogenicity_design


definition:
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.

instance of:
    PerturbationalDesign
properties:
    unique_identifier MO_807

individual pathway_record


definition:
a record which identifies and describes biological pathways, e.g. a KEGG record

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_780

individual pearson_correlation_coefficient


definition:
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.

instance of:
    NodeValueType
properties:
    unique_identifier MO_558

individual pedigree_record


definition:
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

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_969

individual peer_review_quality_control


definition:
An experiment which has a peer reviewed publication attached.

instance of:
    QualityControlDescriptionType
properties:
    unique_identifier MO_365

individual percent_confluence


definition:
A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_378

individual percent_purity


definition:
A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy.

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_482

individual percent_vol_per_vol


definition:
percentage volume per volume, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_916

individual percent_weight_per_vol


definition:
percent weight per volume, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_420

individual percent_weight_per_weight


definition:
percent weight per weight, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_474

individual pfu_per_ml


definition:
the number of plaque forming units per ml

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_768

individual pg


definition:
picogram, mass unit

instance of:
    MassUnit
properties:
    unique_identifier MO_363

individual phylogeny_record


definition:
A record which describes and identifies the relationship between species and is computationally determined and based on sequences e.g. Treebase record

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_662

individual physical_characteristics


definition:
A descriptor for FactorValue where PhysicalCharacteristics are compared.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_863

individual physiological_process_design


definition:
Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. This includes those processes that exhibit an endogenous periodicity independently of any daily variation in the environment such as circadian rhythm or aging.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_1029

individual pl


definition:
picoliter, volume unit

instance of:
    VolumeUnit
properties:
    unique_identifier MO_905

individual place


definition:
The procedure of putting a physical object in a container/physical space.

instance of:
    AtomicAction
properties:
    unique_identifier MO_470

individual planting


definition:
The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing.

instance of:
    InitialTimePoint
properties:
    unique_identifier MO_495

individual plasmid


definition:
sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_439
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual pmol


definition:
picomoles, quantity unit

instance of:
    QuantityUnit
properties:
    unique_identifier MO_688

individual polyA_RNA


definition:
RNA which has been obtained by selection for polyA tracts. Exact synonym: polyA+_RNA Non-exact synonym: mRNA

instance of:
    MaterialType
properties:
    unique_identifier MO_600
    synonym mRNApolyA+_RNA

individual polylysine


definition:
a surface coating for immobilization with the polypeptide, polylysine

instance of:
    SurfaceType
properties:
    unique_identifier MO_569

individual polypeptide


definition:
sequence of a protein, a linear amino acid polymer

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_530
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType PhysicalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType PhysicalBioSequenceType

individual polyploid


definition:
Describes a cell, nucleus or organism with three or more copies of each chromosome.

instance of:
    Ploidy
properties:
    unique_identifier MO_394

individual polysomy


definition:
A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement.

instance of:
    ChromosomalAberrationClassification
properties:
    unique_identifier MO_1030

individual pool


definition:
The process of combining two or more BioMaterials. Exact synonym: combine

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_779
    synonym combine

individual population_density


definition:
The concentration range of the organism.

instance of:
    EnvironmentalFactorCategory
properties:
    unique_identifier MO_650

individual positive


definition:
true or yes

instance of:
    Result
properties:
    unique_identifier MO_429

individual positive_float


definition:
A float > 0.

instance of:
    DataType
properties:
    unique_identifier MO_501

individual positive_integer


definition:
An integer > 0.

instance of:
    DataType
properties:
    unique_identifier MO_629

individual postmortem


definition:
biomaterial removed after the death of the organism

instance of:
    OrganismStatus
properties:
    unique_identifier MO_416

individual predicted_gene


definition:
gene sequence which has been computationally predicted

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.3.1.1
    unique_identifier MO_838
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual premortem


definition:
sample which has been removed prior to the death of an organism

instance of:
    OrganismStatus
properties:
    unique_identifier MO_705

individual preservation


definition:
The type of protocol used to preserve (including storage or keep in stasis) the biomaterial.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_415

individual primary_protein_structure_record


definition:
A record which describes and identifies an experimentally derived protein structure e.g. MSD

instance of:
    DatabaseEntryType
properties:
    unique_identifier MO_785

individual primary_site


definition:
the organism part in which the tumor originated

instance of:
    CancerSite
properties:
    unique_identifier MO_408

individual promoter


definition:
genomic sequence 5' to a gene where the transcription initiation complex forms.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_911
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual protein


definition:
Polymer of amino acids.

instance of:
    MaterialType
    PolymerType
properties:
    unique_identifier MO_683

individual purify


definition:
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).

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_406

individual quality_control_testing_design


definition:
A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_981

individual quantile_normalization


definition:
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.

instance of:
    NormalizationDescriptionType
properties:
    unique_identifier MO_951

individual quantile_normalization_protocol_type


definition:
Application of a normalization of type quantile_normalization.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_457

individual rRNA_gene


definition:
sequence from gene coding for ribosomal RNA exact synonym: ribosomal RNA gene

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_955
    synonym ribosomal RNA gene
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual ratio


definition:
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.

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_597

individual ratio_statistics_normalization


definition:
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.

instance of:
    NormalizationDescriptionType
properties:
    unique_identifier MO_349

individual real_time_PCR_quality_control


definition:
A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes.

instance of:
    QualityControlDescriptionType
properties:
    unique_identifier MO_434

individual rectangular_feature


definition:
The shape of the feature on the array is rectangular.

instance of:
    FeatureShape
properties:
    unique_identifier MO_897

individual reference_design


definition:
A reference experiment design type is where all samples are compared to a common reference.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_699

individual relative


definition:
a measurement where the value is dependent on another measurement

instance of:
    MeasurementType
properties:
    unique_identifier MO_396

individual relative_humidity


definition:
The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding.

instance of:
    EnvironmentalFactorCategory
properties:
    unique_identifier MO_453

individual remove


definition:
The procedure of extracting/taking out a part of a reaction/contents of a container.

instance of:
    AtomicAction
properties:
    unique_identifier MO_713

individual replaced_term


definition:
The term name was changed to one more appropriate to the intent of the definition.

instance of:
    DeprecationReason
properties:
    unique_identifier MO_1026

individual replicate_analysis


definition:
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.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_433

individual replicate_design


definition:
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.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_885

individual resuspend


definition:
The procedure in which solid material is dispensed or dissolved in a liquid.

instance of:
    AtomicAction
properties:
    unique_identifier MO_466

individual reverse


definition:
the reverse strand exact synonym: -

instance of:
    StrandType
properties:
    unique_identifier MO_402
    synonym -

individual reverse_transcription


definition:
Generation of a DNA strand from an RNA strand using reverse transcriptase.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_480

individual reverse_transcription_PCR_quality_control


definition:
A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes.

instance of:
    QualityControlDescriptionType
properties:
    unique_identifier MO_986

individual sacrifice


definition:
The procedure of euthanizing an organism.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_602

individual sampling_time_point


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

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_866

individual seconds


definition:
time unit

instance of:
    TimeUnit
properties:
    unique_identifier MO_391

individual secreted_protein_identification_design


definition:
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.

instance of:
    BioMolecularAnnotation
properties:
    unique_identifier MO_694

individual seed_dormancy


definition:
preservation type whereby the seed is maintained in a dormant state

instance of:
    PreservationType
properties:
    unique_identifier MO_666

individual self_vs_self_design


definition:
A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_490

individual semisolid


definition:
semisolid media type

instance of:
    Media
properties:
    unique_identifier MO_635

individual set_temperature


definition:
An action where the temperature is specified.

instance of:
    AtomicAction
properties:
    unique_identifier MO_393

individual sex


definition:
A descriptor for FactorValue where Sex is compared.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_680

individual sex_design


definition:
A sex experiment design type assays differences associated with an organism's sex, gender or mating type.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_575

individual short_oligo


definition:
An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes).

instance of:
    DesignElement
properties:
    unique_identifier MO_749

individual signal


definition:
A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software).

instance of:
    DerivedBioAssayType
properties:
    unique_identifier MO_534

individual signal_log_ratio


definition:
The change in expression level for a transcript between a baseline and an experiment array. This change is expressed as the log2 ratio. A signal log ratio of 1 is the same as a Fold Change of 2.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.7
    unique_identifier MO_941
    deprecation_reason deleted_term
    deprecation_replacement_term DerivedBioAssayType
    deprecation_old_parent DerivedBioAssayType

individual silicon


definition:
the array is made on silicon

instance of:
    SubstrateType
properties:
    unique_identifier MO_382

individual single_stranded


definition:
a nucleic acid consisting of a single polynucleotide chain.

instance of:
    StrandType
properties:
    unique_identifier MO_576

individual sister


definition:
A female having the same genetic parents as another, or one genetic parent in common with another.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_723

individual slice_analysis


definition:
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.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_531
    deprecation_reason deleted_term
    deprecation_replacement_term NormalizationDescriptionType
    deprecation_old_parent NormalizationDescriptionType

individual snRNA_gene


definition:
sequence from gene coding for small nuclear RNA exact synonym: small nuclear RNA gene

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_961
    synonym small nuclear RNA gene
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent deleted_term

individual software_manufacturer


definition:
Person or organization that manufactured the software.

instance of:
    Roles
properties:
    unique_identifier MO_475

individual software_variation_design


definition:
A software variation design type compares different types of software for performance, accuracy, precision and reproducibility.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_643

individual soil


definition:
soil, growth media for plants and other soil living organisms

instance of:
    Media
properties:
    unique_identifier MO_821

individual son


definition:
The male offspring of the patient or individual under study.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_465

individual sonicator


definition:
An instrument for sonicating biomaterials.

instance of:
    HardwareType
properties:
    unique_identifier MO_477

individual sowing


definition:
the process of placing a seed or spore in some media with the intention to invoke germination.

instance of:
    InitialTimePoint
properties:
    unique_identifier MO_748

individual species_design


definition:
A species experiment design type assays differences between distinct species.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_675

individual species_specific_design_element_group_type


definition:
A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species.

instance of:
    DesignElementGroupType
properties:
    unique_identifier MO_395

individual specified_biomaterial_action


definition:
Conceptual action for specified protocol applied in treatment.

instance of:
    AtomicAction
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_968

individual spectrophotometer


definition:
Hardware for measuring light at different wavelengths.

instance of:
    HardwareType
properties:
    unique_identifier MO_716
    synonym thermocycler

individual spike_quality_control


definition:
An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes.

instance of:
    QualityControlDescriptionType
properties:
    unique_identifier MO_937

individual spin


definition:
The procedure of applying a centrifugal force to a physical object. Exact synonym: centrifuge

instance of:
    AtomicAction
properties:
    unique_identifier MO_879
    synonym centrifuge

individual split


definition:
The procedure of separating a BioMaterial into two or more BioMaterials of similar composition e.g. aliquoting a sample. The BioMaterial may be a BioSource (e.g., a tissue) or a BioSample (e.g. RNA extracted from a BioSource). Non exact Synonym: sample

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_835
    synonym sample

individual split_term


definition:
the term has been decomposed into more specific terms

instance of:
    DeprecationReason
properties:
    unique_identifier MO_1027

individual spotted_antibody_features


definition:
TechnologyType of FeatureGroup where antibodies are spotted directly.

instance of:
    TechnologyType
properties:
    unique_identifier MO_483

individual spotted_colony_features


definition:
TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.

instance of:
    TechnologyType
properties:
    unique_identifier MO_618

individual spotted_ds_DNA_features


definition:
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.

instance of:
    TechnologyType
properties:
    unique_identifier MO_499

individual spotted_protein_features


definition:
TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly.

instance of:
    TechnologyType
properties:
    unique_identifier MO_996

individual spotted_ss_PCR_amplicon_features


definition:
A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array.

instance of:
    TechnologyType
properties:
    unique_identifier MO_921

individual spotted_ss_oligo_features


definition:
The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.

instance of:
    TechnologyType
properties:
    unique_identifier MO_579

individual square_feature


definition:
The shape of the feature on the array is square.

instance of:
    FeatureShape
properties:
    unique_identifier MO_817

individual ss_oligo


definition:
sequence of a single stranded synthesized oligonucleotide

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_570
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual starvation


definition:
Depriving an organism of food or nutrients

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_370

individual stimulated_design_type


definition:
A design in which a behavior is invoked by a variable controlled by the experimenter - e.g. administration of a drug that effects aggressivity.

instance of:
    PerturbationalDesign
properties:
    unique_identifier MO_958

individual stimulus_or_stress_design


definition:
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.

instance of:
    PerturbationalDesign
properties:
    unique_identifier MO_568

individual store


definition:
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.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_442

individual strain_or_line


definition:
A descriptor of FactorValue where comparisons of strains or lines are made.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_859

individual strain_or_line_design


definition:
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.

instance of:
    BiologicalProperty
properties:
    unique_identifier MO_462

individual string_datatype


definition:
The values are a sequence of one or more characters.

instance of:
    DataType
properties:
    unique_identifier MO_352

individual subcutaneous


definition:
Delivery method whereby a drug or compound is administered under the skin of the organism.

instance of:
    DeliveryMethod
properties:
    unique_identifier MO_960

individual submitter


definition:
Person who is the primary contact for data submitted to a database.

instance of:
    Roles
properties:
    unique_identifier MO_882

individual synthetic_DNA


definition:
DNA which is generated by chemical or enzymatic (non cellular) means. non-exact synonym: cDNA

instance of:
    MaterialType
properties:
    unique_identifier MO_577
    synonym cDNA

individual synthetic_RNA


definition:
RNA which is generated by chemical or enzymatic (non cellular) means. E.g. T7 promotor generated RNA. Non-exact synonym: cRNA, complementary RNA aRNA, amplified RNA

instance of:
    MaterialType
properties:
    unique_identifier MO_543
    synonym complementary RNAcRNAaRNAamplified RNA

individual tRNA_gene


definition:
sequence from a gene coding for transfer RNA exact synonym: transfer RNA gene

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_850
    synonym transfer RNA gene
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual tau_rank_correlation


definition:
a nonparametric measure of the agreement between two rankings

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.7
    unique_identifier MO_673
    deprecation_reason deleted_term
    deprecation_replacement_term NodeValueType
    deprecation_old_parent NodeValueType

individual technical_replicate


definition:
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.

instance of:
    QualityControlDescriptionType
    ReplicateDescriptionType
properties:
    unique_identifier MO_641

individual temperature


definition:
Temperature associated with a particular environment.

instance of:
    EnvironmentalFactorCategory
properties:
    unique_identifier MO_791

individual thermal_cycler


definition:
An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR. Exact Synonym: thermocycler

instance of:
    HardwareType
properties:
    unique_identifier MO_854

individual tiling_path_design


definition:
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.

instance of:
    BioMolecularAnnotation
properties:
    unique_identifier MO_507

individual time_series_design


definition:
Groups of assays that are related as part of a time series.

instance of:
    MethodologicalDesign
properties:
    unique_identifier MO_887

individual timepoint


definition:
Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point.

instance of:
    ComplexAction
properties:
    unique_identifier MO_738

individual total_RNA


definition:
Total cellular and nuclear RNA.

instance of:
    MaterialType
properties:
    unique_identifier MO_373

individual total_intensity_normalization


definition:
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.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_441
    deprecation_reason deleted_term
    deprecation_replacement_term NormalizationDescriptionType
    deprecation_old_parent NormalizationDescriptionType

individual total_intensity_normalization_paired


definition:
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.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_686

individual total_intensity_normalization_single


definition:
A normalization method that uses as a coefficient the sum of all intensities in the data set, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). The intensities are normalized through division by such a coefficient (and possible subsequent multiplication by a target constant). Note that a normalization method that employs the average intensity rather than the sum (of all data points, or an appropriate subset) falls into this category as well.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_472

individual transcript


definition:
sequence that represents the product of an RNA polymerase engaged in transcription

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.3.1.1
    unique_identifier MO_827
    deprecation_reason deleted_term
    deprecation_replacement_term TheoreticalBioSequenceType
    deprecation_old_parent TheoreticalBioSequenceType

individual transcript_identification_design


definition:
A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome.

instance of:
    BioMolecularAnnotation
    TechnologicalDesign
properties:
    unique_identifier MO_533
    synonym transcription_profilinggene expressionexpression_profilinggene_expressiontranscription profilingexpression profiling

individual transfect


definition:
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.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_849

individual transfection


definition:
Introduction of genetic material into an organism often in the form of a plasmid.

instance of:
    GeneticModification
properties:
    unique_identifier MO_366

individual translational_bias_design


definition:
A translational bias is an experiment design which characterizes the association of transcripts and translation machinery.

instance of:
    BioMolecularAnnotation
properties:
    unique_identifier MO_939

individual trisomy


definition:
The possession of a third chromosome of any one type in an otherwise diploid cell.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.9
    unique_identifier MO_494
    deprecation_reason replaced_term
    replaced_with_term polysomy
    deprecation_old_parent ChromosomalAberrationClassification

individual tumor_grading


definition:
A descriptor used in cancer biology to describe abnormalities of tumor cells.

instance of:
    BioMaterialCharacteristicCategory
properties:
    unique_identifier MO_843

individual uM


definition:
Micromole per liter or micromolar, concentration unit

instance of:
    ConcentrationUnit
properties:
    unique_identifier MO_740

individual ug


definition:
microgram, unit of mass

instance of:
    MassUnit
properties:
    unique_identifier MO_438

individual ul


definition:
microliter, unit of volume

instance of:
    VolumeUnit
properties:
    unique_identifier MO_926

individual um


definition:
micrometer, unit of distance

instance of:
    DistanceUnit
properties:
    unique_identifier MO_421

individual umol


definition:
micromoles, quantity unit

instance of:
    QuantityUnit
properties:
    unique_identifier MO_752

individual uncentered_Pearson_correlation


definition:
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.

instance of:
    NodeValueType
properties:
    unique_identifier MO_974

individual uncle


definition:
The brother of one's father or mother.

instance of:
    FamilyRelationship
properties:
    unique_identifier MO_950

individual unknown_basis_feature


definition:
Sequence feature whose derivation is unknown.

instance of:
    SeqFeatureBasis
properties:
    unique_identifier MO_525

individual unknown_experiment_design_type


definition:
ExperimentDesignType of unknown type.

instance of:
    BioMolecularAnnotation
    BiologicalProperty
    EpidemiologicalDesign
    MethodologicalDesign
    PerturbationalDesign
properties:
    unique_identifier MO_634

individual unknown_protocol_type


definition:
ProtocolType of unknown type.

instance of:
    ExperimentalProtocolType
properties:
    unique_identifier MO_460

individual unknown_sequence


definition:
BioSequence of unknown type

instance of:
    PhysicalBioSequenceType
    TheoreticalBioSequenceType
properties:
    unique_identifier MO_535

individual unknown_sex


definition:
organism(s) whose sex is unknown

instance of:
    Sex
properties:
    unique_identifier MO_999

individual unknown_substrate_type


definition:
SubstrateType of unknown type.

instance of:
    SubstrateType
properties:
    unique_identifier MO_484

individual unknown_surface_type


definition:
A SurfaceType of unknown type.

instance of:
    SurfaceType
properties:
    unique_identifier MO_359

individual unscaled


definition:
The values are unordered and have no scale.

instance of:
    Scale
properties:
    unique_identifier MO_542

individual urine


definition:
The fluid and dissolved substances excreted by the kidney.

instance of:
    BioSourceType
properties:
    unique_identifier MO_399

individual us


definition:
microsecond, unit of time

instance of:
    TimeUnit
properties:
    unique_identifier MO_795

individual vacuum_dryer


definition:
An instrument designed to remove excess liquid by vacuum and heating.

instance of:
    HardwareType
properties:
    unique_identifier MO_696

individual vector


definition:
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.

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.2.0
    unique_identifier MO_551
    deprecation_reason deleted_term
    deprecation_replacement_term PhysicalBioSequenceType
    deprecation_old_parent PhysicalBioSequenceType

individual version_1.1.7


definition:
Version of the MGED Ontology.

used in classes:
    ChromosomalAberration
instance of:
    MGEDOntologyVersion
properties:
    unique_identifier MO_1031

individual version_1.1.8


definition:
Version of the MGED Ontology.

instance of:
    MGEDOntologyVersion
properties:
    unique_identifier MO_469

individual version_1.1.9


definition:
Version of the MGEDOntology.

used in classes:
    FactorValueDependency
    FactorValueSet
instance of:
    MGEDOntologyVersion
properties:
    unique_identifier MO_1032

individual version_1.2.0


definition:
Version of the MGEDOntology.

used in classes:
    IndividualChromosomalAbnormality
instance of:
    MGEDOntologyVersion
properties:
    unique_identifier MO_1033

individual version_1.3.0


definition:
Version of the MGEDOntology.

instance of:
    MGEDOntologyVersion
properties:
    unique_identifier MO_440

individual version_1.3.1


definition:
Version of the MGED Ontology.

instance of:
    MGEDOntologyVersion
properties:
    unique_identifier MO_1034

individual virus


definition:
one or more DNA or RNA based non cellular infective agent, including bacteriophage

instance of:
    MaterialType
properties:
    unique_identifier MO_372

individual vortexer


definition:
An instrument that mixes by rapid oscillation.

instance of:
    HardwareType
properties:
    unique_identifier MO_983

individual wait


definition:
Allow time to pass. It's measurement should be a unit of time.

instance of:
    AtomicAction
properties:
    unique_identifier MO_988

individual wash


definition:
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.

instance of:
    ComplexAction
    ExperimentalProtocolType
properties:
    unique_identifier MO_596

individual wash_station


definition:
An instrument designed to mechanically wash or stain arrays.

instance of:
    HardwareType
properties:
    unique_identifier MO_626

individual water


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

instance of:
    EnvironmentalFactorCategory
properties:
    unique_identifier MO_380

individual waterbath


definition:
A device for controlling temperature by immersion in water.

instance of:
    HardwareType
properties:
    unique_identifier MO_541

individual weeks


definition:
7 days, unit of time

instance of:
    TimeUnit
properties:
    unique_identifier MO_842

individual whole_organism


definition:
one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria

instance of:
    MaterialType
properties:
    unique_identifier MO_566

individual wild_type


definition:
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.

instance of:
    Allele
    Genotype
properties:
    unique_identifier MO_605

individual within_bioassay_data_set_function


definition:
A function applied to subsets of values from the same Measured/Derived bioassay data set.

instance of:
    DataTransformationProtocolType
properties:
    unique_identifier MO_668

individual x_times


definition:
multiple of stock solution concentration, concentration unit

instance of:
    ConcentrationUnitOther
properties:
    unique_identifier MO_496

individual years


definition:
365 days, time unit

instance of:
    TimeUnit
properties:
    unique_identifier MO_948

individual yes


definition:
true

instance of:
    DeprecatedTerms
properties:
    deprecation_in_version 1.1.7
    unique_identifier MO_540
    deprecation_reason deleted_term

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