Ontology Working Group |
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| Projects :: Software :: Ontologies :: MGED.org | March 15, 2025 |
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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.
- definition:
- Procedures used during treatment.
- properties: unique_identifier MO_193
- 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).
- properties: unique_identifier MO_178
- 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.
- properties: unique_identifier MO_58
- definition:
- MAGE package that describes the array layout and design. The array may be physical or virtual.
- properties: unique_identifier MO_33
- definition:
- An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays.
- properties: unique_identifier MO_34
- definition:
- MAGE package for describing the process by which arrays were manufactured.
- properties: unique_identifier MO_107
- definition:
- The atmospheric conditions used to culture or grow an organism.
- properties: unique_identifier MO_219
- definition:
- An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add
- properties: unique_identifier MO_68
- definition:
- MAGE package for contacts including organizations and people.
- properties: unique_identifier MO_172
- definition:
- Rating of containment system for the protection of organisms from infectious agents.
- properties: unique_identifier MO_97
- definition:
- Refers to the bedding material present in an animals housing.
- properties: unique_identifier MO_154
- definition:
- A bibliographic reference is a published citation in a journal, book, other format e.g. web resource
- properties: unique_identifier MO_201
- definition:
- A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays.
- properties: unique_identifier MO_56
- definition:
- BioAssayData refers to the data files including images generated from one or more BioAssays.
- properties: unique_identifier MO_40
- definition:
- A grouping of bioassay data that has been organized by one or more mathematical functions into nodes.
- properties: unique_identifier MO_116
- definition:
- MAGE package for BioAssayData.
- properties: unique_identifier MO_186
- definition:
- MAGE package for bioassay.
- properties: unique_identifier MO_0
- definition:
- Description of the processing state of the biomaterial for use in the microarray hybridization.
- properties: unique_identifier MO_226
- 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.
- properties: unique_identifier MO_100
- definition:
- Properties of the biomaterial before treated in any manner for the purposes of the experiment.
- properties: unique_identifier MO_5
- definition:
- Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.
- properties: unique_identifier MO_182
- definition:
- A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells.
- properties: unique_identifier MO_20
- 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.
- properties: unique_identifier MO_213
- definition:
- The BioSource after any treatment.
- properties: unique_identifier MO_93
- definition:
- Used to tell when the BioSample is an extract or not.
- properties: unique_identifier MO_161
- definition:
- A representation of a DNA, RNA, or protein sequence.
- properties: unique_identifier MO_163
- definition:
- MAGE package for biological sequences (biosequence).
- properties: unique_identifier MO_191
- 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).
- properties: unique_identifier MO_152
- definition:
- The BioSource is the original source material before any treatment events.
- properties: unique_identifier MO_77
- definition:
- The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial.
- properties: unique_identifier MO_230
- 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.
- properties: unique_identifier MO_95
- definition:
- Factors that relate to properties of the biomaterial, its treatment, or its growth.
- properties: unique_identifier MO_190
- definition:
- A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined.
- properties: unique_identifier MO_224
- definition:
- Physical properties of the BioMaterial e. g. mass or height
- properties: unique_identifier MO_129
- definition:
- class to hold instances used as the filler for the property has_cancer_site
- properties: unique_identifier MO_26
- definition:
- The identifier for the established culture of a metazoan cell if one was used as a biomaterial.
- properties: unique_identifier MO_49
- definition:
- Database of cell line information.
- properties: unique_identifier MO_145
- 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.
- properties: unique_identifier MO_135
- definition:
- Database of cell type information.
- properties: unique_identifier MO_141
- 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).
- properties: unique_identifier MO_1020
- definition:
- A resource for terms to describe cellular components, e.g. GO Cellular Component ontology.
- properties: unique_identifier MO_1021
- 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.
- properties: deprecation_old_restriction some|has_chromosomal_aberration_classification|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.
- properties: unique_identifier MO_6
- definition:
- The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.
- properties: unique_identifier MO_189
- definition:
- The current clinical treatment(s) of the patient from which the biosource is derived.
- properties: unique_identifier MO_69
- definition:
- Database of clinical treatment information
- properties: unique_identifier MO_114
- definition:
- Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification.
- properties: unique_identifier MO_90
- definition:
- A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
- properties: unique_identifier MO_70
- definition:
- Database of compound information.
- properties: unique_identifier MO_151
- definition:
- Units used for concentration measurements.
- properties: unique_identifier MO_61
- definition:
- Concentration units not specified in MAGE.
- properties: unique_identifier MO_86
- definition:
- Organizations or individuals that may be contacted.
- properties: unique_identifier MO_147
- definition:
- Controlled terms for descriptors for the type of control design element.
- properties: unique_identifier MO_50
- definition:
- a plant variety obtained in agriculture in horticulture
- properties: unique_identifier MO_124
- definition:
- The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays.
- properties: unique_identifier MO_165
- definition:
- Primitive data types found in computing languages such as float, boolean, etc.
- properties: unique_identifier MO_125
- definition:
- Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.
- properties: unique_identifier MO_118
- 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).
- properties: unique_identifier MO_157
- definition:
- Defects associated with features or zones such as those that are missing or moved.
- properties: unique_identifier MO_16
- definition:
- Method used to deliver a compound for treatment.
- properties: unique_identifier MO_223
- definition:
- Class to hold deprecated instances and classes.
- properties: unique_identifier MO_206
- definition:
- class to hold instances used as the filler for the property has_reason_for_deprecation
- properties: unique_identifier MO_94
- definition:
- A BioAssay that is created by the transformation of measured or derived BioAssays.
- properties: unique_identifier MO_209
- 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.
- properties: unique_identifier MO_111
- definition:
- MAGE package for description of annotations and references to annotations.
- properties: unique_identifier MO_167
- definition:
- Design elements are reporters, features, and composite elements as defined by MAGE.
- properties: unique_identifier MO_173
- definition:
- A DesignElementGroup holds information on Features, Reporters, or CompositeSequences.
- properties: unique_identifier MO_128
- definition:
- Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence.
- properties: unique_identifier MO_14
- definition:
- The MAGE package for describing the elements located on the array.
- properties: unique_identifier MO_15
- definition:
- The developmental stage of the organism's life cycle during which the biomaterial was extracted.
- properties: unique_identifier MO_120
- definition:
- Database of developmental stage information.
- properties: unique_identifier MO_215
- definition:
- Anatomical location(s) of disease.
- properties: unique_identifier MO_37
- definition:
- The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
- properties: unique_identifier MO_133
- definition:
- Database of disease staging information
- properties: unique_identifier MO_225
- 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.
- properties: unique_identifier MO_126
- definition:
- Database of disease state information.
- properties: unique_identifier MO_181
- definition:
- Units used for distance measurements.
- properties: unique_identifier MO_4
- definition:
- Distance units not specified in MAGE.
- properties: unique_identifier MO_143
- definition:
- a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
- properties: unique_identifier MO_71
- definition:
- Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth.
- properties: unique_identifier MO_117
- definition:
- A description of the conditions the organism has been exposed to that are not one of the variables under study.
- properties: unique_identifier MO_55
- 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
- properties: unique_identifier MO_227
- definition:
- An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history.
- properties: unique_identifier MO_142
- 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.
- properties: unique_identifier MO_112
- 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.
- properties: unique_identifier MO_170
- definition:
- The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc.
- properties: unique_identifier MO_158
- definition:
- The descriptions associated with the Experiment package of MAGE
- properties: unique_identifier MO_31
- definition:
- The factors in the study that are experimental parameters or regarded as influencing the experimental results.
- properties: unique_identifier MO_10
- definition:
- A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML.
- properties: unique_identifier MO_205
- definition:
- All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment.
- properties: unique_identifier MO_75
- definition:
- The value of an ExperimentFactor.
- properties: unique_identifier MO_203
- 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.
- properties: deprecation_old_restriction some|has_value|string
- 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.
- properties: deprecation_old_restriction some|has_value|string
- definition:
- Controlled terms for descriptors of failures (as in PCR) associated with reporters.
- properties: unique_identifier MO_98
- definition:
- Relevant aspects of genetic preconditions or family member's clinical history.
- properties: unique_identifier MO_59
- definition:
- Member of the biosource's family.
- properties: unique_identifier MO_188
- definition:
- A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother.
- properties: unique_identifier MO_36
- definition:
- A technical manufacturer described defect for features.
- properties: unique_identifier MO_138
- definition:
- Technology-based grouping of features representing individual locations on the array.
- properties: unique_identifier MO_54
- definition:
- The expected shape of the feature on the array.
- properties: unique_identifier MO_8
- definition:
- A marking on the surface of the array that can be used to identify the origin of the array.
- properties: unique_identifier MO_136
- definition:
- A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark.
- properties: unique_identifier MO_17
- 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.
- properties: unique_identifier MO_43
- 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.
- properties: unique_identifier MO_137
- 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.
- properties: unique_identifier MO_122
- 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.
- properties: unique_identifier MO_51
- definition:
- A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference.
- properties: unique_identifier MO_132
- definition:
- Database of geographic locations.
- properties: unique_identifier MO_35
- 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.
- properties: unique_identifier MO_183
- definition:
- The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed.
- properties: unique_identifier MO_146
- definition:
- The machine or instrument used.
- properties: unique_identifier MO_134
- definition:
- Controlled terms for descriptors of types of hardware.
- properties: unique_identifier MO_113
- definition:
- The effects of different hardware, types of hardware, or models of hardware on experimental results are studied.
- properties: unique_identifier MO_81
- definition:
- MAGE package for HigherLevelAnalysis
- properties: unique_identifier MO_228
- definition:
- A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging).
- properties: unique_identifier MO_47
- definition:
- Microscopic morphology of tissues.
- properties: unique_identifier MO_194
- definition:
- Database of histology information.
- properties: unique_identifier MO_175
- 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).
- properties: unique_identifier MO_82
- definition:
- Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells).
- properties: unique_identifier MO_101
- definition:
- The humidity that the biosource is exposed to.
- properties: unique_identifier MO_29
- properties: unique_identifier MO_22
- definition:
- Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.)
- properties: unique_identifier MO_211
- definition:
- Identifier or name of the individual organism from which the biomaterial was derived.
- properties: unique_identifier MO_169
- 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.
- properties: deprecation_in_version 1.2.0
- definition:
- The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
- properties: unique_identifier MO_66
- definition:
- The point from which measurements of age were taken.
- properties: unique_identifier MO_80
- definition:
- Compounds that are used for labeling extracts.
- properties: unique_identifier MO_13
- definition:
- The BioSample after labeling for detection of the nucleic acids.
- properties: unique_identifier MO_221
- definition:
- The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
- properties: unique_identifier MO_60
- definition:
- Units for measuring the intensity of light.
- properties: unique_identifier MO_119
- definition:
- An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents.
- properties: unique_identifier MO_57
- 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
- properties: unique_identifier MO_196
- 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.
- properties: unique_identifier MO_174
- definition:
- The version of the MGED Ontology.
- properties: unique_identifier MO_115
- definition:
- Units used for mass measurements.
- properties: unique_identifier MO_149
- definition:
- Mass units not specified in MAGE.
- properties: unique_identifier MO_11
- 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.
- properties: unique_identifier MO_32
- definition:
- Measured values and units.
- properties: unique_identifier MO_144
- definition:
- MAGE package for measurement.
- properties: unique_identifier MO_89
- definition:
- class to hold instances used as the filler for the property has_measurement_type
- properties: unique_identifier MO_72
- definition:
- The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) .
- properties: unique_identifier MO_19
- definition:
- A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop.
- properties: unique_identifier MO_2
- 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.
- properties: unique_identifier MO_85
- definition:
- A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes.
- properties: unique_identifier MO_73
- definition:
- Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm.
- properties: unique_identifier MO_104
- definition:
- Controlled set of terms for describing the type of values (e.g., Euclidean distance).
- properties: unique_identifier MO_160
- definition:
- NormalizationDescription provides details of the normalization strategy for the experiment.
- properties: unique_identifier MO_131
- definition:
- Controlled descriptors for the normalization strategy used for the experiment.
- properties: unique_identifier MO_27
- definition:
- The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
- properties: unique_identifier MO_127
- definition:
- Observation will record the macroscopic examination of the biomaterial.
- properties: unique_identifier MO_53
- definition:
- Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations.
- properties: unique_identifier MO_91
- definition:
- External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology.
- properties: unique_identifier MO_87
- definition:
- The effects of different investigators, laboratories, or organizations on experimental results are studied.
- properties: unique_identifier MO_38
- definition:
- The genus and species (and subspecies) of the organism from which the biomaterial is derived from.
- properties: unique_identifier MO_229
- definition:
- Database of taxonomic information.
- properties: unique_identifier MO_64
- 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).
- properties: unique_identifier MO_1
- definition:
- Database of organism part information.
- properties: unique_identifier MO_200
- definition:
- The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
- properties: unique_identifier MO_84
- definition:
- The organization (e.g. company, hospital) to contact to obtain or purchase something.
- properties: unique_identifier MO_177
- definition:
- Other units are those types not specified in MAGE such as lumens, radioactivity, etc.
- properties: unique_identifier MO_199
- definition:
- A parameter is a variable within a protocol.
- properties: unique_identifier MO_110
- definition:
- Tests and results for pathogens infecting organism from which the biosource is derived
- properties: unique_identifier MO_184
- definition:
- The individual to contact regarding something provided such as a biomaterial.
- properties: unique_identifier MO_24
- definition:
- A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification
- properties: unique_identifier MO_106
- 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.
- properties: unique_identifier MO_192
- definition:
- Database of phenotype information
- properties: unique_identifier MO_39
- definition:
- Descriptions pertaining to the array.
- properties: unique_identifier MO_212
- definition:
- A physical bioassay is the combination of arrays and biomaterials as in a hybridization.
- properties: unique_identifier MO_99
- definition:
- A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC.
- properties: unique_identifier MO_92
- definition:
- The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.
- properties: unique_identifier MO_220
- definition:
- Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence.
- properties: unique_identifier MO_102
- definition:
- The concentration range of the organism.
- properties: unique_identifier MO_46
- definition:
- Method and type of preserving the organism or biosource (i.e. keeping it in stasis).
- properties: unique_identifier MO_176
- definition:
- The type of method used to preserve (keep in stasis) the organism or biosource.
- properties: unique_identifier MO_195
- definition:
- Documentation of the set of steps taken in a procedure.
- properties: unique_identifier MO_214
- definition:
- The MAGE package for protocols.
- properties: unique_identifier MO_63
- definition:
- Descriptors for protocol parameter types, e.g. compound concentration, media type.
- properties: unique_identifier MO_164
- definition:
- A controlled set of terms to provide a descriptor for the type of protocol.
- properties: unique_identifier MO_150
- definition:
- The effects of different protocols or changes in protocols on experimental results are studied.
- properties: unique_identifier MO_140
- definition:
- Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.).
- properties: unique_identifier MO_208
- definition:
- QualityControlDescription provides details of the quality control aspects of the experiment.
- properties: unique_identifier MO_88
- definition:
- Controlled descriptors for the quality control strategy for an experiment.
- properties: unique_identifier MO_121
- definition:
- The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix.
- properties: unique_identifier MO_67
- definition:
- The MAGE package for defining classes for quantitation.
- properties: unique_identifier MO_130
- definition:
- Units used for quantity measurements.
- properties: unique_identifier MO_210
- definition:
- Quantity units not specified in MAGE.
- properties: unique_identifier MO_156
- definition:
- Units for measuring decay of a radioactive isotope over time.
- properties: unique_identifier MO_204
- definition:
- ReplicateDescription provides details about the type of replication used in the experiment.
- properties: unique_identifier MO_162
- definition:
- Controlled descriptors for the type of replication.
- properties: unique_identifier MO_52
- definition:
- Description of the material placed on a feature (spot).
- properties: unique_identifier MO_74
- definition:
- class to hold instances used as the filler for the property has_result
- properties: unique_identifier MO_65
- definition:
- Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider.
- properties: unique_identifier MO_180
- 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.
- properties: unique_identifier MO_139
- definition:
- The scale (linear, log10, ln, etc) used to represent the value.
- properties: unique_identifier MO_108
- definition:
- Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.)
- properties: unique_identifier MO_207
- definition:
- Descriptors of biosequence based on the Sequence Ontology (SO) project.
- properties: unique_identifier MO_25
- definition:
- Database for sequence annotation information.
- properties: unique_identifier MO_83
- definition:
- An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods
- properties: unique_identifier MO_159
- 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.
- properties: unique_identifier MO_168
- definition:
- The software application used.
- properties: unique_identifier MO_109
- definition:
- Controlled terms that provide descriptors for the type of software.
- properties: unique_identifier MO_202
- definition:
- The effects of different software, software packages, or software versions on experimental results are studied.
- properties: unique_identifier MO_222
- definition:
- The organism has had non-genetic parts removed, added, or rearranged.
- properties: unique_identifier MO_44
- 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.
- properties: unique_identifier MO_9
- definition:
- Database of strain, line, cultivar or ecotype information.
- properties: unique_identifier MO_30
- definition:
- A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse
- properties: unique_identifier MO_7
- definition:
- Controlled terms for descriptors of types of array substrates.
- properties: unique_identifier MO_79
- definition:
- Controlled terms for descriptors for coating of the substrate.
- properties: unique_identifier MO_198
- 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.
- properties: unique_identifier MO_123
- definition:
- Database of targeted cell type information.
- properties: unique_identifier MO_45
- 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.
- properties: unique_identifier MO_21
- definition:
- The technology type or platform of the reporters on the array.
- properties: unique_identifier MO_18
- definition:
- The temperature that a biosource is exposed to.
- properties: unique_identifier MO_171
- definition:
- Units used for temperature measurements.
- properties: unique_identifier MO_48
- definition:
- An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry.
- properties: unique_identifier MO_197
- definition:
- TestResult is the recorded value of the test outcome.
- properties: unique_identifier MO_96
- definition:
- Descriptor of the Test performed e.g. Leukocyte count
- properties: unique_identifier MO_218
- definition:
- Database of codes for clinical findings.
- properties: unique_identifier MO_76
- definition:
- A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron.
- properties: unique_identifier MO_42
- definition:
- Units used for time measurements.
- properties: unique_identifier MO_166
- definition:
- Time units not specified in MAGE.
- properties: unique_identifier MO_103
- 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.
- properties: unique_identifier MO_216
- definition:
- A treatment is the process or action by which a biomaterial is created from an input biomaterial.
- properties: unique_identifier MO_23
- definition:
- A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus.
- properties: unique_identifier MO_28
- definition:
- Database of tumor grading information
- properties: unique_identifier MO_187
- definition:
- Uniform Resource Identifier
- properties: unique_identifier MO_12
- definition:
- Units of measure.
- properties: unique_identifier MO_3
- definition:
- User is a way to id a person in a database
- properties: unique_identifier MO_62
- definition:
- Units used for volume measurements.
- properties: unique_identifier MO_179
- definition:
- Volume units not specified in MAGE.
- properties: unique_identifier MO_155
- definition:
- Controlled terms for descriptors of the warnings associated with reporters.
- properties: unique_identifier MO_41
- definition:
- Water consumed by or enveloping the organism that the biosource is derived from.
- properties: unique_identifier MO_153
- definition:
- A technical manufactured described defect for zones.
- properties: unique_identifier MO_105
- 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.
- 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.
- definition:
- An entity responsible for making contributions to the content of the resource.
- definition:
- The extent or scope of the content of the resource.
- definition:
- An entity primarily responsible for making the content of the resource.
- definition:
- A date associated with an event in the life cycle of the resource.
- definition:
- An account of the content of the resource.
- definition:
- The physical or digital manifestation of the resource.
- definition:
- An unambiguous reference to the resource within a given context.
- definition:
- A language of the intellectual content of the resource.
- definition:
- An entity responsible for making the resource available
- definition:
- A reference to a related resource.
- definition:
- Information about rights held in and over the resource.
- definition:
- A reference to a resource from which the present resource is derived.
- definition:
- The topic of the content of the resource.
- definition:
- A name given to the resource.
- definition:
- The nature or genre of the content of the resource.
- definition:
- property indicating the version of the MGED Ontology that the term was deprecated from
- definition:
- The value of the property indicates what version of the ontology the term was deprecated from.
- definition:
- The value indicates the parent of the term before the term was deprecated.
- 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.
- definition:
- Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_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.
- definition:
- property indicating that the class has an identifier
- definition:
- property indicating that the class has an association to a MAGE description
- definition:
- property indicating that the class has a URI
- definition:
- property indicating that the class has an accession number
- definition:
- property indicating that the class has an accession number version
- definition:
- property indicating that the class has an action
- definition:
- property indicating that the class has an additive
- definition:
- property indicating that the class has an address
- definition:
- property indicating that the class has an affiliation to an institution
- definition:
- property indicating that the class has an atmospheric component
- definition:
- property indicating that the class has authors
- definition:
- property indicating that the class has been treated
- definition:
- property indicating that the class has bioassaydata
- definition:
- property indicating that the class has bioassays
- definition:
- property indicating that the class has biomaterial characteristics
- definition:
- property indicating that the class has a biosource type
- definition:
- property indicating that the class has a cancer site
- definition:
- property indicating that the class has a category
- definition:
- property indicating that the class has a chromosomal aberration classification
- definition:
- property indicating that the class has a citation
- definition:
- property indicating that the class has a clinical finding
- definition:
- property indicating that the class has a clinical record
- definition:
- property indicating that the class has a clinical treatment
- definition:
- property indicating that the class has a compound
- definition:
- property indicating that the class contains a cubic volume measurement
- definition:
- property indicating that the class has a database
- definition:
- property indicating that the class has a database entry type
- definition:
- property indicating that the class has a description
- definition:
- property indicating that the class has a diameter
- definition:
- property indicating the location of the disease.
- definition:
- property indicating that the class has disease staging
- definition:
- property indicating that the class has a disease state
- definition:
- property indicating that the class has a donor
- definition:
- property indicating that the class has an editor
- definition:
- property indicating that the class has an email address
- definition:
- property indicating that the class has an experiment design
- definition:
- property indicating that the class has an experiment design type
- definition:
- property indicating that the class has experiment factors
- definition:
- property indicating that the class has a factor value
- definition:
- property indicating that the class has an ontology entry
- definition:
- property indicating that the class has a family member
- definition:
- property indicating that the class has a family relationship
- definition:
- property indicating that the class has a fax
- definition:
- property indicating that the class has a feature shape
- definition:
- property indicating that the class has fiducials
- definition:
- property indicating that the class has a first name
- definition:
- property indicating that the class has hardware
- definition:
- property indicating that the class has a height
- definition:
- property indicating that the class has a host
- definition:
- property indicating that the class has a host part
- definition:
- property indicating that the contents found at this uri are human readable
- definition:
- property indicating that the class has an image format
- definition:
- property indicating that the class has an individual
- definition:
- property indicating that the class has individual genetic characteristics
- definition:
- property indicating that the class has an individual time point
- definition:
- property indicating that the class has an issue
- definition:
- property indicating that the class has a laboratory test
- definition:
- property indicating that the class has a last name
- definition:
- property indicating that the contents found at this uri are machine readable (i.e. in a standard format)
- definition:
- property indicating that the class has a make
- definition:
- property indicating that the class has a manufacturer
- definition:
- property indicating that the class has a mass
- definition:
- property indicating that the class has a maximum measurement
- definition:
- property indicating that the class has a measurement
- definition:
- property indicating that the class has a measurement type
- definition:
- property indicating that the class has a middle initials
- definition:
- property indicating that the class has a model
- definition:
- property indicating that the class has a name
- definition:
- property indicating that the class has a node value
- definition:
- property indicating that the class has a node value type
- definition:
- property indicating that the class has a node
- definition:
- property indicating that the class has a nutrient component
- definition:
- property indicating that the class has an order
- definition:
- property indicating that the class has an organism part
- definition:
- property indicating that the class has an owner
- definition:
- property indicating that the class has pages
- definition:
- property indicating that the class has a parent organization
- definition:
- property indicating that the class has a modified part
- definition:
- property indicating that the protocol has a performer or contact person
- definition:
- property indicating that the class has a phone
- definition:
- property indicating that the class has a prior disease state
- definition:
- property indicating that the class has a property set
- definition:
- property indicating that the class has a protocol
- definition:
- property indicating that the class has providers
- definition:
- property indicating that the class has a publication
- definition:
- property indicating that the class has a publisher
- definition:
- property to indicate the reason for deprecating a term
- definition:
- property indicating the class has a result
- definition:
- property indicating that the class has a scale
- definition:
- property indicating that the class has software
- definition:
- property indicating that the class has species
- definition:
- property indicating that the test has a test protocol
- definition:
- property indicating that the test has a test result
- definition:
- property indicating that the class has a clinical test
- definition:
- property indicating that the class has text
- definition:
- property indicating that the class has a title
- definition:
- property indicating that the class has a toll free phone
- definition:
- property indicating that the class has a treatment
- definition:
- property indicating that the class has a type
- definition:
- property indicating that the class has units
- definition:
- property indicating that the class has a value
- definition:
- property indicating that the class has a version
- definition:
- property indicating that the class has a volume
- definition:
- property indicating that the class has a year
- definition:
- property indicating that the class is a solvent
- definition:
- property indicating that the class is user defined
- definition:
- The value of the property indicates the replacement term.
- definition:
- The value of the property indicates a replacement term since the term was split.
- 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.
- definition:
- A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123.
- definition:
- instance property to indicate what the term was replaced by
- definition:
- property indicating that the class was tested for
- definition:
- Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer
- definition:
- database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses
- definition:
- This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28).
- definition:
- A proprietary image data format that is lossless and containing one channel of data.
- 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.
- definition:
- sequence from a bacterial artificial chromosome exact synonym: bacterial artificial chromosome
- 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.
- 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.
- 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.
- definition:
- Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc.
- 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.
- 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.
- definition:
- a controlled vocabulary provided by CBIL
- 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.
- definition:
- Ontology describing anatomical and physiological relationships.
- 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.
- definition:
- Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds.
- 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).
- definition:
- fluorophore used for labeling/detection purposes
- definition:
- fluorophore used for labeling/detection purposes
- definition:
- Deoxyribonucleic acid.
- definition:
- An instrument that produces DNA sequences.
- definition:
- The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth.
- definition:
- Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences.
- 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).
- definition:
- mating type indicating the presence of F plasmid in a bacterial cell
- 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.
- definition:
- mating type indicating the absence of F plasmid in a bacterial cell
- definition:
- uri for FlyBase developmental stage terms
- definition:
- curated database containing information on Drosophila genes, alleles etc
- definition:
- Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss.
- definition:
- A Comparative Mapping Resource for Grains.
- definition:
- The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
- definition:
- Ontology of human developmental anatomy for Carnegie stages 1-20.
- definition:
- High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome
- definition:
- Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.
- 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.
- definition:
- A resource of vocabularies for describing clinical tests, e.g. blood chemistry.
- definition:
- Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.
- definition:
- Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss.
- definition:
- Kelvin, unit of temperature
- definition:
- liter, unit of volume
- definition:
- Database resource for universal identifiers for laboratory and other clinical observations
- definition:
- Mole per liter or molarity, concentration unit
- definition:
- database entry from mouse anatomical dictionary for developmental stage term
- 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.
- 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.
- 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.
- 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.
- definition:
- database entry from MESH, medical subject headings vocabulary resource
- definition:
- Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors.
- definition:
- A community effort to provide standard terms for annotating phenotypic data.
- definition:
- The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.
- definition:
- identifier for a taxon provided by the NCBI taxonomy database
- definition:
- A description logic namespace that contains controlled terminology used at NCI.
- definition:
- a controlled vocabulary of cell types
- definition:
- a controlled vocabulary for compounds
- definition:
- a controlled vocabulary for disease stages
- definition:
- a controlled vocabulary for disease states
- definition:
- a controlled vocabulary for geographic locations
- definition:
- a controlled vocabulary for histology
- definition:
- a controlled vocabulary of organism parts
- definition:
- a controlled vocabulary for strains or lines
- definition:
- a controlled vocabulary of targeted cell types
- definition:
- a controlled vocabulary of tumor grading terms
- 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.
- definition:
- sequence from a P1 artificial chromosome
- definition:
- Polymerase chain reaction. An element generated using this procedure.
- definition:
- BioSequence generated by means of polymerase chain reaction
- definition:
- Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle.
- definition:
- PCR where no products of any kind appear in gel-separated reaction products.
- definition:
- single oligo used for polymerase chain reaction direction unspecified
- definition:
- single stranded oligo used for polymerase chain reaction
- definition:
- single stranded oligo used for polymerase chain reaction
- definition:
- PCR with multiple bands, or smear, in gel-separated reaction products
- definition:
- Portable Network Graphic, a lossless image data format.
- definition:
- database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice
- definition:
- The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations.
- definition:
- Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg.
- 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.
- definition:
- Ribonucleic acid.
- definition:
- A RNA stability experiment design type examines the stability and/or decay of RNA transcripts.
- 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.
- 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.
- definition:
- The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence.
- definition:
- Computed as the ordinary Pearson correlation coefficient between two groups of rankings.
- definition:
- The Arabidopsis Information Resource.
- definition:
- A structured controlled vocabulary for the anatomy of Arabidopsis.
- definition:
- An ontology of stages of growth and development of the model plant Arabidopsis thaliana.
- definition:
- Toxicology Data Management System, a database resource for systems, organs, pathology, etc.
- 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.
- definition:
- Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH.
- definition:
- units per liter
- definition:
- units per week, e.g. the number of units of alcohol consumed over a period of 7 days
- definition:
- database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions
- definition:
- sequence from yeast artificial chromosome
- definition:
- 32 P, radioactive isotope of phosphorus used for labeling/detection purposes
- definition:
- 33 P, radioactive isotope of phosphorus, used for labeling/detection purposes.
- definition:
- a measurement where the value is independent of other measurements
- definition:
- The action of stabilizing an organism prior to treatment
- definition:
- The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data.
- definition:
- The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data.
- definition:
- The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data.
- definition:
- The mean and variance values resulting from computationally combining 2 or more sets of bioassay data.
- 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.
- definition:
- Units of defined biological activity, e.g. cytokine stimulation, per ml.
- definition:
- A delivery method for compounds/drugs where the compound or drug is freely available.
- definition:
- The procedure of placing one physical object in the same container/physical space as another.
- definition:
- A type of solid media commonly used for growing organisms
- definition:
- agar stab, a cell culture inoculated into agar for long term storage
- definition:
- A descriptor for FactorValue where age is compared.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- definition:
- An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
- definition:
- A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record
- definition:
- a surface coating type for immobilization with the compound aminosilane
- definition:
- attomole, quantity unit
- definition:
- Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n).
- definition:
- glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen
- definition:
- Software to control an arrayer.
- definition:
- Person or organization that manufactured the array.
- definition:
- The process of physically creating the array.
- definition:
- An experiment in which the array platform is compared, e.g. Agilent versus Affy.
- definition:
- An instrument capable of acquiring images of arrays.
- definition:
- An instrument capable of manufacturing arrays by spotting material.
- definition:
- The atmospheric conditions used to culture or grow an organism.
- definition:
- The sister of one's father or mother.
- 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.
- definition:
- The rating of containment system used to protect organisms from infectious agents.
- definition:
- The material (e.g. straw) that an animal sleeps on
- definition:
- time point that indicates the start of some developmental stage
- 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.
- 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.
- definition:
- The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.)
- definition:
- A record which describes and identifies a paper publication e.g. a medline record
- definition:
- A binding site identification design type investigates protein binding sites on nucleic acids non-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP
- definition:
- Software used to transform the Measured or DerivedBioAssay data e.g. normalization. Non-exact synonym: normalization software
- 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.
- 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.
- definition:
- A replicate that consists of independent biological replicates made from different individual BioSources.
- definition:
- A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list
- definition:
- Term used to describe a role or factor value for the person or organization that provides a BioMaterial.
- definition:
- The process of removing tissue from a living organism.
- definition:
- Provider of biosequences (clones, oligos etc) for deposition on the array.
- definition:
- a compound used for labeling/detection purposes
- definition:
- the action of emergence and separation of offspring from the mother.
- definition:
- A biomaterial obtained as fluid consisting of plasma, blood cells and platelets.
- definition:
- A publication type which has an ISBN.
- definition:
- The values are either TRUE or FALSE, which can be expressed as 1 and 0.
- definition:
- A male having the same genetic parents as another, or one genetic parent in common with another.
- 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
- 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
- definition:
- Unit of brightness or luminance.
- definition:
- a cubic centimeter, volume unit
- definition:
- One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms.
- definition:
- A design in which RNA from different cell components is examined.
- 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.
- definition:
- A descriptor for FactorValue where CellLine is compared.
- definition:
- cell lysate, a collection of cells whose membranes have been disrupted
- definition:
- database of cell ontology terms
- definition:
- A descriptor for FactorValue where CellType is compared.
- definition:
- A cell type comparison design experiment design type compares cells of different type for example different cell lines.
- definition:
- the number of cells per ml
- definition:
- A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
- 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.
- definition:
- An instrument capable of applying centrifugal force to tubes or microtiter plates.
- definition:
- the number of colony forming units per ml
- definition:
- Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. Non exact synonym: change growth condition, change environment
- definition:
- The action of changing the relative humidity, e.g. from 1% to 10%.
- definition:
- Change in light intensity or wavelength.
- definition:
- Change in temperature.
- definition:
- the chrome border on an Affymetrix type array which is used as a point of reference for orientation (fiducial)
- definition:
- The loss of a segment of the genetic material from a chromosome.
- definition:
- An irregularity in the number of chromosomes, usually in the form of a gain of genetic material.
- 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.
- 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.
- 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.
- 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.
- definition:
- Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome.
- 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.
- definition:
- A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
- definition:
- A descriptor for FactorValue where ClinicalInformation is compared.
- definition:
- record which describes and identifies clinical information about an organism
- definition:
- A descriptor for a clinical treatment for a patient.
- definition:
- Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown.
- definition:
- Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance.
- definition:
- Software used to cluster the data.
- definition:
- centimeter, a unit of distance
- 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
- definition:
- the physical act of copulation that occurs during the process of sexual reproduction synonyms: copulation, insemination
- 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.
- definition:
- Experiment design type in which genomic content is studied using an array based assay.
- 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.
- definition:
- a record which describes and identifies a compound e.g. drug record part of NCI thesaurus
- 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.
- definition:
- Computationally derived sequence feature.
- definition:
- a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM
- definition:
- A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record
- definition:
- a record which describes and identifies a protein structure e.g. PDB
- definition:
- A device capable of applying software.
- definition:
- Increasing the concentration of solutes in a solution or suspension.
- 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.
- definition:
- DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input
- definition:
- mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input.
- definition:
- A member of a consortium of institutions.
- 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.
- 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.
- definition:
- A Reporter where only buffer was deposited on the array
- 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.
- definition:
- A Reporter where no material or buffer was deposited on the array
- definition:
- A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA.
- 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).
- definition:
- Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone.
- definition:
- A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency.
- 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.
- definition:
- A Reporter indicated as being a control of unknown type.
- 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.
- definition:
- sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size
- definition:
- Unit for a simple count of things
- definition:
- counts per minute, unit of light emissions produced by ionizing radiation.
- definition:
- ctDNA: sequence from the chloroplast synonym: chloroplast DNA
- definition:
- A record which describes and identifies an amino acid sequence which has been curated
- 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
- definition:
- A record which identifies a nucleic acid sequence feature(s) and which has been curated.
- definition:
- person who checks the consistency of the data and MAGE-ML file
- definition:
- RNA obtained from the cytoplasm.
- definition:
- A contact who performs data analysis, e.g. statistician.
- definition:
- person who prepares the MAGE-ML file
- definition:
- Time stated in terms of the day, month, and year.
- definition:
- The female offspring of the patient or individual under study.
- definition:
- 24 hours, time unit
- definition:
- Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma).
- definition:
- degrees celsius, unit of temperature
- definition:
- degrees Fahrenheit, unit of temperature
- definition:
- The term was deleted from the MGED CoreOntology.
- 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.
- definition:
- A descriptor for FactorValue where DevelopmentalStage is compared.
- definition:
- The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.
- definition:
- An analysis aimed at identifying differentially expressed genes in two or more conditions.
- definition:
- A software implementing a Higher Level Analysis protocol of type differential_expresssion.
- definition:
- Decreasing the concentration of solutes in a solution or suspension.
- definition:
- Describes a cell, nucleus or an organism with two copies of each chromosome.
- definition:
- The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
- definition:
- A descriptor for FactorValue where DiseaseState is compared.
- 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.
- definition:
- The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).
- definition:
- The action of removing one or more organism parts.
- definition:
- deciliter, unit of volume
- 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).
- 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.
- 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.
- definition:
- a double stranded oligonucleotide
- definition:
- An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
- 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.
- definition:
- Indicates that a dye swap was performed for some or all hybridizations within an experiment
- 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.
- 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.
- definition:
- Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.
- definition:
- Emergence of an adult insect from its pupa or cocoon.
- definition:
- The point at which the egg(s) is laid by an organism.
- definition:
- protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design
- definition:
- The shape of the feature on the array is circular or oval.
- 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.
- 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.
- 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.
- definition:
- sequence which represents regions of a transcript that are joined to another exon during splicing
- definition:
- Sequence features derived by both computational and experimental methods.
- definition:
- A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial.
- definition:
- An experimentally defined sequence feature.
- definition:
- The BioSample immediately before labeling.
- definition:
- femtomolar, concentration unit
- definition:
- A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied
- definition:
- A male parent.
- definition:
- The process of obtaining quantifiable values from the scanned image of the array. Exact synonyms: image analysis, image quantification
- definition:
- Software to create MeasuredBioAssayData from images. Exact Synonym: image analysis software, image quantification software.
- definition:
- A biosource obtained as fecal matter.
- definition:
- Delivery method where a compound/drug is administered in food or water.
- definition:
- of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes.
- definition:
- The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO)
- definition:
- femtogram, unit of mass
- definition:
- Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold.
- definition:
- femtoliter, unit of volume
- 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).
- 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.
- definition:
- A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34).
- definition:
- femtomole, unit of quantity
- definition:
- the forward strand exact synonym: +
- 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).
- definition:
- A biomaterial that has been lyophilized or dried by freezing under a vacuum.
- 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.
- definition:
- A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat.
- definition:
- A biomaterial obtained frozen
- definition:
- Storage where the thing stored is stored below 0 degrees celsius.
- definition:
- a record which identifies and describes the function of a gene product, e.g. E.C. record
- definition:
- Contact which provides funding for experiments.
- definition:
- gram, unit of mass
- definition:
- grams per liter, concentration unit
- 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
- definition:
- sequence of part of a gene, which is missing one or both ends
- 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.
- 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.
- definition:
- An action whereby an organism(s) has had genetic material removed, added, or rearranged.
- definition:
- A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out
- definition:
- A descriptor for FactorValue where GeneticVariation is compared.
- definition:
- high molecular weight DNA
- definition:
- increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification
- definition:
- A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
- 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).
- definition:
- The array is made on a glass slide.
- definition:
- grams per deciliter, concentration unit
- definition:
- A daughter of one's son or daughter.
- definition:
- The father of one's father or mother.
- definition:
- The mother of one's father or mother.
- definition:
- A son of one's son or daughter.
- definition:
- A ComplexAction or ProtocolType describing growth of an organism or cell culture.
- 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.
- 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.
- definition:
- Describes a cell, nucleus or an organism with one copy of each chromosome.
- definition:
- Person or organization that manufactured the hardware.
- definition:
- A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.
- definition:
- The process of harvesting cells from culture.
- definition:
- The point at which an organism emerges from an egg.
- definition:
- A device for controlling temperature.
- definition:
- The Zone is excluded due to smearing, streaking, or dense background in the Zone.
- definition:
- an organism with both male and female sexual organs in one individual synonym: intersex
- definition:
- The action of preparing a slide for the microscopical examination of organism parts or cell types.
- definition:
- An instrument which fragments tissues or other biomaterials.
- definition:
- 60 minutes, time unit
- definition:
- The process of incubating one or more labeled extracts with an array.
- definition:
- A chamber in which the hybridization is performed which maintains constant conditions.
- definition:
- An instrument which controls hybridization conditions, into which a hybridization chamber may fit.
- definition:
- The process of generating an image from the array.
- definition:
- Software to control a scanner and manipulate and save images. Exact synonym: scanning software
- definition:
- A record which describes and identifies an image, e.g. an image from the mouse atlas
- 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.
- definition:
- Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment).
- definition:
- The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)
- definition:
- An experiment done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
- definition:
- An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
- definition:
- a result which can not be interpreted as positive or negative
- definition:
- The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product.
- definition:
- A descriptor for FactorValue where BioSources are compared.
- definition:
- A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.
- definition:
- An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared.
- definition:
- The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.
- definition:
- The organism (or organism part) has been exposed to a virus or pathogen.
- definition:
- An injury experiment design type is where the response of an organism(s) to injury or damage is studied.
- definition:
- A design in which the innate behavior of the organism is examined, e.g. path finding in bees.
- definition:
- The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism.
- definition:
- A contact's affiliation, e.g. university, research institute or business.
- definition:
- A value which is a whole number (e.g. 10).
- definition:
- sequence from the region between genes
- definition:
- Delivery method for a compound or drug where the substance is administered via an injection into the muscle.
- definition:
- A delivery method for compound or drug whereby the substance is administered via the peritoneum.
- definition:
- delivery method whereby a compound or drug is administered via a vein
- definition:
- sequence spliced out from a transcript
- definition:
- Person who contributed to the study.
- definition:
- treatment of a biomaterial with radiation e.g. electromagnetic radiation
- definition:
- The perimeter of the spotted DNA on the slide is irregular.
- 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.
- definition:
- A design aimed at identifying genes expressed in biomaterials of interest.
- 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.
- 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.
- definition:
- A article published in a print or online journal having an ISSN.
- definition:
- katal per liter, catalytic-activity concentration unit
- definition:
- kilogram, 1000 grams, unit of mass
- 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
- definition:
- The procedure of labeling a biosample.
- definition:
- mark made on slide using a laser which is used as a point of reference for orientation (fiducial)
- definition:
- The length of the light period that a sample is subjected to. Exact synonym:photoperiod
- 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.
- 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
- 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.
- definition:
- The scale is a standard base 10, non logarithmic scale.
- 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.
- 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.
- definition:
- media type, usually some sort of broth
- definition:
- Hardware for automated liquid transfer and handling.
- definition:
- Software used to control automated liquid handler.
- definition:
- An ordered, finite set of booleans.
- definition:
- An ordered, finite set of floats.
- definition:
- An ordered, finite set of integers.
- definition:
- An ordered, finite set of negative floats.
- definition:
- An ordered, finite set of negative integers.
- definition:
- An ordered, finite set of nonnegative floats.
- definition:
- An ordered, finite set of nonnegative integers.
- definition:
- An ordered, finite set of nonpositive floats.
- definition:
- An ordered, finite set of nonpositive integers.
- definition:
- An ordered, finite set of positive floats.
- definition:
- An ordered, finite set of positive integers.
- definition:
- An ordered, finite set of strings.
- 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.
- 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.
- 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.
- definition:
- Application of a scale adjustment following loess_group_normalization, to render the group variances similar.
- definition:
- The values presented are logarithm, base 10.
- definition:
- The values presented are logarithm, base 2.
- definition:
- The values presented are logarithm, base e.
- definition:
- Logarithmic transformation of ratio data.
- definition:
- An element that is an oligonucleotide of at least 50 nucleotides in length.
- definition:
- A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
- 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.
- 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.
- 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.
- 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.
- definition:
- Application of a scale adjustment following lowess_group_normalization, to render the group variances similar.
- definition:
- The unit of total light output from a light source.
- 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.
- definition:
- meter, distance unit
- definition:
- milliliters per liter, concentration unit
- definition:
- milimolar, concentration unit
- definition:
- osmolality per kilogram of water, concentration of the solute per unit of solvent
- definition:
- sequence of a processed transcript capable of directing protein synthesis
- definition:
- individual whose sex organs contain only male gametes
- 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.
- definition:
- Mating type of S. cerevisiae.
- definition:
- Mating type of S. cerevisiae.
- definition:
- Mating type of S.pombe.
- definition:
- Mating type of S.pombe.
- definition:
- the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData
- 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.
- definition:
- the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData
- definition:
- the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData
- definition:
- the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData
- 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).
- definition:
- Application of a normalization of type mean_log_centering.
- definition:
- The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil)
- 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).
- definition:
- Application of a normalization of type median_log_centering.
- definition:
- the term has been subsumed into a more general term
- definition:
- the organism part in which additional tumors are identified remote from the primary site
- definition:
- milligram, mass unit
- definition:
- milligram per kilogram per day
- definition:
- milligrams per milliliter, concentration unit
- definition:
- A record which describes and identifies a microarray experiment e.g. GEO
- 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).
- 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).
- 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.
- definition:
- 60 seconds, unit of time
- 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.
- definition:
- Mix through the process of inverting.
- definition:
- Mix by drawing up and down with a pipette.
- definition:
- Mix through the use of a vortexer.
- definition:
- The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas.
- definition:
- a design element group consisting of multiple types
- definition:
- A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites.
- definition:
- milliliter, volume unit
- definition:
- milliliter per kilogram
- definition:
- millimeter, unit of distance
- definition:
- mole, unit of quantity
- definition:
- an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins
- definition:
- number of molecules, quantity unit
- definition:
- Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1.
- definition:
- Unit of time corresponding to approx. one cycle of the moon's phases.
- definition:
- A female parent.
- 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.
- definition:
- millisecond, time unit
- definition:
- sequence from the mitochondrial genome
- 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.
- definition:
- false or no
- definition:
- A float that is < 0.
- definition:
- An integer < 0.
- definition:
- nanogram, a mass unit
- definition:
- The array is made on a nitrocellulose filter.
- definition:
- nanoliter unit of volume
- definition:
- nanometer distance unit
- definition:
- nanomoles, quantity unit
- definition:
- false
- 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.
- definition:
- A float greater than or equal to 0.
- definition:
- An integer >= 0.
- definition:
- A float less than or equal to zero.
- definition:
- An integer less than or equal to zero.
- definition:
- A normalization testing experiment design tests different normalization procedures.
- 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.
- 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.
- definition:
- The BioSample at any stage other than immediately before labeling.
- definition:
- The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter.
- definition:
- The source DNA for a Feature was not uniformly deposited.
- definition:
- RNA obtained from the nucleus.
- definition:
- The procedure of extracting nucleic acid from the biomaterial.
- definition:
- A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank
- definition:
- number of items or events per day
- definition:
- The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
- definition:
- The array is made on a nylon membrane.
- definition:
- Hardware for synthesizing oligos.
- definition:
- A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement.
- definition:
- A publication type which is available online and which is not an online journal article, e.g. a web site or service.
- definition:
- A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD
- 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.
- definition:
- Software upon which other software runs.
- definition:
- An operator variation experiment design type assesses the operator performance and relation to data consistency and quality.
- definition:
- sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes
- definition:
- An operon identification experiment type is designed to identify locations and members of operons in a genome.
- definition:
- An optimization experiment design type is where different protocols or protocol parameters are compared.
- definition:
- delivery method for drug or compound whereby the drug is administered via the mouth
- definition:
- DNA from organelles such as the mitochondria or chloroplast.
- definition:
- RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus.
- definition:
- one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
- 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).
- definition:
- An organism part comparison experiment design type compares tissues, regions, organs within or between organisms
- definition:
- The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
- definition:
- A design that compares samples from live and dead organisms.
- definition:
- potential of hydrogen
- definition:
- picomolar, concentration unit
- definition:
- A biomaterial obtained embedded in paraffin (wax).
- 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.
- definition:
- a record which identifies and describes biological pathways, e.g. a KEGG record
- 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.
- 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
- definition:
- An experiment which has a peer reviewed publication attached.
- definition:
- A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.
- definition:
- A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy.
- definition:
- percentage volume per volume, concentration unit
- definition:
- percent weight per volume, concentration unit
- definition:
- percent weight per weight, concentration unit
- definition:
- the number of plaque forming units per ml
- definition:
- picogram, mass unit
- definition:
- A record which describes and identifies the relationship between species and is computationally determined and based on sequences e.g. Treebase record
- definition:
- A descriptor for FactorValue where PhysicalCharacteristics are compared.
- 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.
- definition:
- picoliter, volume unit
- definition:
- The procedure of putting a physical object in a container/physical space.
- definition:
- The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing.
- definition:
- sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts
- definition:
- picomoles, quantity unit
- definition:
- RNA which has been obtained by selection for polyA tracts. Exact synonym: polyA+_RNA Non-exact synonym: mRNA
- definition:
- a surface coating for immobilization with the polypeptide, polylysine
- definition:
- sequence of a protein, a linear amino acid polymer
- definition:
- Describes a cell, nucleus or organism with three or more copies of each chromosome.
- definition:
- A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement.
- definition:
- The process of combining two or more BioMaterials. Exact synonym: combine
- definition:
- The concentration range of the organism.
- definition:
- true or yes
- definition:
- A float > 0.
- definition:
- An integer > 0.
- definition:
- biomaterial removed after the death of the organism
- definition:
- gene sequence which has been computationally predicted
- definition:
- sample which has been removed prior to the death of an organism
- definition:
- The type of protocol used to preserve (including storage or keep in stasis) the biomaterial.
- definition:
- A record which describes and identifies an experimentally derived protein structure e.g. MSD
- definition:
- the organism part in which the tumor originated
- definition:
- genomic sequence 5' to a gene where the transcription initiation complex forms.
- definition:
- Polymer of amino acids.
- 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).
- definition:
- A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance
- 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.
- definition:
- Application of a normalization of type quantile_normalization.
- definition:
- sequence from gene coding for ribosomal RNA exact synonym: ribosomal RNA gene
- 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.
- 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.
- definition:
- A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes.
- definition:
- The shape of the feature on the array is rectangular.
- definition:
- A reference experiment design type is where all samples are compared to a common reference.
- definition:
- a measurement where the value is dependent on another measurement
- definition:
- The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding.
- definition:
- The procedure of extracting/taking out a part of a reaction/contents of a container.
- definition:
- The term name was changed to one more appropriate to the intent of the definition.
- 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.
- 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.
- definition:
- The procedure in which solid material is dispensed or dissolved in a liquid.
- definition:
- the reverse strand exact synonym: -
- definition:
- Generation of a DNA strand from an RNA strand using reverse transcriptase.
- definition:
- A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes.
- definition:
- The procedure of euthanizing an organism.
- 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
- definition:
- time unit
- 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.
- definition:
- preservation type whereby the seed is maintained in a dormant state
- definition:
- A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.
- definition:
- semisolid media type
- definition:
- An action where the temperature is specified.
- definition:
- A descriptor for FactorValue where Sex is compared.
- definition:
- A sex experiment design type assays differences associated with an organism's sex, gender or mating type.
- definition:
- An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes).
- definition:
- A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software).
- 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.
- definition:
- the array is made on silicon
- definition:
- a nucleic acid consisting of a single polynucleotide chain.
- definition:
- A female having the same genetic parents as another, or one genetic parent in common with another.
- 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.
- definition:
- sequence from gene coding for small nuclear RNA exact synonym: small nuclear RNA gene
- definition:
- Person or organization that manufactured the software.
- definition:
- A software variation design type compares different types of software for performance, accuracy, precision and reproducibility.
- definition:
- soil, growth media for plants and other soil living organisms
- definition:
- The male offspring of the patient or individual under study.
- definition:
- An instrument for sonicating biomaterials.
- definition:
- the process of placing a seed or spore in some media with the intention to invoke germination.
- definition:
- A species experiment design type assays differences between distinct species.
- definition:
- A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species.
- definition:
- Conceptual action for specified protocol applied in treatment.
- definition:
- Hardware for measuring light at different wavelengths.
- definition:
- An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes.
- definition:
- The procedure of applying a centrifugal force to a physical object. Exact synonym: centrifuge
- 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
- definition:
- the term has been decomposed into more specific terms
- definition:
- TechnologyType of FeatureGroup where antibodies are spotted directly.
- definition:
- TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.
- 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.
- definition:
- TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly.
- definition:
- A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array.
- definition:
- The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.
- definition:
- The shape of the feature on the array is square.
- definition:
- sequence of a single stranded synthesized oligonucleotide
- definition:
- Depriving an organism of food or nutrients
- 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.
- 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.
- 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.
- definition:
- A descriptor of FactorValue where comparisons of strains or lines are made.
- definition:
- A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
- definition:
- The values are a sequence of one or more characters.
- definition:
- Delivery method whereby a drug or compound is administered under the skin of the organism.
- definition:
- Person who is the primary contact for data submitted to a database.
- definition:
- DNA which is generated by chemical or enzymatic (non cellular) means. non-exact synonym: cDNA
- 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
- definition:
- sequence from a gene coding for transfer RNA exact synonym: transfer RNA gene
- definition:
- a nonparametric measure of the agreement between two rankings
- 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.
- definition:
- Temperature associated with a particular environment.
- definition:
- An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR. Exact Synonym: thermocycler
- 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.
- definition:
- Groups of assays that are related as part of a time series.
- definition:
- Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point.
- definition:
- Total cellular and nuclear RNA.
- 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.
- 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.
- 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.
- definition:
- sequence that represents the product of an RNA polymerase engaged in transcription
- definition:
- A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome.
- 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.
- definition:
- Introduction of genetic material into an organism often in the form of a plasmid.
- definition:
- A translational bias is an experiment design which characterizes the association of transcripts and translation machinery.
- definition:
- The possession of a third chromosome of any one type in an otherwise diploid cell.
- definition:
- A descriptor used in cancer biology to describe abnormalities of tumor cells.
- definition:
- Micromole per liter or micromolar, concentration unit
- definition:
- microgram, unit of mass
- definition:
- microliter, unit of volume
- definition:
- micrometer, unit of distance
- definition:
- micromoles, quantity unit
- 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.
- definition:
- The brother of one's father or mother.
- definition:
- Sequence feature whose derivation is unknown.
- definition:
- ExperimentDesignType of unknown type.
- definition:
- ProtocolType of unknown type.
- definition:
- BioSequence of unknown type
- definition:
- organism(s) whose sex is unknown
- definition:
- SubstrateType of unknown type.
- definition:
- A SurfaceType of unknown type.
- definition:
- The values are unordered and have no scale.
- definition:
- The fluid and dissolved substances excreted by the kidney.
- definition:
- microsecond, unit of time
- definition:
- An instrument designed to remove excess liquid by vacuum and heating.
- 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.
- definition:
- Version of the MGED Ontology.
- definition:
- Version of the MGED Ontology.
- definition:
- Version of the MGEDOntology.
- definition:
- Version of the MGEDOntology.
- definition:
- Version of the MGEDOntology.
- definition:
- Version of the MGED Ontology.
- definition:
- one or more DNA or RNA based non cellular infective agent, including bacteriophage
- definition:
- An instrument that mixes by rapid oscillation.
- definition:
- Allow time to pass. It's measurement should be a unit of time.
- 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.
- definition:
- An instrument designed to mechanically wash or stain arrays.
- definition:
- Water consumed by or enveloping the organism that the biosource is derived from.
- definition:
- A device for controlling temperature by immersion in water.
- definition:
- 7 days, unit of time
- definition:
- one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
- 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.
- definition:
- A function applied to subsets of values from the same Measured/Derived bioassay data set.
- definition:
- multiple of stock solution concentration, concentration unit
- definition:
- 365 days, time unit
- definition:
- true
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 ZoneDefectProperties
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:totalDigitsIndividuals
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 yesclass Action
superclasses:
BioMaterialPackage
BiologicalFactorCategory
known subclasses:
AtomicAction
ComplexAction
class_role abstract
class_source ontology
class Age
superclasses:
BioMaterialCharacteristics
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
superclasses:
IndividualGeneticCharacteristics
class_role concrete
class_source ontology
used in individuals:
wild_type
class ArrayDesignPackage
superclasses:
MGEDCoreOntology
known subclasses:
DesignElementGroup
DesignElementGroupType
FeatureShape
PhysicalArrayDesign
SurfaceType
TechnologyType
class_role abstract
class_source mage
class ArrayGroup
superclasses:
ArrayPackage
class_role concrete
class_source mage
constraints:
restriction: has_fiducials has-class Fiducial
restriction: has_type has-class SubstrateType
class ArrayPackage
superclasses:
MGEDCoreOntology
known subclasses:
ArrayGroup
DefectType
FeatureDefect
Fiducial
FiducialType
SubstrateType
ZoneDefect
class_role abstract
class_source mage
class Atmosphere
superclasses:
GrowthCondition
class_role abstract
class_source ontology
constraints:
restriction: has_atmospheric_component has-class Compound
class AtomicAction
superclasses:
Action
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
superclasses:
MGEDCoreOntology
known subclasses:
Contact
Roles
class_role abstract
class_source mage
class BarrierFacility
superclasses:
GrowthCondition
class_role abstract
class_source ontology
class Bedding
superclasses:
EnvironmentalHistory
class_role place_holder
class_source ontology
class BibliographicReference
superclasses:
DescriptionPackage
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
superclasses:
BioAssayPackage
known subclasses:
DerivedBioAssay
PhysicalBioAssay
class_role abstract
class_source mage
class BioAssayData
superclasses:
BioAssayDataPackage
class BioAssayDataCluster
superclasses:
HigherLevelAnalysisPackage
class_role concrete
class_source mage
constraints:
restriction: has_nodes has-class Node
class BioAssayDataPackage
superclasses:
MGEDExtendedOntology
known subclasses:
BioAssayData
Transformation
class BioAssayPackage
superclasses:
MGEDCoreOntology
known subclasses:
BioAssay
DerivedBioAssayType
ImageFormat
class_role abstract
class_source mage
class BioMaterial
superclasses:
BioMaterialPackage
known subclasses:
BioSample
BioSource
LabeledExtract
class_role abstract
class_source mage
constraints:
restriction: has_type has-class MaterialType
restriction: has_biomaterial_characteristics has-class BioMaterialCharacteristics
class BioMaterialCharacteristicCategory
superclasses:
BiologicalFactorCategory
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
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
class_role abstract
class_source ontology
class BioMaterialPackage
superclasses:
MGEDCoreOntology
known subclasses:
Action
BioMaterial
BioMaterialCharacteristics
BioSampleType
FamilyMember
FamilyRelationship
InitialTimePoint
MaterialType
Treatment
class_role abstract
class_source mage
class BioMaterialPurity
superclasses:
BioMaterialCharacteristics
class_role abstract
class_source ontology
class BioMolecularAnnotation
superclasses:
ExperimentDesignType
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
superclasses:
BioMaterial
class_role concrete
class_source mage
constraints:
restriction: has_type has-class BioSampleType
restriction: has_been_treated has-class Treatment
class BioSampleType
superclasses:
BioMaterialPackage
class_role concrete
class_source ontology
used in individuals:
extract
not_extract
class BioSequence
superclasses:
BioSequencePackage
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
superclasses:
MGEDCoreOntology
known subclasses:
BioSequence
BioSequenceType
PolymerType
SeqFeatureBasis
class_role abstract
class_source mage
class BioSequenceType
superclasses:
BioSequencePackage
known subclasses:
PhysicalBioSequenceType
TheoreticalBioSequenceType
class_role abstract
class_source ontology
class BioSource
superclasses:
BioMaterial
class_role concrete
class_source mage
class BioSourceProvider
superclasses:
BioMaterialCharacteristics
class_role abstract
class_source ontology
constraints:
restriction: has_owner has-class Person
restriction: has_donor has-class Organization
class BioSourceType
superclasses:
BioMaterialCharacteristics
class_role concrete
class_source ontology
used in individuals:
agar_stab
freeze_dried_sample
fresh_sample
frozen_sample
paraffin_sample
urine
class BiologicalFactorCategory
superclasses:
ExperimentalFactorCategory
known subclasses:
Action
BioMaterialCharacteristicCategory
BioMaterialCharacteristics
Compound
class_role abstract
class_source ontology
class BiologicalProperty
superclasses:
ExperimentDesignType
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
superclasses:
BioMaterialCharacteristics
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
superclasses:
MGEDCoreOntology
class_role concrete
class_source ontology
used in individuals:
metastatic_site
primary_site
class CellLine
superclasses:
OntologyEntry
BioMaterialCharacteristics
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class CellLineDatabase
class CellLineDatabase
superclasses:
Database
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
superclasses:
BioMaterialCharacteristics
OntologyEntry
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class CellTypeDatabase
class CellTypeDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
CBIL_CV
NCI_cell_type_database
TAIR
cell_ontology
eVOC
class CellularComponent
superclasses:
OntologyEntry
BioMaterialCharacteristics
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class CellularComponentDatabase
class CellularComponentDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
GeneOntology
class ChromosomalAberration
superclasses:
DeprecatedTerms
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
superclasses:
BioMaterialCharacteristics
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
superclasses:
EnvironmentalHistory
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
superclasses:
BioMaterialCharacteristics
OntologyEntry
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class ClinicalTreatmentDatabase
class ClinicalTreatmentDatabase
superclasses:
Database
class_role concrete
class_source ontology
class ComplexAction
superclasses:
Action
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
superclasses:
OntologyEntry
BiologicalFactorCategory
known subclasses:
LabelCompound
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
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
ChEBI
ChemID
NCI_compound_database
class ConcentrationUnit
superclasses:
Unit
known subclasses:
ConcentrationUnitOther
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
superclasses:
ConcentrationUnit
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
superclasses:
AuditAndSecurityPackage
known subclasses:
Organization
Person
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
superclasses:
DesignElementPackage
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
superclasses:
StrainOrLine
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class StrainOrLineDatabase
class DataTransformationProtocolType
superclasses:
ProtocolType
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
superclasses:
MGEDCoreOntology
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
superclasses:
DescriptionPackage
known subclasses:
CellLineDatabase
CellTypeDatabase
CellularComponentDatabase
ClinicalTreatmentDatabase
CompoundDatabase
DevelopmentalStageDatabase
DiseaseStagingDatabase
DiseaseStateDatabase
GeographicLocationDatabase
HistologyDatabase
ObservationDatabase
OrganismDatabase
OrganismPartDatabase
PhenotypeDatabase
SequenceOntologyDatabase
StrainOrLineDatabase
TargetedCellTypeDatabase
TestTypeDatabase
TumorGradingDatabase
class_role abstract
class_source ontology
constraints:
restriction: has_version has-class string
restriction: has_URI has-class URI
class DatabaseEntryType
superclasses:
DescriptionPackage
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
superclasses:
ArrayPackage
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
superclasses:
MGEDExtendedOntology
used in individuals:
ad_libitum
feeding
in_medium
intramuscular_injection
intraperitoneal_injection
intravenous
oral_gavage
subcutaneous
class DeprecatedTerms
superclasses:
MGEDCoreOntology
known subclasses:
ChromosomalAberration
FactorValueDependency
FactorValueSet
IndividualChromosomalAbnormality
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
superclasses:
MGEDCoreOntology
class_role concrete
class_source ontology
used in individuals:
deleted_term
merged_term
replaced_term
split_term
class DerivedBioAssay
superclasses:
BioAssay
class_role concrete
class_source mage
constraints:
restriction: has_type has-class DerivedBioAssayType
class DerivedBioAssayType
superclasses:
BioAssayPackage
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
superclasses:
MGEDCoreOntology
known subclasses:
BibliographicReference
Database
DatabaseEntryType
Image
OntologyEntry
PublicationType
class_role abstract
class_source mage
class DesignElement
superclasses:
DesignElementPackage
known subclasses:
Reporter
class_role concrete
class_source ontology
constraints:
restriction: has_type has-class ControlType
used in individuals:
PCR
long_oligo
short_oligo
class DesignElementGroup
superclasses:
ArrayDesignPackage
known subclasses:
FeatureGroup
class_role abstract
class_source mage
constraints:
restriction: has_species has-class Organism
restriction: has_type has-class DesignElementGroupType
class DesignElementGroupType
superclasses:
ArrayDesignPackage
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
superclasses:
MGEDCoreOntology
known subclasses:
ControlType
DesignElement
FailType
WarningType
class_role abstract
class_source mage
class DevelopmentalStage
superclasses:
OntologyEntry
BioMaterialCharacteristics
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class DevelopmentalStageDatabase
class DevelopmentalStageDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
EMAP
FlyBase_developmental_stage_database
HUMAT
MAD_stage
TAIR_arabidopsis_development_ontology
eVOC
class DiseaseLocation
superclasses:
OrganismPart
class_role concrete
class_source ontology
constraints:
restriction: has_cancer_site has-class CancerSite
class DiseaseStaging
superclasses:
BioMaterialCharacteristics
OntologyEntry
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class DiseaseStagingDatabase
class DiseaseStagingDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
NCI_disease_staging_database
class DiseaseState
superclasses:
OntologyEntry
BioMaterialCharacteristics
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
superclasses:
Database
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
superclasses:
Unit
known subclasses:
DistanceUnitOther
class_role concrete
class_source ontology
used in individuals:
A
cm
m
mm
nm
um
class DistanceUnitOther
superclasses:
DistanceUnit
class_role place_holder
class_source ontology
class Ecotype
superclasses:
StrainOrLine
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class StrainOrLineDatabase
class EnvironmentalFactorCategory
superclasses:
ExperimentalFactorCategory
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
superclasses:
BioMaterialCharacteristics
known subclasses:
Bedding
ClinicalHistory
FamilyHistory
Generation
GeographicLocation
GrowthCondition
Host
PathogenTest
SamplingTimePoint
class_role abstract
class_source ontology
used in individuals:
environmental_history_design
class EnvironmentalStress
superclasses:
MGEDExtendedOntology
constraints:
restriction: has_measurement has-class Measurement
class EpidemiologicalDesign
superclasses:
ExperimentDesignType
class_role concrete
class_source ontology
used in individuals:
clinical_history_design
disease_state_design
family_history_design
unknown_experiment_design_type
class Experiment
superclasses:
ExperimentPackage
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
superclasses:
ExperimentPackage
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
superclasses:
ExperimentPackage
known subclasses:
BiologicalProperty
BioMolecularAnnotation
EpidemiologicalDesign
MethodologicalDesign
PerturbationalDesign
TechnologicalDesign
class_role abstract
class_source ontology
class ExperimentPackage
superclasses:
MGEDCoreOntology
known subclasses:
Experiment
ExperimentalFactor
ExperimentalFactorCategory
ExperimentDesign
ExperimentDesignType
FactorValue
FactorValueDependency
FactorValueSet
NormalizationDescription
NormalizationDescriptionType
QualityControlDescription
QualityControlDescriptionType
ReplicateDescription
ReplicateDescriptionType
class_role abstract
class_source mage
class ExperimentalFactor
superclasses:
ExperimentPackage
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
superclasses:
ExperimentPackage
known subclasses:
BiologicalFactorCategory
EnvironmentalFactorCategory
MethodologicalFactorCategory
class_role abstract
class_source ontology
class ExperimentalProtocolType
superclasses:
ProtocolType
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
superclasses:
ExperimentPackage
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
superclasses:
DeprecatedTerms
ExperimentPackage
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
superclasses:
DeprecatedTerms
ExperimentPackage
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
superclasses:
DesignElementPackage
class_role concrete
class_source ontology
used in individuals:
PCR_fail
PCR_questionable
class FamilyHistory
superclasses:
EnvironmentalHistory
class_role abstract
class_source ontology
constraints:
restriction: has_family_member has-class FamilyMember
class FamilyMember
superclasses:
BioMaterialPackage
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
superclasses:
BioMaterialPackage
class_role concrete
class_source ontology
used in individuals:
aunt
brother
daughter
father
granddaughter
grandfather
grandmother
grandson
mother
sister
son
uncle
class FeatureDefect
superclasses:
ArrayPackage
class_role concrete
class_source mage
constraints:
restriction: has_type has-class DefectType
class FeatureGroup
superclasses:
DesignElementGroup
class_role concrete
class_source mage
constraints:
restriction: has_feature_shape has-class FeatureShape
restriction: has_type has-class TechnologyType
class FeatureShape
superclasses:
ArrayDesignPackage
class_role concrete
class_source ontology
used in individuals:
ellipsoid_feature
rectangular_feature
square_feature
class Fiducial
superclasses:
ArrayPackage
class_role concrete
class_source mage
constraints:
restriction: has_type has-class FiducialType
class FiducialType
superclasses:
ArrayPackage
class_role concrete
class_source ontology
used in individuals:
chrome_border
laser_ablation_mark
class Generation
superclasses:
EnvironmentalHistory
class_role place_holder
class_source ontology
class GeneticMaterial
superclasses:
MGEDExtendedOntology
class GeneticModification
superclasses:
BioMaterialCharacteristics
class_role concrete
class_source ontology
used in individuals:
chromosomal_substitution
gene_knock_in
gene_knock_out
induced_mutation
transfection
class Genotype
superclasses:
IndividualGeneticCharacteristics
class_role concrete
class_source ontology
used in individuals:
wild_type
class GeographicLocation
superclasses:
OntologyEntry
EnvironmentalHistory
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class GeographicLocationDatabase
class GeographicLocationDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
NCI_geographic_location_database
class GrowthCondition
superclasses:
EnvironmentalHistory
known subclasses:
Atmosphere
BarrierFacility
Humidity
Light
Media
Nutrients
PopulationDensity
Temperature
Water
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
superclasses:
IndividualGeneticCharacteristics
class_role place_holder
class_source ontology
class Hardware
superclasses:
ProtocolPackage
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
superclasses:
ProtocolPackage
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
superclasses:
MethodologicalFactorCategory
class_role place_holder
class_source ontology
class HigherLevelAnalysisPackage
superclasses:
MGEDCoreOntology
known subclasses:
BioAssayDataCluster
Node
NodeValue
NodeValueType
class_role abstract
class_source mage
class HigherLevelAnalysisProtocolType
superclasses:
ProtocolType
class_role concrete
class_source ontology
used in individuals:
condition_specificity
differential_expression
multiple_testing_correction
class Histology
superclasses:
OntologyEntry
BioMaterialCharacteristics
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
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
NCI_histology_database
Pathbase
TDMS
class HistoryFactor
superclasses:
MGEDExtendedOntology
class Host
superclasses:
EnvironmentalHistory
class_role abstract
class_source ontology
constraints:
restriction: has_host_part has-class OrganismPart
restriction: has_host has-class Organism
class Humidity
superclasses:
GrowthCondition
class_role abstract
class_source ontology
class Image
superclasses:DescriptionPackage
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
superclasses:
BioAssayPackage
class_role concrete
class_source ontology
used in individuals:
Affymetrix_DAT
GIF
JPEG
PNG
TIFF
class Individual
superclasses:
BioMaterialCharacteristics
class_role place_holder
class_source ontology
class IndividualChromosomalAbnormality
superclasses:
DeprecatedTerms
IndividualGeneticCharacteristics
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
superclasses:
BioMaterialCharacteristics
known subclasses:
Allele
Genotype
Haplotype
IndividualChromosomalAbnormality
Ploidy
class_role abstract
class_source ontology
constraints:
restriction: has_value has-class string
class InitialTimePoint
superclasses:
BioMaterialPackage
class_role concrete
class_source ontology
used in individuals:
beginning_of_stage
birth
coitus
eclosion
egg_laying
fertilization
germination
hatching
planting
sowing
class LabelCompound
superclasses:
Compound
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
superclasses:
BioMaterial
class_role concrete
class_source mage
constraints:
restriction: has_compound has-class LabelCompound
restriction: has_been_treated has-class Treatment
class Light
superclasses:
GrowthCondition
class_role abstract
class_source ontology
class LightUnit
superclasses:
OtherUnit
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
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
class_role abstract
class_source ontology
constraints:
restriction: has_ID has-class string
class MGEDExtendedOntology
superclasses:
MGEDOntology
known subclasses:
BioAssayDataPackage
DeliveryMethod
EnvironmentalStress
GeneticMaterial
HistoryFactor
Preservation
PreservationType
ProtocolParameterType
ProtocolVariation
SomaticModification
StrandType
User
class MGEDOntology
superclasses:
owl:Thing
known subclasses:
MGEDCoreOntology
MGEDExtendedOntology
class_role abstract
class_source ontology
constraints:
restriction: is_user_defined has-class Contact
restriction: is_user_defined has-class BibliographicReference
class MGEDOntologyVersion
superclasses:
MGEDCoreOntology
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
superclasses:
Unit
known subclasses:
MassUnitOther
class_role concrete
class_source ontology
used in individuals:
fg
g
kg
mg
ng
pg
ug
class MassUnitOther
superclasses:
MassUnit
class_role place_holder
class_source ontology
class MaterialType
superclasses:
BioMaterialPackage
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
superclasses:
MeasurementPackage
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
superclasses:
MGEDCoreOntology
known subclasses:
Measurement
Unit
class_role abstract
class_source mage
class MeasurementType
superclasses:
MGEDCoreOntology
class_role concrete
class_source ontology
used in individuals:
absolute
relative
class Media
superclasses:
GrowthCondition
class_role concrete
class_source ontology
used in individuals:
agar
liquid
semisolid
soil
class MethodologicalDesign
superclasses:
ExperimentDesignType
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
superclasses:
ExperimentalFactorCategory
known subclasses:
HardwareVariation
OperatorVariation
ProtocolType
SoftwareVariation
class_role abstract
class_source ontology
class Node
superclasses:
HigherLevelAnalysisPackage
class_role concrete
class_source mage
constraints:
restriction: has_node_value has-class NodeValue
class NodeValue
superclasses:
HigherLevelAnalysisPackage
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
superclasses:
HigherLevelAnalysisPackage
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
superclasses:
ExperimentPackage
class_role abstract
class_source ontology
constraints:
restriction: has_type has-class NormalizationDescriptionType
class NormalizationDescriptionType
superclasses:
ExperimentPackage
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
superclasses:
GrowthCondition
class_role abstract
class_source ontology
constraints:
restriction: has_nutrient_component has-class Compound
class Observation
superclasses:
BioMaterialCharacteristics
class_role abstract
class_source ontology
constraints:
restriction: has_performer has-class Contact
restriction: has_database has-class ObservationDatabase
class ObservationDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
Mammalian_Phenotype_Ontology
class OntologyEntry
superclasses:
DescriptionPackage
known subclasses:
CellLine
CellType
CellularComponent
ClinicalTreatment
Compound
DevelopmentalStage
DiseaseStaging
DiseaseState
GeographicLocation
Histology
Organism
OrganismPart
Phenotype
SequenceOntologyBioSequenceType
StrainOrLine
TargetedCellType
TestType
TumorGrading
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
superclasses:
MethodologicalFactorCategory
class_role place_holder
class_source ontology
class Organism
superclasses:
BioMaterialCharacteristics
OntologyEntry
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class OrganismDatabase
class OrganismDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
NCBI_taxonomy
class OrganismPart
superclasses:
BioMaterialCharacteristics
OntologyEntry
known subclasses:
DiseaseLocation
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class OrganismPartDatabase
class OrganismPartDatabase
superclasses:
Database
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
superclasses:
BioMaterialCharacteristics
class_role concrete
class_source ontology
used in individuals:
postmortem
premortem
class Organization
superclasses:
Contact
class_role concrete
class_source mage
constraints:
restriction: has_name has-class string
restriction: has_parent_organization has-class Organization
class OtherUnit
superclasses:
Unit
known subclasses:
LightUnit
RadiationUnit
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
superclasses:
ProtocolPackage
class_role concrete
class_source mage
constraints:
restriction: has_units has-class Unit
restriction: has_type has-class DataType
class PathogenTest
superclasses:
EnvironmentalHistory
class_role abstract
class_source ontology
constraints:
restriction: was_tested_for has-class Organism
restriction: has_result has-class Result
class Person
superclasses:
Contact
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
superclasses:
ExperimentDesignType
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
superclasses:
OntologyEntry
BioMaterialCharacteristics
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class PhenotypeDatabase
class PhenotypeDatabase
superclasses:
Database
class_role concrete
class_source ontology
class PhysicalArrayDesign
superclasses:
ArrayDesignPackage
class_role concrete
class_source mage
constraints:
restriction: has_type has-class SurfaceType
class PhysicalBioAssay
superclasses:
BioAssay
class_role concrete
class_source mage
constraints:
restriction: has_image_format has-class ImageFormat
class PhysicalBioSequenceType
superclasses:
BioSequenceType
known subclasses:
SequenceOntologyBioSequenceType
class_role concrete
class_source ontology
used in individuals:
antibody
clone_of_unknown_source
unknown_sequence
class Ploidy
superclasses:
IndividualGeneticCharacteristics
class_role concrete
class_source ontology
used in individuals:
aneuploid
diploid
haploid
polyploid
class PolymerType
superclasses:
BioSequencePackage
class_role concrete
class_source ontology
used in individuals:
DNA
RNA
protein
class PopulationDensity
superclasses:
GrowthCondition
class_role abstract
class_source ontology
class Preservation
superclasses:
MGEDExtendedOntology
constraints:
restriction: has_protocol has-class Protocol
restriction: has_type has-class PreservationType
class PreservationType
superclasses:
MGEDExtendedOntology
used in individuals:
frozen_storage
seed_dormancy
class Protocol
superclasses:
ProtocolPackage
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
superclasses:
MGEDCoreOntology
known subclasses:
Hardware
HardwareType
Parameter
Protocol
ProtocolType
Software
SoftwareType
class_role abstract
class_source mage
class ProtocolParameterType
superclasses:
MGEDExtendedOntology
class ProtocolType
superclasses:
ProtocolPackage
MethodologicalFactorCategory
known subclasses:
DataTransformationProtocolType
ExperimentalProtocolType
HigherLevelAnalysisProtocolType
class_role abstract
class_source ontology
class ProtocolVariation
superclasses:
MGEDExtendedOntology
class PublicationType
superclasses:
DescriptionPackage
class_role concrete
class_source ontology
used in individuals:
book
journal_article
online_resource
class QualityControlDescription
superclasses:
ExperimentPackage
class_role abstract
class_source ontology
constraints:
restriction: has_type has-class QualityControlDescriptionType
class QualityControlDescriptionType
superclasses:
ExperimentPackage
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
superclasses:
QuantitationTypePackage
class_role abstract
class_source mage
constraints:
restriction: has_scale has-class Scale
restriction: has_type has-class DataType
class QuantitationTypePackage
superclasses:
MGEDCoreOntology
known subclasses:
QuantitationType
class_role abstract
class_source mage
class QuantityUnit
superclasses:
Unit
known subclasses:
QuantityUnitOther
class_role concrete
class_source ontology
used in individuals:
IU
amol
fmol
mol
molecules
nmol
pmol
umol
class QuantityUnitOther
superclasses:
QuantityUnit
class_role concrete
class_source ontology
used in individuals:
count
class RadiationUnit
superclasses:
OtherUnit
class_role concrete
class_source ontology
used in individuals:
Ci
R
Rad
Rem
cpm
dpm
class ReplicateDescription
superclasses:
ExperimentPackage
class_role abstract
class_source ontology
constraints:
restriction: has_type has-class ReplicateDescriptionType
class ReplicateDescriptionType
superclasses:
ExperimentPackage
class_role concrete
class_source ontology
used in individuals:
biological_replicate
dye_swap_replicate
technical_replicate
class Reporter
superclasses:
DesignElement
class_role concrete
class_source mage
constraints:
restriction: has_type has-class WarningType
restriction: has_type has-class FailType
class Result
superclasses:
MGEDCoreOntology
class_role concrete
class_source ontology
used in individuals:
inconclusive
negative
positive
class Roles
superclasses:
AuditAndSecurityPackage
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
superclasses:
EnvironmentalHistory
class_role abstract
class_source ontology
class Scale
superclasses:
MGEDCoreOntology
class_role concrete
class_source ontology
used in individuals:
linear_scale
log_base_10
log_base_2
log_base_e
unscaled
class SeqFeatureBasis
superclasses:
BioSequencePackage
class_role concrete
class_source ontology
used in individuals:
computational_feature
experimental_and_computational_feature
experimental_feature
unknown_basis_feature
class SequenceOntologyBioSequenceType
superclasses:
OntologyEntry
PhysicalBioSequenceType
TheoreticalBioSequenceType
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class SequenceOntologyDatabase
class SequenceOntologyDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
SequenceOntology
class Serotype
superclasses:
BioMaterialCharacteristics
class_role place_holder
class_source ontology
class Sex
superclasses:
BioMaterialCharacteristics
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
superclasses:
ProtocolPackage
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
superclasses:
ProtocolPackage
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
superclasses:
MethodologicalFactorCategory
class_role place_holder
class_source ontology
class SomaticModification
superclasses:
MGEDExtendedOntology
constraints:
restriction: has_part_modified has-class OrganismPart
class StrainOrLine
superclasses:
OntologyEntry
BioMaterialCharacteristics
known subclasses:
Cultivar
Ecotype
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class StrainOrLineDatabase
restriction: has_species has-class Organism
class StrainOrLineDatabase
superclasses:
Database
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
superclasses:
MGEDExtendedOntology
used in individuals:
double_stranded
forward
reverse
single_stranded
class SubstrateType
superclasses:
ArrayPackage
class_role concrete
class_source ontology
used in individuals:
glass
nitrocellulose
nylon
silicon
unknown_substrate_type
class SurfaceType
superclasses:
ArrayDesignPackage
class_role concrete
class_source ontology
used in individuals:
aminosilane
polylysine
unknown_surface_type
class TargetedCellType
superclasses:
OntologyEntry
BioMaterialCharacteristics
class_role abstract
class_source ontology
class TargetedCellTypeDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
CBIL_CV
MAD_stage
NCI_targeted_cell_type_database
cell_ontology
class TechnologicalDesign
superclasses:
ExperimentDesignType
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
superclasses:
ArrayDesignPackage
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
superclasses:
GrowthCondition
class_role abstract
class_source ontology
class TemperatureUnit
superclasses:
Unit
class_role concrete
class_source ontology
used in individuals:
K
degrees_C
degrees_F
class Test
superclasses:
BioMaterialCharacteristics
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
superclasses:
BioMaterialCharacteristics
class_role abstract
class_source ontology
constraints:
restriction: has_measurement has-class Measurement
class TestType
superclasses:
BioMaterialCharacteristics
OntologyEntry
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class TestTypeDatabase
class TestTypeDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
IUPAC_Clinical_Chemistry_Guidelines
LOINC
TDMS
class TheoreticalBioSequenceType
superclasses:
BioSequenceType
known subclasses:
SequenceOntologyBioSequenceType
class_role concrete
class_source ontology
used in individuals:
unknown_sequence
class TimeUnit
superclasses:
Unit
known subclasses:
TimeUnitOther
class_role concrete
class_source ontology
used in individuals:
days
hours
minutes
months
ms
seconds
us
weeks
years
class TimeUnitOther
superclasses:
TimeUnit
class_role concrete
class_source ontology
used in individuals:
half-life
class Transformation
superclasses:
BioAssayDataPackage
constraints:
restriction: has_protocol has-class Protocol
class Treatment
superclasses:
BioMaterialPackage
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
superclasses:
BioMaterialCharacteristics
OntologyEntry
class_role abstract
class_source ontology
constraints:
restriction: has_database has-class TumorGradingDatabase
class TumorGradingDatabase
superclasses:
Database
class_role concrete
class_source ontology
used in individuals:
NCI_tumor_grading_database
class URI
superclasses:
MGEDCoreOntology
class_role abstract
class_source ontology
class Unit
superclasses:
MeasurementPackage
known subclasses:
ConcentrationUnit
DistanceUnit
MassUnit
OtherUnit
QuantityUnit
TemperatureUnit
TimeUnit
VolumeUnit
class_role abstract
class_source ontology
class User
superclasses:
MGEDExtendedOntology
constraints:
restriction: has_ID has-class string
class VolumeUnit
superclasses:
Unit
known subclasses:
VolumeUnitOther
class_role concrete
class_source ontology
used in individuals:
L
cc
dl
fl
ml
nl
pl
ul
class VolumeUnitOther
superclasses:
VolumeUnit
class_role place_holder
class_source ontology
class WarningType
superclasses:
DesignElementPackage
class_role concrete
class_source ontology
used in individuals:
is_contaminated
not_sequence_verified
class Water
superclasses:
GrowthCondition
class_role abstract
class_source ontology
constraints:
restriction: has_treatment has-class Protocol
restriction: has_additive has-class Compound
class ZoneDefect
superclasses:
ArrayPackage
class_role concrete
class_source mage
constraints:
restriction: has_type has-class DefectType
property class_role
range:
owl:oneOf{"abstract" "place_holder" "concrete"}
property class_source
range:
owl:oneOf{"mage" "ontology"}
property dc:contributor
property dc:coverage
property dc:creator
property dc:date
property dc:description
property dc:format
property dc:identifier
property dc:language
property dc:publisher
property dc:relation
property dc:rights
property dc:source
property dc:subject
property dc:title
property dc:type
property deprecated_from_version
used in classes:
ChromosomalAberration
FactorValueDependency
FactorValueSet
IndividualChromosomalAbnormality
property deprecation_in_version
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
property deprecation_old_restriction
property deprecation_reason
range:
owl:oneOf{"deleted_term" "split_term" "merged_term" "replaced_term"}
property deprecation_replacement_term
property has_ID
used in classes:
MGEDCoreOntology
User
property has_MAGE_description
used in classes:
ExperimentDesign
property has_URI
used in classes:
BibliographicReference
Contact
Database
Image
Protocol
property has_accession
used in classes:
OntologyEntry
property has_accession_version
used in classes:
OntologyEntry
property has_action
used in classes:
Treatment
property has_additive
used in classes:
Water
property has_address
used in classes:
Contact
property has_affiliation
used in classes:
Person
property has_atmospheric_component
used in classes:
Atmosphere
property has_authors
used in classes:
BibliographicReference
property has_been_treated
used in classes:
BioSample
LabeledExtract
property has_bioassay_data
used in classes:
Experiment
property has_bioassays
used in classes:
Experiment
ExperimentDesign
property has_biomaterial_characteristics
used in classes:
BioMaterial
property has_biosource_type
domain:
BioSourceProvider
property has_cancer_site
used in classes:
DiseaseLocation
property has_category
used in classes:
ExperimentalFactor
property has_chromosomal_aberration_classification
used in classes:
ChromosomalAberration
property has_citation
used in classes:
Experiment
Protocol
property has_clinical_finding
used in classes:
ClinicalHistory
property has_clinical_record
used in classes:
ClinicalHistory
FamilyMember
property has_clinical_treatment
used in classes:
ClinicalHistory
property has_compound
used in classes:
LabeledExtract
property has_cubic_volume
used in classes:
Biometrics
property has_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
used in classes:
OntologyEntry
property has_description
used in classes:
ExperimentDesign
OntologyEntry
Protocol
property has_diameter
used in classes:
Biometrics
property has_disease_location
used in classes:
DiseaseState
property has_disease_staging
used in classes:
DiseaseState
property has_disease_state
used in classes:
FamilyMember
property has_donor
used in classes:
BioSourceProvider
property has_editor
used in classes:
BibliographicReference
property has_email
used in classes:
Contact
property has_experiment_design
used in classes:
Experiment
property has_experiment_design_type
used in classes:
ExperimentDesign
property has_experiment_factors
used in classes:
ExperimentDesign
property has_factor_value
used in classes:
ExperimentalFactor
property has_factor_value_ontology_entry
used in classes:
FactorValue
property has_family_member
used in classes:
FamilyHistory
property has_family_relationship
used in classes:
FamilyMember
property has_fax
used in classes:
Contact
property has_feature_shape
used in classes:
FeatureGroup
property has_fiducials
used in classes:
ArrayGroup
property has_first_name
used in classes:
Person
property has_hardware
used in classes:
Protocol
Software
property has_height
used in classes:
Biometrics
property has_host
domain:
Host
used in classes:
Host
property has_host_part
domain:
Host
used in classes:
Host
property has_human_readable_URI
property has_image_format
domain:
PhysicalBioAssay
used in classes:
Image
PhysicalBioAssay
property has_individual
used in classes:
Biometrics
property has_individual_genetic_characteristics
used in classes:
FamilyMember
property has_initial_time_point
domain:
Age
used in classes:
Age
property has_issue
domain:
BibliographicReference
used in classes:
BibliographicReference
property has_laboratory_test
property has_last_name
used in classes:
Person
property has_length
used in classes:
Biometrics
property has_machine_readable_URI
property has_make
domain:
Hardware
used in classes:
Hardware
property has_manufacturer
used in classes:
Hardware
Software
property has_mass
used in classes:
Biometrics
property has_maximum_measurement
domain:
Age
used in classes:
Age
GrowthCondition
property has_measurement
used in classes:
Age
Compound
EnvironmentalStress
FactorValue
GrowthCondition
TestResult
property has_measurement_type
domain:
Measurement
used in classes:
Measurement
property has_mid_initials
used in classes:
Person
property has_model
domain:
Hardware
used in classes:
Hardware
property has_name
used in classes:
Organization
property has_node_value
used in classes:
Node
property has_node_value_type
used in classes:
NodeValue
property has_nodes
used in classes:
BioAssayDataCluster
property has_nutrient_component
used in classes:
Nutrients
property has_order
used in classes:
Treatment
property has_organism_part
used in classes:
Biometrics
Histology
property has_owner
used in classes:
BioSourceProvider
property has_pages
domain:
BibliographicReference
used in classes:
BibliographicReference
property has_parent_organization
used in classes:
Organization
property has_part_modified
used in classes:
SomaticModification
property has_performer
used in classes:
Histology
Observation
Test
property has_phone
used in classes:
Contact
property has_prior_disease_state
used in classes:
ClinicalHistory
property has_property_set
used in classes:
FactorValue
property has_protocol
used in classes:
Preservation
Transformation
Treatment
property has_providers
used in classes:
Experiment
property has_publication
used in classes:
BibliographicReference
property has_publisher
used in classes:
BibliographicReference
property has_reason_for_deprecation
used in classes:
ChromosomalAberration
DeprecatedTerms
FactorValueDependency
FactorValueSet
IndividualChromosomalAbnormality
property has_result
used in classes:
PathogenTest
property has_scale
used in classes:
NodeValue
QuantitationType
property has_software
used in classes:
Hardware
Protocol
Software
property has_species
used in classes:
BioSequence
DesignElementGroup
StrainOrLine
property has_test_protocol
property has_test_result
used in classes:
Test
property has_test_type
used in classes:
ClinicalHistory
Test
property has_text
used in classes:
Protocol
property has_title
used in classes:
BibliographicReference
Protocol
property has_toll_free_phone
used in classes:
Contact
property has_treatment
used in classes:
Water
property has_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
used in classes:
Measurement
Parameter
property has_value
used in classes:
FactorValueDependency
FactorValueSet
GrowthCondition
IndividualGeneticCharacteristics
Measurement
OntologyEntry
property has_version
used in classes:
Database
property has_volume
domain:
BibliographicReference
used in classes:
BibliographicReference
property has_year
used in classes:
BibliographicReference
property is_solvent
used in classes:
Compound
property 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
property split_to_term
property synonym
range:
string
property unique_identifier
property was_replaced_by
property 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
instance of:
DistanceUnit
properties:
unique_identifier MO_515
individual ATCC_Cultures
instance of:
CellLineDatabase
StrainOrLineDatabase
properties:
unique_identifier MO_979
individual Adult_Mouse_Anatomy
instance of:
OrganismPartDatabase
properties:
unique_identifier MO_992
individual Affymetrix_DAT
instance of:
ImageFormat
properties:
unique_identifier MO_786
individual Affymetrix_average_difference
instance of:
DerivedBioAssayType
properties:
unique_identifier MO_649
individual BAC
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
instance of:
StrainOrLineDatabase
properties:
unique_identifier MO_1008
individual CABRI_Filamentous_Fungi_Strains
instance of:
StrainOrLineDatabase
properties:
unique_identifier MO_1009
individual CABRI_HLA_typed_B_Cell_lines
instance of:
CellLineDatabase
properties:
unique_identifier MO_1005
individual CABRI_Human_and_Animal_Cell_lines
instance of:
CellLineDatabase
properties:
unique_identifier MO_536
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individual days
instance of:
TimeUnit
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ComplexAction
ExperimentalProtocolType
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individual degrees_C
instance of:
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individual degrees_F
instance of:
TemperatureUnit
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BiologicalProperty
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individual developmental_stage
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BioMaterialCharacteristicCategory
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HigherLevelAnalysisProtocolType
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individual differential_expression_software
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AtomicAction
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BioMaterialCharacteristicCategory
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individual disease_state
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BioMaterialCharacteristicCategory
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EpidemiologicalDesign
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instance of:
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ExperimentalProtocolType
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individual dl
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individual dose_response_design
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individual double_stranded
instance of:
StrandType
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individual dpm
instance of:
RadiationUnit
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individual ds_oligo
instance of:
DeprecatedTerms
properties:
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deprecation_reason deleted_term
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individual dye_swap_replicate
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individual dye_swap_replicate_reduction
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individual eVOC
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CellTypeDatabase
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individual eclosion
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individual egg_laying
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InitialTimePoint
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individual ellipsoid_feature
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individual environmental_history_design
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EnvironmentalHistory
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individual ex_vivo_design
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MethodologicalDesign
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individual exemplar_mRNA
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individual exon
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individual experimental_design_element_group_type
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individual experimental_feature
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SeqFeatureBasis
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individual extract
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BioSampleType
properties:
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individual fM
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ConcentrationUnit
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unique_identifier MO_898
individual family_history_design
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EpidemiologicalDesign
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individual father
instance of:
FamilyRelationship
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unique_identifier MO_762
individual feature_extraction
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ExperimentalProtocolType
properties:
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individual feature_extraction_software
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individual feces
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properties:
deprecation_in_version 1.1.9
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deprecation_reason deleted_term
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individual female
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individual fertilization
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InitialTimePoint
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individual fg
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individual filtered_data
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DerivedBioAssayType
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individual fl
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individual flag_filter
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individual flip-dye_consistency
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individual float
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individual fmol
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individual forward
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ExperimentalProtocolType
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individual freeze_dried_sample
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BioSourceType
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individual french_railway_distance
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BioSourceType
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individual frozen_sample
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BioSourceType
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individual frozen_storage
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individual function_record
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DatabaseEntryType
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individual funder
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unique_identifier MO_520
individual g
instance of:
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unique_identifier MO_825
individual g_per_L
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ConcentrationUnit
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individual gene
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DeprecatedTerms
properties:
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deprecation_reason deleted_term
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individual gene_fragment
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individual gene_knock_out
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individual genetic_modification
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ComplexAction
ExperimentalProtocolType
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individual genetic_modification_design
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individual genetic_variation
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DeprecatedTerms
properties:
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deprecation_reason deleted_term
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properties:
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individual genomic_region_amplification
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ChromosomalAberrationClassification
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individual genotyping_design
instance of:
BioMolecularAnnotation
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individual germination
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InitialTimePoint
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individual glass
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individual gram_percent
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ConcentrationUnit
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individual granddaughter
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FamilyRelationship
properties:
unique_identifier MO_703
individual grandfather
instance of:
FamilyRelationship
properties:
unique_identifier MO_478
individual grandmother
instance of:
FamilyRelationship
properties:
unique_identifier MO_924
individual grandson
instance of:
FamilyRelationship
properties:
unique_identifier MO_831
individual grow
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ComplexAction
ExperimentalProtocolType
properties:
unique_identifier MO_758
individual growth_condition_design
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PerturbationalDesign
properties:
unique_identifier MO_588
individual half-life
instance of:
TimeUnitOther
properties:
unique_identifier MO_595
individual haploid
instance of:
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unique_identifier MO_719
individual hardware_manufacturer
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individual hardware_variation_design
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ExperimentalProtocolType
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individual hatching
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InitialTimePoint
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individual heating_block
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individual heavy_background
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individual hermaphrodite
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ExperimentalProtocolType
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individual homogenizer
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individual hours
instance of:
TimeUnit
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individual hybridization_chamber
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individual hybridization_station
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individual image_acquisition
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individual image_acquisition_software
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individual in_vivo_design
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instance of:
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individual incubate
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ExperimentalProtocolType
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individual individual
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BioMaterialCharacteristicCategory
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individual individual_genetic_characteristic
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BioMaterialCharacteristicCategory
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BiologicalProperty
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individual induced_mutation
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individual infect
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individual injury_design
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individual innate_behavior_design
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individual inoculate
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ExperimentalProtocolType
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individual integer
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individual intergenic
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individual intravenous
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DeliveryMethod
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individual intron
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BiologicalProperty
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individual kg
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individual kg_per_m2
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individual mRNA
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