An ontology for microarray experiments in support of MAGE v.1.
February 9, 2007
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
The MGED Ontology
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
1.3.1.1
ontology
MO_26
concrete
class to hold instances used as the filler for the property has_cancer_site
Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.
MO_182
mage
abstract
ontology
abstract
MO_9
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.
Water consumed by or enveloping the organism that the biosource is derived from.
ontology
abstract
MO_153
The MAGE package for defining classes for quantitation.
abstract
mage
MO_130
The developmental stage of the organism's life cycle during which the biomaterial was extracted.
abstract
MO_120
ontology
Refers to the bedding material present in an animals housing.
place_holder
MO_154
ontology
concrete
mage
A parameter is a variable within a protocol.
MO_110
ontology
concrete
Database for sequence annotation information.
MO_83
abstract
MAGE package for measurement.
MO_89
mage
Database of tumor grading information
ontology
concrete
MO_187
Measured values and units.
mage
concrete
MO_144
MO_198
Controlled terms for descriptors for coating of the substrate.
ontology
concrete
ontology
class to hold instances used as the filler for the property has_result
MO_65
concrete
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.
concrete
MO_213
ontology
The expected shape of the feature on the array.
concrete
ontology
MO_8
abstract
ontology
The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.
MO_189
ontology
MO_188
Member of the biosource's family.
abstract
Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.)
MO_207
ontology
concrete
MO_40
BioAssayData refers to the data files including images generated from one or more BioAssays.
Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider.
MO_180
concrete
ontology
MO_113
concrete
Controlled terms for descriptors of types of hardware.
ontology
MO_226
mage
Description of the processing state of the biomaterial for use in the microarray hybridization.
abstract
concrete
ontology
MO_156
Quantity units not specified in MAGE.
MO_216
The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data.
abstract
MO_101
Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells).
ontology
ontology
A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference.
abstract
MO_132
MO_165
The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays.
concrete
ontology
A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop.
ontology
MO_2
concrete
ontology
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).
abstract
MO_178
place_holder
MO_38
ontology
The effects of different investigators, laboratories, or organizations on experimental results are studied.
ontology
abstract
MO_162
ReplicateDescription provides details about the type of replication used in the experiment.
ontology
Physical properties of the BioMaterial e. g. mass or height
abstract
MO_129
ontology
MO_41
Controlled terms for descriptors of the warnings associated with reporters.
concrete
concrete
MO_6
ontology
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.
concrete
ontology
MO_117
Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth.
MO_64
concrete
ontology
Database of taxonomic information.
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.
ontology
MO_174
abstract
place_holder
MO_169
ontology
Identifier or name of the individual organism from which the biomaterial was derived.
MO_136
mage
A marking on the surface of the array that can be used to identify the origin of the array.
concrete
The value of an ExperimentFactor.
mage
concrete
MO_203
MO_221
concrete
The BioSample after labeling for detection of the nucleic acids.
mage
MO_109
concrete
The software application used.
mage
MO_170
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.
mage
concrete
concrete
MO_30
Database of strain, line, cultivar or ecotype information.
ontology
MAGE package for BioAssayData.
MO_186
An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays.
MO_34
concrete
mage
MO_5
Properties of the biomaterial before treated in any manner for the purposes of the experiment.
abstract
ontology
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).
abstract
MO_152
ontology
place_holder
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.
ontology
MO_43
MO_195
The type of method used to preserve (keep in stasis) the organism or biosource.
ontology
Microscopic morphology of tissues.
abstract
MO_194
A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse
MO_7
mage
concrete
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.
MO_112
abstract
MO_15
The MAGE package for describing the elements located on the array.
mage
Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.)
concrete
ontology
MO_211
mage
A technical manufacturer described defect for features.
concrete
MO_138
mage
MO_191
abstract
MAGE package for biological sequences (biosequence).
ontology
concrete
MO_160
Controlled set of terms for describing the type of values (e.g., Euclidean distance).
The organism has had non-genetic parts removed, added, or rearranged.
MO_44
place_holder
The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed.
ontology
MO_146
Concentration units not specified in MAGE.
ontology
concrete
MO_86
abstract
ontology
MO_135
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.
Uniform Resource Identifier
MO_12
ontology
abstract
Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD).
concrete
ontology
MO_157
mage
The MAGE package for protocols.
MO_63
abstract
TestResult is the recorded value of the test outcome.
ontology
MO_96
abstract
MO_31
The descriptions associated with the Experiment package of MAGE
abstract
mage
Units used for volume measurements.
concrete
ontology
MO_179
concrete
MO_202
ontology
Controlled terms that provide descriptors for the type of software.
Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.).
concrete
MO_208
ontology
mage
Description of the material placed on a feature (spot).
MO_74
concrete
concrete
MO_201
A bibliographic reference is a published citation in a journal, book, other format e.g. web resource
mage
Descriptor of the Test performed e.g. Leukocyte count
ontology
abstract
MO_218
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).
abstract
MO_1020
ontology
MO_185
MO_1033
Version of the MGEDOntology.
ontology
deleted_term
The term was deleted from the MGED CoreOntology.
MO_1023
1.2.0
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.
place_holder
mage
MO_228
abstract
MAGE package for HigherLevelAnalysis
The genus and species (and subspecies) of the organism from which the biomaterial is derived from.
abstract
ontology
MO_229
MAGE package that describes the array layout and design. The array may be physical or virtual.
abstract
MO_33
mage
concrete
MO_94
ontology
class to hold instances used as the filler for the property has_reason_for_deprecation
Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.
ontology
MO_118
abstract
MO_168
ontology
concrete
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.
concrete
MO_95
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.
ontology
abstract
ontology
MO_184
Tests and results for pathogens infecting organism from which the biosource is derived
concrete
MO_91
Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations.
ontology
The identifier for the established culture of a metazoan cell if one was used as a biomaterial.
ontology
abstract
MO_49
MO_61
Units used for concentration measurements.
concrete
ontology
MO_90
ontology
Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification.
concrete
ontology
MO_98
concrete
Controlled terms for descriptors of failures (as in PCR) associated with reporters.
MO_148
Version of the MGEDOntology.
MO_1032
deleted_term
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.
place_holder
ontology
1.1.9
some|has_value|string
MO_45
ontology
concrete
Database of targeted cell type information.
Units used for mass measurements.
concrete
ontology
MO_149
MO_55
ontology
abstract
A description of the conditions the organism has been exposed to that are not one of the variables under study.
abstract
The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial.
MO_230
ontology
concrete
MO_52
ontology
Controlled descriptors for the type of replication.
MAGE package for description of annotations and references to annotations.
mage
abstract
MO_167
abstract
MO_126
ontology
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.
MO_46
ontology
The concentration range of the organism.
abstract
Units used for time measurements.
MO_166
concrete
ontology
A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging).
concrete
ontology
MO_47
ontology
An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry.
MO_197
abstract
MO_181
concrete
Database of disease state information.
ontology
concrete
MO_22
mage
Controlled terms for descriptors of types of array substrates.
MO_79
ontology
concrete
place_holder
MO_155
ontology
Volume units not specified in MAGE.
A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus.
MO_28
abstract
ontology
ontology
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.
concrete
MO_58
MO_107
mage
MAGE package for describing the process by which arrays were manufactured.
abstract
MO_214
mage
concrete
Documentation of the set of steps taken in a procedure.
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.
MO_137
MO_19
The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) .
ontology
concrete
MO_73
mage
concrete
A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes.
MO_158
ontology
abstract
The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc.
MO_77
concrete
mage
The BioSource is the original source material before any treatment events.
The point from which measurements of age were taken.
ontology
MO_80
concrete
class to hold instances used as the filler for the property has_measurement_type
concrete
MO_72
ontology
MO_119
ontology
Units for measuring the intensity of light.
concrete
abstract
Rating of containment system for the protection of organisms from infectious agents.
ontology
MO_97
abstract
ontology
MO_20
A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells.
abstract
External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology.
MO_87
ontology
Units used for distance measurements.
concrete
MO_4
ontology
Distance units not specified in MAGE.
MO_143
place_holder
ontology
ontology
The effects of different hardware, types of hardware, or models of hardware on experimental results are studied.
MO_81
place_holder
mage
MO_116
A grouping of bioassay data that has been organized by one or more mathematical functions into nodes.
concrete
MO_176
Method and type of preserving the organism or biosource (i.e. keeping it in stasis).
ontology
concrete
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.
MO_51
concrete
The version of the MGED Ontology.
MO_115
ontology
MO_100
General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue.
concrete
ontology
Database of developmental stage information.
MO_215
abstract
Organizations or individuals that may be contacted.
MO_147
mage
ontology
abstract
The humidity that the biosource is exposed to.
MO_29
MO_163
mage
A representation of a DNA, RNA, or protein sequence.
concrete
MO_205
ontology
A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML.
abstract
MO_48
ontology
concrete
Units used for temperature measurements.
concrete
Controlled terms for descriptors for the type of control design element.
MO_50
ontology
ontology
concrete
Used to tell when the BioSample is an extract or not.
MO_161
ontology
concrete
MO_121
Controlled descriptors for the quality control strategy for an experiment.
ontology
MO_224
A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined.
concrete
ontology
concrete
Database of disease staging information
MO_225
A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark.
ontology
MO_17
concrete
The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.
concrete
MO_220
ontology
MO_75
All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment.
concrete
ontology
mage
A treatment is the process or action by which a biomaterial is created from an input biomaterial.
MO_23
concrete
MO_88
abstract
QualityControlDescription provides details of the quality control aspects of the experiment.
ontology
Design elements are reporters, features, and composite elements as defined by MAGE.
ontology
concrete
MO_173
MO_68
ontology
An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add
concrete
A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays.
MO_56
abstract
mage
concrete
ontology
MO_142
An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history.
abstract
MO_193
ontology
Procedures used during treatment.
ontology
MO_92
A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC.
concrete
abstract
ontology
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.
MO_139
Observation will record the macroscopic examination of the biomaterial.
abstract
MO_53
ontology
concrete
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.
ontology
MO_32
MO_10
The factors in the study that are experimental parameters or regarded as influencing the experimental results.
mage
concrete
The machine or instrument used.
concrete
mage
MO_134
MO_84
ontology
The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
concrete
concrete
ontology
MO_37
Anatomical location(s) of disease.
The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
MO_60
abstract
ontology
ontology
MO_69
abstract
The current clinical treatment(s) of the patient from which the biosource is derived.
concrete
Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm.
mage
MO_104
concrete
MO_175
Database of histology information.
ontology
ontology
abstract
MO_71
a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
abstract
ontology
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.
MO_123
mage
MO_54
Technology-based grouping of features representing individual locations on the array.
concrete
ontology
abstract
A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
MO_70
Database of compound information.
concrete
MO_151
ontology
1.1.7
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.
deleted_term
abstract
MO_78
MO_1031
Version of the MGED Ontology.
some|has_chromosomal_aberration_classification|ChromosomalAberrationClassification
ontology
abstract
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.
MO_85
ontology
MO_99
A physical bioassay is the combination of arrays and biomaterials as in a hybridization.
concrete
mage
Units for measuring decay of a radioactive isotope over time.
ontology
MO_204
concrete
MO_164
Descriptors for protocol parameter types, e.g. compound concentration, media type.
Database of organism part information.
ontology
concrete
MO_200
concrete
MO_24
mage
The individual to contact regarding something provided such as a biomaterial.
MO_122
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.
concrete
ontology
ontology
Primitive data types found in computing languages such as float, boolean, etc.
MO_125
concrete
A controlled set of terms to provide a descriptor for the type of protocol.
ontology
abstract
MO_150
MO_196
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
abstract
ontology
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).
MO_1
MO_159
An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods
place_holder
ontology
ontology
The effects of different software, software packages, or software versions on experimental results are studied.
place_holder
MO_222
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.
concrete
MO_21
ontology
concrete
Time units not specified in MAGE.
ontology
MO_103
Units of measure.
ontology
abstract
MO_3
MO_82
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).
MO_140
The effects of different protocols or changes in protocols on experimental results are studied.
concrete
ontology
Class to hold deprecated instances and classes.
MO_206
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.
ontology
MO_183
abstract
ontology
MO_76
concrete
Database of codes for clinical findings.
Controlled descriptors for the normalization strategy used for the experiment.
ontology
MO_27
concrete
Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence.
ontology
concrete
MO_14
ontology
MO_36
A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother.
concrete
concrete
MO_42
ontology
A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron.
mage
MO_172
MAGE package for contacts including organizations and people.
abstract
MO_171
The temperature that a biosource is exposed to.
ontology
abstract
concrete
ontology
Units used for quantity measurements.
MO_210
abstract
MO_219
The atmospheric conditions used to culture or grow an organism.
ontology
abstract
MO_0
mage
MAGE package for bioassay.
A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification
ontology
concrete
MO_106
mage
MO_128
A DesignElementGroup holds information on Features, Reporters, or CompositeSequences.
abstract
concrete
mage
The BioSource after any treatment.
MO_93
ontology
MO_16
concrete
Defects associated with features or zones such as those that are missing or moved.
place_holder
Mass units not specified in MAGE.
MO_11
ontology
deleted_term
place_holder
MO_217
1.1.9
some|has_value|string
ontology
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.
MO_141
Database of cell type information.
concrete
ontology
ontology
MO_133
The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
abstract
ontology
Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence.
MO_102
concrete
User is a way to id a person in a database
MO_62
concrete
ontology
Database of phenotype information
MO_39
abstract
MO_66
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
ontology
ontology
NormalizationDescription provides details of the normalization strategy for the experiment.
MO_131
abstract
MO_108
ontology
The scale (linear, log10, ln, etc) used to represent the value.
concrete
ontology
concrete
Database of cell line information.
MO_145
MO_223
Method used to deliver a compound for treatment.
Factors that relate to properties of the biomaterial, its treatment, or
its growth.
ontology
abstract
MO_190
abstract
MO_59
Relevant aspects of genetic preconditions or family member's clinical history.
ontology
ontology
Other units are those types not specified in MAGE such as lumens, radioactivity, etc.
MO_199
concrete
MO_127
The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
abstract
ontology
abstract
MO_67
mage
The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix.
MO_212
mage
Descriptions pertaining to the array.
concrete
MO_114
Database of clinical treatment information
concrete
ontology
ontology
MO_192
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.
abstract
A technical manufactured described defect for zones.
concrete
MO_105
mage
mage
concrete
The organization (e.g. company, hospital) to contact to obtain or purchase something.
MO_177
ontology
concrete
The technology type or platform of the reporters on the array.
MO_18
a plant variety obtained in agriculture in horticulture
abstract
ontology
MO_124
MO_13
concrete
ontology
Compounds that are used for labeling extracts.
MO_227
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
ontology
MO_57
abstract
An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents.
MO_25
ontology
abstract
Descriptors of biosequence based on the Sequence Ontology (SO) project.
ontology
A resource for terms to describe cellular components, e.g. GO Cellular Component ontology.
MO_1021
concrete
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.
ontology
concrete
MO_111
ontology
Database of geographic locations.
MO_35
concrete
A BioAssay that is created by the transformation of measured or derived BioAssays.
MO_209
mage
concrete
MO_319
property indicating that the class has a type
property indicating that the class has a factor value
MO_236
property indicating that the class has an association to a MAGE description
MO_260
property indicating that the class has a clinical finding
MO_316
property indicating that the class has a nutrient component
MO_321
property indicating that the class has a node value type
MO_264
property to indicate the reason for deprecating a term
MO_306
property indicating that the class has a measurement type
MO_242
property indicating that the class has an ontology entry
MO_263
MO_328
property indicating that the class has experiment factors
property indicating that the class has a host
MO_313
property indicating that the class has a height
MO_317
MO_320
property indicating that the class has species
MO_248
property indicating that the class has a cancer site
MO_249
property indicating that the class has a category
property indicating that the class has a chromosomal aberration classification
MO_253
property indicating that the class has a mass
MO_280
property indicating that the class has a clinical test
MO_311
MO_252
property indicating that the class has bioassaydata
MO_324
property indicating the class has a result
property indicating that the class has a citation
MO_274
MO_290
property indicating the location of the disease.
MO_259
property indicating that the class has an atmospheric component
property indicating that the class has an action
MO_312
property indicating that the class has a family member
MO_243
property indicating the version of the MGED Ontology that the term was deprecated from
MO_299
MO_303
property indicating that the class has providers
property indicating that the class has a compound
MO_302
MO_257
property indicating that the class has a parent organization
MO_314
property indicating that the class has an additive
MO_269
property indicating that the class has units
property indicating that the class has a modified part
MO_241
property indicating that the class has a family relationship
MO_250
MO_307
property indicating that the class has a node
MO_291
property indicating that the class has an experiment design
MO_232
property indicating that the class has a manufacturer
property indicating that the class has a node value
MO_310
MO_262
property indicating that the class has a treatment
MO_265
property indicating that the class was tested for
MO_304
instance property to indicate what the term was replaced by
property indicating that the class has a database
MO_233
property indicating that the class has disease staging
MO_275
property indicating that the class has an experiment design type
MO_288
MO_279
property indicating that the class is user defined
MO_301
property indicating that the class has a diameter
property indicating that the test has a test result
MO_261
property indicating that the class has a feature shape
MO_268
MO_267
property indicating that the class has fiducials
property indicating that the class has individual genetic characteristics
MO_254
property indicating that the class has a prior disease state
MO_276
property indicating that the class has an individual
MO_327
MO_240
property indicating that the class has a database entry type
MO_244
property indicating that the test has a test protocol
MO_273
property indicating that the protocol has a performer or contact person
property indicating that the class has software
MO_284
MO_285
property indicating that the class has an organism part
property indicating that the class has a protocol
MO_300
MO_286
property indicating that the class has hardware
MO_297
property indicating that the class has a maximum measurement
property indicating that the class has a disease state
MO_305
MO_247
property indicating that the class has a clinical record
property indicating that the class has an affiliation to an institution
MO_309
property indicating that the class has a scale
MO_287
property indicating that the class has an image format
MO_234
MO_283
property indicating that the class has a host part
property indicating that the class has a laboratory test
MO_281
property indicating that the class has a property set
MO_266
MO_238
property indicating that the class has bioassays
MO_272
property indicating that the class has biomaterial characteristics
MO_325
property indicating that the class has a measurement
property indicating that the class has a clinical treatment
MO_282
property indicating that the class contains a cubic volume measurement
MO_245
property indicating that the class has an editor
MO_256
MO_251
property indicating that the class has a publication
MO_335
property indicating that the class has an order
MO_296
property indicating that the class has a name
property indicating that the class has an issue
MO_294
property indicating that the class has a first name
MO_258
property indicating that the class has an accession number version
MO_339
MO_289
property indicating that the class has a fax
property indicating that the class has an email address
MO_293
MO_295
property indicating that the class has a publisher
MO_323
property indicating that the class has an identifier
MO_246
property indicating that the class has pages
MO_271
property indicating that the class has a make
property indicating that the class has a model
MO_270
MO_330
property indicating that the contents found at this uri are human readable
property indicating that the class has a phone
MO_235
property indicating that the class has a version
MO_239
property indicating that the class has a year
MO_322
property indicating that the class has a value
MO_326
property indicating that the class has a toll free phone
MO_329
MO_334
property indicating that the class has a description
property indicating that the class has an address
MO_277
property indicating that the class has an accession number
MO_231
MO_308
property indicating that the class has a volume
property indicating that the class has a last name
MO_255
property indicating that the class has text
MO_298
property indicating that the contents found at this uri are machine readable (i.e. in a standard format)
MO_336
property indicating that the class has a middle initials
MO_237
property indicating that the class has a title
MO_337
MO_318
property indicating that the class has authors
property indicating that the class is a solvent
MO_332
property indicating that the class has an owner
MO_278
MO_342
property indicating that the class has a donor
MO_341
property indicating that the class has been treated
property indicating that the class has a URI
MO_340
property indicating that the class has a biosource type
MO_315
property indicating that the class has an individual time point
MO_292
Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss.
MO_963
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.
MO_1012
MO_767
The point at which the egg(s) is laid by an organism.
A chamber in which the hybridization is performed which maintains constant conditions.
MO_563
nanoliter unit of volume
MO_754
MO_650
The concentration range of the organism.
MO_905
picoliter, volume unit
MO_696
An instrument designed to remove excess liquid by vacuum and heating.
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.
MO_756
MO_527
An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared.
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.
MO_902
MO_469
Version of the MGED Ontology.
MO_581
deleted_term
1.3.1.1
sequence from the mitochondrial genome
a measurement where the value is independent of other measurements
MO_741
d
24 hours, time unit
MO_513
MO_614
Kelvin, unit of temperature
MO_825
gram, unit of mass
deleted_term
MO_463
sequence from the region between genes
1.2.0
MO_965
The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product.
MO_1028
A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement.
MO_674
The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.)
MO_976
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.
MO_627
A publication type which has an ISBN.
MO_498
The atmospheric conditions used to culture or grow an organism.
An operon identification experiment type is designed to identify locations and members of operons in a genome.
MO_772
MO_694
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.
MO_669
The perimeter of the spotted DNA on the slide is irregular.
An experiment in which the array platform is compared, e.g. Agilent versus
Affy.
MO_899
A delivery method for compound or drug whereby the substance is administered via the peritoneum.
MO_473
Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle.
MO_358
The value of the property indicates a replacement term since the term was split.
MO_1017
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.
MO_417
MO_984
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.
Time stated in terms of the day, month, and year.
MO_587
MO_865
uri for FlyBase developmental stage terms
http://cvs.sourceforge.net/viewcvs.py/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.ontology?content-type=text/plain&rev=1.1
MO_561
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.
Depriving an organism of food or nutrients
MO_370
sample which has been removed prior to the death of an organism
MO_705
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.
MO_1015
MO_629
An integer > 0.
MO_952
A replicate that consists of independent biological replicates made from different individual BioSources.
MO_740
Micromole per liter or micromolar, concentration unit
MO_516
Sequence features derived by both computational and experimental methods.
MO_547
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.
Database resource for universal identifiers for laboratory and other clinical observations
MO_731
http://www.loinc.org/download
MO_797
a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM
MO_573
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.
MO_518
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.
The process of incubating one or more labeled extracts with an array.
MO_884
MO_542
The values are unordered and have no scale.
MO_430
A article published in a print or online journal having an ISSN.
Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone.
MO_708
Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds.
http://chem.sis.nlm.nih.gov/chemidplus
MO_426
MO_847
Software upon which other software runs.
A translational bias is an experiment design which characterizes the association of transcripts and translation machinery.
MO_939
MO_918
Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n).
MO_641
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.
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
MO_462
MO_544
A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied
A RNA stability experiment design type examines the stability and/or decay of RNA transcripts.
MO_553
MO_926
microliter, unit of volume
The value of the property indicates what version of the ontology the term was deprecated from.
1.1.7
1.1.9
1.3.1.1
1.3.0
1.1.8
1.2.0
MO_1014
MO_500
Unit for a simple count of things
Person who contributed to the study.
MO_769
MO_991
A publication type which is available online and which is not an online journal article, e.g. a web site or service.
deleted_term
1.2.0
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.
MO_531
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.
MO_499
MO_451
A record which describes and identifies an amino acid sequence which has been curated
MO_726
An injury experiment design type is where the response of an organism(s) to injury or damage is studied.
The values are a sequence of one or more characters.
MO_352
The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination.
MO_489
MO_929
The process of generating an image from the array.
A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites.
MO_436
liter, unit of volume
MO_444
MO_796
nanogram, a mass unit
MO_631
Unit of time corresponding to approx. one cycle of the moon's phases.
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.
MO_401
MO_365
An experiment which has a peer reviewed publication attached.
MO_379
The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.
http://arabidopsis.info/catalogue.html
MO_819
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28076
a controlled vocabulary of tumor grading terms
MO_856
Experiment design type in which genomic content is studied using an array based assay.
array_CGH
array CGH
CGH
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
MO_832
thermocycler
MO_716
Hardware for measuring light at different wavelengths.
a controlled vocabulary for compounds
MO_376
http://nciterm.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C1908
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.
MO_345
MO_949
milligram, mass unit
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.
MO_994
A descriptor for FactorValue where GeneticVariation is compared.
1.1.8
deleted_term
MO_557
A record which identifies a nucleic acid sequence feature(s) and which has been curated.
MO_644
MO_757
A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank
Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc.
http://www.cabri.org/HyperCat/cells/all.htm
MO_536
MO_626
An instrument designed to mechanically wash or stain arrays.
http://tumor.informatics.jax.org
MO_942
Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors.
An instrument which controls hybridization conditions, into which a hybridization chamber may fit.
MO_497
the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData
MO_458
An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes.
MO_937
http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12596
a controlled vocabulary of targeted cell types
MO_351
MO_564
The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.
MO_484
SubstrateType of unknown type.
MO_403
milliliter per kilogram
MO_384
A descriptor for a clinical treatment for a patient.
http://www.cabri.org/HyperCat/yeast/all_A.htm
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.
MO_1010
MO_967
http://portal.bioengineering.elyt.ods.org/ontology/
Ontology describing anatomical and physiological relationships.
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.
MO_861
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).
MO_642
micromoles, quantity unit
MO_752
the term has been decomposed into more specific terms
MO_1027
MO_809
A structured controlled vocabulary for the anatomy of Arabidopsis.
http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/Arabidopsis/Attic/arabidopsis_anatomy.ontology
Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH.
http://www.nlm.nih.gov/research/umls/
MO_947
MO_375
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.
Delivery method for a compound or drug where the substance is administered via an injection into the muscle.
MO_617
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.
MO_364
Sequence feature whose derivation is unknown.
MO_525
intersex
MO_356
an organism with both male and female sexual organs in one individual
synonym: intersex
http://www.cbil.upenn.edu/anatomy.php3
a controlled vocabulary provided by CBIL
MO_886
deleted_term
1.3.1.1
MO_361
DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input
A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species.
MO_395
MO_658
kg/m2
The mass of an object in kilograms divided by the surface area in meters squared. Also known as the Body Mass Index (when applied to a person) which is a measure of leaness/obesity. Exact synonym:kg/m2
potential of hydrogen
MO_814
The rating of containment system used to protect organisms from infectious agents.
MO_511
MO_575
A sex experiment design type assays differences associated with an organism's sex, gender or mating type.
The action of changing the relative humidity, e.g. from 1% to 10%.
MO_917
an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins
MO_889
MO_449
A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA.
MO_950
The brother of one's father or mother.
MO_482
A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy.
MO_691
A record which describes and identifies an image, e.g. an image from the mouse atlas
MO_538
a record which identifies and describes the function of a gene product, e.g. E.C. record
The value of the property indicates the replacement term.
MO_1018
1.2.0
deleted_term
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.
MO_551
MO_717
mating type indicating the presence of F plasmid in a bacterial cell
http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo
MO_1022
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
MO_622
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.
1.3.0
The organism (or organism part) has been exposed to a virus or pathogen.
MO_559
The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism.
infect
MO_440
Version of the MGEDOntology.
replaced_term
The term name was changed to one more appropriate to the intent of the definition.
MO_1026
MO_616
MO_803
sequence of a processed transcript capable of directing protein synthesis
deleted_term
1.2.0
MO_492
The array is made on a nylon membrane.
An irregularity in the number of chromosomes, usually in the form of a gain of genetic material.
MO_1002
MO_723
A female having the same genetic parents as another, or one genetic parent in common with another.
An experiment done in a test tube or a culture dish, e.g.
A bacterial invasion assay in an established cell culture.
MO_347
percent weight per volume, concentration unit
MO_420
MO_893
person who checks the consistency of the data and MAGE-ML file
TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly.
MO_996
An experimentally defined sequence feature.
MO_452
A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency.
MO_431
MO_894
The BioSample at any stage other than immediately before labeling.
MO_864
An integer < 0.
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C7057
MO_790
a controlled vocabulary for disease states
The action of stabilizing an organism prior to treatment
MO_776
MO_679
RNA obtained from the nucleus.
MO_897
The shape of the feature on the array is rectangular.
micrometer, unit of distance
MO_421
time point that indicates the start of some developmental stage
MO_608
MO_394
Describes a cell, nucleus or organism with three or more copies of each chromosome.
Mating type of S.pombe.
MO_407
The values presented are logarithm, base e.
MO_554
femtomolar, concentration unit
MO_898
MO_859
A descriptor of FactorValue where comparisons of strains or lines are made.
complementary RNA
cRNA
aRNA
amplified RNA
RNA which is generated by chemical or enzymatic (non cellular) means. E.g. T7 promotor generated RNA.
Non-exact synonym:
cRNA, complementary RNA
aRNA, amplified RNA
MO_543
MO_476
An instrument capable of applying centrifugal force to tubes or microtiter plates.
MO_607
The procedure of extracting nucleic acid from the biomaterial.
a controlled vocabulary for strains or lines
MO_397
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16403
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.
MO_938
MO_637
Mating type of S. cerevisiae.
A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list
MO_989
MO_422
http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28108
a controlled vocabulary for disease stages
one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
MO_566
http://obo.sourceforge.net/list.shtml
MO_844
Ontology of human developmental anatomy for Carnegie stages 1-20.
MO_331
A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123.
the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData
MO_445
MO_873
An ordered, finite set of positive integers.
MO_524
Indicates that a dye swap was performed for some or all hybridizations within an experiment
the term has been subsumed into a more general term
MO_1025
An ordered, finite set of nonpositive floats.
MO_1000
A proprietary image data format that is lossless and containing one channel of data.
MO_786
MO_763
Person or organization that manufactured the hardware.
MO_594
Ribonucleic acid.
International unit
UI
MO_1011
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.
MO_855
Mating type of S.pombe.
MO_457
Application of a normalization of type quantile_normalization.
Version of the MGED Ontology.
MO_1034
A design in which a behavior is invoked by a variable controlled by the experimenter - e.g. administration of a drug that effects aggressivity.
MO_958
MO_609
increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification
MO_852
record which describes and identifies clinical information about an organism
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.
MO_798
MO_405
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.
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.
MO_974
MO_534
A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software).
MO_583
disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument.
MO_760
An ordered, finite set of floats.
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.
MO_493
A binding site identification design type investigates protein binding sites on nucleic acids
non-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP
MO_933
chromatin immunoprecipitation
chromatin IP
chromatin_immunoprecipitation
ChIP-chip
MO_615
The material (e.g. straw) that an animal sleeps on
deleted_term
1.1.7
scanning software
MO_1003
Software to control a scanner and manipulate and save images.
Exact synonym: scanning software
Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg.
MO_725
A community effort to provide standard terms for annotating phenotypic data.
http://www.informatics.jax.org/searches/Phat.cgi?id=MP:0000001
MO_704
MO_941
1.1.7
deleted_term
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.
MO_460
ProtocolType of unknown type.
MO_523
protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design
MO_427
33 P, radioactive isotope of phosphorus, used for labeling/detection purposes.
degrees celsius, unit of temperature
MO_980
MO_920
millisecond, time unit
RNA obtained from the cytoplasm.
MO_978
MO_433
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.
A Reporter where no material or buffer was deposited on the array
MO_830
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
MO_773
identifier for a taxon provided by the NCBI taxonomy database
MO_713
The procedure of extracting/taking out a part of a reaction/contents of a container.
MO_969
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
MO_823
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.
MO_853
sequence of part of a gene, which is missing one or both ends
1.3.1.1
deleted_term
Allow time to pass. It's measurement should be a unit of time.
MO_988
http://sig.biostr.wahington.edu/projects/fm/
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.
MO_468
MO_645
DNA from organelles such as the mitochondria or chloroplast.
MO_914
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.
MO_883
Increasing the concentration of solutes in a solution or suspension.
MO_687
a controlled vocabulary of cell types
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=12596
Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma).
MO_389
Application of a normalization of type mean_log_centering.
MO_657
MO_571
The Zone is excluded due to smearing, streaking, or dense background in the Zone.
Water consumed by or enveloping the organism that the biosource is derived from.
MO_380
MO_983
An instrument that mixes by rapid oscillation.
MO_881
Provider of biosequences (clones, oligos etc) for deposition on the array.
MO_888
1.2.0
sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size
deleted_term
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).
MO_1024
A biomaterial obtained as fluid consisting of plasma, blood cells and platelets.
1.1.9
deleted_term
MO_409
A Reporter where only buffer was deposited on the array
MO_505
A descriptor for FactorValue where DiseaseState is compared.
MO_787
1.3.1.1
gene sequence which has been computationally predicted
MO_838
deleted_term
MO_744
a result which can not be interpreted as positive or negative
A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes.
MO_434
A device for controlling temperature by immersion in water.
MO_541
milliliter, volume unit
MO_488
The values presented are logarithm, base 10.
MO_735
MO_948
365 days, time unit
Delivery method whereby a drug or compound is administered under the skin of the organism.
MO_960
The mean and variance values resulting from computationally combining 2 or more sets of bioassay data.
MO_400
microgram, unit of mass
MO_438
A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD
MO_529
MO_1006
http://www.cabri.org/HyperCat/cells/hybrid.htm
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.
MO_665
The female offspring of the patient or individual under study.
MO_971
agar stab, a cell culture inoculated into agar for long term storage
MO_700
Mix through the process of inverting.
split_term
A design in which the innate behavior of the organism is examined, e.g.
path finding in bees.
MO_355
1.1.9
MO_532
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.
Person or organization that manufactured the array.
MO_890
MO_677
Change in temperature.
http://www.informatics.jax.org/mgihome/GXD/AD/
MO_693
database entry from mouse anatomical dictionary for developmental stage term
MO_707
number of molecules, quantity unit
MO_558
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.
MO_739
fluorophore used for labeling/detection purposes
The process of obtaining quantifiable values from the scanned image of the
array. Exact synonyms: image analysis, image quantification
image analysis
image quantification
MO_928
deleted_term
sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes
MO_759
1.2.0
An ordered, finite set of nonnegative floats.
MO_360
MO_804
An ordered, finite set of nonpositive integers.
The type of protocol used to preserve (including storage or keep in stasis) the biomaterial.
MO_415
centrifuge
The procedure of applying a centrifugal force to a physical object.
Exact synonym: centrifuge
MO_879
deleted_term
MO_621
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.
1.3.1.1
MO_782
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.
place_holder
concrete
abstract
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.
MO_338
An integer less than or equal to zero.
MO_623
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.
MO_750
replaced_term
MO_766
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.
1.1.9
femtoliter, unit of volume
MO_721
MO_968
Conceptual action for specified protocol applied in treatment.
deciliter, unit of volume
MO_624
The procedure of putting a physical object in a container/physical space.
MO_470
MO_779
The process of combining two or more BioMaterials.
Exact synonym: combine
combine
MO_711
The process of removing tissue from a living organism.
MO_826
The values are either TRUE or FALSE, which can be expressed as 1 and 0.
<pre>The time point that a sample was taken. Not to be used where the sample is part of a time
course. SamplingTimePoint is not related to age. An instance could be summer, a date, a time, or a range value</pre>
MO_866
MO_746
Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss.
Emergence of an adult insect from its pupa or cocoon.
MO_876
Polymerase chain reaction. An element generated using this procedure.
MO_915
The process of physically creating the array.
MO_818
MO_582
grams per deciliter, concentration unit
MO_600
mRNA
polyA+_RNA
RNA which has been obtained by selection for polyA tracts.
Exact synonym: polyA+_RNA
Non-exact synonym: mRNA
An action whereby an organism(s) has had genetic material removed, added, or rearranged.
MO_927
soil, growth media for plants and other soil living organisms
MO_821
MO_591
Term used to describe a role or factor value for the person or organization that provides a BioMaterial.
A male having the same genetic parents as another, or one genetic parent in common with another.
MO_655
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.
MO_857
http://www.ebi.ac.uk/chebi
Delivery method where a compound/drug is administered in food or water.
MO_993
MO_548
A descriptor for FactorValue where CellType is compared.
1.1.9
A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement.
MO_1030
MO_494
replaced_term
The possession of a third chromosome of any one type in an otherwise diploid cell.
MO_576
a nucleic acid consisting of a single polynucleotide chain.
MO_359
A SurfaceType of unknown type.
MO_333
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.
MO_604
photoperiod
The length of the light period that a sample is subjected to.
Exact synonym:photoperiod
An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
MO_454
MO_692
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.
milligrams per milliliter, concentration unit
MO_522
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.
MO_512
http://www.item.fraunhofer.de/reni/index/htm
MO_737
database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions
bacterial artificial chromosome
sequence from a bacterial artificial chromosome
exact synonym: bacterial artificial chromosome
MO_985
1.2.0
deleted_term
Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point.
MO_738
MO_411
Computationally derived sequence feature.
MO_562
A descriptor for FactorValue where CellLine is compared.
1.2.0
small nuclear RNA gene
sequence from gene coding for small nuclear RNA
exact synonym: small nuclear RNA gene
MO_961
deleted_term
deleted_term
MO_643
A software variation design type compares different types of software for performance, accuracy, precision and reproducibility.
MO_535
BioSequence of unknown type
MO_597
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.
MO_872
The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify).
MO_515
Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer
MO_911
1.2.0
genomic sequence 5' to a gene where the transcription initiation complex forms.
deleted_term
MO_831
A son of one's son or daughter.
MO_659
Mating type of S. cerevisiae.
A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat.
MO_730
MO_368
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.
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.
MO_613
http://www.opengalen.org/open/crm/crm-anatomy.html
The action of removing one or more organism parts.
MO_374
MO_367
meter, distance unit
Microeinstein per minute and square meter (µE m-2 min-1 or uEinstein m-2 min-1). One einstein is one mole or 6.02x10e23 (avogadro constant) photons. It is commonly used as a unit for photosynthetically active radiation (PAR), however the einstein is not an SI unit. Therefore, microEinsteins per m2 per second is identical to micromoles per m2 per second (SI unit for light irradiance). i.e. (1000 µE m-2 s-1 = 1000 µmol m-2 s-1).
MO_526
The values presented are logarithm, base 2.
MO_647
the action of emergence and separation of offspring from the mother.
MO_710
MO_701
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO)
MO_867
The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
MO_794
deleted_term
1.2.0
sequence from yeast artificial chromosome
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.
MO_828
A descriptor for FactorValue where Sex is compared.
MO_680
MO_913
A record which describes and identifies nucleic acid sequence which has been identified as a gene by a curator. e.g. Flybase gene record
MO_357
The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth.
http://genex.hgu.mrc.ac.uk
The procedure of euthanizing an organism.
MO_602
A biomaterial obtained frozen
MO_610
MO_749
An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes).
A contact who performs data analysis, e.g. statistician.
MO_753
A male parent.
MO_762
Temperature associated with a particular environment.
MO_791
An instrument capable of acquiring images of arrays.
MO_824
MO_682
mating type indicating the absence of F plasmid in a bacterial cell
MO_1016
The value indicates the parent of the term before the term was deprecated.
MO_663
A device for controlling temperature.
MO_742
The array is made on a glass slide.
MO_648
millimeter, unit of distance
centimeter, a unit of distance
MO_837
MO_386
A float greater than or equal to 0.
complementary DNA
cDNA
MO_966
deleted_term
1.2.0
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
A record which describes and identifies an experimentally derived protein structure e.g. MSD
MO_785
The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data.
MO_946
MO_560
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
MO_795
microsecond, unit of time
one or more DNA or RNA based non cellular infective agent, including bacteriophage
MO_372
A device capable of applying software.
MO_510
MO_432
delivery method whereby a compound or drug is administered via a vein
MO_885
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.
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.
MO_461
MO_520
Contact which provides funding for experiments.
1.2.0
sequence of a single stranded synthesized oligonucleotide
deleted_term
MO_570
MO_385
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).
MO_775
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.
An optimization experiment design type is where different protocols or protocol parameters are compared.
MO_934
MO_423
mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input.
deleted_term
1.3.1.1
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.
MO_1029
A biosource obtained as fecal matter.
deleted_term
1.1.9
MO_636
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.
MO_686
MO_354
The sister of one's father or mother.
MO_992
http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology?rev=1.1&view=markup
This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28).
replaced_term
1.1.7
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.
MO_539
MO_812
degrees Fahrenheit, unit of temperature
MO_931
Application of a normalization of type median_log_centering.
mage
ontology
MO_343
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.
MO_862
nanometer distance unit
A loop experiment design is where labeled extracts are compared in consecutive pairs.
synonym: circular design
circular design
MO_912
An operator variation experiment design type assesses the operator performance and relation to data consistency and quality.
MO_519
MO_599
high molecular weight DNA
MO_903
cell lysate, a collection of cells whose membranes have been disrupted
MO_887
Groups of assays that are related as part of a time series.
MO_448
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.
MO_907
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.
MO_474
percent weight per weight, concentration unit
A daughter of one's son or daughter.
MO_703
MO_764
A cell type comparison design experiment design type compares cells of different type for example different cell lines.
An instrument capable of manufacturing arrays by spotting material.
MO_697
split_term
replaced_term
merged_term
deleted_term
MO_1013
Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term.
MO_580
http://www.nlm.nih.gov/mesh/filelist.html
database entry from MESH, medical subject headings vocabulary resource
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.
MO_638
The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter.
MO_970
MO_720
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.
MO_808
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.
MO_702
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.
1.2.0
deleted_term
1.2.0
deleted_term
sequence of a protein, a linear amino acid polymer
MO_530
deleted_term
Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome.
1.2.0
MO_578
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.
MO_517
MO_829
A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record
kilogram, 1000 grams, unit of mass
MO_846
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.
MO_901
preservation type whereby the seed is maintained in a dormant state
MO_666
a design element group consisting of multiple types
MO_528
deleted_term
false
1.1.7
MO_556
MO_836
Describes a cell, nucleus or an organism with two copies of each chromosome.
deleted_term
MO_381
1.2.0
single stranded oligo used for polymerase chain reaction
A type of solid media commonly used for growing organisms
MO_935
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.
MO_908
Logarithmic transformation of ratio data.
MO_896
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).
MO_590
The procedure of placing one physical object in the same container/physical space as another.
MO_815
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.
MO_987
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.
MO_698
A biomaterial obtained embedded in paraffin (wax).
MO_990
MO_765
a record which describes and identifies a protein structure e.g. PDB
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.
MO_437
MO_393
An action where the temperature is specified.
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.
MO_588
MO_601
A contact's affiliation, e.g. university, research institute or business.
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.
MO_377
MO_816
A descriptor for FactorValue where ClinicalInformation is compared.
MO_748
the process of placing a seed or spore in some media with the intention to invoke germination.
The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding.
MO_453
MO_653
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.
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.
MO_664
sequence from a gene coding for transfer RNA
exact synonym: transfer RNA gene
1.2.0
MO_850
deleted_term
transfer RNA gene
MO_496
multiple of stock solution concentration, concentration unit
A software implementing a Higher Level Analysis protocol of type differential_expresssion.
MO_350
MO_428
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.
MO_755
A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial.
The action of preparing a slide for the microscopical examination of organism parts or cell types.
MO_611
1.2.0
MO_709
sequence spliced out from a transcript
deleted_term
units per week, e.g. the number of units of alcohol consumed over a period of 7 days
MO_388
MO_870
Units of defined biological activity, e.g. cytokine stimulation, per ml.
A reference experiment design type is where all samples are compared to a common reference.
MO_699
MO_419
deleted_term
1.1.7
High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome
sequence that represents the product of an RNA polymerase engaged in transcription
MO_827
1.3.1.1
deleted_term
h
MO_486
60 minutes, time unit
MO_869
katal per liter, catalytic-activity concentration unit
deleted_term
ribosomal RNA gene
1.2.0
sequence from gene coding for ribosomal RNA
exact synonym: ribosomal RNA gene
MO_955
A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance
MO_981
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.
MO_567
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.
MO_736
RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus.
MO_574
A float that is < 0.
MO_728
An instrument which fragments tissues or other biomaterials.
MO_714
fluorophore used for labeling/detection purposes
MO_646
1.2.0
MO_439
sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts
deleted_term
MO_435
A value which is a whole number (e.g. 10).
MO_465
The male offspring of the patient or individual under study.
MO_878
A descriptor for FactorValue where DevelopmentalStage is compared.
image quantification software
image analysis software
MO_633
Software to create MeasuredBioAssayData from images.
Exact Synonym: image analysis software, image quantification software.
MO_975
delivery method for drug or compound whereby the drug is administered via the mouth
MO_1005
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.
http://www.cabri.org/HyperCat/cells/hla.htm
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.
MO_956
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
MO_572
candle power
The array is made on a nitrocellulose filter.
MO_455
MO_834
a cubic centimeter, volume unit
MO_683
Polymer of amino acids.
nanomoles, quantity unit
MO_743
MO_945
Deoxyribonucleic acid.
MO_628
picomolar, concentration unit
grams per liter, concentration unit
MO_805
1.1.9
Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1.
replaced_term
MO_424
MO_995
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.
1.1.7
deleted_term
MO_673
a nonparametric measure of the agreement between two rankings
MO_507
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.
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.
MO_964
Toxicology Data Management System, a database resource for systems, organs, pathology, etc.
http://hazel.niehs.nih.gov/user_spt/pct_terms.htm
MO_718
1.2.0
MO_909
deleted_term
sequence from a P1 artificial chromosome
m
MO_877
60 seconds, unit of time
deleted_term
MO_503
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
1.2.0
number of items or events per day
MO_670
MO_477
An instrument for sonicating biomaterials.
The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data.
MO_671
MO_998
mole, unit of quantity
database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses
http://www.atcc.org/Cultures/Products.cfm
MO_979
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.
MO_848
MO_589
A biomaterial that has been lyophilized or dried by freezing under a vacuum.
A member of a consortium of institutions.
MO_778
A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array.
MO_921
time unit
MO_391
MO_925
A Reporter indicated as being a control of unknown type.
MO_999
organism(s) whose sex is unknown
Storage where the thing stored is stored below 0 degrees celsius.
MO_481
TechnologyType of FeatureGroup where antibodies are spotted directly.
MO_483
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.
MO_443
MO_854
An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR.
Exact Synonym: thermocycler
An element that is an oligonucleotide of at least 50 nucleotides in length.
MO_598
MO_745
The point at which an organism emerges from an egg.
MO_491
the chrome border on an Affymetrix type array which is used as a point of
reference for orientation (fiducial)
MO_625
Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold.
MO_783
the physical act of copulation that occurs during the process of sexual reproduction
synonyms: copulation, insemination
insemination
copulation
Application of a scale adjustment following loess_group_normalization, to render the group variances similar.
MO_521
PCR with multiple bands, or smear, in gel-separated reaction products
MO_620
An instrument that produces DNA sequences.
MO_676
MO_774
A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record
MO_406
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).
MO_1019
A design in which RNA from different cell components is examined.
MO_672
normalization software
Software used to transform the Measured or DerivedBioAssay data e.g. normalization.
Non-exact synonym: normalization software
Software used to cluster the data.
MO_464
MO_784
The jackknife Pearson correlation is the lowest Pearson correlation between two data series where one pair of values in the data series are omitted.
MO_467
A descriptor for FactorValue where age is compared.
A delivery method for compounds/drugs where the compound or drug is freely available.
MO_592
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.
MO_606
Application of a scale adjustment following lowess_group_normalization, to render the group variances similar.
MO_410
MO_502
Software to control an arrayer.
MO_678
A Comparative Mapping Resource for Grains.
http://www.gramene.org/
MO_900
An ordered, finite set of negative integers.
MO_858
dye flip
flip dye
An experiment design type where the label orientations are reversed.
exact synonym: flip dye, dye flip
treatment of a biomaterial with radiation e.g. electromagnetic radiation
MO_770
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.
MO_1007
MO_919
http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/developmental/plant_development/Arabidopsis/temporal.tair?rev=1.21&view=markup
An ontology of stages of growth and development of the model plant Arabidopsis thaliana.
MO_822
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.
32 P, radioactive isotope of phosphorus used for labeling/detection purposes
MO_839
MO_348
counts per minute, unit of light emissions produced by ionizing radiation.
An ordered, finite set of positive floats.
MO_777
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.
MO_789
http://www.iupac.org/publications/pac/2000/205/205olesen.html
MO_593
A resource of vocabularies for describing clinical tests, e.g. blood chemistry.
a record which describes and identifies a compound e.g. drug record part of NCI thesaurus
MO_546
MO_973
An ordered, finite set of nonnegative integers.
milliliters per liter, concentration unit
MO_801
MO_533
transcription_profiling
gene expression
expression_profiling
gene_expression
transcription profiling
A transcript identification design type characterizes the length and
position of transcripts and allows identification of all forms of
transcripts in the genome.
expression profiling
MO_916
percentage volume per volume, concentration unit
MO_568
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.
MO_398
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).
Introduction of genetic material into an organism often in the form of a plasmid.
MO_366
MO_475
Person or organization that manufactured the software.
http://song.sourceforge.net/
The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence.
MO_724
1.2.0
deleted_term
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.
MO_441
MO_932
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).
MO_675
A species experiment design type assays differences between distinct species.
MO_940
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.
MO_944
The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas.
MO_807
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.
MO_399
The fluid and dissolved substances excreted by the kidney.
MO_565
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
chloroplast DNA
MO_586
ctDNA: sequence from the chloroplast
synonym: chloroplast DNA
deleted_term
1.3.1.1
MO_751
The scale is a standard base 10, non logarithmic scale.
MO_891
An ordered, finite set of integers.
MO_681
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.
-
MO_402
the reverse strand
exact synonym: -
MO_639
A descriptor for FactorValue where BioSources are compared.
MO_1008
http://www.cabri.org/HyperCat/bact/all_A.htm
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.
MO_378
A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.
MO_603
The unit of total light output from a light source.
Change in light intensity or wavelength.
MO_549
the number of cells per ml
MO_727
The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
MO_871
MO_936
Mole per liter or molarity, concentration unit
A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34).
MO_860
A record which describes and identifies a paper publication e.g. a medline record
MO_923
The shape of the feature on the array is circular or oval.
MO_459
MO_733
Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment).
picomoles, quantity unit
MO_688
MO_349
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.
MO_661
osmolality per kilogram of water, concentration of the solute per unit of solvent
person who prepares the MAGE-ML file
MO_695
The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil)
MO_545
MO_490
A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.
MO_1001
Portable Network Graphic, a lossless image data format.
MO_605
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.
MO_906
The source DNA for a Feature was not uniformly deposited.
Eberwine procedure
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
MO_997
one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
MO_508
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/
MO_504
curated database containing information on Drosophila genes, alleles etc
MO_734
A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.
MO_418
Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance.
MO_977
attomole, quantity unit
Microeinstein per second and square meter (µE m-2 s-1 or uEinstein m-2 s-1). One einstein is one mole or 6.02x10e23 (Avogadro constant) photons. It is commonly used as a unit for photosynthetically active radiation (PAR), however the einstein is not an SI unit. Therefore, microEinsteins per m2 per second is identical to micromoles per m2 per second (SI unit for light irradiance). i.e. (1000 µE m-2 s-1 = 1000 µmol m-2 s-1).
MO_584
http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype
MO_660
The Arabidopsis Information Resource.
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.
MO_596
MO_874
An analysis aimed at identifying differentially expressed genes in two or more conditions.
femtomole, unit of quantity
MO_689
MO_959
The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).
An ordered, finite set of booleans.
MO_712
the organism part in which the tumor originated
MO_408
Unit of brightness or luminance.
MO_813
MO_924
The mother of one's father or mother.
MO_922
The loss of a segment of the genetic material from a chromosome.
The father of one's father or mother.
MO_478
MO_466
The procedure in which solid material is dispensed or dissolved in a liquid.
biomaterial removed after the death of the organism
MO_416
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.
MO_472
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.
MO_771
MO_540
deleted_term
1.1.7
true
deleted_term
MO_412
Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences.
1.2.0
MO_880
Mix through the use of a vortexer.
MO_868
Hardware for automated liquid transfer and handling.
change environment
change growth condition
Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial.
Non exact synonym: change growth condition, change environment
MO_383
MO_662
A record which describes and identifies the relationship between species and is
computationally determined and based on sequences e.g. Treebase record
The BioSample immediately before labeling.
MO_895
Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.
MO_684
http://www.sanbi.ac.za/evoc/ontologies.html
MO_747
a surface coating type for immobilization with the compound aminosilane
A descriptor used in cancer biology to describe abnormalities of tumor cells.
MO_843
MO_842
7 days, unit of time
MO_509
milimolar, concentration unit
MO_943
the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData
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.
MO_810
glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen
MO_833
MO_761
Software used to control automated liquid handler.
Computed as the ordinary Pearson correlation coefficient between two groups of rankings.
MO_552
MO_373
Total cellular and nuclear RNA.
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.
deleted_term
1.2.0
MO_413
A float > 0.
MO_501
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out
MO_447
MO_425
the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData
MO_654
ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2002
Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.
Person who is the primary contact for data submitted to a database.
MO_882
MO_986
A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes.
MO_612
One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms.
MO_690
a controlled vocabulary of organism parts
http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C13007
MO_404
http://cvs.sourceforge.net/views.py/obo/obo/ontology/anatomy/cell_type/cell.ontology?rev=HEAD&content-type=text/vnd.viewcvs-markup
database of cell ontology terms
MO_793
a compound used for labeling/detection purposes
1.1.7
A description logic namespace that contains controlled terminology used at NCI.
split_term
MO_630
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16632
a controlled vocabulary for geographic locations
http://nciterms.nci.nih.gov
MO_456
MO_811
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).
semisolid media type
MO_635
An ordered, finite set of strings.
MO_800
MO_957
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.
deleted_term
BioSequence generated by means of polymerase chain reaction
MO_450
1.2.0
MO_346
A record which describes and identifies a microarray experiment e.g. GEO
sequence which represents regions of a transcript that are joined to another exon during splicing
deleted_term
MO_619
1.2.0
MO_640
single stranded oligo used for polymerase chain reaction
1.2.0
deleted_term
MO_656
A float less than or equal to zero.
The procedure of labeling a biosample.
MO_471
+
MO_820
the forward strand
exact synonym: +
The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations.
MO_632
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.
MO_799
MO_863
A descriptor for FactorValue where PhysicalCharacteristics are compared.
MO_634
ExperimentDesignType of unknown type.
MO_982
The process of harvesting cells from culture.
A design that compares samples from live and dead organisms.
MO_841
MO_537
a controlled vocabulary for histology
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C4741
TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.
MO_618
Describes a cell, nucleus or an organism with one copy of each chromosome.
MO_719
MO_577
cDNA
DNA which is generated by chemical or enzymatic (non cellular) means.
non-exact synonym: cDNA
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.
MO_892
An organism part comparison experiment design type compares tissues, regions, organs within or between organisms
MO_953
database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice
MO_972
http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php
MO_904
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
guilt by association
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.
MO_362
MO_446
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.
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.
MO_585
of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes.
MO_506
a record which identifies and describes biological pathways, e.g. a KEGG record
MO_780
MO_930
Hardware for synthesizing oligos.
MO_835
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
sample
An integer >= 0.
MO_390
MO_649
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.
MO_729
A normalization testing experiment design tests different normalization procedures.
A ComplexAction or ProtocolType describing growth of an organism or cell culture.
MO_758
A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.
MO_722
MO_806
the organism part in which additional tumors are identified remote from the primary site
media type, usually some sort of broth
MO_715
MO_392
A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
RNAi
MO_768
the number of plaque forming units per ml
The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)
MO_514
MO_371
Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown.
MO_442
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.
deleted_term
MO_651
single oligo used for polymerase chain reaction direction unspecified
1.2.0
MO_792
The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
MO_849
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.
MO_1009
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.
http://www.cabri.org/HyperCat/fun/all_A.htm
a measurement where the value is dependent on another measurement
MO_396
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
MO_555
MO_845
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.
MO_817
The shape of the feature on the array is square.
MO_685
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.
a surface coating for immobilization with the polypeptide, polylysine
MO_569
The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.
MO_781
Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.
http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml
MO_369
MO_353
milligram per kilogram per day
The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing.
MO_495
MO_429
true or yes
MO_487
A design aimed at identifying genes expressed in biomaterials of interest.
MO_788
the number of colony forming units per ml
1.3.0
replaced_term
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.
MO_706
An ordered, finite set of negative floats.
MO_851
femtogram, unit of mass
MO_732
MO_485
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).
A female parent.
MO_387
MO_910
mark made on slide using a laser which is used as a point of reference for orientation (fiducial)
MO_802
false or no
a double stranded oligonucleotide
deleted_term
1.2.0
MO_344
Decreasing the concentration of solutes in a solution or suspension.
MO_962
MO_550
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.
picogram, mass unit
MO_363
MO_875
units per liter
individual whose sex organs contain only male gametes
MO_652
MO_951
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.
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.
MO_595
MO_667
PCR where no products of any kind appear in gel-separated reaction products.
A function applied to subsets of values from the same Measured/Derived bioassay data set.
MO_668
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.
MO_414
MO_954
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).
Mix by drawing up and down with a pipette.
MO_479
MO_480
Generation of a DNA strand from an RNA strand using reverse transcriptase.
MO_579
The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.
the array is made on silicon
MO_382
MO_840
The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data.