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.
The value of the property indicates the replacement term.
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.
The value of the property indicates a replacement term since the term was split.
A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123.
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.
The value of the property indicates what version of the ontology the term was deprecated from.
Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term.
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.
The value indicates the parent of the term before the term was deprecated.
This property is used to indicate additional terms that have the same meaning as the term that the property is applied to. The terms that have the same meaning as the term that this property is applied to will be the value of the property.
property indicating the version of the MGED Ontology that the term was deprecated from
property indicating that the class has an association to a MAGE description
property indicating that the class has a URI
property indicating that the class has an action
property indicating that the class has an additive
property indicating that the class has an affiliation to an institution
property indicating that the class has an atmospheric component
property indicating that the class has been treated
property indicating that the class has bioassaydata
property indicating that the class has bioassays
property indicating that the class has biomaterial characteristics
property indicating that the class has a biosource type
property indicating that the class has a cancer site
property indicating that the class has a category
property indicating that the class has a chromosomal aberration classification
property indicating that the class has a citation
property indicating that the class has a clinical finding
property indicating that the class has a clinical record
property indicating that the class has a clinical treatment
property indicating that the class has a compound
property indicating that the class contains a cubic volume measurement
property indicating that the class has a database
property indicating that the class has a database entry type
property indicating that the class has a diameter
property indicating the location of the disease.
property indicating that the class has disease staging
property indicating that the class has a disease state
property indicating that the class has a donor
property indicating that the class has an experiment design
property indicating that the class has an experiment design type
property indicating that the class has experiment factors
property indicating that the class has a factor value
property indicating that the class has an ontology entry
property indicating that the class has a family member
property indicating that the class has a family relationship
property indicating that the class has a feature shape
property indicating that the class has fiducials
property indicating that the class has hardware
property indicating that the class has a height
property indicating that the class has a host
property indicating that the class has a host part
property indicating that the class has an image format
property indicating that the class has an individual
property indicating that the class has individual genetic characteristics
property indicating that the class has an individual time point
property indicating that the class has a laboratory test
property indicating that the class has a manufacturer
property indicating that the class has a mass
property indicating that the class has a maximum measurement
property indicating that the class has a measurement
property indicating that the class has a measurement type
property indicating that the class has a node value
property indicating that the class has a node value type
property indicating that the class has a node
property indicating that the class has a nutrient component
property indicating that the class has an organism part
property indicating that the class has an owner
property indicating that the class has a parent organization
property indicating that the class has a modified part
property indicating that the protocol has a performer or contact person
property indicating that the class has a prior disease state
property indicating that the class has a property set
property indicating that the class has a protocol
property indicating that the class has providers
property to indicate the reason for deprecating a term
property indicating the class has a result
property indicating that the class has a scale
property indicating that the class has software
property indicating that the class has species
property indicating that the test has a test protocol
property indicating that the test has a test result
property indicating that the class has a clinical test
property indicating that the class has a treatment
property indicating that the class has a type
property indicating that the class has units
property indicating that the class is user defined
instance property to indicate what the term was replaced by
property indicating that the class was tested for
property indicating that the class has an identifier
property indicating that the class has an accession number
property indicating that the class has an accession number version
property indicating that the class has an address
property indicating that the class has authors
property indicating that the class has a description
property indicating that the class has an editor
property indicating that the class has an email address
property indicating that the class has a fax
property indicating that the class has a first name
property indicating that the contents found at this uri are human readable
property indicating that the class has an issue
property indicating that the class has a last name
property indicating that the contents found at this uri are machine readable (i.e. in a standard format)
property indicating that the class has a make
property indicating that the class has a middle initials
property indicating that the class has a model
property indicating that the class has a name
property indicating that the class has an order
property indicating that the class has pages
property indicating that the class has a phone
property indicating that the class has a publication
property indicating that the class has a publisher
property indicating that the class has text
property indicating that the class has a title
property indicating that the class has a toll free phone
property indicating that the class has a value
property indicating that the class has a version
property indicating that the class has a volume
property indicating that the class has a year
property indicating that the class is a solvent
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).
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.
MAGE package that describes the array layout and design. The array may be physical or virtual.
An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays.
MAGE package for describing the process by which arrays were manufactured.
The atmospheric conditions used to culture or grow an organism.
An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add
MAGE package for contacts including organizations and people.
Rating of containment system for the protection of organisms from infectious agents.
Refers to the bedding material present in an animals housing.
A bibliographic reference is a published citation in a journal, book, other format e.g. web resource
A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays.
BioAssayData refers to the data files including images generated from one or more BioAssays.
A grouping of bioassay data that has been organized by one or more mathematical functions into nodes.
Description of the processing state of the biomaterial for use in the microarray hybridization.
General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue.
Properties of the biomaterial before treated in any manner for the purposes of the experiment.
Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.
A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells.
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.
Used to tell when the BioSample is an extract or not.
A representation of a DNA, RNA, or protein sequence.
MAGE package for biological sequences (biosequence).
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).
The BioSource is the original source material before any treatment events.
The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial.
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.
Factors that relate to properties of the biomaterial, its treatment, or its growth.
A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined.
Physical properties of the BioMaterial e. g. mass or height
class to hold instances used as the filler for the property has_cancer_site
The identifier for the established culture of a metazoan cell if one was used as a biomaterial.
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.
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).
A resource for terms to describe cellular components, e.g. GO Cellular Component ontology.
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.
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.
The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.
The current clinical treatment(s) of the patient from which the biosource is derived.
Database of clinical treatment information
Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification.
A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
Units used for concentration measurements.
Concentration units not specified in MAGE.
Organizations or individuals that may be contacted.
Controlled terms for descriptors for the type of control design element.
a plant variety obtained in agriculture in horticulture
The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays.
Primitive data types found in computing languages such as float, boolean, etc.
Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.
Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD).
Defects associated with features or zones such as those that are missing or moved.
Method used to deliver a compound for treatment.
Class to hold deprecated instances and classes.
class to hold instances used as the filler for the property has_reason_for_deprecation
A BioAssay that is created by the transformation of measured or derived BioAssays.
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.
MAGE package for description of annotations and references to annotations.
Design elements are reporters, features, and composite elements as defined by MAGE.
A DesignElementGroup holds information on Features, Reporters, or CompositeSequences.
Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence.
The MAGE package for describing the elements located on the array.
The developmental stage of the organism's life cycle during which the biomaterial was extracted.
Database of developmental stage information.
The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
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.
a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth.
A description of the conditions the organism has been exposed to that are not one of the variables under study.
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
An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history.
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.
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.
The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc.
The descriptions associated with the Experiment package of MAGE
The factors in the study that are experimental parameters or regarded as influencing the experimental results.
A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML.
All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment.
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.
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.
Controlled terms for descriptors of failures (as in PCR) associated with reporters.
Relevant aspects of genetic preconditions or family member's clinical history.
A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother.
A technical manufacturer described defect for features.
Technology-based grouping of features representing individual locations on the array.
The expected shape of the feature on the array.
A marking on the surface of the array that can be used to identify the origin of the array.
A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark.
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.
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.
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.
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.
A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference.
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.
The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed.
Controlled terms for descriptors of types of hardware.
The effects of different hardware, types of hardware, or models of hardware on experimental results are studied.
A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging).
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).
Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells).
The humidity that the biosource is exposed to.
Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.)
Identifier or name of the individual organism from which the biomaterial was derived.
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.
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
The point from which measurements of age were taken.
Compounds that are used for labeling extracts.
The BioSample after labeling for detection of the nucleic acids.
The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
Units for measuring the intensity of light.
An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents.
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
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.
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.
class to hold instances used as the filler for the property has_measurement_type
The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) .
A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop.
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.
A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes.
Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm.
Controlled set of terms for describing the type of values (e.g., Euclidean distance).
NormalizationDescription provides details of the normalization strategy for the experiment.
Controlled descriptors for the normalization strategy used for the experiment.
The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
Observation will record the macroscopic examination of the biomaterial.
Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations.
External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology.
The effects of different investigators, laboratories, or organizations on experimental results are studied.
The genus and species (and subspecies) of the organism from which the biomaterial is derived from.
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).
The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
The organization (e.g. company, hospital) to contact to obtain or purchase something.
Other units are those types not specified in MAGE such as lumens, radioactivity, etc.
A parameter is a variable within a protocol.
Tests and results for pathogens infecting organism from which the biosource is derived
The individual to contact regarding something provided such as a biomaterial.
A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification
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.
A physical bioassay is the combination of arrays and biomaterials as in a hybridization.
A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC.
The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.
Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence.
The concentration range of the organism.
Method and type of preserving the organism or biosource (i.e. keeping it in stasis).
The type of method used to preserve (keep in stasis) the organism or biosource.
Documentation of the set of steps taken in a procedure.
Descriptors for protocol parameter types, e.g. compound concentration, media type.
A controlled set of terms to provide a descriptor for the type of protocol.
The effects of different protocols or changes in protocols on experimental results are studied.
Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.).
QualityControlDescription provides details of the quality control aspects of the experiment.
Controlled descriptors for the quality control strategy for an experiment.
The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix.
The MAGE package for defining classes for quantitation.
Units for measuring decay of a radioactive isotope over time.
ReplicateDescription provides details about the type of replication used in the experiment.
Controlled descriptors for the type of replication.
Description of the material placed on a feature (spot).
class to hold instances used as the filler for the property has_result
Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider.
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.
The scale (linear, log10, ln, etc) used to represent the value.
Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.)
Descriptors of biosequence based on the Sequence Ontology (SO) project.
Database for sequence annotation information.
An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods
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.
Controlled terms that provide descriptors for the type of software.
The effects of different software, software packages, or software versions on experimental results are studied.
The organism has had non-genetic parts removed, added, or rearranged.
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.
Database of strain, line, cultivar or ecotype information.
A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse
Controlled terms for descriptors of types of array substrates.
Controlled terms for descriptors for coating of the substrate.
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.
Database of targeted cell type information.
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.
The technology type or platform of the reporters on the array.
The temperature that a biosource is exposed to.
Units used for temperature measurements.
An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry.
TestResult is the recorded value of the test outcome.
Descriptor of the Test performed e.g. Leukocyte count
Database of codes for clinical findings.
A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron.
The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data.
A treatment is the process or action by which a biomaterial is created from an input biomaterial.
A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus.
User is a way to id a person in a database
Controlled terms for descriptors of the warnings associated with reporters.
Water consumed by or enveloping the organism that the biosource is derived from.
A technical manufactured described defect for zones.
Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer
database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses
This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28).
A proprietary image data format that is lossless and containing one channel of data.
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.
sequence from a bacterial artificial chromosome exact synonym: bacterial artificial chromosome
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.
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.
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.
Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc.
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.
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.
a controlled vocabulary provided by CBIL
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.
Ontology describing anatomical and physiological relationships.
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.
Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds.
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).
fluorophore used for labeling/detection purposes
An instrument that produces DNA sequences.
The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth.
Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences.
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).
mating type indicating the presence of F plasmid in a bacterial cell
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.
mating type indicating the absence of F plasmid in a bacterial cell
uri for FlyBase developmental stage terms
curated database containing information on Drosophila genes, alleles etc
Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss.
A Comparative Mapping Resource for Grains.
The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
Ontology of human developmental anatomy for Carnegie stages 1-20.
High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome
Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.
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.
A resource of vocabularies for describing clinical tests, e.g. blood chemistry.
Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.
Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss.
Database resource for universal identifiers for laboratory and other clinical observations
Mole per liter or molarity, concentration unit
database entry from mouse anatomical dictionary for developmental stage term
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.
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.
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.
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.
database entry from MESH, medical subject headings vocabulary resource
Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors.
A community effort to provide standard terms for annotating phenotypic data.
The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.
identifier for a taxon provided by the NCBI taxonomy database
A description logic namespace that contains controlled terminology used at NCI.
a controlled vocabulary for disease stages
a controlled vocabulary for disease states
a controlled vocabulary for geographic locations
a controlled vocabulary of organism parts
a controlled vocabulary for strains or lines
a controlled vocabulary of targeted cell types
a controlled vocabulary of tumor grading terms
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.
sequence from a P1 artificial chromosome
Polymerase chain reaction. An element generated using this procedure.
BioSequence generated by means of polymerase chain reaction
Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle.
PCR where no products of any kind appear in gel-separated reaction products.
single oligo used for polymerase chain reaction direction unspecified
single stranded oligo used for polymerase chain reaction
PCR with multiple bands, or smear, in gel-separated reaction products
Portable Network Graphic, a lossless image data format.
database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice
The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations.
Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg.
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.
A RNA stability experiment design type examines the stability and/or decay of RNA transcripts.
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.
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.
The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence.
Computed as the ordinary Pearson correlation coefficient between two groups of rankings.
A structured controlled vocabulary for the anatomy of Arabidopsis.
An ontology of stages of growth and development of the model plant Arabidopsis thaliana.
Toxicology Data Management System, a database resource for systems, organs, pathology, etc.
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.
Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH.
units per week, e.g. the number of units of alcohol consumed over a period of 7 days
database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions
sequence from yeast artificial chromosome
32 P, radioactive isotope of phosphorus used for labeling/detection purposes
33 P, radioactive isotope of phosphorus, used for labeling/detection purposes.
a measurement where the value is independent of other measurements
The action of stabilizing an organism prior to treatment
The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data.
The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data.
The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data.
The mean and variance values resulting from computationally combining 2 or more sets of bioassay data.
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.
Units of defined biological activity, e.g. cytokine stimulation, per ml.
A delivery method for compounds/drugs where the compound or drug is freely available.
The procedure of placing one physical object in the same container/physical space as another.
A type of solid media commonly used for growing organisms
agar stab, a cell culture inoculated into agar for long term storage
A descriptor for FactorValue where age is compared.
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.
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.
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.
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.
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.
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.
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.
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.
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.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record
a surface coating type for immobilization with the compound aminosilane
Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n).
glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen
Person or organization that manufactured the array.
The process of physically creating the array.
An experiment in which the array platform is compared, e.g. Agilent versus Affy.
An instrument capable of acquiring images of arrays.
An instrument capable of manufacturing arrays by spotting material.
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.
The rating of containment system used to protect organisms from infectious agents.
The material (e.g. straw) that an animal sleeps on
time point that indicates the start of some developmental stage
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.
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.
The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.)
A record which describes and identifies a paper publication e.g. a medline record
A binding site identification design type investigates protein binding sites on nucleic acids non-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP
Software used to transform the Measured or DerivedBioAssay data e.g. normalization. Non-exact synonym: normalization software
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.
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 replicate that consists of independent biological replicates made from different individual BioSources.
A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list
Term used to describe a role or factor value for the person or organization that provides a BioMaterial.
The process of removing tissue from a living organism.
Provider of biosequences (clones, oligos etc) for deposition on the array.
a compound used for labeling/detection purposes
the action of emergence and separation of offspring from the mother.
A biomaterial obtained as fluid consisting of plasma, blood cells and platelets.
The values are either TRUE or FALSE, which can be expressed as 1 and 0.
A male having the same genetic parents as another, or one genetic parent in common with another.
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
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
One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms.
A design in which RNA from different cell components is examined.
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.
A descriptor for FactorValue where CellLine is compared.
cell lysate, a collection of cells whose membranes have been disrupted
A descriptor for FactorValue where CellType is compared.
A cell type comparison design experiment design type compares cells of different type for example different cell lines.
A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
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.
An instrument capable of applying centrifugal force to tubes or microtiter plates.
the number of colony forming units per ml
Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. Non exact synonym: change growth condition, change environment
The action of changing the relative humidity, e.g. from 1% to 10%.
Change in light intensity or wavelength.
the chrome border on an Affymetrix type array which is used as a point of reference for orientation (fiducial)
The loss of a segment of the genetic material from a chromosome.
An irregularity in the number of chromosomes, usually in the form of a gain of genetic material.
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.
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.
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.
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.
Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome.
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.
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
A descriptor for FactorValue where ClinicalInformation is compared.
record which describes and identifies clinical information about an organism
A descriptor for a clinical treatment for a patient.
Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown.
Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance.
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
the physical act of copulation that occurs during the process of sexual reproduction synonyms: copulation, insemination
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.
Experiment design type in which genomic content is studied using an array based assay.
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.
a record which describes and identifies a compound e.g. drug record part of NCI thesaurus
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Computationally derived sequence feature.
a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM
A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record
a record which describes and identifies a protein structure e.g. PDB
Increasing the concentration of solutes in a solution or suspension.
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.
DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input
mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input.
A member of a consortium of institutions.
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.
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.
A Reporter where only buffer was deposited on the array
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.
A Reporter where no material or buffer was deposited on the array
A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA.
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).
Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone.
A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency.
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.
A Reporter indicated as being a control of unknown type.
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.
sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size
counts per minute, unit of light emissions produced by ionizing radiation.
ctDNA: sequence from the chloroplast synonym: chloroplast DNA
A record which describes and identifies an amino acid sequence which has been curated
A record which describes and identifies nucleic acid sequence which has been identified as a gene by a curator. e.g. Flybase gene record
A record which identifies a nucleic acid sequence feature(s) and which has been curated.
person who checks the consistency of the data and MAGE-ML file
A contact who performs data analysis, e.g. statistician.
Time stated in terms of the day, month, and year.
The female offspring of the patient or individual under study.
Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma).
The term was deleted from the MGED CoreOntology.
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.
A descriptor for FactorValue where DevelopmentalStage is compared.
The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.
An analysis aimed at identifying differentially expressed genes in two or more conditions.
A software implementing a Higher Level Analysis protocol of type differential_expresssion.
Decreasing the concentration of solutes in a solution or suspension.
Describes a cell, nucleus or an organism with two copies of each chromosome.
A descriptor for FactorValue where DiseaseState is 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.
The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).
The action of removing one or more organism parts.
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 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.
disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument.
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
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.
Indicates that a dye swap was performed for some or all hybridizations within an experiment
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.
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.
Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.
Emergence of an adult insect from its pupa or cocoon.
The point at which the egg(s) is laid by an organism.
protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design
The shape of the feature on the array is circular or oval.
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.
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.
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.
sequence which represents regions of a transcript that are joined to another exon during splicing
Sequence features derived by both computational and experimental methods.
A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial.
An experimentally defined sequence feature.
The BioSample immediately before labeling.
A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied
The process of obtaining quantifiable values from the scanned image of the array. Exact synonyms: image analysis, image quantification
Software to create MeasuredBioAssayData from images. Exact Synonym: image analysis software, image quantification software.
Delivery method where a compound/drug is administered in food or water.
of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes.
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO)
Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold.
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).
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.
A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34).
The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify).
A biomaterial that has been lyophilized or dried by freezing under a vacuum.
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.
A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat.
Storage where the thing stored is stored below 0 degrees celsius.
a record which identifies and describes the function of a gene product, e.g. E.C. record
Contact which provides funding for experiments.
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
sequence of part of a gene, which is missing one or both ends
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.
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.
An action whereby an organism(s) has had genetic material removed, added, or rearranged.
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out
A descriptor for FactorValue where GeneticVariation is compared.
increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
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).
A ComplexAction or ProtocolType describing growth of an organism or cell culture.
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.
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.
Describes a cell, nucleus or an organism with one copy of each chromosome.
Person or organization that manufactured the hardware.
A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.
The process of harvesting cells from culture.
The point at which an organism emerges from an egg.
The Zone is excluded due to smearing, streaking, or dense background in the Zone.
an organism with both male and female sexual organs in one individual synonym: intersex
The action of preparing a slide for the microscopical examination of organism parts or cell types.
An instrument which fragments tissues or other biomaterials.
The process of incubating one or more labeled extracts with an array.
A chamber in which the hybridization is performed which maintains constant conditions.
An instrument which controls hybridization conditions, into which a hybridization chamber may fit.
The process of generating an image from the array.
Software to control a scanner and manipulate and save images. Exact synonym: scanning software
A record which describes and identifies an image, e.g. an image from the mouse atlas
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.
Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment).
The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)
An experiment done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
a result which can not be interpreted as positive or negative
The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product.
A descriptor for FactorValue where BioSources are compared.
A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.
An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared.
The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.
The organism (or organism part) has been exposed to a virus or pathogen.
An injury experiment design type is where the response of an organism(s) to injury or damage is studied.
A design in which the innate behavior of the organism is examined, e.g. path finding in bees.
The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism.
A contact's affiliation, e.g. university, research institute or business.
A value which is a whole number (e.g. 10).
Delivery method for a compound or drug where the substance is administered via an injection into the muscle.
A delivery method for compound or drug whereby the substance is administered via the peritoneum.
delivery method whereby a compound or drug is administered via a vein
treatment of a biomaterial with radiation e.g. electromagnetic radiation
The perimeter of the spotted DNA on the slide is irregular.
The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination.
A design aimed at identifying genes expressed in biomaterials of interest.
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.
The jackknife Pearson correlation is the lowest Pearson correlation between two data series where one pair of values in the data series are omitted.
A article published in a print or online journal having an ISSN.
katal per liter, catalytic-activity concentration unit
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
mark made on slide using a laser which is used as a point of reference for orientation (fiducial)
The length of the light period that a sample is subjected to. Exact synonym:photoperiod
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.
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
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.
The scale is a standard base 10, non logarithmic scale.
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.
Hardware for automated liquid transfer and handling.
Software used to control automated liquid handler.
An ordered, finite set of negative floats.
An ordered, finite set of negative integers.
An ordered, finite set of nonnegative floats.
An ordered, finite set of nonnegative integers.
An ordered, finite set of nonpositive floats.
An ordered, finite set of nonpositive integers.
An ordered, finite set of positive floats.
An ordered, finite set of positive integers.
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.
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.
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.
Application of a scale adjustment following loess_group_normalization, to render the group variances similar.
The values presented are logarithm, base 10.
The values presented are logarithm, base 2.
The values presented are logarithm, base e.
Logarithmic transformation of ratio data.
An element that is an oligonucleotide of at least 50 nucleotides in length.
A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
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.
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.
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.
Application of a scale adjustment following lowess_group_normalization, to render the group variances similar.
The unit of total light output from a light source.
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.
milliliters per liter, concentration unit
osmolality per kilogram of water, concentration of the solute per unit of solvent
sequence of a processed transcript capable of directing protein synthesis
individual whose sex organs contain only male gametes
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.
the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData
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.
the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData
the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData
the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData
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).
Application of a normalization of type mean_log_centering.
A method of normalizing log ratio data by subtraction of the median log ratios computed across all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins).
Application of a normalization of type median_log_centering.
the term has been subsumed into a more general term
the organism part in which additional tumors are identified remote from the primary site
milligrams per milliliter, concentration unit
A record which describes and identifies a microarray experiment e.g. GEO
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).
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).
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.
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.
Mix by drawing up and down with a pipette.
The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas.
a design element group consisting of multiple types
A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites.
an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins
Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1.
Unit of time corresponding to approx. one cycle of the moon's phases.
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.
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.
The array is made on a nitrocellulose filter.
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.
A normalization testing experiment design tests different normalization procedures.
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.
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.
The BioSample at any stage other than immediately before labeling.
The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter.
The source DNA for a Feature was not uniformly deposited.
The procedure of extracting nucleic acid from the biomaterial.
A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank
A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement.
A publication type which is available online and which is not an online journal article, e.g. a web site or service.
A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD
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.
Software upon which other software runs.
An operator variation experiment design type assesses the operator performance and relation to data consistency and quality.
sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes
An operon identification experiment type is designed to identify locations and members of operons in a genome.
An optimization experiment design type is where different protocols or protocol parameters are compared.
delivery method for drug or compound whereby the drug is administered via the mouth
DNA from organelles such as the mitochondria or chloroplast.
RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus.
one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
An organism part comparison experiment design type compares tissues, regions, organs within or between organisms
A design that compares samples from live and dead organisms.
A biomaterial obtained embedded in paraffin (wax).
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.
a record which identifies and describes biological pathways, e.g. a KEGG record
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.
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
An experiment which has a peer reviewed publication attached.
A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.
A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy.
percentage volume per volume, concentration unit
percent weight per volume, concentration unit
percent weight per weight, concentration unit
the number of plaque forming units per ml
A record which describes and identifies the relationship between species and is computationally determined and based on sequences e.g. Treebase record
A descriptor for FactorValue where PhysicalCharacteristics are compared.
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.
The procedure of putting a physical object in a container/physical space.
The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing.
sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts
RNA which has been obtained by selection for polyA tracts. Exact synonym: polyA+_RNA Non-exact synonym: mRNA
a surface coating for immobilization with the polypeptide, polylysine
sequence of a protein, a linear amino acid polymer
Describes a cell, nucleus or organism with three or more copies of each chromosome.
A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement.
The process of combining two or more BioMaterials. Exact synonym: combine
biomaterial removed after the death of the organism
gene sequence which has been computationally predicted
sample which has been removed prior to the death of an organism
The type of protocol used to preserve (including storage or keep in stasis) the biomaterial.
A record which describes and identifies an experimentally derived protein structure e.g. MSD
the organism part in which the tumor originated
genomic sequence 5' to a gene where the transcription initiation complex forms.
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).
A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance
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.
Application of a normalization of type quantile_normalization.
sequence from gene coding for ribosomal RNA exact synonym: ribosomal RNA gene
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.
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.
A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes.
The shape of the feature on the array is rectangular.
A reference experiment design type is where all samples are compared to a common reference.
a measurement where the value is dependent on another measurement
The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding.
The procedure of extracting/taking out a part of a reaction/contents of a container.
The term name was changed to one more appropriate to the intent of the definition.
A transformation method in which replicate intensity or ratio data sets are combined. Analysis of the mean and standard deviation values for replicate data points can be used to identify and potentially exclude low quality data.
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.
The procedure in which solid material is dispensed or dissolved in a liquid.
Generation of a DNA strand from an RNA strand using reverse transcriptase.
A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes.
The procedure of euthanizing an organism.
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
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.
preservation type whereby the seed is maintained in a dormant state
A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.
An action where the temperature is specified.
A descriptor for FactorValue where Sex is compared.
A sex experiment design type assays differences associated with an organism's sex, gender or mating type.
An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes).
A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software).
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.
a nucleic acid consisting of a single polynucleotide chain.
A female having the same genetic parents as another, or one genetic parent in common with another.
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.
sequence from gene coding for small nuclear RNA exact synonym: small nuclear RNA gene
Person or organization that manufactured the software.
A software variation design type compares different types of software for performance, accuracy, precision and reproducibility.
soil, growth media for plants and other soil living organisms
The male offspring of the patient or individual under study.
An instrument for sonicating biomaterials.
the process of placing a seed or spore in some media with the intention to invoke germination.
A species experiment design type assays differences between distinct species.
A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species.
Conceptual action for specified protocol applied in treatment.
Hardware for measuring light at different wavelengths.
An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes.
The procedure of applying a centrifugal force to a physical object. Exact synonym: centrifuge
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
the term has been decomposed into more specific terms
TechnologyType of FeatureGroup where antibodies are spotted directly.
TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.
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.
TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly.
A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array.
The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.
The shape of the feature on the array is square.
sequence of a single stranded synthesized oligonucleotide
Depriving an organism of food or nutrients
A design in which a behavior is invoked by a variable controlled by the experimenter - e.g. administration of a drug that effects aggressivity.
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.
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.
A descriptor of FactorValue where comparisons of strains or lines are made.
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
The values are a sequence of one or more characters.
Delivery method whereby a drug or compound is administered under the skin of the organism.
Person who is the primary contact for data submitted to a database.
DNA which is generated by chemical or enzymatic (non cellular) means. non-exact synonym: cDNA
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
sequence from a gene coding for transfer RNA exact synonym: transfer RNA gene
a nonparametric measure of the agreement between two rankings
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.
Temperature associated with a particular environment.
An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR. Exact Synonym: thermocycler
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.
Groups of assays that are related as part of a time series.
Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point.
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.
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.
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.
sequence that represents the product of an RNA polymerase engaged in transcription
A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome.
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.
Introduction of genetic material into an organism often in the form of a plasmid.
A translational bias is an experiment design which characterizes the association of transcripts and translation machinery.
The possession of a third chromosome of any one type in an otherwise diploid cell.
A descriptor used in cancer biology to describe abnormalities of tumor cells.
Micromole per liter or micromolar, concentration unit
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.
Sequence feature whose derivation is unknown.
The values are unordered and have no scale.
The fluid and dissolved substances excreted by the kidney.
An instrument designed to remove excess liquid by vacuum and heating.
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.
one or more DNA or RNA based non cellular infective agent, including bacteriophage
An instrument that mixes by rapid oscillation.
Allow time to pass. It's measurement should be a unit of time.
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.
An instrument designed to mechanically wash or stain arrays.
A device for controlling temperature by immersion in water.
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.
A function applied to subsets of values from the same Measured/Derived bioassay data set.
multiple of stock solution concentration, concentration unit