The MGED Ontology
Chris Stoeckert, Helen Parkinson, Trish Whetzel, Paul Spellman, Catherine A. Ball, Joseph White, John Matese, Liju Fan, Gilberto Fragoso, Mervi Heiskanen, Susanna Sansone, Helen Causton, Laurence Game, Chris Taylor
Concepts, definitions, terms, and resources for standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1
1.3.0.1
May 17, 2006
An ontology for microarray experiments in support of MAGE v.1.
mage
MAGE package for bioassay.
abstract
ontology
The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm).
abstract
abstract
Units of measure.
ontology
ontology
concrete
A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop.
concrete
ontology
Units used for distance measurements.
ontology
abstract
Properties of the biomaterial before treated in any manner for the purposes of the experiment.
concrete
ontology
An irregularity in the number or structure of chromosomes, usually in the form of a gain (duplication), loss (deletion), exchange (translocation), or alteration in sequence (inversion) of genetic material. Excludes simple changes in sequence such as mutations, and is usually detectable by cytogenetic and microscopic techniques such as FISH.
A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse
The expected shape of the feature on the array.
concrete
ontology
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.
abstract
ontology
mage
concrete
The factors in the study that are experimental parameters or regarded as influencing the experimental results.
Mass units not specified in MAGE.
place_holder
ontology
abstract
ontology
Uniform Resource Identifier
Compounds that are used for labeling extracts.
ontology
concrete
Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence.
ontology
concrete
The MAGE package for describing the elements located on the array.
abstract
mage
Defects associated with features or zones such as those that are missing or moved.
ontology
concrete
concrete
The technology type or platform of the reporters on the array.
ontology
A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark.
ontology
concrete
ontology
concrete
The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) .
A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells.
ontology
abstract
concrete
ontology
The purpose(s) for which the array is used within an experiment, e.g. to
assess the transcriptome, the genomic content, or to identify
transcription factor binding sites.
concrete
mage
concrete
A treatment is the process or action by which a biomaterial is created from an input biomaterial.
mage
The individual to contact regarding something provided such as a biomaterial.
concrete
mage
Descriptors of biosequence based on the Sequence Ontology (SO) project.
abstract
ontology
class to hold instances used as the filler for the property has_cancer_site
ontology
concrete
concrete
ontology
Controlled descriptors for the normalization strategy used for the experiment.
abstract
A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus.
ontology
ontology
abstract
The humidity that the biosource is exposed to.
concrete
ontology
Database of strain, line, cultivar or ecotype information.
abstract
mage
The descriptions associated with the Experiment package of MAGE
ontology
concrete
Controlled terms for the state of the BioMaterial. Each state (BioSource, different BioSamples, and LabeledExtract) have MaterialTypes. Examples are population of an organism, organism, organism part, cell, etc.
MAGE package that describes the array layout and design. The array may be physical or virtual.
abstract
mage
An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays.
concrete
mage
ontology
concrete
Database of geographic locations.
concrete
A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother.
ontology
the organism part in which additional tumors are identified remote from the primary site
the organism part in which the tumor originated
ontology
Anatomical location(s) of disease.
concrete
place_holder
The effects of different investigators, laboratories, or organizations on experimental results are studied.
ontology
concrete
Database of phenotype information
ontology
BioAssayData refers to the data files including images generated from one or more BioAssays.
ontology
concrete
Controlled terms for descriptors of the warnings associated with reporters.
concrete
ontology
A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron.
place_holder
ontology
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.
The organism has had non-genetic parts removed, added, or rearranged.
concrete
Database of targeted cell type information.
ontology
The concentration range of the organism.
ontology
abstract
ontology
A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging).
concrete
ontology
Units used for temperature measurements.
concrete
The identifier for the established culture of a metazoan cell if one was used as a biomaterial.
ontology
abstract
Controlled terms for descriptors for the type of control design element.
concrete
ontology
ontology
concrete
The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism
either prior to or during the experiment.
Controlled descriptors for the type of replication.
ontology
concrete
abstract
ontology
Observation will record the macroscopic examination of the biomaterial.
Technology-based grouping of features representing individual locations on the array.
mage
concrete
ontology
A description of the conditions the organism has been exposed to that are not one of the variables under study.
abstract
A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays.
mage
abstract
ontology
An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents.
abstract
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.
ontology
concrete
Relevant aspects of genetic preconditions or family member's clinical history.
abstract
ontology
ontology
The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
abstract
ontology
Units used for concentration measurements.
concrete
mage
abstract
The MAGE package for protocols.
User is a way to id a person in a database
concrete
Database of taxonomic information.
ontology
class to hold instances used as the filler for the property has_result
ontology
concrete
ontology
abstract
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix.
mage
abstract
An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add
concrete
ontology
The current clinical treatment(s) of the patient from which the biosource is derived.
abstract
ontology
ontology
A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
abstract
a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler
abstract
ontology
ontology
class to hold instances used as the filler for the property has_measurement_type
concrete
concrete
A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes.
mage
concrete
mage
Description of the material placed on a feature (spot).
ontology
concrete
All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment.
ontology
Database of codes for clinical findings.
concrete
The BioSource is the original source material before any treatment events.
concrete
mage
Version of the MGED Ontology.
abstract
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.
The term was deleted from the MGED CoreOntology.
Controlled terms for descriptors of types of array substrates.
ontology
concrete
ontology
concrete
The point from which measurements of age were taken.
ontology
The effects of different hardware, types of hardware, or models of hardware on experimental results are studied.
place_holder
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).
concrete
ontology
The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
ontology
concrete
Database for sequence annotation information.
abstract
The effects on results of changing protocols, hardware, software, or people performing the experiments are studied Examples are comparison of data across different labeling protocols, scanners, image quantification software, or laboratories.
ontology
ontology
Concentration units not specified in MAGE.
concrete
ontology
abstract
External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology.
ontology
abstract
QualityControlDescription provides details of the quality control aspects of the experiment.
MAGE package for measurement.
abstract
mage
Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification.
ontology
concrete
ontology
Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations.
concrete
concrete
ontology
A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC.
The BioSource after any treatment.
concrete
mage
class to hold instances used as the filler for the property has_reason_for_deprecation
ontology
concrete
concrete
The form in which the BioMaterial was obtained/maintained e.g. frozen, fresh etc. Note can be used to describe BioSamples as well as BioSources.
ontology
TestResult is the recorded value of the test outcome.
ontology
abstract
Rating of containment system for the protection of organisms from infectious agents.
ontology
abstract
A physical bioassay is the combination of arrays and biomaterials as in a hybridization.
concrete
mage
concrete
Controlled terms for descriptors of failures (as in PCR) associated with reporters.
ontology
General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue.
abstract
ontology
Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells).
concrete
ontology
Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence.
concrete
ontology
Time units not specified in MAGE.
concrete
Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm.
mage
mage
A technical manufactured described defect for zones.
concrete
concrete
A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification
ontology
abstract
MAGE package for describing the process by which arrays were manufactured.
mage
ontology
concrete
The scale (linear, log10, ln, etc) used to represent the value.
concrete
mage
The software application used.
concrete
mage
A parameter is a variable within a protocol.
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.
concrete
ontology
concrete
The complete set of bioassays (hybridizations) and their descriptions performed as an experiment for a common purpose. Here we take experiment to mean an observational or perturbing study. An experiment will be often equivalent to a publication.
mage
ontology
Controlled terms for descriptors of types of hardware.
concrete
concrete
ontology
Database of clinical treatment information
concrete
ontology
The version of the MGED Ontology.
concrete
ontology
Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth.
mage
A grouping of bioassay data that has been organized by one or more mathematical functions into nodes.
concrete
ontology
Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.
abstract
ontology
concrete
Units for measuring the intensity of light.
The developmental stage of the organism's life cycle during which the biomaterial was extracted.
abstract
ontology
Controlled descriptors for the quality control strategy for an experiment.
concrete
ontology
The genetic modification introduced into the organism from which the biomaterial was derived. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection.
concrete
ontology
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.
abstract
ontology
abstract
a plant variety obtained in agriculture in horticulture
ontology
ontology
Primitive data types found in computing languages such as float, boolean, etc.
concrete
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.
abstract
ontology
The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
abstract
ontology
A DesignElementGroup holds information on Features, Reporters, or CompositeSequences.
abstract
mage
ontology
Physical properties of the BioMaterial e. g. mass or height
abstract
The MAGE package for defining classes for quantitation.
mage
abstract
abstract
ontology
NormalizationDescription provides details of the normalization strategy for the experiment.
A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference.
abstract
ontology
The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
abstract
ontology
mage
The machine or instrument used.
concrete
ontology
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.
abstract
concrete
mage
A marking on the surface of the array that can be used to identify the origin of the array.
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.
concrete
A technical manufacturer described defect for features.
mage
ontology
A descriptor of the time point that a sample was taken. Not to be used
where the sample is part of a time course. SamplingTimePoint is not
related to age. An instance could be summer, a date, a time, or a range
value.
abstract
The effects of different protocols or changes in protocols on experimental results are studied.
concrete
Database of cell type information.
ontology
concrete
ontology
An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history.
Distance units not specified in MAGE.
ontology
place_holder
Measured values and units.
a measurement where the value is independent of other measurements
Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial.
Non exact synonym: change growth conditions, change environment
a measurement where the value is dependent on another measurement
concrete
mage
ontology
concrete
Database of cell line information.
place_holder
The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed.
ontology
abstract
Organizations or individuals that may be contacted.
mage
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.
Version of the MGEDOntology.
place_holder
ontology
concrete
Units used for mass measurements.
ontology
A controlled set of terms to provide a descriptor for the type of protocol.
abstract
ontology
concrete
ontology
Database of compound information.
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).
ontology
abstract
abstract
Water consumed by or enveloping the organism that the biosource is derived from.
ontology
place_holder
ontology
Refers to the bedding material present in an animals housing.
Volume units not specified in MAGE.
ontology
place_holder
concrete
Quantity units not specified in MAGE.
ontology
Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD).
concrete
ontology
The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc.
ontology
abstract
ontology
An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods
place_holder
concrete
ontology
Controlled set of terms for describing the type of values (e.g., Euclidean distance).
concrete
ontology
Used to tell when the BioSample is an extract or not.
ontology
abstract
ReplicateDescription provides details about the type of replication used in the experiment.
A representation of a DNA, RNA, or protein sequence.
mage
concrete
Descriptors for protocol parameter types, e.g. compound concentration, media type.
concrete
The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays.
ontology
concrete
ontology
Units used for time measurements.
abstract
MAGE package for description of annotations and references to annotations.
mage
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.
ontology
concrete
Identifier or name of the individual organism from which the biomaterial was derived.
ontology
place_holder
ExperimentDesign refers to both observational and experimental (perturbational) studies. The organizing principles of the study including the relationships between assays and the steps taken to interpret the data.
mage
concrete
abstract
The temperature that a biosource is exposed to.
ontology
MAGE package for contacts including organizations and people.
abstract
mage
concrete
Design elements are reporters, features, and composite elements as defined by MAGE.
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.
abstract
ontology
Database of histology information.
concrete
ontology
Method and type of preserving the organism or biosource (i.e. keeping it in stasis).
concrete
The organization (e.g. company, hospital) to contact to obtain or purchase something.
mage
abstract
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).
ontology
concrete
Units used for volume measurements.
ontology
concrete
ontology
Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider.
Database of disease state information.
ontology
concrete
abstract
mage
Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.
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.
abstract
ontology
Tests and results for pathogens infecting organism from which the biosource is derived
abstract
ontology
a result which can not be interpreted as positive or negative
false or no
true or yes
place_holder
Version of the MGEDOntology.
ontology
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.
MAGE package for BioAssayData.
ontology
concrete
Database of tumor grading information
ontology
Member of the biosource's family.
abstract
ontology
The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.
abstract
Factors that relate to properties of the biomaterial, its treatment, or
its growth.
abstract
ontology
abstract
mage
MAGE package for biological sequences (biosequence).
abstract
ontology
The observable form taken by some character (or group of characters) in an individual or an organism, excluding pathology and disease. The detectable outward manifestations of a specific genotype.
abstract
ontology
Procedures used during treatment.
ontology
Microscopic morphology of tissues.
abstract
The type of method used to preserve (keep in stasis) the organism or biosource.
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
An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry.
abstract
ontology
Controlled terms for descriptors for coating of the substrate.
concrete
ontology
concrete
ontology
Other units are those types not specified in MAGE such as lumens, radioactivity, etc.
ontology
Database of organism part information.
concrete
mage
concrete
A bibliographic reference is a published citation in a journal, book, other format e.g. web resource
ontology
concrete
Controlled terms that provide descriptors for the type of software.
The value of an ExperimentFactor.
concrete
mage
Units for measuring decay of a radioactive isotope over time.
ontology
concrete
A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML.
ontology
abstract
ontology
Class to hold deprecated instances and classes.
concrete
the term has been subsumed into a more general term
The term name was changed to one more appropriate to the intent of the definition.
the term has been decomposed into more specific terms
concrete
Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.)
ontology
concrete
ontology
Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.).
mage
A BioAssay that is created by the transformation of measured or derived BioAssays.
concrete
concrete
ontology
Units used for quantity measurements.
concrete
Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.)
ontology
Descriptions pertaining to the array.
concrete
mage
concrete
BioMolecularAnnotation experiment design types are those which are designed to investigate functions, processes, locations and identity at the molecular level e.g. binding site identification, genotyping.
ontology
Documentation of the set of steps taken in a procedure.
mage
concrete
ontology
Database of developmental stage information.
concrete
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 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.
ontology
place_holder
ontology
Descriptor of the Test performed e.g. Leukocyte count
abstract
The atmospheric conditions used to culture or grow an organism.
abstract
ontology
ontology
concrete
The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.
mage
concrete
The BioSample after labeling for detection of the nucleic acids.
Method used to deliver a compound for treatment.
place_holder
ontology
The effects of different software, software packages, or software versions on experimental results are studied.
ontology
A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined.
concrete
ontology
concrete
Database of disease staging information
Description of the processing state of the biomaterial for use in the microarray hybridization.
mage
abstract
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
abstract
mage
MAGE package for HigherLevelAnalysis
The genus and species (and subspecies) of the organism from which the biomaterial is derived from.
ontology
abstract
ontology
abstract
The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial.
property indicating that the class has an accession number
property indicating that the class has a manufacturer
property indicating that the class has a database
property indicating that the class has an image format
property indicating that the class has a phone
property indicating that the class has a factor value
property indicating that the class has bioassays
property indicating that the class has a middle initials
property indicating that the class has a version
property indicating that the class has a database entry type
property indicating that the class has a modified part
property indicating that the class has a measurement type
property indicating that the class has a family member
property indicating that the test has a test protocol
property indicating that the class contains a cubic volume measurement
property indicating that the class has pages
property indicating that the class has a clinical record
property indicating that the class has a cancer site
property indicating that the class has a category
property indicating that the class has a family relationship
property indicating that the class has a publication
property indicating that the class has bioassaydata
property indicating that the class has a chromosomal aberration classification
property indicating that the class has individual genetic characteristics
property indicating that the class has a last name
property indicating that the class has an editor
property indicating that the class has a parent organization
property indicating that the class has a first name
property indicating that the class has an atmospheric component
property indicating that the class has an association to a MAGE description
property indicating that the test has a test result
property indicating that the class has a treatment
property indicating that the class has an ontology entry
property indicating that the class has a node value type
property indicating that the class was tested for
property indicating that the class has a property set
property indicating that the class has fiducials
property indicating that the class has a feature shape
property indicating that the class has units
property indicating that the class has a model
property indicating that the class has a make
property indicating that the class has biomaterial characteristics
property indicating that the protocol has a performer or contact person
property indicating that the class has a citation
property indicating that the class has disease staging
property indicating that the class has a prior disease state
property indicating that the class has an address
property indicating that the class has an owner
property indicating that the class is user defined
property indicating that the class has a mass
property indicating that the class has a laboratory test
property indicating that the class has a clinical treatment
property indicating that the class has a host part
property indicating that the class has software
property indicating that the class has an organism part
property indicating that the class has hardware
property indicating that the class has a scale
property indicating that the class has an experiment design type
property indicating that the class has a fax
property indicating the location of the disease.
property indicating that the class has an experiment design
property indicating that the class has an individual time point
property indicating that the class has an email address
property indicating that the class has an issue
property indicating that the class has a publisher
property indicating that the class has a name
property indicating that the class has a maximum measurement
property indicating that the class has text
property indicating the version of the MGED Ontology that the term was deprecated from
property indicating that the class has a protocol
property indicating that the class has a compound
property indicating that the class has providers
instance property to indicate what the term was replaced by
property indicating that the class has a disease state
property to indicate the reason for deprecating a term
property indicating that the class has a node
property indicating that the class has a volume
property indicating that the class has an affiliation to an institution
property indicating that the class has a node value
property indicating that the class has a clinical test
property indicating that the class has an action
property indicating that the class has a host
property indicating that the class has an additive
property indicating that the class has a biosource type
property indicating that the class has a clinical finding
property indicating that the class has a height
property indicating that the class has authors
property indicating that the class has a type
property indicating that the class has species
property indicating that the class has a nutrient component
property indicating that the class has a year
property indicating that the class has an identifier
property indicating the class has a result
property indicating that the class has a measurement
property indicating that the class has a value
property indicating that the class has an individual
property indicating that the class has experiment factors
property indicating that the class has a toll free phone
property indicating that the contents found at this uri are human readable
property indicating that the class is a solvent
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 that the class has a description
property indicating that the class has an order
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 title
abstract
place_holder
concrete
This property is used to identify the type of class of the term. The value "abstract" indicates that the class is used for organizational purposes. The value "instantiated" indicates that the class contains Individuals that can be used as annotation terms. The value "abstract" indicates that the class is used to provide organization within the MGED Ontology. The value "place_holder" indicates that this class represents the location in the ontology where terms of this class would be located.
property indicating that the class has an accession number version
property indicating that the class has a URI
property indicating that the class has been treated
property indicating that the class has a donor
ontology
mage
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.
a double stranded oligonucleotide
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.
A record which describes and identifies a microarray experiment e.g. GEO
<pre>An experiment done in a test tube or a culture dish, e.g.
A bacterial invasion assay in an established cell culture</pre>
counts per minute, unit of light emissions produced by ionizing radiation.
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 software implementing a Higher Level Analysis protocol of type differential_expresssion.
a controlled vocabulary of targeted cell types
http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12596
The values are a sequence of one or more characters.
milligram per kilogram per day
The sister of one's father or mother.
an organism with both male and female sexual organs in one individual
synonym: intersex
A design in which the innate behavior of the organism is examined, e.g.
path finding in bees.
http://genex.hgu.mrc.ac.uk
The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth.
Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle.
A SurfaceType of unknown type.
An ordered, finite set of nonnegative floats.
DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input
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.
picogram, mass unit
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.
An experiment which has a peer reviewed publication attached.
meter, distance unit
Introduction of genetic material into an organism often in the form of a plasmid.
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.
Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.
http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml
Depriving an organism of food or nutrients
Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown.
one or more DNA or RNA based non cellular infective agent, including bacteriophage
Total cellular and nuclear RNA.
The action of removing one or more organism parts.
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.
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 controlled vocabulary for compounds
http://nciterm.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C1908
A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.
http://arabidopsis.info/catalogue.html
The Nottingham Arabidopsis Stock Centre (NASC). Provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community.
Water consumed by or enveloping the organism that the biosource is derived from.
single stranded oligo used for polymerase chain reaction
the array is made on silicon
A descriptor for a clinical treatment for a patient.
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).
A float greater than or equal to 0.
A female parent.
units per week, e.g. the number of units of alcohol consumed over a period of 7 days
Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma).
An integer >= 0.
time unit
RNAi
A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
An action where the temperature is specified.
A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species.
Describes a cell, nucleus or organism with three or more copies of each chromosome.
a controlled vocabulary for strains or lines
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16403
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).
The fluid and dissolved substances excreted by the kidney.
The mean and variance values resulting from computationally combining 2 or more sets of bioassay data.
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.
the reverse strand
exact synonym: -
milliliter per kilogram
http://cvs.sourceforge.net/views.py/obo/obo/ontology/anatomy/cell_type/cell.ontology?rev=HEAD&content-type=text/vnd.viewcvs-markup
database of cell ontology terms
The source DNA was not printed for a Feature or Zone on the slide, possibly due to lack of sample, broken or clogged spotting pin.
The 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).
Mating type of S.pombe.
A biomaterial obtained as fluid consisting of plasma, blood cells and platelets.
Application of a scale adjustment following lowess_group_normalization, to render the group variances similar.
Computationally derived sequence feature.
Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences.
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.
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.
The type of protocol used to preserve (including storage or keep in stasis) the biomaterial.
biomaterial removed after the death of the organism
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.
Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance.
High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome
percent weight per volume, concentration unit
micrometer, unit of distance
a controlled vocabulary for disease stages
http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28108
mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input.
Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1.
A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement.
the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData
Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds.
http://chem.sis.nlm.nih.gov/chemidplus
33 P, radioactive isotope of phosphorus, used for labeling/detection purposes.
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.
A article published in a print or online journal having an ISSN.
A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency.
delivery method whereby a compound or drug is administered via a vein
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 PCR based quantitative validation of a subset of the array based data used for experimental QC purposes.
A value which is a whole number (e.g. 10).
A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites.
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.
microgram, unit of mass
sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts
Version of the MGEDOntology.
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.
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.
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.
liter, unit of volume
the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData
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.
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out
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.
A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA.
BioSequence generated by means of polymerase chain reaction
A record which describes and identifies an amino acid sequence which has been curated
An experimentally defined sequence feature.
The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding.
An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
The array is made on a nitrocellulose filter.
http://nciterms.nci.nih.gov
A description logic namespace that contains controlled terminology used at NCI.
Application of a normalization of type quantile_normalization.
the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData
The shape of the feature on the array is circular or oval.
ProtocolType of unknown type.
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.
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
sequence from the region between genes
Software used to cluster the data.
The male offspring of the patient or individual under study.
The procedure in which solid material is dispensed or dissolved in a liquid.
A descriptor for FactorValue where age is compared.
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.
http://sig.biostr.wahington.edu/projects/fm/
The procedure of putting a physical object in a container/physical space.
Version of the MGED Ontology.
The procedure of labeling a biosample.
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.
A delivery method for compound or drug whereby the substance is administered via the peritoneum.
percent weight per weight, concentration unit
Person or organization that manufactured the software.
An instrument capable of applying centrifugal force to tubes or microtiter plates.
An instrument for sonicating biomaterials.
The father of one's father or mother.
Mix by drawing up and down with a pipette.
Generation of a DNA strand from an RNA strand using reverse transcriptase.
Storage where the thing stored is stored below 0 degrees celsius.
A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy.
TechnologyType of FeatureGroup where antibodies are spotted directly.
SubstrateType of unknown type.
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).
h
60 minutes, time unit
A design aimed at identifying genes expressed in biomaterials of interest.
milliliter, volume unit
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 self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.
the chrome border on an Affymetrix type array which is used as a point of
reference for orientation (fiducial)
The array is made on a nylon membrane.
The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing.
The possession of a third chromosome of any one type in an otherwise diploid cell.
A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement.
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.
multiple of stock solution concentration, concentration unit
An instrument which controls hybridization conditions, into which a hybridization chamber may fit.
The atmospheric conditions used to culture or grow an organism.
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.
Unit for a simple count of things
A float > 0.
Software to control an arrayer.
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
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/
curated database containing information on Drosophila genes, alleles etc
A Reporter where only buffer was deposited on the array
of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes.
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.
one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
milimolar, concentration unit
A device capable of applying software.
The rating of containment system used to protect organisms from infectious agents.
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.
d
24 hours, time unit
The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)
Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer
Sequence features derived by both computational and experimental methods.
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.
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.
An operator variation experiment design type assesses the operator performance and relation to data consistency and quality.
Contact which provides funding for experiments.
Application of a scale adjustment following loess_group_normalization, to render the group variances similar.
milligrams per milliliter, concentration unit
protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design
Indicates that a dye swap was performed for some or all hybridizations within an experiment
Sequence feature whose derivation is unknown.
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).
An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared.
a design element group consisting of multiple types
A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD
sequence of a protein, a linear amino acid polymer
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.
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.
gene expression
gene_expression
A transcript identification design type characterizes the length and
position of transcripts and allows identification of all forms of
transcripts in the genome.
expression_profiling
transcription_profiling
expression profiling
transcription profiling
A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software).
BioSequence of unknown type
http://www.cabri.org/CABRI/srs-doc/
Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc.
a controlled vocabulary for histology
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C4741
a record which identifies and describes the function of a gene product, e.g. E.C. record
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.
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.
true
A device for controlling temperature by immersion in water.
The values are unordered and have no scale.
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
A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied
The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil)
a record which describes and identifies a compound e.g. drug record part of NCI thesaurus
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.
A descriptor for FactorValue where CellType is compared.
Change in light intensity or wavelength.
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 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.
Computed as the ordinary Pearson correlation coefficient between two groups of rankings.
A RNA stability experiment design type examines the stability and/or decay of RNA transcripts.
The values presented are logarithm, base e.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
false
A descriptor for FactorValue where GeneticVariation is compared.
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.
The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism.
infect
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
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.
A chamber in which the hybridization is performed which maintains constant conditions.
A descriptor for FactorValue where CellLine is compared.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.
one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
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.
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.
a surface coating for immobilization with the polypeptide, polylysine
The Zone is excluded due to smearing, streaking, or dense background in the Zone.
sequence of a single stranded synthesized oligonucleotide
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
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.
RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus.
A sex experiment design type assays differences associated with an organism's sex, gender or mating type.
a nucleic acid consisting of a single polynucleotide chain.
DNA which is generated by chemical or enzymatic (non cellular) means.
non-exact synonym: cDNA
Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome.
database entry from MESH, medical subject headings vocabulary resource
http://www.nlm.nih.gov/mesh/filelist.html
The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.
sequence from the mitochondrial genome
grams per deciliter, concentration unit
disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument.
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).
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.
ctDNA: sequence from the chloroplast
synonym: chloroplast DNA
Time stated in terms of the day, month, and year.
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.
A biomaterial that has been lyophilized or dried by freezing under a vacuum.
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).
Term used to describe a role or factor value for the person or organization that provides a BioMaterial.
A delivery method for compounds/drugs where the compound or drug is freely available.
http://www.iupac.org/publications/pac/2000/205/205olesen.html
A resource of vocabularies for describing clinical tests, e.g. blood chemistry.
Ribonucleic acid.
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.
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.
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.
An element that is an oligonucleotide of at least 50 nucleotides in length.
high molecular weight DNA
RNA which has been obtained by selection for polyA tracts.
Exact synonym: polyA+_RNA
Non-exact synonym: mRNA
A contact's affiliation, e.g. university, research institute or business.
The procedure of euthanizing an organism.
The unit of total light output from a light source.
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.
The length of the light period that a sample is subjected to.
Exact synonym:photoperiod
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.
The procedure of extracting nucleic acid from the biomaterial.
time point that indicates the start of some developmental stage
increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification
A biomaterial obtained frozen
The action of preparing a slide for the microscopical examination of organism parts or cell types.
One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms.
http://www.opengalen.org/open/crm/crm-anatomy.html
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.
Kelvin, unit of temperature
The material (e.g. straw) that an animal sleeps on
The organism (or organism part) has been exposed to a virus or pathogen.
Delivery method for a compound or drug where the substance is administered via an injection into the muscle.
TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.
sequence which represents regions of a transcript that are joined to another exon during splicing
PCR with multiple bands, or smear, in gel-separated reaction products
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.
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.
An integer less than or equal to zero.
deciliter, unit of volume
Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold.
An instrument designed to mechanically wash or stain arrays.
A publication type which has an ISBN.
picomolar, concentration unit
a controlled vocabulary for geographic locations
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16632
An integer > 0.
Unit of time corresponding to approx. one cycle of the moon's phases.
The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations.
Software to create MeasuredBioAssayData from images.
Exact Synonym: image analysis software, image quantification software.
ExperimentDesignType of unknown type.
semisolid media type
A biosource obtained as fecal matter.
Mating type of S. cerevisiae.
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.
A descriptor for FactorValue where BioSources are compared.
single stranded oligo used for polymerase chain reaction
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.
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).
A software variation design type compares different types of software for performance, accuracy, precision and reproducibility.
A record which identifies a nucleic acid sequence feature(s) and which has been curated.
DNA from organelles such as the mitochondria or chloroplast.
fluorophore used for labeling/detection purposes
The values presented are logarithm, base 2.
millimeter, unit of distance
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.
The concentration range of the organism.
single oligo used for polymerase chain reaction direction unspecified
individual whose sex organs contain only male gametes
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.
ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2002
Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.
A male having the same genetic parents as another, or one genetic parent in common with another.
A float less than or equal to zero.
Application of a normalization of type mean_log_centering.
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
Mating type of S. cerevisiae.
The Arabidopsis Information Resource.
http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype
osmolality per kilogram of water, concentration of the solute per unit of solvent
A record which describes and identifies the relationship between species and is
computationally determined and based on sequences e.g. Treebase record
A device for controlling temperature.
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.
preservation type whereby the seed is maintained in a dormant state
The female offspring of the patient or individual under study.
PCR where no products of any kind appear in gel-separated reaction products.
A function applied to subsets of values from the same Measured/Derived bioassay data set.
The perimeter of the spotted DNA on the slide is irregular.
The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data.
number of items or events per day
Software used to transform the Measured or DerivedBioAssay data e.g. normalization.
Non-exact synonym: normalization software
a nonparametric measure of the agreement between two rankings
The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.)
A species experiment design type assays differences between distinct species.
An instrument that produces DNA sequences.
Change in temperature.
http://www.gramene.org/
A Comparative Mapping Resource for Grains.
RNA obtained from the nucleus.
A descriptor for FactorValue where Sex is compared.
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.
mating type indicating the absence of F plasmid in a bacterial cell
Polymer of amino acids.
Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.
http://www.sanbi.ac.za/evoc/ontologies.html
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 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.
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=12596
a controlled vocabulary of cell types
picomoles, quantity unit
femtomole, unit of quantity
a controlled vocabulary of organism parts
http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C13007
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.
A record which describes and identifies an image, e.g. an image from the mouse atlas
person who prepares the MAGE-ML file
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.
database entry from mouse anatomical dictionary for developmental stage term
http://www.informatics.jax.org/mgihome/GXD/AD/
An instrument designed to remove excess liquid by vacuum and heating.
An instrument capable of manufacturing arrays by spotting material.
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.
A reference experiment design type is where all samples are compared to a common reference.
Mix through the process of inverting.
The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO)
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.
A daughter of one's son or daughter.
A community effort to provide standard terms for annotating phenotypic data.
http://www.informatics.jax.org/searches/Phat.cgi?id=MP:0000001
sample which has been removed prior to the death of an organism
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.
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).
number of molecules, quantity unit
Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone.
sequence spliced out from a transcript
the action of emergence and separation of offspring from the mother.
The process of removing tissue from a living organism.
An ordered, finite set of booleans.
The procedure of extracting/taking out a part of a reaction/contents of a container.
An instrument which fragments tissues or other biomaterials.
media type, usually some sort of broth
Hardware for measuring light at different wavelengths.
mating type indicating the presence of F plasmid in a bacterial cell
Describes a cell, nucleus or an organism with one copy of each chromosome.
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.
Toxicology Data Management System, a database resource for systems, organs, pathology, etc.
http://hazel.niehs.nih.gov/user_spt/pct_terms.htm
femtoliter, unit of volume
A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.
A female having the same genetic parents as another, or one genetic parent in common with another.
The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence.
http://song.sourceforge.net/
Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg.
the number of cells per ml
An injury experiment design type is where the response of an organism(s) to injury or damage is studied.
A float that is < 0.
A normalization testing experiment design tests different normalization procedures.
A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat.
http://www.loinc.org/download
Database resource for universal identifiers for laboratory and other clinical observations
femtogram, unit of mass
Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment).
A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.
The values presented are logarithm, base 10.
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.
http://www.item.fraunhofer.de/reni/index/htm
database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions
Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point.
fluorophore used for labeling/detection purposes
Micromole per liter or micromolar, concentration unit
The array is made on a glass slide.
nanomoles, quantity unit
The point at which an organism emerges from an egg.
a surface coating type for immobilization with the compound aminosilane
Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss.
the process of placing a seed or spore in some media with the intention to invoke germination.
An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes).
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.
The scale is a standard base 10, non logarithmic scale.
micromoles, quantity unit
A contact who performs data analysis, e.g. statistician.
nanoliter unit of volume
A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial.
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.
A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank
A ComplexAction or ProtocolType describing growth of an organism or cell culture.
sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes
An ordered, finite set of floats.
Software used to control automated liquid handler.
A male parent.
Person or organization that manufactured the hardware.
A cell type comparison design experiment design type compares cells of different type for example different cell lines.
a record which describes and identifies a protein structure e.g. PDB
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 point at which the egg(s) is laid by an organism.
the number of plaque forming units per ml
Person who contributed to the study.
treatment of a biomaterial with radiation e.g. electromagnetic radiation
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.
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
identifier for a taxon provided by the NCBI taxonomy database
An operon identification experiment type is designed to identify locations and members of operons in a genome.
A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record
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.
The action of stabilizing an organism prior to treatment
An ordered, finite set of positive floats.
A member of a consortium of institutions.
The process of combining two or more BioMaterials.
Exact synonym: combine
a record which identifies and describes biological pathways, e.g. a KEGG record
The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.
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.
the physical act of copulation that occurs during the process of sexual reproduction
synonyms: copulation, insemination
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 record which describes and identifies an experimentally derived protein structure e.g. MSD
A proprietary image data format that is lossless and containing one channel of data.
A descriptor for FactorValue where DiseaseState is compared.
the number of colony forming units per ml
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.
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C7057
a controlled vocabulary for disease states
Temperature associated with a particular environment.
The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
a compound used for labeling/detection purposes
sequence from yeast artificial chromosome
microsecond, unit of time
nanogram, a mass unit
a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM
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.
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.
An ordered, finite set of strings.
milliliters per liter, concentration unit
sequence of a processed transcript capable of directing protein synthesis
grams per liter, concentration unit
An ordered, finite set of nonpositive integers.
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.
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.
A structured controlled vocabulary for the anatomy of Arabidopsis.
http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/Arabidopsis/Attic/arabidopsis_anatomy.ontology
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.
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).
degrees Fahrenheit, unit of temperature
Unit of brightness or luminance.
potential of hydrogen
The procedure of placing one physical object in the same container/physical space as another.
A descriptor for FactorValue where ClinicalInformation is compared.
The shape of the feature on the array is square.
http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28076
a controlled vocabulary of tumor grading terms
The process of physically creating the array.
the forward strand
exact synonym: +
soil, growth media for plants and other soil living organisms
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 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.
An instrument capable of acquiring images of arrays.
gram, unit of mass
The values are either TRUE or FALSE, which can be expressed as 1 and 0.
sequence that represents the product of an RNA polymerase engaged in transcription
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.
A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record
A Reporter where no material or buffer was deposited on the array
A son of one's son or daughter.
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen
a cubic centimeter, volume unit
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
Describes a cell, nucleus or an organism with two copies of each chromosome.
centimeter, a unit of distance
gene sequence which has been computationally predicted
The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data.
32 P, radioactive isotope of phosphorus used for labeling/detection purposes
7 days, unit of time
A design that compares samples from live and dead organisms.
A descriptor used in cancer biology to describe abnormalities of tumor cells.
Ontology of human developmental anatomy for Carnegie stages 1-20.
http://obo.sourceforge.net/list.shtml
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.
kilogram, 1000 grams, unit of mass
Software upon which other software runs.
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 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.
sequence from a gene coding for transfer RNA
exact synonym: transfer RNA gene
An ordered, finite set of negative floats.
record which describes and identifies clinical information about an organism
An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR.
Exact Synonym: thermocycler
sequence of part of a gene, which is missing one or both ends
Mating type of S.pombe.
CGH
array CGH
Experiment design type in which genomic content is studied using an array based assay.
array_CGH
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.
http://www.ebi.ac.uk/chebi
An experiment design type where the label orientations are reversed.
exact synonym: flip dye, dye flip
A descriptor of FactorValue where comparisons of strains or lines are made.
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.
A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34).
nanometer distance unit
A descriptor for FactorValue where PhysicalCharacteristics are compared.
An integer < 0.
http://cvs.sourceforge.net/viewcvs.py/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.ontology?content-type=text/plain&rev=1.1
uri for FlyBase developmental stage terms
<pre>The time point that a sample was taken. Not to be used where the sample is part of a time
course. SamplingTimePoint is not related to age. An instance could be summer, a date, a time, or a range value</pre>
The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
Hardware for automated liquid transfer and handling.
katal per liter, catalytic-activity concentration unit
Units of defined biological activity, e.g. cytokine stimulation, per ml.
The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify).
An ordered, finite set of positive integers.
An analysis aimed at identifying differentially expressed genes in two or more conditions.
units per liter
Emergence of an adult insect from its pupa or cocoon.
m
60 seconds, unit of time
A descriptor for FactorValue where DevelopmentalStage is compared.
The procedure of applying a centrifugal force to a physical object.
Exact synonym: centrifuge
Mix through the use of a vortexer.
Provider of biosequences (clones, oligos etc) for deposition on the array.
Person who is the primary contact for data submitted to a database.
Increasing the concentration of solutes in a solution or suspension.
The process of incubating one or more labeled extracts with an array.
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.
http://www.cbil.upenn.edu/anatomy.php3
a controlled vocabulary provided by CBIL
Groups of assays that are related as part of a time series.
sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size
an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins
Person or organization that manufactured the array.
person who checks the consistency of the data and MAGE-ML file
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.
An ordered, finite set of integers.
The BioSample at any stage other than immediately before labeling.
Logarithmic transformation of ratio data.
The BioSample immediately before labeling.
The shape of the feature on the array is rectangular.
An ordered, finite set of negative integers.
femtomolar, concentration unit
An experiment in which the array platform is compared, e.g. Agilent versus
Affy.
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.
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.
cell lysate, a collection of cells whose membranes have been disrupted
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
picoliter, volume unit
The source DNA for a Feature was not uniformly deposited.
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.
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.
sequence from a P1 artificial chromosome
mark made on slide using a laser which is used as a point of reference for orientation (fiducial)
genomic sequence 5' to a gene where the transcription initiation complex forms.
A loop experiment design is where labeled extracts are compared in consecutive pairs.
synonym: circular design
A record which describes and identifies nucleic acid sequence which has been identified as a gene by a curator. e.g. Flybase gene record
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.
Polymerase chain reaction. An element generated using this procedure.
percentage volume per volume, concentration unit
The action of changing the relative humidity, e.g. from 1% to 10%.
Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n).
http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/developmental/plant_development/Arabidopsis/temporal.tair?rev=1.21&view=markup
An ontology of stages of growth and development of the model plant Arabidopsis thaliana.
millisecond, time unit
A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array.
The loss of a segment of the genetic material from a chromosome.
A record which describes and identifies a paper publication e.g. a medline record
The mother of one's father or mother.
A Reporter indicated as being a control of unknown type.
microliter, unit of volume
An action whereby an organism(s) has had genetic material removed, added, or rearranged.
The process of obtaining quantifiable values from the scanned image of the
array. Exact synonyms: image analysis, image quantification
The process of generating an image from the array.
Hardware for synthesizing oligos.
Application of a normalization of type median_log_centering.
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).
ChIP-chip
chromatin_immunoprecipitation
A binding site identification design type investigates protein binding sites on nucleic acids
non-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP
chromatin immunoprecipitation
An optimization experiment design type is where different protocols or protocol parameters are compared.
A type of solid media commonly used for growing organisms
Mole per liter or molarity, concentration unit
An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes.
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.
A translational bias is an experiment design which characterizes the association of transcripts and translation machinery.
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.
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.
http://tumor.informatics.jax.org
Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors.
the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData
The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas.
Deoxyribonucleic acid.
The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data.
365 days, time unit
http://www.nlm.nih.gov/research/umls/
Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH.
milligram, mass unit
The brother of one's father or mother.
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.
A replicate that consists of independent biological replicates made from different individual BioSources.
An organism part comparison experiment design type compares tissues, regions, organs within or between organisms
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).
sequence from gene coding for ribosomal RNA
exact synonym: ribosomal RNA gene
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.
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.
A design in which a behavior is invoked by a variable controlled by the experimenter - e.g. administration of a drug that effects aggressivity.
The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).
Delivery method whereby a drug or compound is administered under the skin of the organism.
sequence from gene coding for small nuclear RNA
exact synonym: small nuclear RNA gene
Decreasing the concentration of solutes in a solution or suspension.
Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss.
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 ÒParisÓ point, or is the sum of their distances to the ÒParisÓ point otherwise.
The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product.
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
http://portal.bioengineering.elyt.ods.org/ontology/
Ontology describing anatomical and physiological relationships.
Conceptual action for specified protocol applied in treatment.
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
The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter.
agar stab, a cell culture inoculated into agar for long term storage
An ordered, finite set of nonnegative integers.
http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php
database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice
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.
delivery method for drug or compound whereby the drug is administered via the mouth
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.
attomole, quantity unit
RNA obtained from the cytoplasm.
database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses
http://www.atcc.org/Cultures/Products.cfm
degrees celsius, unit of temperature
A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance
The process of harvesting cells from culture.
An instrument that mixes by rapid oscillation.
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.
sequence from a bacterial artificial chromosome
exact synonym: bacterial artificial chromosome
A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes.
Robust Multiarray Average. A quantitative measure of the relative abundance of a transcript. RMA is a summary measure of related Ôperfect matchÕ Features on an Affymetrix array. The values are background-adjusted, normalized and log-transformed values.
Allow time to pass. It's measurement should be a unit of time.
A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list
A biomaterial obtained embedded in paraffin (wax).
A publication type which is available online and which is not an online journal article, e.g. a web site or service.
This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28).
http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology?rev=1.1&view=markup
Delivery method where a compound/drug is administered in food or water.
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.
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.
TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly.
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
mole, unit of quantity
organism(s) whose sex is unknown
An ordered, finite set of nonpositive floats.
An irregularity in the number of chromosomes, usually in the form of a gain of genetic material.
Portable Network Graphic, a lossless image data format.
Software to control a scanner and manipulate and save images.
Exact synonym: scanning software