property indicating that the class has a biosource type
property indicating that the class has a host
property indicating that the class has a host part
property indicating that the class has an image format
property indicating that the class has an individual time point
property indicating that the class has an issue
property indicating that the class has a make
property indicating that the class has a maximum measurement
property indicating that the class has a measurement type
property indicating that the class has a model
property indicating that the class has pages
property indicating that the class has a volume
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.
One of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on phenotype or sequence. Polymorphisms are included in this definition.
MAGE package that describes the array layout and design. The array may be physical or virtual.
An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays.
MAGE package for describing the process by which arrays were manufactured.
The atmospheric conditions used to culture or grow an organism.
An atomic action is a single step process on the biomaterial, e.g mix by inversion, wait, add
MAGE package for contacts including organizations and people.
Rating of containment system for the protection of organisms from infectious agents.
Refers to the bedding material present in an animals housing.
A bibliographic reference is a published citation in a journal, book, other format e.g. web resource
A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays.
BioAssayData refers to the data files including images generated from one or more BioAssays.
A grouping of bioassay data that has been organized by one or more mathematical functions into nodes.
Description of the processing state of the biomaterial for use in the microarray hybridization.
General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue.
Properties of the biomaterial before treated in any manner for the purposes of the experiment.
Description of the source of the nucleic acid used to generate labeled material for the microarray experiment.
BioMolecularAnnotation experiment design types are those which are designed to investigate functions, processes, locations and identity at the molecular level e.g. binding site identification, genotyping.
Used to tell when the BioSample is an extract or not.
A representation of a DNA, RNA, or protein sequence.
MAGE package for biological sequences (biosequence).
Controlled terms for descriptors indicating the type of biosequence. Types may be physical (e.g BAC, cDNA clone), or computational (e.g unigene cluster, consensus)
The BioSource is the original source material before any treatment events.
The resource (e.g, company, hospital, geographical location) used to obtain or purchase the biomaterial.
The form in which the Biosource is provided, may also be used to describe biosamples e.g. agar stab.
Factors that relate to properties of the biomaterial, its treatment, or its growth.
A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined.
Physical properties of the BioMaterial e. g. mass or height
The identifier for the cell line if one was used as a biomaterial.
CellType, the type of cell used in the experiment if non mixed, if mixed the TargetedCellType should be used, example of instances, epithelial, glial etc.
An abnormality of a chromosome's number or structure, which excludes simple changes in sequence and is usually detectable by cytogentic and microscopic techniques such as FISH.
An irregularity in the number or structure of chromosomes, usually in the form of a gain (duplication), loss (deletion), exchange (translocation), or alteration in sequence (inversion) of genetic material. Excludes simple changes in sequence such as mutations, and is usually detectable by cytogenetic and microscopic techniques such as FISH.
Clinical findings that are distinct from the disease state and can be referred to from an established controlled vocabulary or ontology. An example might be a test performed and/or finding.
The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment.
The current clinical treatment(s) of the patient from which the biosource is derived.
Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification.
A drug, solvent, chemical, etc., with a property that can be measured such as concentration.
Units used for concentration measurements.
Concentration units not specified in MAGE.
Organizations or individuals that may be contacted.
Controlled terms for descriptors for the type of control design element.
a plant variety obtained in in agriculture in horticulture
Primitive data types found in computing languages such as float, boolean, etc.
Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records.
Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD).
Defects associated with features or zones such as those that are missing or moved.
Method used to deliver a compound for treatment.
Class to hold deprecated instances and classes.
A BioAssay that is created by the transformation of measured or derived BioAssays.
Controlled set of descriptors for the type of derivation of the BioAssay such as averaging features, taking ratios of signal QuantitationTypes, and normalizing BioAssay data.
MAGE package for description of annotations and references to annotations.
Design elements are reporters, features, and composite elements as defined by MAGE.
A DesignElementGroup holds information on Features, Reporters, or CompositeSequences.
Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence.
The MAGE package for describing the elements located on the array.
The developmental stage of the organism's life cycle during which the biomaterial was extracted.
Database of developmental stage information.
The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.
The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed.
a biotype resulting from selection in a particular habitat, e.g. the A.thaliana Ecotype Ler
Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth.
A description of the conditions the organism has been exposed to that are not one of the variables under study.
Environmental stress is a treatment where some aspect of the environment is perturbed in order to stress the organism or culture, e.g. temperature shock, osmotic shock
An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history.
The complete set of bioassays (hybridizations) and their descriptions performed as an experiment for a common purpose. Here we take experiment to mean an observational or perturbing study. An experiment will be often equivalent to a publication.
ExperimentDesign refers to both observational and experimental (perturbational) studies. The organizing principles of the study including the relationships between assays and the steps taken to interpret the data.
The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc.
The descriptions associated with the Experiment package of MAGE
The factors in the study that are experimental parameters or regarded as influencing the experimental results.
A factor category describes factors which are under test in the experiment and allowable factor categories can be BioMaterialCharacteristics, Compound (names, concentrations) and Action etc. E.g. in an experiment where leukemia types are compared the factor categories are ALL and AML.
A group of FactorValues which refer to the same condition used to treat or describe a BioMaterial, e.g. 10% glucose, 1 hour OR larval stage, age 24 hours.
A super grouping of FactorValueDependencies or FactorValues which describes combinations of conditions used to treat or describe a BioMaterial applied to a BioAssay, typically separating things on the basis of channels or the concepts of measured and reference samples e.g. 10% glucose, 1 hour AND 10mm NaCl, 2 hours in channel 1.
Controlled terms for descriptors of failures (as in PCR) associated with reporters.
Relevant aspects of genetic preconditions or family member's clinical history.
A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother.
A technical manufacturer described defect for features.
Technology-based grouping of features representing individual locations on the array.
The expected shape of the feature on the array.
A marking on the surface of the array that can be used to identify the origin of the array.
A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark.
The number of cell passages if the organism or organism part that is cultured is unicellular or a cell culture otherwise the number of generations.
Genetic material may be DNA or RNA and identifiable as an entry in a public external database such as EMBL/DDBJ/GenBank or one of the model organism databases.
The genetic modification introduced into the organism from which the biomaterial was derived. Examples of genetic variation include specification of a transgene or the gene knocked-out.
The total sum of the genetic information of an organism that is known and relevant to the experiment being performed.
A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference.
A description of the conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures and open environments such as field studies.
The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed.
Controlled terms for descriptors of types of hardware.
The effects of different hardware, types of hardware, or models of hardware on experimental results are studied.
Factors that are measured or observed parts of the study but not induced or under the control of the experiment. These factors do not have protocols (e.g., epidemiology factors).
Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells).
The humidity that the biosource is exposed to.
Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.)
Identifier or name of the individual organism from which the biomaterial was derived.
An abnormality in the number or structure of chromosomes in the biomaterial from an individual organism, detected by karyotyping or other methods. E.g., a B-cell lymphoma from a patient has an abnormal karyotype 48,XY,t(1;2)(p22;p11),+3,+12.
The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.
The point from which measurements of age were taken.
Compounds that are used for labeling extracts.
The BioSample after labeling for detection of the nucleic acids.
Database of codes for clinical findings.
The photoperiod and type (e.g., natural, restricted wavelength) of light exposure.
Units for measuring the intensity of light.
An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents.
Location for those classes that are not in the Core ontology as they do are not containable in MAGE. It is not yet structured to work with the Core ontology
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.
The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) .
A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g quality control, replicates, loop.
The effects on results of changing protocols, hardware, software, or people performing the experiments are studied Examples are comparison of data across different labeling protocols, scanners, image quantification software, or laboratories.
A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes.
Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm.
Controlled set of terms for describing the type of values (e.g., Euclidean distance).
NormalizationDescription provides details of the normalization strategy for the experiment.
Controlled descriptors for the normalization strategy used for the experiment.
The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.).
External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology.
The effects of different investigators, laboratories, or organizations on experimental results are studied.
The genus and species (and subspecies) of the organism from which the biomaterial is derived from.
The part of the organism's anatomy from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, or body location (arm).
The stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
The organization (e.g, company, hospital) to contact to obtain or purchase something.
Other units are those types not specified in MAGE such as lumens, radioactivity, etc.
A parameter is a variable within a protocol.
Tests and results for pathogens infecting organism from which the biosource is derived
The individual to contact regarding something provided such as a biomaterial.
A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification
The observable form taken by some character (or group of characters) in an individual or an organism, excluding pathology and diesease. The detectable outward manifestations of a specific genotype.
A physical bioassay is the combination of arrays and biomaterials as in a hybridization.
A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g BAC, PAC.
The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc.
Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence.
The concentration range of the organism.
Method and type of preserving the organism or biosource (i.e. keeping it in stasis).
The type of method used to preserve (keep in stasis) the organism or biosource.
Documentation of the set of steps taken in a procedure.
Descriptors for protocol parameter types, e.g. compound concentration, media type.
A controlled set of terms to provide a descriptor for the type of protocol.
The effects of different protocols or changes in protocols on experimental results are studied.
Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.).
QualityControlDescription provides details of the quality control aspects of the experiment.
Controlled descriptors for the quality control strategy for an experiment.
The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix.
The MAGE package for defining classes for quantitation.
Units for measuring decay of a radioactive isotope over time.
ReplicateDescription provides details about the type of replication used in the experiment.
Controlled descriptors for the type of replication.
Description of the material placed on a feature (spot).
Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider.
The scale (linear, log10, ln, etc) used to represent the value.
Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.)
Database for sequence annotation information.
Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny.
Controlled terms that provide descriptors for the type of software.
The effects of different software, software packages, or software versions on experimental results are studied.
The organism has had non-genetic parts removed, added, or rearranged.
Animals or plants that have a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings.
Database of strain, line, cultivar or ecotype information.
A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse
Controlled terms for descriptors of types of array substrates.
Controlled terms for descriptors for coating of the substrate.
The target cell type is the cell of primary interest. The biomaterial may be derived from a mixed population of cells although only one cell type is of interest.
Database of targeted cell type information.
The technology type or platform of the reporters on the array.
The temperature that a biosource is exposed to.
Units used for temperature measurements.
A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron.
The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data.
A treatment is the process or action by which a biomaterial is created from an input biomaterial.
A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus.
User is a way to id a person in a database
Controlled terms for descriptors of the warnings associated with reporters.
Water consumed by or enveloping the organism that the biosource is derived from.
A technical manufactured described defect for zones.
Angstrom, unit of distance, 1 angstrom = 10 nanometers
This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28).
Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc.
a controlled vocabulary provided by CBIL
Ontology describing anatomical and physiological relationships.
Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds.
flurophore used for labeling/detection purposes
An instrument that produces DNA sequences.
The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth.
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.
curated database containing information on Drosophila genes, alleles etc
database entry from GALEN common reference model, a resource for medical coding and terminology
A Comparative Mapping Resource for Grains.
Ontology of human developmental anatomy for Carnegie stages 1-20.
Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001.
A resource of vocabularies for describing clinical tests, e.g. blood chemistry.
Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature.
Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss.
Database resource for universal identifiers for laboratory and other clinical observations
database entry from mouse anatomical dictionary for developmental stage term
database entry from MESH, medical subject headings vocabulary resource
Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors.
identifier for a taxon provided by the NCBI taxonomy database
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.
Polymerase chain reaction. An element generated using this procedure.
BioSequence generated by means of polymerase chain reaction
Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle.
PCR where no products of any kind appear in gel-separated reaction products.
single oligo used for polymerase chain reaction direction unspecified
single stranded oligo used for polymerase chain reaction
PCR with multiple bands, or smear, in gel-separated reaction products
Portable Network Graphic, a lossless image data format.
A RNA stability experiment design type examines the stability and/or decay of RNA transcripts.
Computed as the ordinary Pearson correlation coefficient between two groups of rankings.
Toxicology Data Management System, a database resource for systems, organs, pathology, etc.
Tag Image File Format (TIFF) is a common format to describe and store raster image data from scanners and other imaging devices. TIFFs may contain one or more channels and the data may be compressed using a lossless compression algorithm.
Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH.
database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions
sequence from yeast artificial chromosome
A delivery method for compounds/drugs where the compound or drug is freely available.
The procedure of placing one physical object in the same container/physical space as another.
A type of solid media commonly used for growing organisms
agar stab, a cell culture inoculated into agar for long term storage
A descriptor for FactorValue where age is compared.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record
Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n).
glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen
Person or organization that manufactured the array.
An instrument capable of manufacturing arrays by spotting material.
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. (MAS 4.0 version of the Affymetrix analysis software).
results of data reduction involving computation of the average intensity from identical Features, Reporters or CompositeSequences in different hybridizations.
The rating of containment system used to protect organisms from infectious agents.
time point that indicates the start of some developmental stage
The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.)
A computational procedure used to process or transform one BioAssayDataCube into another.
results of data reduction involving computation of a representative value, e.g. by averaging, for a group of replicated Features, Reporters or CompositeSequences from 2 or more hybridizations.
A replicate that consists of independent biological replicates made from different individual BioSources.
A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list
A descriptor for FactorValue where BioSource providers are compared.
A biomaterial, usually tissue, cells, or fluid from a living organism
Provider of biosequences (clones, oligos etc) for deposition on the array.
a compound used for labeling/detection purposes
the action of emergence and separation of offspring from the mother.
A biomaterial obtained as fluid consisting of plasma, blood cells and platelets.
A male having the same genetic parents as another, or one genetic parent in common with another.
One or more dissociated cell(s) possibly heterogeneous, excluding single cell 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 descriptor for FactorValue where CellLine is compared.
cell lysate, a collection of cells whose membranes have been disrupted
A descriptor for FactorValue where CellType is compared.
A cell type comparison design experiment design type compares cells of different type for example different cell lines.
A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
The action of changing the relative humidity, e.g. from 1% to 10%.
Change in light intensity or wavelength.
The loss of a segment of the genetic material from a chromosome.
An irregularity in the number of chromosomes, usually in the form of a gain of genetic material.
The gain of a segment of the genetic material in a chromosome by fragmentation of a chromosome and transfer of the broken-off portion of another chromosome or other sources.
Chromosome segments that have been turned through 180 degrees with the result that the gene sequence for the segment is reversed with respect to the rest of the chromosome.
A type of aberration characterized by fragmentation of a chromosome and transfer of the broken-off portion to another chromosome, often of a different pair.
Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome.
A circadian rhythm experiment design type assays the events associated with the circadian rhythm which is a biological activity that exhibits an endogenous periodicity independently of any daily variation in the environment.
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
A descriptor for FactorValue where ClinicalInformation is compared.
ecord which describes and identifies clinical information about an organism
A descriptor for a clinical treatment for a patient.
Sequence from some nucleic acid copy and the associated vector
results of an analysis method that groups data based on some measure of similarity, e.g. Pearson correlation coeficient, Euclidean distance.
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.
The treatment is effected by a defined chemical, biological or compound. The compound may be a drug, solvent, chemical, etc., with a property that can be measured such as concentration.
a record which describes and identifies a compound e.g. drug record part of NCI thesaurus
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Computationally derived sequence feature.
a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM
A record which identifies and describes a nucleic sequence feature which has been computationally determined or predeicted E.g. and Ensembl record
a record which describes and identifies a protein structure e.g. PDB
Increasing the concentration of solutes in a solution or suspension.
mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input.
A member of a consortium of institutions.
A contact who provides some service related to some aspect of the experiment which is not data coding or analysis. E.g. help with an experimental design.
A Reporter associated with a BioSequence that has a context dependent predicted signal. e.g. a yeast reporter on a human array is a control_biosequence expected to be of low signal if no spikes are used. If spikes are used, the signal is expected to be high.
A Reporter where only buffer was deposited on the array
A grouping of DesignElements features/Reporters/Composites which are not designed to detect a signal in the biomaterial and which are on the array for control purposes e.g a grouping of controls used for spiking.
A Reporter where no material or buffer was deposited on the array
A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA.
A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency.
A Reporter indicated as being a control of unknown type.
sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size
counts per minute, unit of light emissions produced by ionizing radiation.
A record which describes and identifies an amino acid sequence which has been curated
A record which identifies a nucleic acid sequence feature(s) and which has been curated.
A contact who performs data analysis, e.g. statistician.
Time stated in terms of the day, month, and year.
The female offspring of the patient or individual under study.
A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions.
A descriptor for FactorValue where DevelopmentalStage is compared.
The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter.
Decreasing the concentration of solutes in a solution or suspension.
Describes a cell, nucleus or an organism with two copies of each chromosome.
A descriptor for FactorValue where DiseaseState is compared.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s).
The action of removing one or more OrganismParts.
A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s).
a nucleic acid consiting of two polynucleotide chains having antiparallel orientation and being bound together by hydrogen bonding between the chains. This would apply to DNA and some RNA genomes, but not to rRNA or tRNA, etc.
disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument.
Indicates that a dye swap was performed for some or all hybridizations within an experiment
results of data reduction involving computation of a representative value, e.g. by averaging, for identical Features, Reporters or CompositeSequences from 2 hybridizations utilizing dye-swapped LabeledExtracts.
Ontology of human terms that describe the sample source of human cDNA and SAGE libraries.
Emergence of an adult insect from its pupa or cocoon.
The shape of the feature on the array is circular or oval.
An environmental history design type is where some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
sequence which represents regions of a transcript that are joined to another exon during splicing
Sequence features derived by both computational and experimental methods.
A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial.
An experimentally defined sequence feature.
The BioSample immediately before labeling.
A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied
Delivery method where a compound/drug is administered in food or water.
data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold
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.
The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify).
Storage where the thing stored is stored below 0 degrees celsius.
a record which identifies and describes the function of a gene product, e.g. E.C. record
Contact which provides funding for experiments.
genomic sequence which corresponds to the primary transcript and uses the furthest 5' and 3' UTR's, doesn't include non transcribed regulatory regions. Can be experimentally or computationally determined
sequence of part of a gene, which is missing one or both ends
The modification of an organism that inserts a functional gene at the site of a nonfunctional locus for that gene using recombinant methods.
The modification of an organism that renders a gene non-functional e.g. due to the removal of all, or part of, the gene using recombinant methods.
An action whereby an organism(s) has had genetic material removed, added, or rearranged.
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out
A descriptor for FactorValue where GeneticVariation is compared.
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
A ComplexAction or ProtocolType describing growth of an organism or cell culture.
A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients.
Person or organization that manufactured the hardware.
A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision.
The point at which an organism emerges from an egg.
The Zone is excluded due to smearing, streaking, or dense background in the Zone.
an organism with both male and female sexual organs in one individual
An instrument which fragments tissues or other biomaterials.
The process of incubating one or more labeled extracts with an array.
A chamber in which the hybridization is performed which maintains constant conditions.
An instrument which controls hybridization conditions, into which a hybridization chamber may fit.
The process of generating an image from the array.
A record which describes and identifies an image, e.g. an image from the mouse atlas
The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)
The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product.
A descriptor for FactorValue where BioSources are compared.
A descriptor for FactorValue where IndividualGeneticCharacteristic is compared.
An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared.
The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation.
The organism (or organism part) has been exposed to a virus or pathogen.
An injury experiment design type is where the response of an organism(s) to injury or damage is studied.
A contact's affiliation, e.g. university, research institute or business.
A value which is a whole number (e.g. 10).
Delivery method for a compound or drug where the substance is administered via an injection into the muscle.
A delivery method for compound or drug whereby the substance is administered via the peritoneum.
delivery method whereby a compound or drug is administered via a vein
treatment of a biomaterial with radiation e.g. electromagnetic radiation
The perimeter of the spotted DNA on the slide is irregular.
The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination.
A design aimed at identifying genes expressed in biomaterials of interest.
A method of re-scaling ratio data by subtracting the mean log base 2 ratio from each log2(ratio). This adjusts the mean log2(ratio) to zero.
A article published in a print or online journal having an ISSN.
A method of re-scaling intensity data from one channel relative to another based on regression of the intensities in one channel on those of the other. The slope of the regression line is used to re-scale the intensities in one channel for each Feature. This single parameter method assumes that there is a linear relationship between the intensities in one channel relative to the other.
A transformation method in which low intensities are linearly scaled while high intensities are logarithmically scaled. The transition point is determined by minimizing the absolute deviation of the variance of log ratios.
Hardware for automated liquid transfer and handling.
Software used to control automated liquid handler.
An ordered, finite set of negative floats.
An ordered, finite set of negative integers.
An ordered, finite set of nonpositive floats.
An ordered, finite set of positive integers.
The values presented are logarithm, base 10.
The values presented are logarithm, base 2.
The values presented are logarithm, base e.
An element that is an oligonucleotide of at least 50 nucleotides in length.
A transformation method that involves removal of Features with low intensities in one or both channels from the data set. The threshold for exclusion is usually based on some estimation of local background intensity.
The unit of total light output from a light source.
A metric unit equal to one lumen per square meter. This unit is the modern equivalent of foot-candles where one footcandle is 10.76 lux.
sequence of a processed transcript capable of directing protein synthesis
individual whose sex organs contain only male gametes
the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData
the mean and associated confidence values resulting from combining the data from 2 or more sets of BioAssayData. Confidence indicators include, but are not limited to:confidence interval, standard deviation, coefficient of variation, and p-value.
the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData
the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData
the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData
A record which describes and identifies a microarray experiment e.g. GEO
The source DNA was not printed for a Feature or Zone on the slide, possibly due to lack of sample, broken or clogged spotting pin.
Mix by drawing up and down with a pipette.
The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas.
a designelement group consisting of multiple types
A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites.
an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins
Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1.
Unit of time corresponding to approx. one cycle of the moon's phases.
The array is made on a nitrocellulose filter.
The modification of an organism due to the presence of DNA from another individual, e.g. of a different strain, species or breed. These do not include targeted transgenics such as knock-ins and knock-outs.
A normalization testing experiment design tests different normalization procedures.
intensities from one or both channels resulting from normalization of MeasuredBioAssayData.
ratios resulting from normalization of MeasuredBioAssayData
The BioSample at any stage other than immediately before labeling.
The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter.
The source DNA for a Feature was not uniformly deposited.
The procedure of extracting nucleic acid from the biomaterial.
A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank
A publication type which is available online and which is not an online journal article, e.g. a web site or service.
A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD
Software upon which other software runs.
An operator variation experiment design type assesses the operator performance and relation to data consistency and quality.
An operon identification experiment type is designed to identify locations and members of operons in a genome.
An optimization experiment design type is where different protocols or protocol parameters are compared.
delivery method for drug or compound whereby the drug is administered via the mouth
DNA from organelles such as the mitochondria or chloroplast.
RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus.
one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria
An organism part comparison experiment design type compares tissues, regions, organs within or between organisms
A biomaterial obtained embedded in paraffin (wax).
A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
a record which identifies and describes biological pathways, e.g. a KEGG record
A record which descibes and identifies a pedigree or lineage for a strain, line,individal or cell whose lineage traceable e.g. a wormbase cell lineage record, or a pedigree record for a mouse
An experiment which has a peer reviewed publication attached.
A descriptor for FactorValue where PhysicalCharacteristics are compared.
The procedure of putting a physical object in a container/physical space.
sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts
A chromosomal abnormality in which there are extra complete multiples.
sequence of a protein, a linear amino acid polymer
Describes a cell, nucleus or organism with three or more copies of each chromosome.
biomaterial removed after the death of the organism
gene sequence which has been computationally predicted
sample which has been removed prior to the death of an organism
The type of protocol used to preserve (including storage or keep in statis) the biomaterial.
genomic sequence 5' to a gene where the transcription initiation complex forms.
The action of enriching a BioMaterial (organism, cell, nucleic acid etc) or Compound e.g. for FACS for positive selection or RNA cleanup the Action or ProtocolType is purify (see fractionate).
A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance
results of data reduction involving computation of the ratio of signal intensities obtained from hybridization of two, or more, labelled extracts to one, or more arrays
Interchanges of genetic material among different chromosomes such that the total chromosome complement may still contain all of the genetic material.
The shape of the feature on the array is rectangular.
A reference experiment design type is where all samples are compared to a common reference.
The procedure of extracting/taking out a part of a reaction/contents of a container.
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
The procedure in which solid material is dispensed or dissolved in a liquid.
Generation of a DNA strand from an RNA strand using reverse transcriptase.
Translocation in which the centromeres of two acrocentric chromosomes appear to have fused, forming an abnormal chromosome consisting of the long arms of two different chromosomes with loss of the short arms.
The procedure of euthanizing an organism.
A secreted protein identification design type identifies transcripts associated with a secretory pathway during translation and is used to infer which proteins are secreted or membrane bound.
preservation type whereby the seed is maintained in a dormant state
A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.
An action where the temperature is specified.
A descriptor for FactorValue where Sex is compared.
A sex experiment design type assays differences associated with an organism's sex, gender or mating type.
An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes).
A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software).
a nucleic acid consiting of a single polynucleotide chain.
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.
Person or organization that manufactured the software.
soil, growth media for plants and other soil living organisms
The male offspring of the patient or individual under study.
An instrument for sonicating biomaterials.
A species experiment design type assays differences between distinct species.
A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species.
Conceptual action for specified protocol applied in treatment.
Hardware for measuring light at different wavelengths.
An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes.
TechnologyType of FeatureGroup where antibodies are spotted directly.
TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly.
A descriptor for the TechnologyType for a group of features where double stranded DNA is spotted on the array e.g. a PCR of a cDNA clone.
TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly.
The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate.
The shape of the feature on the array is square.
sequence of a single stranded synthesized oligonucleotide
Depriving an organism of food or nutrients
A stimulus or stress experiment design type is where the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity, for the purposes of keeping it in the same state.
A descriptor of FactorValue where comparisons of strains or lines are made.
A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
The values are a sequence of one or more characters.
Delivery method whereby a drug or compound is administered under the skin of the organism.
Person who is the primary contact for data submitted to a database.
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.
Groups of assays that are related as part of a time series.
sequence that represents the product of an RNA polymerase engaged in transcription
A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome.
The process of bringing about genetic alteration of any cell or organism by a variety of means including recombinant DNA technology, viruses, chemical mutagens, and X-rays.
A translational bias is an experiment design which characterizes the association of transcripts and translation machinery.
The possession of a third chromosome of any one type in an otherwise diploid cell.
A descriptor used in cancer biology to describe abnormalities of tumor cells.
Sequence feature whose derivation is unknown.
The values are unordered and have no scale.
Sequence from a vector, DNA of any transmissible agent e.g. plasmid or virus into which a segment of foreign DNA can be spliced, does not include insert sequence. These terms should be used when other terms such as plasmid, YAC, BAC are used.
one or more DNA or RNA based non cellular infective agent, including bacteriophage
An instrument that mixes by rapid oscillation.
Allow time to pass. It's measurement should be a unit of time.
The process of applying a solvent (e.g. water) or a solution (e.g. SSC/SDS) to a BioMaterial or an array to remove impurities or unwanted compounds.
A device for controlling temperature by immersion in water.
The genotype or phenotype that is found in nature or in standard laboratory stocks for a given organism. For a single locus, the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.