MGED_ONTOLOGY_TERM_ID ONTOLOGY_TERM_TYPE_ID NAME DEFINITION URI EXTERNAL_DATABASE_RELEASE_ID SOURCE_ID 29750 43 species_design A species experiment design type assays differences between distinct species. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #species_design 29751 43 openGALEN OpenGALEN Human Anatomy - opensource database of approx. ten thousand http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #openGALEN 29752 43 fM femtomolar, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #fM 29753 43 transcript sequence that represents the product of an RNA polymerase engaged in transcription http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #transcript 29754 44 TargetedCellType 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TargetedCellType 29755 43 organism_part_comparison_design An organism part comparison experiment design type compares tissues, regions, organs within or between organisms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #organism_part_comparison_design 29756 43 hybridization The process of incubating one or more labeled extracts with an array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #hybridization 29757 43 intramuscular_injection Delivery method for a compound or drug where the substance is administered via an injection into the muscle. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #intramuscular_injection 29758 43 MAD_stage database entry from mouse anatomical dictionary for developmental stage term http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MAD_stage 29759 43 mix_by_pipette Mix by drawing up and down with a pipette. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mix_by_pipette 29760 43 version_1.1.7 a version of the MGED Ontology http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #version_1.1.7 29761 43 NCBI_taxonomy identifier for a taxon provided by the NCBI taxonomy database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCBI_taxonomy 29762 43 self_vs_self_design A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #self_vs_self_design 29763 44 StrainOrLineDatabase Database of strain, line, cultivar or ecotype information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #StrainOrLineDatabase 29764 44 TumorGradingDatabase Database of tumor grading information http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TumorGradingDatabase 29765 43 operator_variation_design An operator variation experiment design type assesses the operator performance and relation to data consistency and quality. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #operator_variation_design 29766 43 unknown_substrate_type SubstrateType of unknown type. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #unknown_substrate_type 29767 43 mating_type_a Mating type of S. cerevisiae. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mating_type_a 29768 43 positive true or yes http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #positive 29769 43 timepoint Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #timepoint 29770 43 control_design_element_group_type 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #control_design_element_group_type 29771 43 behavioral_design_type A design type in which some behavior(s) of an organism is studied. The behavior can be innate, such as path finding in bees. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #behavioral_design_type 29772 44 VolumeUnit Units used for volume measurements. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #VolumeUnit 29773 44 DataType Primitive data types found in computing languages such as float, boolean, etc. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DataType 29774 43 spotted_protein_features TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #spotted_protein_features 29775 43 alexa_660 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #alexa_660 29776 43 submitter Person who is the primary contact for data submitted to a database. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #submitter 29777 43 data_coder person who prepares the MAGE-ML file http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #data_coder 29778 64 has_human_readable_URI property indicating that the contents found at this uri are human readable http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_human_readable_URI 29779 43 wait Allow time to pass. It's measurement should be a unit of time. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #wait 29780 43 control_genomic_DNA A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #control_genomic_DNA 29781 43 change_biomaterial_characteristics Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #change_biomaterial_characteristics 29782 64 has_measurement_type property indicating that the class has a measurement type http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_measurement_type 29783 43 clinical_treatment A descriptor for a clinical treatment for a patient. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #clinical_treatment 29784 64 has_image_format property indicating that the class has an image format http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_image_format 29785 43 Pathbase database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Pathbase 29786 43 F+ mating type indicating the presence of F plasmid in a bacterial cell http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #F+ 29787 43 PNG Portable Network Graphic, a lossless image data format. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PNG 29788 44 SubstrateType Controlled terms for descriptors of types of array substrates. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #SubstrateType 29789 43 father A male parent. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #father 29790 43 umol micromoles, quantity unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #umol 29791 43 filtered_data data from which a subset has been removed based on some criteria, e.g. data below an intensity threshold http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #filtered_data 29792 43 low_intensity_filter 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #low_intensity_filter 29793 44 EnvironmentalHistory A description of the conditions the organism has been exposed to that are not one of the variables under study. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #EnvironmentalHistory 29794 43 pool The process of combining two or more BioMaterials. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #pool 29795 64 has_database property indicating that the class has a database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_database 29796 43 mg milligram, mass unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mg 29797 43 synthetic_DNA DNA which is generated by chemical or enzymatic (non cellular) means. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #synthetic_DNA 29798 43 ORF 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ORF 29799 64 has_feature_shape property indicating that the class has a feature shape http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_feature_shape 29800 64 has_category property indicating that the class has a categeory http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_category 29801 43 http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ uri for NCBI taxonomy database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ 29802 43 cell_ontology database of cell ontology terms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cell_ontology 29803 44 GeographicLocation A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #GeographicLocation 29804 44 SequenceOntologyDatabase Database for sequence annotation information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #SequenceOntologyDatabase 29805 43 alexa_594 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #alexa_594 29806 43 exon sequence which represents regions of a transcript that are joined to another exon during splicing http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #exon 29807 43 disease_staging The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #disease_staging 29808 64 has_authors property indicating that the class has authors http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_authors 29809 43 biosequence_provider Provider of biosequences (clones, oligos etc) for deposition on the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #biosequence_provider 29810 43 individual A descriptor for FactorValue where BioSources are compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #individual 29811 43 replicate_analysis A transformation method in which the intensity or ratio data from Features obtaining the same source DNA are combined. Analysis of the mean and standard deviation values for replicated Features can be used to exclude http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #replicate_analysis 29812 43 cells/ml the number of cells per ml http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cells/ml 29347 43 NCI_histology_database a controlled vocabulary for histology http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_histology_database 29348 43 extract The BioSample immediately before labeling. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #extract 29349 64 has_issue property indicating that the class has an issue http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_issue 29350 43 Ci 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). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Ci 29351 43 ontology_record A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ontology_record 29352 44 BioAssayData BioAssayData refers to the data files including images generated from one or more BioAssays. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioAssayData 29353 43 RNA_stability_design A RNA stability experiment design type examines the stability and/or decay of RNA transcripts. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #RNA_stability_design 29354 43 experimental_design_element_group_type A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #experimental_design_element_group_type 29355 43 us microsecond, unit of time http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #us 29356 43 PCR_questionable PCR with multiple bands, or smear, in gel-separated reaction products http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PCR_questionable 29357 43 organellar_DNA DNA from organelles such as the mitochondria or chloroplast. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #organellar_DNA 29358 44 Allele 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Allele 29359 43 http://genex.hgu.mrc.ac.uk uri for EMAP http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://genex.hgu.mrc.ac.uk 29360 43 genotyping_design A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #genotyping_design 29361 43 spotted_colony_features TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #spotted_colony_features 29362 72 has_been_treated (null) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_been_treated 29363 43 http://sig.biostr.washington.edu/projects/fm/ uri for The Foundational Model of Anatomy (FMA) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://sig.biostr.washington.edu/projects/fm/ 29364 44 HigherLevelAnalysisProtocolType A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #HigherLevelAnalysisProtocolType 29365 64 has_year property indicating that the class has a year http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_year 29366 43 irradiate treatment of a biomaterial with radiation e.g. electromagnetic radiation http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #irradiate 29367 43 software_manufacturer Person or organization that manufactured the software. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #software_manufacturer 29368 43 technical_replicate 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #technical_replicate 29369 43 hardware_variation_design A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #hardware_variation_design 29370 43 DNA_sequencer An instrument that produces DNA sequences. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DNA_sequencer 29371 64 has_ID property indicating that the class has an identifier http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_ID 29372 64 has_prior_disease_state property indicating that the class has a prior disease state http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_prior_disease_state 29373 44 PolymerType Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PolymerType 29374 64 has_hardware property indicating that the class has hardware http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_hardware 29375 43 place The procedure of putting a physical object in a container/physical space. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #place 29376 43 secreted_protein_identification_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #secreted_protein_identification_design 29463 72 has_accession_version (null) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_accession_version 29377 43 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C16403 uri for NCI_strain_or_line_database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C16403 29378 43 organism_part The part of the organism's anatomy from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, or body location (arm). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #organism_part 29379 44 IndividualGeneticCharacteristics The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #IndividualGeneticCharacteristics 29380 44 HardwareType Controlled terms for descriptors of types of hardware. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #HardwareType 29381 43 spotted_ss_oligo_features The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #spotted_ss_oligo_features 29382 44 ReplicateDescription ReplicateDescription provides details about the type of replication used in the experiment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ReplicateDescription 29383 43 deleted_term The term was deleted from the MGED CoreOntology. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #deleted_term 29384 44 MethodologicalFactorCategory 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MethodologicalFactorCategory 29385 43 all_pairs An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #all_pairs 29386 44 ConcentrationUnit Units used for concentration measurements. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ConcentrationUnit 29387 43 nucleic_acid_primary_sequence_record A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nucleic_acid_primary_sequence_record 29388 64 has_test_result property indicating that the test has a test result http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_test_result 29389 64 has_nodes property indicating that the class has a node http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_nodes 29390 43 yes true http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #yes 29391 44 DeprecatedTerms Class to hold deprecated instances and classes. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DeprecatedTerms 29392 43 mtDNA sequence from the mitochondrial genome http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mtDNA 29393 43 amino_acid_primary_sequence_record A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #amino_acid_primary_sequence_record 29394 44 DiseaseStaging The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DiseaseStaging 29395 43 incubate The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #incubate 29396 43 biotin a compound used for labeling/detection purposes http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #biotin 29397 43 mean_and_variance the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mean_and_variance 29398 43 concentrate Increasing the concentration of solutes in a solution or suspension. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #concentrate 29399 43 log_base_10 The values presented are logarithm, base 10. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #log_base_10 29400 43 time_series_design Groups of assays that are related as part of a time series. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #time_series_design 29401 43 A Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #A 29402 64 has_factor_value_ontology_entry property indicating that the class has an ontology entry http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_factor_value_ontology_entry 29403 44 Treatment A treatment is the process or action by which a biomaterial is created from an input biomaterial. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Treatment 29404 43 liquid_handler_software Software used to control automated liquid handler. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #liquid_handler_software 29405 43 rectangular_feature The shape of the feature on the array is rectangular. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #rectangular_feature 29406 43 birth the action of emergence and separation of offspring from the mother. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #birth 29407 43 genomic_region_amplification increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #genomic_region_amplification 29408 43 chromosomal_inversion 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #chromosomal_inversion 29409 44 OntologyEntry External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #OntologyEntry 29410 43 nonpositive_integer An integer less than or equal to zero. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nonpositive_integer 29411 43 cellular_process_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cellular_process_design 29412 64 has_fiducials property indicating that the class has fiducials http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_fiducials 29413 43 cell_line A descriptor for FactorValue where CellLine is compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cell_line 29414 43 MTB_Database Database entry from the mouse tumor biology database, a resource for nomenclature of mouse tumors. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MTB_Database 29415 43 clustered_data results of an analysis method that groups data based on some measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #clustered_data 29416 43 molecules number of molecules, quantity unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #molecules 29417 43 organism_status The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #organism_status 29418 43 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C13007 uri for NCI_organism_part_database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C13007 29419 64 has_mid_initials property indicating that the class has a middle initials http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_mid_initials 29420 43 feeding Delivery method where a compound/drug is administered in food or water. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #feeding 29421 44 Transformation The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Transformation 29422 43 control_buffer A Reporter where only buffer was deposited on the array http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #control_buffer 29423 44 StrandType A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #StrandType 29424 43 eclosion Emergence of an adult insect from its pupa or cocoon. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #eclosion 29425 44 AuditAndSecurityPackage MAGE package for contacts including organizations and people. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #AuditAndSecurityPackage 29426 44 Light The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Light 29427 43 control_empty A Reporter where no material or buffer was deposited on the array http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #control_empty 29428 44 MGEDOntology 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MGEDOntology 29429 43 non-targeted_transgenic_variation_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #non-targeted_transgenic_variation_design 29430 62 is_solvent property indicating that the class is a solvent http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #is_solvent 29431 43 PAC sequence from a P1 artificial chromosome http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PAC 29432 44 DesignElementGroupType Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DesignElementGroupType 29433 43 genomic_DNA high molecular weight DNA http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #genomic_DNA 29434 43 nl nanoliter unit of volume http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nl 29435 64 has_type property indicating that the class has a type http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_type 29436 43 FlyBase_organism_part_database curated database containing information on Drosophila genes, alleles etc http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FlyBase_organism_part_database 29437 43 http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C28076 uri for NCI_tumor_grading database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C28076 29438 44 FailType Controlled terms for descriptors of failures (as in PCR) associated with reporters. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FailType 29439 44 Compound A drug, solvent, chemical, etc., with a property that can be measured such as concentration. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Compound 29440 43 cc a cubic centimeter, volume unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cc 29441 64 has_phone property indicating that the class has a phone http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_phone 29442 43 relative a measurement where the value is dependent on another measurement http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #relative 29443 43 ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2002/ uri of ICD9, international classification of diseases version 9 http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD9-CM/2002/ 29444 44 CellLineDatabase Database of cell line information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #CellLineDatabase 29445 43 Euclidean_distance The Euclidian distance is the square root of the sums of the differences between the squares of each pair of values in a data series. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Euclidean_distance 29446 43 in_medium Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #in_medium 29447 43 pedigree_record 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 http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #pedigree_record 29448 43 feature_extraction_software Software to create MeasuredBioAssayData from images. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #feature_extraction_software 29449 43 version_1.1.8 The version 1.1.8 of the MGED Ontology. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #version_1.1.8 29450 43 chromosomal_duplication An irregularity in the number of chromosomes, usually in the form of a gain of genetic material. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #chromosomal_duplication 29451 64 has_software property indicating that the class has software http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_software 29452 43 candela 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #candela 29453 43 mother A female parent. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mother 29454 43 PCR Polymerase chain reaction. An element generated using this procedure. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PCR 29455 44 MGEDCoreOntology An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MGEDCoreOntology 29456 43 NCI_targeted_cell_type_database a controlled vocabulary of targeted cell types http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_targeted_cell_type_database 29457 64 has_volume property indicating that the class has a volume http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_volume 29458 43 list_of_booleans An ordered, finite set of booleans. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_booleans 29459 43 sonicator An instrument for sonicating biomaterials. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #sonicator 29460 43 consortium_member A member of a consortium of institutions. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #consortium_member 29461 43 compound_treatment_design A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #compound_treatment_design 29462 43 acclimatization The action of stabilizing an organism prior to treatment http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #acclimatization 29464 43 purify 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). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #purify 29465 43 replaced_term The term name was changed to one more appropriate to the intent of the definition. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #replaced_term 29466 43 CBIL_CV a controlled vocabulary provided by CBIL http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #CBIL_CV 29467 43 predicted_gene gene sequence which has been computationally predicted http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #predicted_gene 29468 43 nonnegative_integer An integer >= 0. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nonnegative_integer 29469 43 genetic_modification An action whereby an organism(s) has had genetic material removed, added, or rearranged. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #genetic_modification 29470 44 LabelCompound Compounds that are used for labeling extracts. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #LabelCompound 29471 44 HigherLevelAnalysisPackage MAGE package for HigherLevelAnalysis http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #HigherLevelAnalysisPackage 29472 43 cell_type_comparison_design A cell type comparison design experiment design type compares cells of different type for example different cell lines. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cell_type_comparison_design 29473 43 aminosilane a surface coating type for immobilization with the compound aminosilane http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #aminosilane 29474 43 uncentered_Pearson_correlation 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #uncentered_Pearson_correlation 29475 43 tRNA gene sequence from a gene coding for transfer RNA http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #tRNA gene 29476 43 polylysine a surface coating for immobilization with the polypeptide, polylysine http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #polylysine 29477 44 TimeUnit Units used for time measurements. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TimeUnit 29478 43 gene_knock_out 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #gene_knock_out 29479 64 deprecated_from_version property indicating the version of the MGED Ontology that the term was deprecated from http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #deprecated_from_version 29480 64 has_family_relationship property indicating that the class has a family relationship http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_family_relationship 29481 64 has_maximum_measurement property indicating that the class has a maximum measurement http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_maximum_measurement 29482 43 male individual whose sex organs contain only male gametes http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #male 29483 43 percent_vol/vol percentage volume per volume, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #percent_vol/vol 29484 43 absolute a measurement where the value is independent of other measurements http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #absolute 29485 43 ug microgram, unit of mass http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ug 29486 44 ClinicalTreatmentDatabase Database of clinical treatment information http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ClinicalTreatmentDatabase 29487 43 homogenizer An instrument which fragments tissues or other biomaterials. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #homogenizer 29488 43 beginning_of_stage time point that indicates the start of some developmental stage http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #beginning_of_stage 29489 43 histological_slide_preparation The action of preparing a slide for the microscopical examination of organism parts or cell types. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #histological_slide_preparation 29490 44 DevelopmentalStageDatabase Database of developmental stage information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DevelopmentalStageDatabase 29491 64 has_factor_value property indicating that the class has a factor value http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_factor_value 29492 43 K Kelvin, unit of temperature http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #K 29493 43 haploid Describes a cell, nucleus or an organism with one copy of each chromosome. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #haploid 29494 44 SoftwareType Controlled terms that provide descriptors for the type of software. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #SoftwareType 29495 44 BibliographicReference A bibliographic reference is a published citation in a journal, book, other format e.g. web resource http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BibliographicReference 29496 43 bedding The material (e.g. straw) that an animal sleeps on http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #bedding 29497 43 spotted_antibody_features TechnologyType of FeatureGroup where antibodies are spotted directly. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #spotted_antibody_features 29498 64 has_editor property indicating that the class has an editor http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_editor 29499 43 feature_extraction The process of obtaining quantifiable values from the scanned image of the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #feature_extraction 29500 43 strain_or_line A descriptor of FactorValue where comparisons of strains or lines are made. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #strain_or_line 29501 44 Water Water consumed by or enveloping the organism that the biosource is derived from. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Water 29502 43 array_manufacture_software Software to control an arrayer. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #array_manufacture_software 29503 43 ng nanogram, a mass unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ng 29504 43 Affymetrix_average_difference 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Affymetrix_average_difference 29505 44 MeasurementPackage MAGE package for measurement. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MeasurementPackage 29506 43 heavy_background The Zone is excluded due to smearing, streaking, or dense background in the Zone. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #heavy_background 29507 43 cytoplasmic_RNA RNA obtained from the cytoplasm. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cytoplasmic_RNA 29508 43 transfect 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #transfect 29509 43 control_label Reporter used as a control where some label has been deposited. This includes flour and radioactively labeled oligos and flours alone. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #control_label 29510 64 has_units property indicating that the class has units http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_units 29511 43 glass The array is made on a glass slide. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #glass 29512 64 has_result property indicating the class has a result http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_result 29513 43 snRNA_gene sequence from gene coding for small nuclear RNA http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #snRNA_gene 29514 43 flip-dye_consistency 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #flip-dye_consistency 29515 44 MGEDOntologyVersion The version of the MGED Ontology. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MGEDOntologyVersion 29516 64 has_model property indicating that the class has a model http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_model 29517 43 candelas_per_square_meter Unit of brightness or luminance. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #candelas_per_square_meter 29518 72 has_URI (null) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_URI 29519 72 has_biosource_type (null) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_biosource_type 29520 43 BAC sequence from a bacterial artificial chromosome http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BAC 29521 43 ds_oligo a double stranded oligonucleotide http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ds_oligo 29522 43 http://www.loinc.org/download uri for LOINC http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.loinc.org/download 29523 64 has_machine_readable_URI property indicating that the contents found at this uri are machine readable (i.e. in a standard format) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_machine_readable_URI 29524 43 liquid media type, usually some sort of broth http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #liquid 29525 44 PerturbationalDesign A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PerturbationalDesign 29526 43 list_of_nonpositive_floats An ordered, finite set of nonpositive floats. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_nonpositive_floats 29527 43 gene_knock_in The modification of an organism that inserts a functional gene at the site of a nonfunctional locus for that gene using recombinant methods. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #gene_knock_in 29528 43 funder Contact which provides funding for experiments. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #funder 29529 43 TDMS Toxicology Data Management System, a database resource for systems, organs, pathology, etc. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TDMS 29530 43 mm millimeter, unit of distance http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mm 29531 44 Person The individual to contact regarding something provided such as a biomaterial. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Person 29532 43 unknown_sex organism(s) whose sex is unknown http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #unknown_sex 29533 43 http://www.cbil.upenn.edu/anatomy.php3 uri for CBIL anatomy terms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.cbil.upenn.edu/anatomy.php3 29534 43 antibody glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #antibody 29706 72 has_donor (null) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_donor 29845 72 has_owner (null) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_owner 29535 43 TIFF 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TIFF 29536 44 DistanceUnit Units used for distance measurements. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DistanceUnit 29537 43 ChemID Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ChemID 29538 44 PhenotypeDatabase Database of phenotype information http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PhenotypeDatabase 29539 43 degrees_F degrees Fahrenheit, unit of temperature http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #degrees_F 29540 44 ExperimentDesignType The ExperimentDesignType is the high level description for studies such as "time series", "dose response", etc. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ExperimentDesignType 29541 44 DataTransformationProtocolType The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DataTransformationProtocolType 29542 43 array_manufacturer Person or organization that manufactured the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #array_manufacturer 29543 44 GrowthCondition 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #GrowthCondition 29544 44 BiologicalProperty A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BiologicalProperty 29545 44 Biometrics Physical properties of the BioMaterial e. g. mass or height http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Biometrics 29546 44 TemperatureUnit Units used for temperature measurements. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TemperatureUnit 29547 43 consultant 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #consultant 29548 44 FiducialType A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FiducialType 29549 43 YAC sequence from yeast artificial chromosome http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #YAC 29550 43 primary_protein_structure_record A record which describes and identifies an experimentally derived protein structure e.g. MSD http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #primary_protein_structure_record 29551 64 has_experiment_design property indicating that the class has an experiment design http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_experiment_design 29552 64 has_providers property indicating that the class has providers http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_providers 29553 43 control_biosequence 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #control_biosequence 29554 43 list_of_positive_integers An ordered, finite set of positive integers. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_positive_integers 29555 64 has_biosource_type property indicating that the class has a biosource type http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_biosource_type 29556 44 Histology Microscopic morphology of tissues. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Histology 29557 43 x(times) multiple of stock solution concentration, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #x(times) 29558 64 has_make property indicating that the class has a make http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_make 29559 43 biopsy A biomaterial, usually tissue, cells, fluid or a fresh sample obtained during surgery, from an organism. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #biopsy 29560 64 has_node_value_type property indicating that the class has a node value type http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_node_value_type 29561 43 female of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #female 29562 64 has_address property indicating that the class has an address http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_address 29563 44 TestResult TestResult is the recorded value of the test outcome. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TestResult 29564 44 ArrayGroup An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ArrayGroup 29565 43 Cy5 fluorophore used for labeling/detection purposes http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Cy5 29566 43 Spearmans_rank_correlation Computed as the ordinary Pearson correlation coefficient between two groups of rankings. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Spearmans_rank_correlation 29567 43 http://www.gramene.org/ uri for GRAMENE http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.gramene.org/ 29568 43 http://www.atcc.org/Cultures/Products.cfm uri for ATCC http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.atcc.org/Cultures/Products.cfm 29569 43 clinical_information A descriptor for FactorValue where ClinicalInformation is compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #clinical_information 29570 44 CompoundDatabase Database of compound information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #CompoundDatabase 29571 44 OrganismDatabase Database of taxonomic information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #OrganismDatabase 29572 43 http://www.cabri.org/CABRI/cabri-srs-doc/ uri for cabri, common access to biological resources and information http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.cabri.org/CABRI/cabri-srs-doc/ 29573 44 ConcentrationUnitOther Concentration units not specified in MAGE. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ConcentrationUnitOther 29574 64 has_additive property indicating that the class has an additive http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_additive 29575 43 collapsed_spot_replicate 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://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #collapsed_spot_replicate 29576 43 development_or_differentiation_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #development_or_differentiation_design 29577 44 ImageFormat Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ImageFormat 29578 44 ComplexAction Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ComplexAction 29579 43 uM Micromole per liter or micromolar, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #uM 29580 43 NCI_disease_state_database a controlled vocabulary for disease states http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_disease_state_database 29581 43 clustering_software Software used to cluster the data. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #clustering_software 29582 43 cell_type A descriptor for FactorValue where CellType is compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cell_type 29583 64 has_initial_time_point property indicating that the class has an individual time point http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_initial_time_point 29584 43 operon_identification_design An operon identification experiment type is designed to identify locations and members of operons in a genome. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #operon_identification_design 29585 43 total_RNA Total cellular and nuclear RNA. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #total_RNA 29586 43 list_of_nonnegative_integers An ordered, finite set of nonnegative integers. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_nonnegative_integers 29587 43 grow A ComplexAction or ProtocolType describing growth of an organism or cell culture. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #grow 29588 43 Rad 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Rad 29589 44 GeneticModification 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #GeneticModification 29590 43 PCR_amplification Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PCR_amplification 29591 44 ExperimentDesign 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ExperimentDesign 29592 43 curator person who checks the consistency of the data and MAGE-ML file http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #curator 29593 43 genetic_variation A descriptor for FactorValue where GeneticVariation is compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #genetic_variation 29594 43 computational_feature Computationally derived sequence feature. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #computational_feature 29595 44 BioMaterialPackage Description of the source of the nucleic acid used to generate labeled material for the microarray experiment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioMaterialPackage 29596 44 SomaticModification The organism has had non-genetic parts removed, added, or rearranged. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #SomaticModification 29597 44 FeatureShape The expected shape of the feature on the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FeatureShape 29598 44 SurfaceType Controlled terms for descriptors for coating of the substrate. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #SurfaceType 29599 44 ZoneDefect A technical manufactured described defect for zones. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ZoneDefect 29600 43 translational_bias_design A translational bias is an experiment design which characterizes the association of transcripts and translation machinery. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #translational_bias_design 29601 43 online_resource A publication type which is available online and which is not an online journal article, e.g. a web site or service. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #online_resource 29602 44 NodeValueType Controlled set of terms for describing the type of values (e.g., Euclidean distance). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NodeValueType 29603 43 stimulus_or_stress_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #stimulus_or_stress_design 29604 43 not_uniform The source DNA for a Feature was not uniformly deposited. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #not_uniform 29605 43 chromosome Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #chromosome 29606 44 OrganismPart The part of the organism's anatomy from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, or body location (arm). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #OrganismPart 29607 43 lumen The unit of total light output from a light source. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #lumen 29608 43 genetic_modification_design A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #genetic_modification_design 29609 43 clinical_record record which describes and identifies clinical information about an organism http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #clinical_record 29610 44 LightUnit Units for measuring the intensity of light. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #LightUnit 29611 43 pg picogram, mass unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #pg 29612 64 has_part_modified property indicating that the class has a modified part http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_part_modified 29613 64 has_clinical_record property indicating that the class has a clinical record http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_clinical_record 29614 44 DiseaseState 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DiseaseState 29615 44 Reporter Description of the material placed on a feature (spot). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Reporter 29616 44 CellLine The identifier for the established culture of a metazoan cell if one was used as a biomaterial. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #CellLine 29617 43 L liter, unit of volume http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #L 29618 44 CellType 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #CellType 29619 43 mol mole, unit of quantity http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mol 29620 64 has_action property indicating that the class has an action http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_action 29621 62 has_description property indicating that the class has a description http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_description 29622 44 DiseaseStagingDatabase Database of disease staging information http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DiseaseStagingDatabase 29623 43 TAIR The Arabadopsis Information Resource. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TAIR 29624 43 frozen_sample A biomaterial obtained frozen http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #frozen_sample 29625 43 change_temperature Change in temperature. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #change_temperature 29626 43 NCI_tumor_grading_database a controlled vocabulary of tumor grading terms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_tumor_grading_database 29627 43 rRNA gene sequence from gene coding for ribosomal RNA exact synonym: ribosomal RNA gene http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #rRNA gene 29628 43 http://www.informatics.jax.org/searches/Phat.cgi?id=MP:0000001 uri for the Mammalian Phenotype Browser http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.informatics.jax.org/searches/Phat.cgi?id=MP:0000001 29629 43 ul microliter, unit of volume http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ul 29630 44 PhysicalBioSequenceType A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PhysicalBioSequenceType 29631 43 nuclear_RNA RNA obtained from the nucleus. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nuclear_RNA 29632 44 MeasurementType class to hold instances used as the filler for the property has_measurement_type http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MeasurementType 29633 44 Age 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). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Age 29634 44 DesignElement Design elements are reporters, features, and composite elements as defined by MAGE. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DesignElement 29635 44 TestType Descriptor of the Test performed e.g. Leukocyte count http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TestType 29636 64 has_species property indicating that the class has species http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_species 29637 43 dl deciliter, unit of volume http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #dl 29638 43 reverse the reverse strand http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #reverse 29639 43 arrayer An instrument capable of manufacturing arrays by spotting material. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #arrayer 29640 44 PreservationType The type of method used to preserve (keep in stasis) the organism or biosource. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PreservationType 29641 44 ObservationDatabase Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ObservationDatabase 29642 43 metastatic_site the organism part in which additional tumors are identified remote from the primary site http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #metastatic_site 29643 43 quality_control_testing_design A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #quality_control_testing_design 29644 44 Haplotype The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Haplotype 29645 43 JAX_mouse_strains Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #JAX_mouse_strains 29646 43 unknown_surface_type A SurfaceType of unknown type. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #unknown_surface_type 29647 43 store 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #store 29648 43 wild_type 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #wild_type 29649 43 signal A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #signal 29650 43 percent_weight/vol percent weight per volume, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #percent_weight/vol 29651 43 waterbath A device for controlling temperature by immersion in water. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #waterbath 29652 43 cpm counts per minute, unit of light emissions produced by ionizing radiation. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cpm 29653 43 bioassay_data_transformation_software Software used to transform the Measured or DerivedBioAssay data e.g. normalization. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #bioassay_data_transformation_software 29654 43 subcutaneous Delivery method whereby a drug or compound is administered under the skin of the organism. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #subcutaneous 29655 43 nucleic_acid_extraction The procedure of extracting nucleic acid from the biomaterial. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nucleic_acid_extraction 29656 64 has_disease_staging property indicating that the class has disease staging http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_disease_staging 29657 43 gene 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://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #gene 29658 43 hardware_manufacturer Person or organization that manufactured the hardware. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #hardware_manufacturer 29659 43 split 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 http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #split 29660 62 has_title property indicating that the class has a title http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_title 29661 44 Parameter A parameter is a variable within a protocol. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Parameter 29662 43 bioassay_replicate_reduction 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #bioassay_replicate_reduction 29663 64 has_disease_location property indicating the location of the disease. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_disease_location 29664 44 ChromosomalAberration 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ChromosomalAberration 29665 64 has_individual property indicating that the class has an individual http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_individual 29666 44 Contact Organizations or individuals that may be contacted. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Contact 29667 43 unknown_experiment_design_type ExperimentDesignType of unknown type. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #unknown_experiment_design_type 29668 44 DistanceUnitOther Distance units not specified in MAGE. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DistanceUnitOther 29669 43 alexa_680 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #alexa_680 29670 43 chromosomal_translocation 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #chromosomal_translocation 29671 44 BioMaterialCharacteristics Properties of the biomaterial before treated in any manner for the purposes of the experiment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioMaterialCharacteristics 29672 43 sex A descriptor for FactorValue where Sex is compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #sex 29673 44 Database Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Database 29674 43 media The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #media 29675 64 has_chromosomal_aberration_classification property indicating that the class has a chromosomal aberration classification http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_chromosomal_aberration_classification 29676 43 cell One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cell 29677 44 Measurement Measured values and units. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Measurement 29678 64 has_test_protocol property indicating that the test has a test protocol http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_test_protocol 29679 43 http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype uri for TAIR http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype 29680 43 merged_term the term has been subsumed into a more general term http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #merged_term 29681 43 IUPAC_Clinical_Chemistry_Guidelines A resource of vocabularies for describing clinical tests, e.g. blood chemistry. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #IUPAC_Clinical_Chemistry_Guidelines 29682 44 ControlType Controlled terms for descriptors for the type of control design element. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ControlType 29683 44 FactorValue The value of an ExperimentFactor. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FactorValue 29684 43 EMAP The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy covers the 26 developmental stages (Theiler Stages) from fertilization to birth. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #EMAP 29685 43 cDNA_clone 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://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cDNA_clone 29686 44 MethodologicalDesign A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MethodologicalDesign 29687 43 33P 33 P, radioactive isotope of phosphorus, used for labeling/detection purposes. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #33P 29688 43 image_acquisition_software Software to control a scanner and manipulate and save images. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #image_acquisition_software 29689 43 starvation Depriving an organism of food or nutrients http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #starvation 29690 43 integer A value which is a whole number (e.g. 10). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #integer 29691 44 BioSample The BioSource after any treatment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioSample 29692 43 sex_design A sex experiment design type assays differences associated with an organism's sex, gender or mating type. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #sex_design 29693 43 mean_and_coefficient_of_variation the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mean_and_coefficient_of_variation 29694 43 image_record A record which describes and identifies an image, e.g. an image from the mouse atlas http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #image_record 29695 44 TimeUnitOther Time units not specified in MAGE. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TimeUnitOther 29696 44 URI Uniform Resource Identifier http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #URI 29697 43 grandmother The mother of one's father or mother. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #grandmother 29698 43 normalized_ratios ratios resulting from normalization of MeasuredBioAssayData http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #normalized_ratios 29699 64 was_replaced_by instance property to indicate what the term was replaced by http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #was_replaced_by 29700 44 LabeledExtract The BioSample after labeling for detection of the nucleic acids. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #LabeledExtract 29701 43 clinical_history_design A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #clinical_history_design 29702 43 add The procedure of placing one physical object in the same container/physical space as another. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #add 29703 43 boolean The values are either TRUE or FALSE, which can be expressed as 1 and 0. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #boolean 29704 43 wash 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #wash 29705 44 PathogenTest Tests and results for pathogens infecting organism from which the biosource is derived http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PathogenTest 29707 43 agar_stab agar stab, a cell culture inoculated into agar for long term storage http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #agar_stab 29708 43 displaced_feature_or_zone The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #displaced_feature_or_zone 29709 43 Rem 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Rem 29710 43 clone_of_unkonwn_source Sequence from some nucleic acid copy and the associated vector http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #clone_of_unkonwn_source 29711 43 positive_integer An integer > 0. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #positive_integer 29712 44 PhysicalArrayDesign Descriptions pertaining to the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PhysicalArrayDesign 29713 43 function_record a record which identifies and describes the function of a gene product, e.g. E.C. record http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #function_record 29714 43 list_of_negative_floats An ordered, finite set of negative floats. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_negative_floats 29715 44 Preservation Method and type of preserving the organism or biosource (i.e. keeping it in stasis). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Preservation 29716 44 BioMaterial Description of the processing state of the biomaterial for use in the microarray hybridization. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioMaterial 29717 43 synthetic_RNA RNA which is generated by chemical or enzymatic (non cellular) means. E.g. T7 promotor generated RNA. Non-exact synonym: cRNA, complementary RNA http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #synthetic_RNA 29718 43 biological_resource_record A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #biological_resource_record 29719 43 Mammalian_Phenotype_Ontology A community effort to provide standard terms for annotating phenotypic data. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Mammalian_Phenotype_Ontology 29720 43 oligo_synthesizer Hardware for synthesizing oligos. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #oligo_synthesizer 29721 43 hermaphrodite an organism with both male and female sexual organs in one individual http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #hermaphrodite 29722 43 ss_oligo sequence of a single stranded synthesized oligonucleotide http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ss_oligo 29723 43 linear_amplification 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #linear_amplification 29724 43 growth_condition_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #growth_condition_design 29725 43 CABRI_Human_and_Animal_Cell_lines Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #CABRI_Human_and_Animal_Cell_lines 29726 44 User User is a way to id a person in a database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #User 29727 64 has_affiliation property indicating that the class has an affiliation to an institution http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_affiliation 29728 43 chromosomal_deletion The loss of a segment of the genetic material from a chromosome. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #chromosomal_deletion 29729 43 tumor_grading A descriptor used in cancer biology to describe abnormalities of tumor cells. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #tumor_grading 29730 43 laser_ablation_mark mark made on slide using a laser which is used as a point of reference for orientation (fiducial) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #laser_ablation_mark 29731 43 gene_fragment sequence of part of a gene, which is missing one or both ends http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #gene_fragment 29732 43 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C28108 uri for NCI_disease_staging_database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C28108 29733 43 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C12596 uri for NCI_cell_type_database and NCI_targeted_cell_type_database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C12596 29734 64 has_donor property indicating that the class has a donor http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_donor 29735 43 dpm disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #dpm 29736 44 AtomicAction An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #AtomicAction 29737 44 BioAssayPackage MAGE package for bioassay. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioAssayPackage 29738 43 compound_record a record which describes and identifies a compound e.g. drug record part of NCI thesaurus http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #compound_record 29739 43 biological_replicate A replicate that consists of independent biological replicates made from different individual BioSources. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #biological_replicate 29740 43 dilute Decreasing the concentration of solutes in a solution or suspension. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #dilute 29741 43 total_intensity_normalization 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #total_intensity_normalization 29742 43 degrees_C degrees celsius, unit of temperature http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #degrees_C 29743 43 coitus sexual intercourse or copulation http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #coitus 29744 43 ATCC_Cultures database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ATCC_Cultures 29745 43 list_of_floats An ordered, finite set of floats. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_floats 29746 64 has_node_value property indicating that the class has a node value http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_node_value 29747 43 hybridization_chamber A chamber in which the hybridization is performed which maintains constant conditions. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #hybridization_chamber 29748 43 aunt The sister of one's father or mother. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #aunt 29749 43 daughter The female offspring of the patient or individual under study. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #daughter 30005 43 cell_cycle_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cell_cycle_design 30006 43 unknown_sequence BioSequence of unknown type http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #unknown_sequence 30007 43 Affymetrix_DAT A proprietary image data format that is lossless and containing one channel of data. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Affymetrix_DAT 30008 44 ProtocolParameterType Descriptors for protocol parameter types, e.g. compound concentration, media type. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ProtocolParameterType 30009 43 pl picoliter, volume unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #pl 30010 44 Software The software application used. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Software 30011 64 has_MAGE_description property indicating that the class has an association to a MAGE description http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_MAGE_description 30012 43 negative_integer An integer < 0. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #negative_integer 30013 43 list_of_integers An ordered, finite set of integers. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_integers 30014 44 GeneticMaterial 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #GeneticMaterial 30015 64 has_URI property indicating that the class has a URI http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_URI 30016 64 has_database_entry_type property indicating that the class has a database entry type http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_database_entry_type 30017 43 book A publication type which has an ISBN. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #book 30018 43 trisomy The possession of a third chromosome of any one type in an otherwise diploid cell. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #trisomy 30019 43 slice_analysis 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #slice_analysis 30020 64 has_test_type property indicating that the class has a clinical test http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_test_type 30021 43 dose_response_design 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). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #dose_response_design 30022 43 transcript_identification_design A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #transcript_identification_design 30023 43 grandfather The father of one's father or mother. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #grandfather 30024 43 32P 32 P, radioactive isotope of phosphorus used for labeling/detection purposes http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #32P 30025 43 HUMAT Ontology of human developmental anatomy for Carnegie stages 1-20. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #HUMAT 30026 43 SequenceOntology The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #SequenceOntology 30027 43 reverse_transcription Generation of a DNA strand from an RNA strand using reverse transcriptase. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #reverse_transcription 30028 43 specified_biomaterial_action Conceptual action for specified protocol applied in treatment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #specified_biomaterial_action 30029 43 behavior_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #behavior_design 30030 43 replicate_design 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://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #replicate_design 30031 43 intron sequence spliced out from a transcript http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #intron 30032 43 preservation The type of protocol used to preserve (including storage or keep in statis) the biomaterial. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #preservation 30033 43 lux 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #lux 30034 43 molecular_mixture an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #molecular_mixture 30035 44 ProtocolType A controlled set of terms to provide a descriptor for the type of protocol. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ProtocolType 30036 43 NCI_strain_or_line_database a controlled vocabulary for strains or lines http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_strain_or_line_database 30037 64 has_citation property indicating that the class has a citation http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_citation 30038 64 has_email property indicating that the class has an email address http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_email 30039 43 pM picomolar, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #pM 30040 44 DesignElementGroup A DesignElementGroup holds information on Features, Reporters, or CompositeSequences. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DesignElementGroup 30041 43 heating_block A device for controlling temperature. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #heating_block 30042 44 InitialTimePoint The point from which measurements of age were taken. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #InitialTimePoint 30043 43 alexa_532 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #alexa_532 30044 44 EnvironmentalFactorCategory Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #EnvironmentalFactorCategory 30045 43 curated_nucleic_acid_sequence_feature_record A record which identifies a nucleic acid sequence feature(s) and which has been curated. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #curated_nucleic_acid_sequence_feature_record 30046 43 element_design_protocol protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #element_design_protocol 30047 44 DescriptionPackage MAGE package for description of annotations and references to annotations. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DescriptionPackage 30048 43 http://obo.sourceforge.net/list.shtml uri for HUMAT http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://obo.sourceforge.net/list.shtml 30049 64 has_treatment property indicating that the class has a treatment http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_treatment 30050 43 harvest The process of harvesting cells from culture. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #harvest 30051 64 was_tested_for property indicating that the class was tested for http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #was_tested_for 30052 43 single_stranded a nucleic acid consisting of a single polynucleotide chain. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #single_stranded 30053 43 RNA Ribonucleic acid. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #RNA 30054 43 mean_and_confidence_indicators 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mean_and_confidence_indicators 30055 44 FamilyHistory Relevant aspects of genetic preconditions or family member's clinical history. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FamilyHistory 30056 43 http://nciterms.nci.nih.gov uri of NCI Thesaurus http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://nciterms.nci.nih.gov 30057 43 float A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #float 30058 43 ellipsoid_feature The shape of the feature on the array is circular or oval. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ellipsoid_feature 30059 43 negative false or no http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #negative 30060 43 vortexer An instrument that mixes by rapid oscillation. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #vortexer 30061 43 square_feature The shape of the feature on the array is square. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #square_feature 30062 72 has_value (null) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_value 30063 44 DefectType Defects associated with features or zones such as those that are missing or moved. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DefectType 30064 43 pmol picomoles, quantity unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #pmol 30065 44 Experiment 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Experiment 30066 44 Fiducial A marking on the surface of the array that can be used to identify the origin of the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Fiducial 30067 43 linear_scale The scale is a standard base 10, non logarithmic scale. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #linear_scale 30068 43 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C4741 uri for NCI_histology_database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C4741 30069 44 TumorGrading A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TumorGrading 30070 43 nonpositive_float A float less than or equal to zero. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nonpositive_float 30071 43 FlyBase_developmental_stage_database uri for FlyBase developmental stage terms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FlyBase_developmental_stage_database 30072 43 intergenic sequence from the region between genes http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #intergenic 30073 43 M Mole per liter or molarity, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #M 30074 43 control_unknown_type A Reporter indicated as being a control of unknown type. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #control_unknown_type 30075 44 ClinicalHistory The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ClinicalHistory 30076 43 polypeptide sequence of a protein, a linear amino acid polymer http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #polypeptide 30077 43 frozen_storage Storage where the thing stored is stored below 0 degrees celsius. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #frozen_storage 30078 44 BarrierFacility Rating of containment system for the protection of organisms from infectious agents. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BarrierFacility 30079 43 kat/l katal per liter, catalytic-activity concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #kat/l 30080 43 days 24 hours, time unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #days 30081 44 Humidity The humidity that the biosource is exposed to. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Humidity 30082 64 is_user_defined property indicating that the class is user defined http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #is_user_defined 30083 43 virus one or more DNA or RNA based non cellular infective agent, including bacteriophage http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #virus 30084 64 has_height property indicating that the class has a height http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_height 30085 43 Hfr High frequency recombinant, mating type that indicates that the F plasmid has integrated into the chromosome http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Hfr 30086 44 Temperature The temperature that a biosource is exposed to. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Temperature 30087 64 has_been_treated property indicating that the class has been treated http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_been_treated 30088 43 pfu/ml the number of plaque forming units per ml http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #pfu/ml 30089 43 PCR_fail PCR where no products of any kind appear in gel-separated reaction products. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PCR_fail 30090 43 developmental_stage A descriptor for FactorValue where DevelopmentalStage is compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #developmental_stage 30091 43 PCR_amplicon BioSequence generated by means of polymerase chain reaction http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PCR_amplicon 30092 43 log_ratio result of data reduction involving computation of the ratio of signal intensities from a hybridization of two labeled extracts, followed by log transformation. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #log_ratio 30093 44 TechnologyType The technology type or platform of the reporters on the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TechnologyType 30094 43 unknown_protocol_type ProtocolType of unknown type. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #unknown_protocol_type 30095 44 BioAssayDataPackage MAGE package for BioAssayData. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioAssayDataPackage 30096 43 minutes 60 seconds, unit of time http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #minutes 30097 43 http://chem.sis.nlm.nih.gov/chemidplus uri for the ChemIDplus database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://chem.sis.nlm.nih.gov/chemidplus 30098 43 PCR_primer single oligo used for polymerase chain reaction direction unspecified http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PCR_primer 30099 43 loop_design A loop experiment design is where labeled extracts are compared in consecutive pairs. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #loop_design 30100 44 ExperimentPackage The descriptions associated with the Experiment package of MAGE http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ExperimentPackage 30101 44 MaterialType 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MaterialType 30102 64 has_laboratory_test property indicating that the class has a laboratory test http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_laboratory_test 30103 43 tau_rank_correlation a nonparametric measure of the agreement between two rankings http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #tau_rank_correlation 30104 62 has_order property indicating that the class has an order http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_order 30105 43 list_of_nonpositive_integers An ordered, finite set of nonpositive integers. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_nonpositive_integers 30106 43 ratio results of data reduction involving computation of the ratio of signal intensities obtained from hybridization of two, or more, labeled extracts to one, or more arrays http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ratio 30107 44 PublicationType Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PublicationType 30108 43 signal_log_ratio 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 http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #signal_log_ratio 30109 43 exemplar_mRNA 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #exemplar_mRNA 30110 43 oral_gavage delivery method for drug or compound whereby the drug is administered via the mouth http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #oral_gavage 30111 44 GeographicLocationDatabase Database of geographic locations. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #GeographicLocationDatabase 30112 43 age A descriptor for FactorValue where age is compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #age 30113 64 has_cancer_site property indicating that the class has a cancer site http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_cancer_site 30114 44 SeqFeatureBasis Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #SeqFeatureBasis 30115 43 hatching The point at which an organism emerges from an egg. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #hatching 30116 44 BioSampleType Used to tell when the BioSample is an extract or not. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioSampleType 30117 43 diameter_aberration The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #diameter_aberration 30118 64 has_bioassays property indicating that the class has bioassays http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_bioassays 30119 72 has_initial_time_point (null) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_initial_time_point 30120 43 mM milimolar, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mM 30121 43 FMA 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://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FMA 30122 43 Pearson_correlation The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Pearson_correlation 30123 43 change_light Change in light intensity or wavelength. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #change_light 30124 43 intraperitoneal_injection A delivery method for compound or drug whereby the substance is administered via the peritoneum. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #intraperitoneal_injection 30125 44 DerivedBioAssayType 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DerivedBioAssayType 30126 44 NormalizationDescriptionType Controlled descriptors for the normalization strategy used for the experiment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NormalizationDescriptionType 30127 43 hours 60 minutes, time unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #hours 30128 44 Individual Identifier or name of the individual organism from which the biomaterial was derived. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Individual 30129 43 http://www.opengalen.org/open/crm/crm-anatomy.html uri for open galen http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.opengalen.org/open/crm/crm-anatomy.html 30130 43 alexa_430 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #alexa_430 30131 43 ctDNA ctDNA: sequence from the chloroplast http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ctDNA 30132 44 ChromosomalAberrationClassification 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ChromosomalAberrationClassification 30133 43 normalization_testing_design A normalization testing experiment design tests different normalization procedures. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #normalization_testing_design 30134 43 http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml uri for MGI mouse strain approved terms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml 30135 43 bibliographic_record A record which describes and identifies a paper publication e.g. a medline record http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #bibliographic_record 30136 43 organism one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #organism 30137 43 http://portal.bioengineering.elyt.ods.org/ontology/ uri for CellML http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://portal.bioengineering.elyt.ods.org/ontology/ 30138 43 spectrophotometer Hardware for measuring light at different wavelengths. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #spectrophotometer 30139 44 SoftwareVariation The effects of different software, software packages, or software versions on experimental results are studied. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #SoftwareVariation 30140 44 Hardware The machine or instrument used. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Hardware 30141 43 mRNA sequence of a processed transcript capable of directing protein synthesis http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mRNA 30142 43 log_base_2 The values presented are logarithm, base 2. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #log_base_2 30143 44 ProtocolVariation The effects of different protocols or changes in protocols on experimental results are studied. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ProtocolVariation 30144 43 cosmid sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cosmid 30145 43 compound_based_treatment 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #compound_based_treatment 30146 43 forward the forward strand http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #forward 30147 43 percent_weight/weight percent weight per weight, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #percent_weight/weight 30148 44 OtherUnit Other units are those types not specified in MAGE such as lumens, radioactivity, etc. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #OtherUnit 30149 43 date Time stated in terms of the day, month, and year. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #date 30150 43 sister A female having the same genetic parents as another, or one genetic parent in common with another. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #sister 30151 64 has_publisher property indicating that the class has a publisher http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_publisher 30152 43 chromosomal_insertion 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #chromosomal_insertion 30153 43 ms millisecond, time unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ms 30154 43 Cy3 fluorophore used for labeling/detection purposes http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Cy3 30155 44 DiseaseLocation Anatomical location(s) of disease. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DiseaseLocation 30156 43 seconds time unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #seconds 30157 43 operon sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #operon 30158 43 disease_state_design A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #disease_state_design 30159 43 list_of_nonnegative_floats An ordered, finite set of nonnegative floats. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_nonnegative_floats 30160 43 PCR_primer_reverse single stranded oligo used for polymerase chain reaction http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PCR_primer_reverse 30161 64 has_mass property indicating that the class has a mass http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_mass 30162 44 FactorValueSet 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FactorValueSet 30163 43 physiological_process_design Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. This includes those processes http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #physiological_process_design 30164 44 Organization The organization (e.g. company, hospital) to contact to obtain or purchase something. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Organization 30165 44 BioSource The BioSource is the original source material before any treatment events. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioSource 30166 43 spin The procedure of applying a centrifugal force to a physical object. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #spin 30167 64 has_first_name property indicating that the class has a first name http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_first_name 30168 44 QualityControlDescription QualityControlDescription provides details of the quality control aspects of the experiment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #QualityControlDescription 30169 64 has_owner property indicating that the class has an owner http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_owner 30170 44 OrganismPartDatabase Database of organism part information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #OrganismPartDatabase 30171 64 has_scale property indicating that the class has a scale http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_scale 30172 43 EST Sequence derived from expressed sequence tag. EST's are likely to be partial, single read and low quality sequences. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #EST 30173 43 atmosphere The atmospheric conditions used to culture or grow an organism. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #atmosphere 30174 43 fl femtoliter, unit of volume http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #fl 30175 43 weeks 7 days, unit of time http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #weeks 30176 44 BiologicalFactorCategory Factors that relate to properties of the biomaterial, its treatment, or its growth. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BiologicalFactorCategory 30177 43 species_specific_design_element_group_type A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #species_specific_design_element_group_type 30178 44 ClinicalTreatment The current clinical treatment(s) of the patient from which the biosource is derived. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ClinicalTreatment 30179 43 http://www.iupac.org/publications/pac/2000/7205/7205olesen.html uri for IUPAC_Clinical_Chemistry_Guidelines http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.iupac.org/publications/pac/2000/7205/7205olesen.html 30180 44 BioAssay A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioAssay 30181 43 is_contaminated The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #is_contaminated 30182 43 alexa_546 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://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #alexa_546 30183 43 vacuum_dryer An instrument designed to remove excess liquid by vacuum and heating. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #vacuum_dryer 30184 43 uncle The brother of one's father or mother. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #uncle 30185 43 is_expressed_design A design aimed at identifying genes expressed in biomaterials of interest. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #is_expressed_design 30186 43 lowess_normalization Locally weighted linear regression of the intensities in one channel from a set of Features on those of the other channel. Lowess removes intensity-dependent dye-specific effects from the set of Features. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #lowess_normalization 30187 44 PopulationDensity The concentration range of the organism. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PopulationDensity 30188 43 mean_and_standard_deviation the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mean_and_standard_deviation 30189 43 unknown_basis_feature Sequence feature whose derivation is unknown. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #unknown_basis_feature 30190 43 injury_design An injury experiment design type is where the response of an organism(s) to injury or damage is studied. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #injury_design 30191 44 BioSequence A representation of a DNA, RNA, or protein sequence. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioSequence 30192 43 soil soil, growth media for plants and other soil living organisms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #soil 30193 43 co-expression_design 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) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #co-expression_design 30194 44 OperatorVariation The effects of different investigators, laboratories, or organizations on experimental results are studied. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #OperatorVariation 30195 43 circadian_rhythm_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #circadian_rhythm_design 30196 43 not_sequence_verified The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #not_sequence_verified 30197 43 postmortem biomaterial removed after the death of the organism http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #postmortem 30198 64 has_pages property indicating that the class has pages http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_pages 30199 44 ExperimentalProtocolType All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ExperimentalProtocolType 30200 43 set_temperature An action where the temperature is specified. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #set_temperature 30201 43 diploid Describes a cell, nucleus or an organism with two copies of each chromosome. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #diploid 30202 64 has_measurement property indicating that the class has a measurement http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_measurement 30203 43 investigator Person who contributed to the study. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #investigator 30204 44 EnvironmentalStress 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 http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #EnvironmentalStress 30205 43 http://www.item.fraunhofer.de/reni/index.htm uri for RENI http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.item.fraunhofer.de/reni/index.htm 30206 44 IndividualChromosomalAbnormality 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #IndividualChromosomalAbnormality 30207 44 HistoryFactor 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). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #HistoryFactor 30208 44 FamilyMember Member of the biosource's family. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FamilyMember 30209 43 mix_by_inversion Mix through the process of inverting. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mix_by_inversion 30210 44 QualityControlDescriptionType Controlled descriptors for the quality control strategy for an experiment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #QualityControlDescriptionType 30211 43 paraffin_sample A biomaterial obtained embedded in paraffin (wax). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #paraffin_sample 30212 43 software_variation_design A software variation design type compares different types of software for performance, accuracy, precision and reproducibility. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #software_variation_design 30213 44 Action Procedures used during treatment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Action 30214 43 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C16632 uri for NCI_geographic_location_database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C16632 30215 43 physical_characteristics A descriptor for FactorValue where PhysicalCharacteristics are compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #physical_characteristics 30216 43 protein Polymer of amino acids. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #protein 30217 43 http://www.nlm.nih.gov/mesh/filelist.html uri for MESH http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.nlm.nih.gov/mesh/filelist.html 30218 43 chrome_border the chrome border on an Affymetrix type array which is used as a point of reference for orientation (fiducial) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #chrome_border 30219 43 decontaminate Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #decontaminate 30220 43 PCR_primer_forward single stranded oligo used for polymerase chain reaction http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PCR_primer_forward 30221 43 behavioral_stimulus The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #behavioral_stimulus 30222 43 LOINC Database resource for universal identifiers for laboratory and other clinical observations http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #LOINC 30223 43 cell_lysate cell lysate, a collection of cells whose membranes have been disrupted http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cell_lysate 30224 64 has_accession_version property indicating that the class has an accession number version http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_accession_version 30225 43 NCI_compound_database a controlled vocabulary for compounds http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_compound_database 30226 43 pathogenicity_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #pathogenicity_design 30227 64 has_fax property indicating that the class has a fax http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_fax 30228 43 mating_type_alpha Mating type of S. cerevisiae. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mating_type_alpha 30229 43 primary_site the organism part in which the tumor originated http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #primary_site 30230 43 sacrifice The procedure of euthanizing an organism. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #sacrifice 30231 43 centrifuge An instrument capable of applying centrifugal force to tubes or microtiter plates. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #centrifuge 30232 44 ProtocolPackage The MAGE package for protocols. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ProtocolPackage 30233 44 TargetedCellTypeDatabase Database of targeted cell type information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TargetedCellTypeDatabase 30234 43 disease_state A descriptor for FactorValue where DiseaseState is compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #disease_state 30235 43 http://cvs.sourceforge.net/viewcvs.py/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology?content-type=text/plain&rev=1.1 uri for mouse anatomical dictionary for the adult mouse http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://cvs.sourceforge.net/viewcvs.py/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology?content-type=text/plain&rev=1.1 30236 43 intravenous delivery method whereby a compound or drug is administered via a vein http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #intravenous 30237 43 aneuploid Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #aneuploid 30238 44 MassUnit Units used for mass measurements. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MassUnit 30239 43 Adult_Mouse_Anatomy This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Adult_Mouse_Anatomy 30240 43 alexa_633 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #alexa_633 30241 43 list_of_strings An ordered, finite set of strings. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_strings 30242 43 institution A contact's affiliation, e.g. university, research institute or business. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #institution 30243 43 computed_amino_acid_sequence_feature_record a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #computed_amino_acid_sequence_feature_record 30244 43 ICD-9-CM Database entry from ICD 9 2001, international classification of diseases 9, clinical modification 2001. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ICD-9-CM 30245 43 ad_libitum A delivery method for compounds/drugs where the compound or drug is freely available. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ad_libitum 30246 43 MESH database entry from MESH, medical subject headings vocabulary resource http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MESH 30247 43 dye_swap_replicate_reduction 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #dye_swap_replicate_reduction 30248 43 linlog_normalization 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #linlog_normalization 30249 43 JPEG Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #JPEG 30250 64 has_text property indicating that the class has text http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_text 30251 44 Atmosphere The atmospheric conditions used to culture or grow an organism. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Atmosphere 30252 43 normalized_intensities intensities from one or both channels resulting from normalization of MeasuredBioAssayData. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #normalized_intensities 30253 43 strain_or_line_design A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #strain_or_line_design 30254 43 water Water consumed by or enveloping the organism that the biosource is derived from. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #water 30255 43 negative_float A float that is < 0. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #negative_float 30256 43 missing_feature_or_zone 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #missing_feature_or_zone 30257 43 ratio_statistics_normalization A method of re-scaling intensity data from one channel relative to another based on an iterative method of calculating single parameter linear normalization factors. This method allows calculation of confidence intervals for the data set. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ratio_statistics_normalization 30258 64 has_parent_organization property indicating that the class has a parent organization http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_parent_organization 30259 43 son The male offspring of the patient or individual under study. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #son 30260 44 Result class to hold instances used as the filler for the property has_result http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Result 30261 44 BioSourceProvider The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioSourceProvider 30262 43 mL/L milliliters per liter, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mL/L 30263 43 control_spike_calibration 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #control_spike_calibration 30264 64 has_publication property indicating that the class has a publication http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_publication 30265 44 Bedding Refers to the bedding material present in an animals housing. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Bedding 30266 43 no false http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #no 30267 43 irregular_shape The perimeter of the spotted DNA on the slide is irregular. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #irregular_shape 30268 43 microarray_experiment_record A record which describes and identifies a microarray experiment e.g. GEO http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #microarray_experiment_record 30269 64 has_host_part property indicating that the class has a host part http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_host_part 30270 43 alexa_568 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://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #alexa_568 30271 44 DeprecationReason class to hold instances used as the filler for the property has_reason_for_deprecation http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DeprecationReason 30272 43 UMLS Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #UMLS 30273 44 DeliveryMethod Method used to deliver a compound for treatment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DeliveryMethod 30274 43 array_scanner An instrument capable of acquiring images of arrays. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #array_scanner 30275 44 Sex 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Sex 30276 43 spike_quality_control An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #spike_quality_control 30277 43 GIF Graphics Interchange Format , a common image data format containing RGB data compressed with fairly high data loss. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #GIF 30278 43 dissect The action of removing one or more OrganismParts. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #dissect 30279 43 peer_review_quality_control An experiment which has a peer reviewed publication attached. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #peer_review_quality_control 30280 43 http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/ uri for FlyBase organism part database terms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fly/ 30281 43 kg kilogram, 1000 grams, unit of mass http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #kg 30282 43 percent_confluence A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #percent_confluence 30283 43 cellular_modification_design A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cellular_modification_design 30284 44 ArrayPackage MAGE package for describing the process by which arrays were manufactured. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ArrayPackage 30285 43 computer A device capable of applying software. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #computer 30286 43 experimental_and_computational_feature Sequence features derived by both computational and experimental methods. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #experimental_and_computational_feature 30287 44 BioSequencePackage MAGE package for biological sequences (biosequence). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioSequencePackage 30288 43 log_base_e The values presented are logarithm, base e. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #log_base_e 30289 43 vector 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #vector 30290 44 Scale The scale (linear, log10, ln, etc) used to represent the value. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Scale 30291 43 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C7057 uri for NCI_disease_state_database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C7057 30292 43 iterative_mean_log_centering 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #iterative_mean_log_centering 30293 44 Test An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. erythrocyte count http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Test 30294 44 HistologyDatabase Database of histology information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #HistologyDatabase 30295 64 has_name property indicating that the class has a name http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_name 30296 43 premortem sample which has been removed prior to the death of an organism http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #premortem 30297 43 NCI_Thesaurus A description logic namespace that contains controlled terminology used at NCI. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_Thesaurus 30298 64 has_organism_part property indicating that the class has an organism part http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_organism_part 30299 43 http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C1908 uri for NCI_compound_database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI+Thesaurus&code=C1908 30300 43 curated_gene_record A record which describes and identifies nucleic acid sequence which has been identified as a gene by a curator. e.g. Flybase gene record http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #curated_gene_record 30301 44 TestTypeDatabase Database of codes for clinical findings. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TestTypeDatabase 30302 43 list_of_negative_integers An ordered, finite set of negative integers. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_negative_integers 30303 43 semisolid semisolid media type http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #semisolid 30304 64 has_experiment_design_type property indicating that the class has an experiment design type http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_experiment_design_type 30305 43 cfu/ml the number of colony forming units per ml http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cfu/ml 30306 43 curated_amino_acid_sequence_record A record which describes and identifies an amino acid sequence which has been curated http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #curated_amino_acid_sequence_record 30307 44 DiseaseStateDatabase Database of disease state information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DiseaseStateDatabase 30308 43 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 http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://cvs.sourceforge.net/viewcvs.py/*checkout*/obo/obo/ontology/developmental/animal_development/fly/fly_development.ontology?content-type=text/plain&rev=1.1 30309 43 family_history_design A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #family_history_design 30310 43 g gram, unit of mass http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #g 30311 43 mix_by_vortex Mix through the use of a vortexer. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mix_by_vortex 30313 84 thing (null) (null) 8015 #thing 30315 83 string (null) (null) 8015 #string 29813 43 alexa_350 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #alexa_350 29814 44 WarningType Controlled terms for descriptors of the warnings associated with reporters. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #WarningType 29815 43 optimization_design An optimization experiment design type is where different protocols or protocol parameters are compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #optimization_design 29816 43 eVOC Ontology of human terms that describe the sample source of human cDNA and SAGE libraries. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #eVOC 29817 43 half-life 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #half-life 29818 43 agar A type of solid media commonly used for growing organisms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #agar 29819 44 QuantityUnitOther Quantity units not specified in MAGE. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #QuantityUnitOther 29820 64 has_nutrient_component property indicating that the class has a nutrient component http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_nutrient_component 29821 44 RadiationUnit Units for measuring decay of a radioactive isotope over time. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #RadiationUnit 29822 44 Generation 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Generation 29823 43 nmol nanomoles, quantity unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nmol 29824 43 hybridization_station An instrument which controls hybridization conditions, into which a hybridization chamber may fit. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #hybridization_station 29825 43 mean_and_p_values the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mean_and_p_values 29826 44 BioSequenceType 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). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioSequenceType 29827 44 Media The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) . http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Media 29828 43 silicon the array is made on silicon http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #silicon 29829 44 NodeValue Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NodeValue 29830 43 consensus_mRNA mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #consensus_mRNA 29831 44 Ploidy The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Ploidy 29832 43 NCI_organsim_part_database a controlled vocabulary of organism parts http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_organsim_part_database 29833 64 has_reason_for_deprecation property to indicate the reason for deprecating a term http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_reason_for_deprecation 29834 43 polyploid Describes a cell, nucleus or organism with three or more copies of each chromosome. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #polyploid 29835 43 nutrients The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nutrients 29836 64 has_compound property indicating that the class has a compound http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_compound 29837 43 brother A male having the same genetic parents as another, or one genetic parent in common with another. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #brother 29838 64 has_manufacturer property indicating that the class has a manufacturer http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_manufacturer 29839 64 has_biomaterial_characteristics property indicating that the class has biomaterial characteristics http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_biomaterial_characteristics 29840 43 pathway_record a record which identifies and describes biological pathways, e.g. a KEGG record http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #pathway_record 29841 44 Genotype The total sum of the genetic information of an organism that is known and relevant to the experiment being performed. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Genotype 29842 64 has_disease_state property indicating that the class has a disease state http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_disease_state 29843 43 planting time point at which a seed was planted http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #planting 29848 64 has_protocol property indicating that the class has a protocol http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_protocol 29849 44 Organism The genus and species (and subspecies) of the organism from which the biomaterial is derived from. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Organism 29850 43 journal_article A article published in a print or online journal having an ISSN. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #journal_article 29851 44 BioAssayDataCluster A grouping of bioassay data that has been organized by one or more mathematical functions into nodes. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioAssayDataCluster 29852 43 thermal_cycler An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #thermal_cycler 29853 44 FeatureDefect A technical manufacturer described defect for features. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FeatureDefect 29854 43 list_of_positive_floats An ordered, finite set of positive floats. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #list_of_positive_floats 29855 43 feces A biosource obtained as fecal matter. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #feces 29856 43 m meter, distance unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #m 29857 64 has_bioassay_data property indicating that the class has bioassaydata http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_bioassay_data 29858 43 g/L grams per liter, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #g/L 29859 43 individual_genetic_characteristic A descriptor for FactorValue where IndividualGeneticCharacteristic is compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #individual_genetic_characteristic 29860 44 DesignElementPackage The MAGE package for describing the elements located on the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DesignElementPackage 29861 44 Observation Observation will record the macroscopic examination of the biomaterial. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Observation 29862 44 VolumeUnitOther Volume units not specified in MAGE. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #VolumeUnitOther 29863 44 BioMaterialCharacteristicCategory General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioMaterialCharacteristicCategory 29864 44 BioMolecularAnnotation 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioMolecularAnnotation 29865 43 organellar_RNA RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #organellar_RNA 29866 43 computed_nucleic_acid_sequence_feature_record A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #computed_nucleic_acid_sequence_feature_record 29867 43 count Unit for a simple count of things http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #count 29868 44 Protocol Documentation of the set of steps taken in a procedure. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Protocol 29869 43 WebRENI database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #WebRENI 29870 64 has_toll_free_phone property indicating that the class has a toll free phone http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_toll_free_phone 29871 43 cm centimeter, a unit of distance http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #cm 29872 43 http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/cell_type/cell.ontology?rev=HEAD&content-type=text/vnd.viewcvs-markup uri for cell ontology http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/cell_type/cell.ontology?rev=HEAD&content-type=text/vnd.viewcvs-markup 29873 44 Node A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Node 29874 44 FactorValueDependency 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FactorValueDependency 29875 43 individual_genetic_characteristics_design An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #individual_genetic_characteristics_design 29876 43 barrier_facility The rating of containment system used to protect organisms from infectious agents. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #barrier_facility 29877 43 consensus_DNA DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #consensus_DNA 29944 43 mixed_design_element_group_type a design element group consisting of multiple types http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mixed_design_element_group_type 29945 43 biological_fluid_collection 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #biological_fluid_collection 29946 43 remove The procedure of extracting/taking out a part of a reaction/contents of a container. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #remove 29947 44 Nutrients The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Nutrients 29948 43 http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php uri for Pathbase http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php 29949 43 differential_expression An analysis aimed at identifying differentially expressed genes in two or more conditions. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #differential_expression 29950 43 ml milliliter, volume unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ml 29951 43 mixed_sex A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mixed_sex 29952 43 DNA Deoxyribonucleic acid. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DNA 29953 43 linear_regression_normalization 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #linear_regression_normalization 29954 43 operating_system Software upon which other software runs. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #operating_system 29955 43 array_manufacturing_protocol The process of physically creating the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #array_manufacturing_protocol 29956 44 ExperimentalFactorCategory 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ExperimentalFactorCategory 29957 43 blood A biomaterial obtained as fluid consisting of plasma, blood cells and platelets. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #blood 29958 43 granddaughter A daughter of one's son or daughter. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #granddaughter 29959 43 jackknife_Pearson_correlation The jackknife Pearson correlation is the lowest Pearson correlation between two data series where one pair of values in the data series are omitted. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #jackknife_Pearson_correlation 29960 44 Cultivar a plant variety obtained in agriculture in horticulture http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Cultivar 29961 64 has_family_member property indicating that the class has a family member http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_family_member 29962 43 um micrometer, unit of distance http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #um 29963 43 ml/kg milliliter per kilogram http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ml/kg 29964 44 StrainOrLine For animals or plants, these are offspring that have a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings. For microbes, these are isolates derived from nature or in the laboratory. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #StrainOrLine 29965 43 NCI_geographic_location_database a controlled vocabulary for geographic locations http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_geographic_location_database 29966 44 NormalizationDescription NormalizationDescription provides details of the normalization strategy for the experiment. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NormalizationDescription 29967 43 split_term the term has been decomposed into more specific terms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #split_term 29968 43 long_oligo An element that is an oligonucleotide of at least 50 nucleotides in length. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #long_oligo 29969 43 computed_protein_structure_record a record which describes and identifies a protein structure e.g. PDB http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #computed_protein_structure_record 29970 43 resuspend The procedure in which solid material is dispensed or dissolved in a liquid. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #resuspend 29971 43 fmol femtomole, unit of quantity http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #fmol 29972 44 ReplicateDescriptionType Controlled descriptors for the type of replication. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ReplicateDescriptionType 29973 43 pH potential of hydrogen http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #pH 29974 43 short_oligo An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #short_oligo 29975 43 polyA_RNA RNA which has been obtained by selection for polyA tracts. Exact synonym: polyA+_RNA http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #polyA_RNA 29976 43 image_acquisition The process of generating an image from the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #image_acquisition 29977 64 has_atmospheric_component property indicating that the class has an atmospheric component http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_atmospheric_component 29978 43 positive_float A float > 0. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #positive_float 29979 44 QuantityUnit Units used for quantity measurements. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #QuantityUnit 29980 64 has_clinical_finding property indicating that the class has a clinical finding http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_clinical_finding 29981 44 ExperimentalFactor The factors in the study that are experimental parameters or regarded as influencing the experimental results. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ExperimentalFactor 29982 44 SequenceOntologyBioSequenceType Descriptors of biosequence based on the Sequence Ontology (SO) project. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #SequenceOntologyBioSequenceType 29983 43 http://tumor.informatics.jax.org uri for Mouse Tumor Biology Database http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://tumor.informatics.jax.org 29984 44 FeatureGroup Technology-based grouping of features representing individual locations on the array. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FeatureGroup 29985 43 seed_dormancy preservation type whereby the seed is maintained in a dormant state http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #seed_dormancy 29986 43 plasmid sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #plasmid 29987 44 DatabaseEntryType Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DatabaseEntryType 29988 43 F- mating type indicating the absence of F plasmid in a bacterial cell http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #F- 29989 43 labeling The procedure of labeling a biosample. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #labeling 29990 43 dye_swap_quality_control Indicates that a dye swap was performed for some or all hybridizations within an experiment http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #dye_swap_quality_control 29991 43 nonnegative_float A float greater than or equal to 0. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nonnegative_float 29992 44 DevelopmentalStage The developmental stage of the organism's life cycle during which the biomaterial was extracted. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DevelopmentalStage 29993 43 environmental_history_design 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #environmental_history_design 29994 43 http://www.sanbi.ac.za/evoc/ontologies.html uri for eVOC http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.sanbi.ac.za/evoc/ontologies.html 29995 43 reference_design A reference experiment design type is where all samples are compared to a common reference. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #reference_design 29996 44 MassUnitOther Mass units not specified in MAGE. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MassUnitOther 29997 43 mix_general The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mix_general 29998 44 HardwareVariation The effects of different hardware, types of hardware, or models of hardware on experimental results are studied. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #HardwareVariation 29999 44 Phenotype 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Phenotype 30000 64 has_property_set property indicating that the class has a property set http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_property_set 30001 43 monosomy Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #monosomy 30002 43 induced_mutation The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #induced_mutation 30003 43 control_reporter_size A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #control_reporter_size 30004 43 binding_site_identification_design A binding site identification design type investigates protein binding sites on nucleic acids http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #binding_site_identification_design 29878 44 ArrayDesignPackage MAGE package that describes the array layout and design. The array may be physical or virtual. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #ArrayDesignPackage 29879 43 fg femtogram, unit of mass http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #fg 29880 43 http://www.informatics.jax.org/mgihome/GXD/AD/ uri for jax mouse gene indices http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://www.informatics.jax.org/mgihome/GXD/AD/ 29881 44 Unit Units of measure. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Unit 29882 72 has_accession (null) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_accession 29883 44 Ecotype a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Ecotype 29884 43 population_density The concentration range of the organism. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #population_density 29885 43 double_stranded 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #double_stranded 29886 44 QuantitationType The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #QuantitationType 29887 43 spotted_ds_DNA_features 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #spotted_ds_DNA_features 29888 44 MGEDExtendedOntology 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 http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #MGEDExtendedOntology 29889 43 nm nanometer distance unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nm 29890 44 TheoreticalBioSequenceType A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #TheoreticalBioSequenceType 29891 43 fractionate The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #fractionate 29892 43 nitrocellulose The array is made on a nitrocellulose filter. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nitrocellulose 29893 43 infect The organism (or organism part) has been exposed to a virus or pathogen. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #infect 29894 44 OrganismStatus The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #OrganismStatus 29895 64 has_clinical_treatment property indicating that the class has a clinical treatment http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_clinical_treatment 29896 43 wash_station An instrument designed to mechanically wash or stain arrays. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #wash_station 29897 43 biomaterial_provider Term used to describe a role or factor value for the person or organization that provides a BioMaterial. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #biomaterial_provider 29898 43 averaged_intensity results of data reduction involving computation of the average intensity from identical Features, Reporters or CompositeSequences in different hybridizations. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #averaged_intensity 29899 44 CellTypeDatabase Database of cell type information. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #CellTypeDatabase 29900 64 has_accession property indicating that the class has an accession number http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_accession 29901 64 has_last_name property indicating that the class has a last name http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_last_name 29902 43 experimental_feature An experimentally defined sequence feature. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #experimental_feature 29903 64 has_host property indicating that the class has a host http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_host 29904 43 change_humidity The action of changing the relative humidity, e.g. from 1% to 10%. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #change_humidity 29905 43 string_datatype The values are a sequence of one or more characters. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #string_datatype 29906 43 GRAMENE A Comparative Mapping Resource for Grains. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #GRAMENE 29907 64 has_value property indicating that the class has a value http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_value 29908 44 EpidemiologicalDesign An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #EpidemiologicalDesign 29909 44 FamilyRelationship A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #FamilyRelationship 29910 44 BioSourceType The form in which the Biosource is provided, may also be used to describe biosamples e.g. agar stab. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #BioSourceType 29911 43 whole_organism one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #whole_organism 29912 43 mg/mL milligrams per milliliter, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mg/mL 29913 44 PhysicalBioAssay A physical bioassay is the combination of arrays and biomaterials as in a hybridization. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #PhysicalBioAssay 29914 43 R Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #R 29915 43 months Unit of time corresponding to approx. one cycle of the moon's phases. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #months 29916 43 unscaled The values are unordered and have no scale. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #unscaled 29917 64 has_experiment_factors property indicating that the class has experiment factors http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_experiment_factors 29918 43 NCI_disease_staging_database a controlled vocabulary for disease stages http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_disease_staging_database 29919 43 NCI_cell_type_database a controlled vocabulary of cell types http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #NCI_cell_type_database 29920 64 has_individual_genetic_characteristics property indicating that the class has individual genetic characteristics http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_individual_genetic_characteristics 29921 43 http://song.sourceforge.net/ The Sequence Ontology Project http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://song.sourceforge.net/ 29922 43 dye_swap_design An experiment design type where the label orientations are reversed. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #dye_swap_design 29923 43 mg/kg/day milligram per kilogram per day http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mg/kg/day 29924 43 promoter genomic sequence 5' to a gene where the transcription initiation complex forms. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #promoter 29925 43 liquid_handler Hardware for automated liquid transfer and handling. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #liquid_handler 29926 43 http://hazel.niehs.nih.gov/user_spt/pct_terms.htm uri for NIEHS database of controlled pathology terms http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #http://hazel.niehs.nih.gov/user_spt/pct_terms.htm 29927 44 Roles Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Roles 29928 43 gram_percent grams per deciliter, concentration unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #gram_percent 29929 44 CancerSite class to hold instances used as the filler for the property has_cancer_site http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #CancerSite 29930 44 QuantitationTypePackage The MAGE package for defining classes for quantitation. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #QuantitationTypePackage 29931 43 years 365 days, time unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #years 29932 43 CellML Ontology describing anatomical and physiological relationships. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #CellML 29933 64 has_performer property indicating that the protocol has a performer or contact person http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_performer 29934 64 has_version property indicating that the class has a version http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #has_version 29935 43 inconclusive a result which can not be interpreted as positive or negative http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #inconclusive 29936 43 amol attomole, quantity unit http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #amol 29937 43 alexa_488 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. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #alexa_488 29938 43 nylon The array is made on a nylon membrane. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #nylon 29939 43 not_extract The BioSample at any stage other than immediately before labeling. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #not_extract 29940 43 phylogeny_record A record which describes and identifies the relationship between species and is http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #phylogeny_record 29941 43 grandson A son of one's son or daughter. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #grandson 29942 43 data_analyst A contact who performs data analysis, e.g. statistician. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #data_analyst 29943 43 in_situ_oligo_features The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent) http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #in_situ_oligo_features 29844 44 DerivedBioAssay A BioAssay that is created by the transformation of measured or derived BioAssays. http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #DerivedBioAssay 29846 43 mOsm/kg H2O osmolality per kilogram of water, concentration of the solute per unit of solvent http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #mOsm/kg H2O 29847 44 Host Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells). http://mged.sourceforge.net/ontologies/MGEDontology.php 8015 #Host