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ontology ID label editor preferred term has curation status alternative term IEDB Alternative Terms definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class obsolete obsolescence reason replacement term Randi's notes on obsolescence
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A IEDB alternative term A definition A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A ontology term requester A term tracker item CLASS_TYPE C % AT deprecated^^xsd:boolean AI has obsolescence reason AI term replaced by
OBI:0000050 obsolete_platform IAO:0000123 A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. OBI Instrument branch OBI Instrument branch subclass Obsolete Class true IAO:0000103
OBI:0000100 obsolete_role of being first subject treated IAO:0000120 First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study OBI Rat 1A; first enrolled patient to receive treatment Role Branch subclass Obsolete Class true IAO:0000103
OBI:0000109 biological vector role IAO:0000120 a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. OBI and Wikipedia 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.|Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 GROUP: Role Branch subclass Obsolete Class true IAO:0000103
OBI:0000140 obsolete_label role IAO:0000428 label Label role is a role which inheres in a material entity and which is realized in a detection of label assay OBI Role Branch subclass Obsolete Class true IAO:0000228 OBI:0002743
OBI:0000205 obsolete_dropout role IAO:0000120 Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role. OBI Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study) Role Branch subclass Obsolete Class true IAO:0000103
OBI:0000207 obsolete health care provider role IAO:0000120 health care provider a worker role of providing medical care either within or outside the study timeline Person:Jennifer Fostel subclass Obsolete Class true OMRSE:00000012
OBI:0000223 obsolete_blinded medication role IAO:0000120 Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance 115 patients received ipilimumab and blinded medication|Inert pill shaped like aspirin tablet Jennifer Fostel|Person:Helen Parkinson subclass Obsolete Class true IAO:0000103
OBI:0000233 obsolete_defined_material IAO:0000121 Place holder class, Utility class to gather the defined classes OBI Biomaterial derived Susanna Sansone subclass Obsolete Class true IAO:0000226
OBI:0000264 obsolete_sample population IAO:0000120 recruited population A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. GROUP: OBI Biomaterial Branch Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458 PERSON: Jennifer Fostel|PERSON: Philippe Rocca-Serra subclass Obsolete Class true IAO:0000227
OBI:0000296 obsolete_enrollment IAO:0000125 enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules IEDB Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 Bjoern Peters subclass Obsolete Class true IAO:0000227
OBI:0000323 obsolete_peritoneum IAO:0000002 is the serous membrane that forms the lining of the abdominal cavity subclass Obsolete Class true IAO:0000228
OBI:0000340 obsolete_documenting IAO:0000125 wikipedia http://en.wikipedia.org/wiki/Documenting Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. Bjoern Peters subclass Obsolete Class true IAO:0000228 IAO:0000572
OBI:0000420 obsolete_trypsinized material IAO:0000002 A material entity that has undergone a process of digestion with trypsin A trypsinized suspension of cells Person:Bjoern Peters subclass Obsolete Class true IAO:0000103
OBI:0000442 obsolete_heart IAO:0000002 The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions http://en.wikipedia.org/wiki/Heart Alan Ruttenberg's heart Person:Bjoern Peters subclass Obsolete Class true IAO:0000230
OBI:0000446 obsolete_identification IAO:0000124 a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 Philippe Rocca-Serra subclass Obsolete Class true IAO:0000103
OBI:0000449 obsolete_defined_output IAO:0000121 This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process. example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation. PERSON: Alan Ruttenberg|PERSON: James Malone|PERSON: Melanie Courtot subclass Obsolete Class true IAO:0000226
OBI:0000577 obsolete_molecular concentration IAO:0000123 A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity. Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. the phosphate concentration should be 0.1M PERSON: Alan Ruttenberg subclass Obsolete Class true IAO:0000228
OBI:0000665 obsolete intracellular cytokine staining assay IAO:0000120 ICCS|ICS intracellular cytokine staining (ICS) The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. IEDB Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies IEDB subclass Obsolete Class true IAO:0000227 OBI:0000916
OBI:0000667 obsolete MHC multimer staining assay IAO:0000120 MHC tetramer assay MHC tetramer/multimer staining An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer IEDB Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes. IEDB subclass Obsolete Class true IAO:0000227 OBI:1110179
OBI:0000682 obsolete_study result IAO:0000120 Study result is an information content entity that is a specified data output of a study. GROUP: OBI subclass Obsolete Class true IAO:0000230
OBI:0000698 obsolete_DNA ligase IAO:0000123 ligase A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule Kevin Clancy, Bjoern Peters subclass Obsolete Class true IAO:0000228
OBI:0000797 obsolete_primary structure of protein The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together SIINFEKL' is the primary structure of a peptide Person:Bjoern Peters subclass Obsolete Class true IAO:0000228
OBI:0000830 obsolete_primary structure of sequence macromolecule A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds Person:Bjoern Peters subclass Obsolete Class true IAO:0000228
OBI:0000851 obsolete_diethyl pyrocarbonate subclass Obsolete Class true IAO:0000228
OBI:0000856 obsolete intracellular material detection by flow cytometry assay IAO:0000123 intracellular staining An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. subclass Obsolete Class true IAO:0000227 OBI:0000916
OBI:0000926 obsolete_ambidexterious handedness subclass Obsolete Class true IAO:0000103
OBI:0000929 obsolete_training service provider role IAO:0000123 a service provider role which is realized by a servicer provider organization performing some training OBI EBI provides training on databases and tools and has a training service provider role PERSON:Helen Parkinson subclass Obsolete Class true IAO:0000103
OBI:0000936 obsolete_material access provider role IAO:0000123 a service provider role which is realized by a servicer provider organization performing access to some material OBI A person or organization who provides access to a DNA sequencer. PERSON:Helen Parkinson subclass Obsolete Class true IAO:0000103
OBI:0000937 obsolete_left handedness subclass Obsolete Class true IAO:0000228
OBI:0000956 obsolete_handedness subclass Obsolete Class true IAO:0000228 PATO:0002201
OBI:0000972 obsolete_electrically powered device a processed material created to have a function and which requires electrical power to execute subclass Obsolete Class true IAO:0000103
OBI:0000974 obsolete_right handedness subclass Obsolete Class true IAO:0000228
OBI:0000980 obsolete_protocol service provider role IAO:0000120 a service provider role which is realized by a servicer provider organization performing a protocol execution DNA sequencing of a sample by a core lab which returns data to the consumer PERSON:Helen Parkinson subclass Obsolete Class true IAO:0000103
OBI:0000986 obsolete_DNA sequencing training service IAO:0000123 A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments subclass Obsolete Class true IAO:0000103
OBI:0000987 obsolete_general scalar measurement datum IAO:0000124 subclass Obsolete Class true IAO:0000103
OBI:0001009 obsolete_qualitative binding detection assay IAO:0000123 A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum subclass Obsolete Class true IAO:0000103
OBI:0001037 obsolete_specimen fixation function IAO:0000123 A specimen fixation function is a function that holds or fastens an entity in a fixed position. EAGLE-I subclass Obsolete Class true IAO:0000227
OBI:0001250 obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation IAO:0000122 T cell degranulation by intracellular staining An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000227 OBI:0000916
OBI:0001540 obsolete T cell recognition of eluted MHC ligand assay IAO:0000120 T cell recognition An assay that identifies an MHC ligand using a T cell response assay as a readout IEDB Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell. PERSON: Randi Vita, Bjoern Peters subclass Obsolete Class true IAO:0000227 OBI:0001469
OBI:0001560 obsolete cell lysate MHC binding constant determination assay IAO:0000120 An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant. IEDB PERSON: Bjoern Peters subclass Obsolete Class true IAO:0000103
OBI:0001572 obsolete cell bound MHC binding constant determination assay IAO:0000120 An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant. IEDB PERSON: Bjoern Peters subclass Obsolete Class true IAO:0000103
OBI:0001574 obsolete cell lysate MHC competitive binding assay using radioactivity detection IAO:0000122 cell lysate MHC competitive binding using radioactivity competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000227 OBI:0001544
OBI:0001576 obsolete purified MHC binding constant determination assay IAO:0000120 An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant. IEDB PERSON: Bjoern Peters subclass Obsolete Class true IAO:0000103
OBI:0001582 obsolete cell bound MHC direct binding assay IAO:0000122 cell bound MHC direct binding direct binding assay measuring MHC ligand binding using MHC derived from a cell IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000103
OBI:0001611 obsolete purified MHC direct binding assay IAO:0000122 purified MHC direct binding direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000103
OBI:0001712 obsolete B cell epitope direct binding assay IAO:0000122 direct binding assay A direct binding assay using a assay IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000103
OBI:0001715 obsolete B cell epitope competitive binding assay IAO:0000122 competitive binding assay A competitive inhibition of binding assay using a assay IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000103
OBI:0001737 obsolete B cell epitope specific X-ray crystallography assay IAO:0000122 X-ray crystallography [Ã…] A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters subclass Obsolete Class true IAO:0000227 OBI:0001738
OBI:0100015 obsolete_anatomical entity IAO:0000121 An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' MO Tissue, organ, system, sperm, blood or body location (arm). Bjoern Peters|Philippe Rocca-Serra|Tina Boussard subclass Obsolete Class true IAO:0000228
OBI:0100035 obsolete_immortal cell IAO:0000120 a cell derived from a multicellular organism that has the potential to replicate indefinitely GROUP: OBI Biomaterial Branch a single Hela cell PERSON: Bjoern Peters subclass Obsolete Class true IAO:0000228
OBI:0100039 obsolete_fragment derived from protein IAO:0000123 A material entity which is derived from a protein GROUP: IEDB the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme PERSON: Bjoern Peters subclass Obsolete Class true IAO:0000103
OBI:0100055 obsolete_cell line cell IAO:0000120 A material entity that represents generations of a primary culture. GROUP: OBI Biomaterial Branch PERSON: Susanna Sansone subclass Obsolete Class true IAO:0000228
OBI:0100056 obsolete_immortal cell line culture IAO:0000120 immortal cell line sample|permanent cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. PERSON:Matthew Brush PERSON:Matthew Brush subclass Obsolete Class true IAO:0000228 CLO:0009828
OBI:0100062 obsolete_cell line IAO:0000120 cell line sample A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture). OBI-CLO Alignment Working Group (Spring 2013) A split of HeLa cells in active culture, or stored in frozen aliquots. Populations of HEK 293 cells used in experiments such as those documented in Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592.|He, Tong-Chuan, et al. ""Identification of c-MYC as a target of the APC pathway."" Science 281.5382 (1998): 1509-1512. - ""To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene"". Note that common usage in the literature is often of the form ""a human colorectal cancer cell line"", as seen above. But such references to studies in ""a line"" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'."" PERSON:Matthew Brush subclass Obsolete Class true IAO:0000228 CLO:0000031
OBI:0100069 obsolete_polymer IAO:0000120 A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. TERM: CHEBI:33839 James Malone|Philippe Rocca-Serra subclass Obsolete Class true IAO:0000228
OBI:0302714 obsolete_collection (of entities of organismal origin) IAO:0000120 set|group|ensemble a collection is a bfo:aggregate object, that is a set of material object of the same kind PERSON: Philippe Rocca-Serra PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings] PERSON: Susanna Sansone subclass Obsolete Class true IAO:0000103
OBI:0302743 obsolete_liver IAO:0000125 liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates GROUP: OBI Biomaterial Branch PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology. AJR Am J Roentgenol. 1990 Jan;154(1):87-93. PERSON: Philippe Rocca-Serra subclass Obsolete Class true IAO:0000228
OBI:0302745 obsolete_adipose tissue IAO:0000125 adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates. GROUP: OBI Biomaterial derived PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4. PERSON: Philippe Rocca-Serra subclass Obsolete Class true IAO:0000228
OBI:0302901 obsolete_activation IAO:0000124 a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!) OBI-Branch PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63. Philippe Rocca-Serra subclass Obsolete Class true IAO:0000103
OBI:0600065 obsolete_defined processes IAO:0000121 Place holder class, see editor note OBI branch derived PlanAndPlannedProcess Branch subclass Obsolete Class true IAO:0000226
OBI:1110002 obsolete_occurrence of disease IAO:0000123 An occurrence of disease is a process involving pathologic changes within an organism IEDB IEDB subclass Obsolete Class true IAO:0000228
OBI:1110055 obsolete_disease IAO:0000121 placeholder to be imported from disease ontology IEDB IEDB subclass Obsolete Class true IAO:0000228 OGMS:0000031
REO:0000171 obsolete molecular label role IAO:0000122 molecular tracer role A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. OBI developer call, 3-12-12 Group: OBI subclass Obsolete Class true OBI:0002743
REO:0000280 obsolete molecular label IAO:0000122 molecular tracer A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay OBI developer call, 3-12-12 Group: OBI subclass Obsolete Class true OBI:0002744