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Changing templates to use @en
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cmungall committed Jun 20, 2024
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2 changes: 1 addition & 1 deletion src/ontology/templates/biobank-specimens.tsv
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ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type specimen collection process gross anatomical part collection process input URI
ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| 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 specimen and (is_specified_output_of some %) C specimen and (is_specified_output_of some 'specimen collection process') and ('derives from' some %) C specimen and (is_specified_output_of some ('specimen collection process' and has_specified_input some %))
ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=|AL 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 specimen and (is_specified_output_of some %) C specimen and (is_specified_output_of some 'specimen collection process') and ('derives from' some %) C specimen and (is_specified_output_of some ('specimen collection process' and has_specified_input some %))
OBI:0002500 amniotic fluid specimen ready for release A specimen that is derived from amniotic fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism amniotic fluid UBERON_0000173
OBI:0002501 bile specimen ready for release A specimen that is derived from bile. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism bile UBERON_0001970
OBI:0002502 cerebrospinal fluid specimen ready for release A specimen that is derived from cerbrospinal fluid. Chris Stoeckert, Penn Medicine Biobank Chris Stoeckert equivalent collecting specimen from organism cerebrospinal fluid UBERON_0001359
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2 changes: 1 addition & 1 deletion src/ontology/templates/biopsy.tsv
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ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class material anatomical entity input device output entity
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| 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 CI C 'has_specified_input' some % C 'has_specified_input' some % C 'has_specified_output' some %
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=|AL 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 CI C 'has_specified_input' some % C 'has_specified_input' some % C 'has_specified_output' some %
OBI:0002650 biopsy ready for release A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. https://en.wikipedia.org/wiki/Biopsy Biopsy of a potentially cancerous mole. Nicole Vasilevsky|Damion Dooley subclass collecting specimen from organism material anatomical entity device pre-mortem specimen
OBI:0002651 image guided biopsy ready for release image-guided biopsy|imaging guided biopsy|image guided needle biopsy A biopsy which uses an imaging procedure to guide a needle biopsy. https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland. Damion Dooley subclass needle biopsy
OBI:0002652 computed tomography assisted biopsy ready for release Computed Tomography Assisted Biopsy|CT Guided Biopsy|CT Assisted Biopsy|Computed Tomography-Guided Needle Biopsy A needle biopsy guided by real-time computed tomography (CT) scan images. http://purl.obolibrary.org/obo/NCIT_C137909 A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle. Damion Dooley subclass image guided biopsy computed tomography scanner
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2 changes: 1 addition & 1 deletion src/ontology/templates/devices.tsv
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ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class function has part part of manufactured by associated axioms
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| 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 % C 'has function' some % SPLIT=| C 'has part' some % SPLIT=| C 'part of' some % C is_manufactured_by value % C % SPLIT=|
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=|AL 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 % C 'has function' some % SPLIT=| C 'has part' some % SPLIT=| C 'part of' some % C is_manufactured_by value % C % SPLIT=|
OBI:0000038 chromatography column chromatography column metadata incomplete Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. http://en.wikipedia.org/wiki/Column_chromatography Frank Gibson open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 device ('material separation function' and ('realized in' only 'preparative chromatography')) container
OBI:0000041 pump valve switch pump valve switch metadata incomplete A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. OBI OBI Instrument branch FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument device mechanical function
OBI:0000048 chromatography device chromatography device metadata complete chromatography instrument A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a ""mobile phase"" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. http://en.wikipedia.org/wiki/Chromatography Frank Gibson open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 device contain function|environment control function|measure function|material separation function
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2 changes: 1 addition & 1 deletion src/ontology/templates/epitope-assays.tsv
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Ontology ID label editor preferred term has curation status alternative term IEDB alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class material processing technique detection technique reagent input output MHC source target entity target context unit
ID A rdfs: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 % C 'has part' some % SPLIT=| C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some %) and (realizes some ('reagent role' and ('inheres in' some %))) C has_specified_input some % C has_specified_output some % C has_specified_input some (% and ('has part' some 'MHC protein complex')) C has_specified_output some ('is about' some %) C has_specified_output some ('is about' some ( 'has assay target context' some %)) C has_specified_output some ('has measurement unit label' value %)
ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| A IEDB alternative termAL 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 % C 'has part' some % SPLIT=| C 'has part' some ( % and 'detection technique') SPLIT=| C (has_specified_input some %) and (realizes some ('reagent role' and ('inheres in' some %))) C has_specified_input some % C has_specified_output some % C has_specified_input some (% and ('has part' some 'MHC protein complex')) C has_specified_output some ('is about' some %) C has_specified_output some ('is about' some ( 'has assay target context' some %)) C has_specified_output some ('has measurement unit label' value %)
OBI:0001194 ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells TGFb release|ELISPOT An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent enzyme-linked immunospot assay ('transforming growth factor beta production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))
OBI:0001196 cytometric bead array assay measuring epitope specific IP-10 production by T cells CXCL10/IP-10 release|cytometric bead array A cytometric bead array assay that detects IP-10 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent antigen detection by cytometric bead array assay ('IP-10 production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))
OBI:0001198 assay measuring epitope specific interleukin-27 production by T cells IL-27 release|biological activity A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters equivalent assay ('interleukin-27 production' and ('process is result of' some 'MHC:epitope complex binding to TCR'))
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2 changes: 1 addition & 1 deletion src/ontology/templates/obsolete.tsv
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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 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
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| A IEDB alternative termAL 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 metadata incomplete 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 metadata complete 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 obsolete biological vector role metadata complete 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
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2 changes: 1 addition & 1 deletion src/ontology/templates/organizations.tsv
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ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type type
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| 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 TYPE SPLIT=|
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=|AL 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 TYPE SPLIT=|
OBI:0000462 Affymetrix Affymetrix An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix supplied microarray manufacturer|material supplier
OBI:0000752 Thermo Thermo Philippe Rocca-Serra manufacturer
OBI:0000753 Waters Waters Philippe Rocca-Serra manufacturer
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2 changes: 1 addition & 1 deletion src/ontology/templates/sample-collection.tsv
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ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class specimen type
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| 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 % C has_specified_output some (% and 'has role' some 'specimen role')
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=|AL 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 % C has_specified_output some (% and 'has role' some 'specimen role')
OBI:0002904 adult arthropod specimen collection process collection of adults A live arthropod specimen collection process in which the arthropods are in the adult stage. MIRO:30000052 John Judkins https://github.com/obi-ontology/obi/issues/1217 live arthropod specimen collection process
OBI:0002905 animal-biting arthropod specimen collection by aspiration animal biting catch An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. MIRO:30000012 John Judkins https://github.com/obi-ontology/obi/issues/1217 arthropod specimen collection by aspiration
OBI:0002906 animal-biting outdoor arthropod specimen collection by aspiration animal biting catch - outdoors An animal-biting arthropod specimen collection by aspiration that occurs outside a building. MIRO:30000014 John Judkins https://github.com/obi-ontology/obi/issues/1217 animal-biting arthropod specimen collection by aspiration
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2 changes: 1 addition & 1 deletion src/ontology/templates/specimen-assay-data.tsv
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ontology ID label editor preferred term has curation status alternative term definition definition source example of usage term editor editor note curator note ontology term requester term tracker item axiom
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=| 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 EC %
ID LABEL A editor preferred term AI has curation status A alternative term SPLIT=|AL 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 EC %
OBI:0003243 blood assay datum A data item that is the specified output of a blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'blood assay')
OBI:0003244 blood microbiology datum An organism detection datum that is the specified output of a blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'blood microbiology assay')
OBI:0003245 feces assay datum A data item that is the specified output of a feces assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'feces assay')
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