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Replace alternative term with alternative label in all templates
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sebastianduesing committed Nov 22, 2024
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4 changes: 2 additions & 2 deletions src/ontology/templates/administration.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 logical note parent class target of administration material administered administration technique objective associated axiom
ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| 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 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C achieves_planned_objective some % C %
ontology ID label editor preferred term has curation status alternative label definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class target of administration material administered administration technique objective associated axiom
ID A rdfs:label A editor preferred term AI has curation status A alternative label SPLIT=| AL definition@en SPLIT=| 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 'realizes' some ('target of material addition role' and ('role of' some %)) SPLIT=| C 'realizes' some ('material to be added role' and ('role of' some %)) SPLIT=| C 'has part' some % SPLIT=| C achieves_planned_objective some % C %
OBI:0000281 intraperitoneal injection intraperitoneal injection is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe BP equivalent intraperitoneal administration ('realizes' some ('function' and ('inheres in' some 'syringe')))
OBI:0000429 intraperitoneal administration intraperitoneal administration The administration of a substance into the peritoneum of an organism Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h Person:Bjoern Peters equivalent administering substance in vivo peritoneum
OBI:0000837 oral ingestion of pill oral ingestion of pill An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case equivalent oral administration pill ('has specified input' some 'pill')
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4 changes: 2 additions & 2 deletions src/ontology/templates/antibody-purification.tsv
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id rdfs 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 output
ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| 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 SPLIT=| A term tracker item SPLIT=| CLASS_TYPE C % C 'has specified output' some %
id rdfs label editor preferred term has curation status alternative label definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent output
ID A rdfs:label A editor preferred term AI has curation status A alternative label SPLIT=| AL definition@en SPLIT=| 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 SPLIT=| A term tracker item SPLIT=| CLASS_TYPE C % C 'has specified output' some %
OBI:0003616 antibody purification of MHC class I protein complex An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of MHC protein complex MHC class I protein complex
OBI:0003617 antibody purification of human MHC class I protein complex An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class I protein complex, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of MHC class I protein complex human MHC class I protein complex
OBI:0003618 antibody purification of HLA protein complex with A2 serotype An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype, while others contain impurities and are not of interest. Randi Vita Randi Vita|Sebastian Duesing equivalent antibody purification of human MHC class I protein complex HLA protein complex with A2 serotype
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4 changes: 2 additions & 2 deletions src/ontology/templates/assays.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 logical note parent class material processing technique detection technique evaluant measurand analyte device reagent molecular label input output target entity target context objective associated axioms
ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| 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 'has role' some 'evaluant role')) and (realizes some ('evaluant role' and ('role of' some %))) SPLIT=| C ('has specified input' some %) and (realizes some ('measurand role' and ('inheres in' some %))) C ('has specified input' some %) and (realizes some ('analyte role' and ('inheres in' some %))) C ('has specified input' some %) and (realizes some (function and ('inheres in' some %))) SPLIT=| C ('has specified input' some %) and (realizes some ('reagent role' and ('inheres in' some %))) C ('has specified input' some %) and (realizes some ('molecular label role' and ('inheres in' some %))) C 'has specified input' some % C 'has specified output' some % C 'has specified output' some ('is about' some %) C 'has specified output' some ('is about' some ( 'has assay target context' some %)) C achieves_planned_objective some % C %
ontology ID label editor preferred term has curation status alternative label definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type logical note parent class material processing technique detection technique evaluant measurand analyte device reagent molecular label input output target entity target context objective associated axioms
ID A rdfs:label A editor preferred term AI has curation status A alternative label SPLIT=| AL definition@en SPLIT=| 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 'has role' some 'evaluant role')) and (realizes some ('evaluant role' and ('role of' some %))) SPLIT=| C ('has specified input' some %) and (realizes some ('measurand role' and ('inheres in' some %))) C ('has specified input' some %) and (realizes some ('analyte role' and ('inheres in' some %))) C ('has specified input' some %) and (realizes some (function and ('inheres in' some %))) SPLIT=| C ('has specified input' some %) and (realizes some ('reagent role' and ('inheres in' some %))) C ('has specified input' some %) and (realizes some ('molecular label role' and ('inheres in' some %))) C 'has specified input' some % C 'has specified output' some % C 'has specified output' some ('is about' some %) C 'has specified output' some ('is about' some ( 'has assay target context' some %)) C achieves_planned_objective some % C %
CHMO:0000087 fluorescence microscopy assay fluorescence imaging|fluorescence microscopic imaging|FM Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. CHMO subclass light microscopy assay ('material entity' and ('bearer of' some fluorescence))
CHMO:0000089 confocal fluorescence microscopy assay CLSM|confocal fluorescence imaging|confocal laser scanning fluorescence microscopy|confocal laser scanning microscopy|confocal-laser scanning microscopy|fluorescence confocal microscopy|fluorescence confocal scanning laser microscopy|LSCM|scanning confocal fluorescence microscopy Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. CHMO subclass microscopy assay
CHMO:0000102 light microscopy assay light microscopy|OM|optical microscopy Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. CHMO subclass microscopy assay
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4 changes: 2 additions & 2 deletions 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=| AL definition@en 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 %
ontology ID label editor preferred term has curation status alternative label 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 label SPLIT=| AL definition@en 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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4 changes: 2 additions & 2 deletions src/ontology/templates/data-sets.tsv
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ontology ID label 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 is about is specified output of has member
ID A rdfs:label AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| 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 'is about' some % C 'is specified output of' some % C 'has member' some %
ontology ID label has curation status alternative label definition definition source example of usage term editor editor note curator note ontology term requester term tracker item logical type parent class is about is specified output of has member
ID A rdfs:label AI has curation status A alternative label SPLIT=| AL definition@en SPLIT=| 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 'is about' some % C 'is specified output of' some % C 'has member' some %
OBI:0003327 image data set A data set that is comprised of multidimensional structured measurements and metadata required for a morphological representation of an entity. An image data set can be the source from which an image (such as a 2D image using pixels or a 3D image using voxels) is produced. The output produced by a digital imaging technique, such as microscopy, MRI, or CT. https://orcid.org/0000-0001-9625-1899 ""William D. Duncan"",https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie"",https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik"",https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl"",https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra"",https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 subclass data set entity
OBI:0003328 magnetic resonance image data set An image data set whose information content originates from some MR imaging assay and is about some MRI participant. MRI at a Glance, ISBN 10: 1119053552 The DICOM file produced by an MRI machine when a multiple sclerosis patient undergoes a brain scan. https://orcid.org/0000-0001-9625-1899 ""William D. Duncan"",https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie"",https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik"",https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl"",https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra"",https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 equivalent image data set magnetic resonance imaging participant
OBI:0003331 raw image data set An image data set that encodes measurement values produced by some instrument before undergoing a data transformation. The untransformed (""k-space"") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. https://orcid.org/0000-0001-9625-1899 ""William D. Duncan"",https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie"",https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik"",https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl"",https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra"",https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"",https://orcid.org/0000-0002-1604-3078 ""Alan Ruttenberg"" https://github.com/obi-ontology/obi/issues/1481 subclass image data set
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4 changes: 2 additions & 2 deletions src/ontology/templates/data-transformations.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 term tracker item logical type parent class input output objective associated axioms
ID A rdfs:label A editor preferred term AI has curation status A alternative term SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A term tracker item CLASS_TYPE C % C 'has specified input' some % C 'has specified output' some % C achieves_planned_objective some % C %
ontology ID label editor preferred term has curation status alternative label definition definition source example of usage term editor editor note curator note term tracker item logical type parent class input output objective associated axioms
ID A rdfs:label A editor preferred term AI has curation status A alternative label SPLIT=| AL definition@en SPLIT=| A definition source SPLIT=| A example of usage SPLIT=| A term editor SPLIT=| A editor note SPLIT=| A curator note SPLIT=| A term tracker item CLASS_TYPE C % C 'has specified input' some % C 'has specified output' some % C achieves_planned_objective some % C %
OBI:0003355 image data set analysis The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik""|https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl""|https://orcid.org/0000-0001-9625-1899 ""William D. Duncan""|https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra""|https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie""|https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 subclass data transformation image data set
OBI:0003356 raw magnetic resonance image data set reconstruction A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. A Fourier transform of raw ""k-space"" data produced into an image data set that represents the anatomical structure of the tissue examined. https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik""|https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl""|https://orcid.org/0000-0001-9625-1899 ""William D. Duncan""|https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra""|https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie""|https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith"" https://github.com/obi-ontology/obi/issues/1481 equivalent image data set analysis raw magnetic resonance image data set reconstructed magnetic resonance image data set
OBI:0003647 tandem mass spectrometry analysis tandem mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a tandem mass spectrometry assay. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1684 equivalent mass spectrometry analysis ('data item' and 'is specified output of' some 'tandem mass spectrometry assay')
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