From 8a1044c9f6d85a0c68e46436ec8ff86f068b6731 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Mon, 5 Aug 2024 10:47:26 -0500 Subject: [PATCH 01/38] Switch non-versioned OMO import to the current version of OMO. --- src/ontology/obi-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index f0ece3b6..f718c89e 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -14,7 +14,6 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - @@ -59,6 +58,7 @@ + en Ontology for Biomedical Investigations From 0ed714a7f9435a41e7dc761f7ba17b84dc446a7a Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Mon, 5 Aug 2024 13:33:39 -0500 Subject: [PATCH 02/38] Replace RO-core import with OntoFox RO import. --- src/ontology/OntoFox_inputs/RO_input.txt | 28 +++ src/ontology/OntoFox_outputs/RO_imports.owl | 186 ++++++++++++++++++++ src/ontology/catalog-v001.xml | 1 + src/ontology/obi-edit.owl | 2 +- 4 files changed, 216 insertions(+), 1 deletion(-) create mode 100644 src/ontology/OntoFox_inputs/RO_input.txt create mode 100644 src/ontology/OntoFox_outputs/RO_imports.owl diff --git a/src/ontology/OntoFox_inputs/RO_input.txt b/src/ontology/OntoFox_inputs/RO_input.txt new file mode 100644 index 00000000..a80ba27d --- /dev/null +++ b/src/ontology/OntoFox_inputs/RO_input.txt @@ -0,0 +1,28 @@ +[URI of the OWL(RDF/XML) output file] +http://purl.obolibrary.org/obo/obi/dev/import/RO_imports.owl + +[Source ontology] +# OBO Relations Ontology +RO + +[Low level source term URIs] +http://purl.obolibrary.org/obo/RO_0000081 # role of +http://purl.obolibrary.org/obo/RO_0000087 # has role +http://purl.obolibrary.org/obo/RO_0000091 # has disposition +http://purl.obolibrary.org/obo/RO_0000092 # disposition of +http://purl.obolibrary.org/obo/RO_0000085 # has function +http://purl.obolibrary.org/obo/RO_0000079 # function of +http://purl.obolibrary.org/obo/RO_0000086 # has quality +http://purl.obolibrary.org/obo/RO_0000080 # quality of +http://purl.obolibrary.org/obo/RO_0002351 # has member +http://purl.obolibrary.org/obo/RO_0001025 # located in + +[Top level source term URIs and target direct superclass URIs] + +[Source term retrieval setting] +includeAllIntermediates + +[Source annotation URIs] +http://www.w3.org/2000/01/rdf-schema#label +copyTo http://purl.obolibrary.org/obo/IAO_0000111 +http://purl.obolibrary.org/obo/IAO_0000115 diff --git a/src/ontology/OntoFox_outputs/RO_imports.owl b/src/ontology/OntoFox_outputs/RO_imports.owl new file mode 100644 index 00000000..0d90f61d --- /dev/null +++ b/src/ontology/OntoFox_outputs/RO_imports.owl @@ -0,0 +1,186 @@ + + + + + + + + + + + + + + + editor preferred term + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + editor preferred term + + + + + + + + definition + definition + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + definition + definition + + + + + + + + imported from + + + + + + + + + + + + + + + + + + + function of + a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence + + function of + + + + + + + + quality of + a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence + + quality of + + + + + + + + role of + a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence + + role of + + + + + + + + has function + a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence + + has function + + + + + + + + has quality + a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence + + has quality + + + + + + + + has role + a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence + + has role + + + + + + + + has disposition + a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + + has disposition + + + + + + + + disposition of + inverse of has disposition + + disposition of + + + + + + + + + located in + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + + located in + + + + + + + + + has member + has member is a mereological relation between a collection and an item. + + has member + + + + + + + diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 37551192..fa8abb2f 100755 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -21,6 +21,7 @@ + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index f718c89e..2d01e82b 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -35,6 +35,7 @@ + @@ -59,7 +60,6 @@ - en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester From 43990a342e552fb9941a4b3ff0c4b2facb4e9a14 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Mon, 5 Aug 2024 13:38:52 -0500 Subject: [PATCH 03/38] Prepare IAO import module. --- src/ontology/OntoFox_inputs/IAO_input.txt | 3 +- src/ontology/OntoFox_outputs/IAO_imports.owl | 104 +------------------ 2 files changed, 7 insertions(+), 100 deletions(-) diff --git a/src/ontology/OntoFox_inputs/IAO_input.txt b/src/ontology/OntoFox_inputs/IAO_input.txt index 15dfb4cd..99926b52 100644 --- a/src/ontology/OntoFox_inputs/IAO_input.txt +++ b/src/ontology/OntoFox_inputs/IAO_input.txt @@ -46,6 +46,7 @@ http://purl.obolibrary.org/obo/IAO_0000235 # denoted by http://purl.obolibrary.org/obo/IAO_0000300 # textual entity http://purl.obolibrary.org/obo/IAO_0000306 # table http://purl.obolibrary.org/obo/IAO_0000310 # document +http://purl.obolibrary.org/obo/IAO_0000311 # publication http://purl.obolibrary.org/obo/IAO_0000312 # publication about an investigation http://purl.obolibrary.org/obo/IAO_0000401 # one dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000407 # has coordinate unit label @@ -73,7 +74,7 @@ http://purl.obolibrary.org/obo/IAO_0000572 # documenting subClassOf http://purl.obolibrary.org/obo/OBI_0000011 # planned process [Source term retrieval setting] -includeAllIntermediates +includeComputedIntermediates [Source annotation URIs] http://www.w3.org/2000/01/rdf-schema#label diff --git a/src/ontology/OntoFox_outputs/IAO_imports.owl b/src/ontology/OntoFox_outputs/IAO_imports.owl index 40cfcb4a..113517d4 100644 --- a/src/ontology/OntoFox_outputs/IAO_imports.owl +++ b/src/ontology/OntoFox_outputs/IAO_imports.owl @@ -194,52 +194,6 @@ - - - - - entity - - entity - - - - - - - - - continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - - continuant - - - - - - - - - quality - - quality - - - - - - - - - specifically dependent continuant - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - specifically dependent continuant - - - - @@ -340,7 +294,7 @@ interpreted by or directly executed by a processing unit. - + information carrier A quality of an information bearer that imparts the information content @@ -424,7 +378,7 @@ interpreted by or directly executed by a processing unit. - + graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. @@ -460,7 +414,7 @@ interpreted by or directly executed by a processing unit. - + curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. @@ -530,18 +484,6 @@ Example: The ISO document specifying what encompasses an XML document; The instr - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - - data about an ontology part - - - - @@ -679,18 +621,6 @@ clustering algorithm. - - - - - diagram - A figure that expresses one or more propositions - - diagram - - - - @@ -727,22 +657,10 @@ clustering algorithm. - - - - - cartesian spatial coordinate datum - A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude - - cartesian spatial coordinate datum - - - - - + one dimensional cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region @@ -862,7 +780,7 @@ points together with a line. - + centrally registered identifier registry A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. @@ -883,18 +801,6 @@ points together with a line. - - - - - code set - An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. - - code set - - - - From 19d4e323b10716cfcf64a4e5bc0d65665ce2ebfe Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Mon, 5 Aug 2024 13:41:09 -0500 Subject: [PATCH 04/38] Remove BFO import. --- src/ontology/obi-edit.owl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 2d01e82b..407f4c54 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -14,7 +14,6 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - From bce2c6b1acffb59291f94009fea003b1e2faca75 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 6 Aug 2024 15:49:52 -0500 Subject: [PATCH 05/38] Add COB import --- src/ontology/catalog-v001.xml | 1 + src/ontology/obi-edit.owl | 2 ++ 2 files changed, 3 insertions(+) diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index fa8abb2f..cae333f8 100755 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -1,5 +1,6 @@ + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 407f4c54..b2139cf3 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -9,11 +9,13 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + From 9fe2471f167d357fcfc78c5fe863a25895d9ff4a Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 6 Aug 2024 15:51:28 -0500 Subject: [PATCH 06/38] Rename 'alternative term' column to 'alternative label' in all templates --- src/ontology/templates/administration.tsv | 4 ++-- src/ontology/templates/antibody-purification.tsv | 4 ++-- src/ontology/templates/assays.tsv | 4 ++-- src/ontology/templates/biobank-specimens.tsv | 4 ++-- src/ontology/templates/biopsy.tsv | 4 ++-- src/ontology/templates/data-sets.tsv | 4 ++-- src/ontology/templates/data-transformations.tsv | 4 ++-- src/ontology/templates/devices.tsv | 4 ++-- src/ontology/templates/epitope-assays.tsv | 4 ++-- src/ontology/templates/medical-history.tsv | 4 ++-- src/ontology/templates/obsolete.tsv | 4 ++-- src/ontology/templates/organizations.tsv | 4 ++-- src/ontology/templates/physical-examination.tsv | 4 ++-- src/ontology/templates/sample-collection.tsv | 4 ++-- src/ontology/templates/sequence-analysis.tsv | 4 ++-- src/ontology/templates/specimen-assay-data.tsv | 4 ++-- src/ontology/templates/study-designs.tsv | 4 ++-- src/ontology/templates/value-specifications.tsv | 4 ++-- 18 files changed, 36 insertions(+), 36 deletions(-) diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index aed4b76d..aa085b77 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -1,5 +1,5 @@ -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') diff --git a/src/ontology/templates/antibody-purification.tsv b/src/ontology/templates/antibody-purification.tsv index 7227c734..ca6b2148 100644 --- a/src/ontology/templates/antibody-purification.tsv +++ b/src/ontology/templates/antibody-purification.tsv @@ -1,5 +1,5 @@ -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 diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 47c9115b..40442d6d 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -1,5 +1,5 @@ -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 diff --git a/src/ontology/templates/biobank-specimens.tsv b/src/ontology/templates/biobank-specimens.tsv index 7e8c0c84..d4205b5a 100644 --- a/src/ontology/templates/biobank-specimens.tsv +++ b/src/ontology/templates/biobank-specimens.tsv @@ -1,5 +1,5 @@ -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=| 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 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 %)) +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 specimen collection process gross anatomical part collection process input URI +ID A rdfs: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 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 diff --git a/src/ontology/templates/biopsy.tsv b/src/ontology/templates/biopsy.tsv index 3d8e352c..3aa976ba 100644 --- a/src/ontology/templates/biopsy.tsv +++ b/src/ontology/templates/biopsy.tsv @@ -1,5 +1,5 @@ -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 diff --git a/src/ontology/templates/data-sets.tsv b/src/ontology/templates/data-sets.tsv index d1551234..95dc5f53 100644 --- a/src/ontology/templates/data-sets.tsv +++ b/src/ontology/templates/data-sets.tsv @@ -1,5 +1,5 @@ -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 diff --git a/src/ontology/templates/data-transformations.tsv b/src/ontology/templates/data-transformations.tsv index dbe7caa6..bb2f1947 100644 --- a/src/ontology/templates/data-transformations.tsv +++ b/src/ontology/templates/data-transformations.tsv @@ -1,5 +1,5 @@ -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') diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index ee8e777e..8796211c 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -1,5 +1,5 @@ -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=| 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 C % C 'has function' some % SPLIT=| C 'has part' some % SPLIT=| C 'part of' some % C is_manufactured_by value % C % SPLIT=| +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 function has part part of manufactured by associated axioms +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 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 diff --git a/src/ontology/templates/epitope-assays.tsv b/src/ontology/templates/epitope-assays.tsv index bdd2534c..8557f7ea 100644 --- a/src/ontology/templates/epitope-assays.tsv +++ b/src/ontology/templates/epitope-assays.tsv @@ -1,5 +1,5 @@ -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 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 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 %) +Ontology ID label editor preferred term has curation status alternative label 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 label SPLIT=| A IEDB alternative term 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 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')) diff --git a/src/ontology/templates/medical-history.tsv b/src/ontology/templates/medical-history.tsv index 3dafc77d..c1ccb4d3 100644 --- a/src/ontology/templates/medical-history.tsv +++ b/src/ontology/templates/medical-history.tsv @@ -1,5 +1,5 @@ -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 -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 % +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 +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 % OBI:0002368 clinical history of cancer A clinical history in which there is a diagnosis of cancer. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass clinical history OBI:0002369 clinical history devoid of cancer clinical history of no cancer A clinical history in which there was no diagnosis of cancer. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass clinical history OBI:0002370 unknown clinical history of cancer A clinical history in which it is not known whether there was a diagnosis of cancer. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass clinical history diff --git a/src/ontology/templates/obsolete.tsv b/src/ontology/templates/obsolete.tsv index 39f14605..fdaba18a 100755 --- a/src/ontology/templates/obsolete.tsv +++ b/src/ontology/templates/obsolete.tsv @@ -1,5 +1,5 @@ -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 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 C % AT deprecated^^xsd:boolean AI has obsolescence reason AI term replaced by +ontology ID label editor preferred term has curation status alternative label 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 label SPLIT=| A IEDB alternative term 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 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 diff --git a/src/ontology/templates/organizations.tsv b/src/ontology/templates/organizations.tsv index dd3c57c6..17735113 100644 --- a/src/ontology/templates/organizations.tsv +++ b/src/ontology/templates/organizations.tsv @@ -1,5 +1,5 @@ -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=| 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 TYPE SPLIT=| +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 type +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 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 diff --git a/src/ontology/templates/physical-examination.tsv b/src/ontology/templates/physical-examination.tsv index 7aeb49b3..4dbf9169 100644 --- a/src/ontology/templates/physical-examination.tsv +++ b/src/ontology/templates/physical-examination.tsv @@ -1,5 +1,5 @@ -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 detection technique evaluant device input output anatomical site assessed biological trait -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 ( % 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 (function and ('inheres in' some %))) SPLIT=| C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is quality measurement of' 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 logical note parent class detection technique evaluant device input output anatomical site assessed biological trait +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 ( % 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 (function and ('inheres in' some %))) SPLIT=| C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is quality measurement of' some %) OBI:0003501 functional assessment of individual A physical examination of an organism's ability to perform functional activities. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass physical examination of an organism OBI:0003502 facial atrophy assessment An observational assessment of the loss of facial muscle tissue due to inactivity or disease. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass observational assessment of individual facial muscle facial muscle performance OBI:0003503 tongue atrophy assessment An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass observational assessment of individual tongue facial muscle performance diff --git a/src/ontology/templates/sample-collection.tsv b/src/ontology/templates/sample-collection.tsv index c2731ddf..0319846f 100644 --- a/src/ontology/templates/sample-collection.tsv +++ b/src/ontology/templates/sample-collection.tsv @@ -1,5 +1,5 @@ -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=| 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 C % C has_specified_output some (% and 'has role' some 'specimen role') +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 specimen type +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 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 diff --git a/src/ontology/templates/sequence-analysis.tsv b/src/ontology/templates/sequence-analysis.tsv index 9fb69b27..7c43a66c 100644 --- a/src/ontology/templates/sequence-analysis.tsv +++ b/src/ontology/templates/sequence-analysis.tsv @@ -1,5 +1,5 @@ -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 output input input of output of objective -ID A rdfs:label A editor preferred term AL 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_specified_output' some % C 'has_specified_input' some % C is_specified_input_of some % C is_specified_output_of some % C achieves_planned_objective 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 output input input of output of objective +ID A rdfs:label A editor preferred term AL 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_specified_output' some % C 'has_specified_input' some % C is_specified_input_of some % C is_specified_output_of some % C achieves_planned_objective some % OBI:0002565 adapter-sequence trimming A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). Dan Berrios Dan Berrios subclass sequence trimming adapter-trimmed sequence data 'adapter sequence data' OBI:0002566 file merge A data transformation in which data contained in 2 or more files are merged into a single file. Dan Berrios Dan Berrios subclass data transformation OBI:0002567 sequence alignment A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. Dan Berrios Dan Berrios subclass sequence analysis data transformation aligned sequence data sequence data diff --git a/src/ontology/templates/specimen-assay-data.tsv b/src/ontology/templates/specimen-assay-data.tsv index 84caaf7d..ea6871dc 100644 --- a/src/ontology/templates/specimen-assay-data.tsv +++ b/src/ontology/templates/specimen-assay-data.tsv @@ -1,5 +1,5 @@ -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=| 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 EC % +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 axiom +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 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') diff --git a/src/ontology/templates/study-designs.tsv b/src/ontology/templates/study-designs.tsv index 50ae1a83..b0c2389d 100644 --- a/src/ontology/templates/study-designs.tsv +++ b/src/ontology/templates/study-designs.tsv @@ -1,5 +1,5 @@ -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 objective independent variable dependent variable assay associated superclasses associated equivalent classes -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 C % C 'has part' some % SPLIT=| C 'has part' some ('study design independent variable' and ('is about' some %)) SPLIT=| C 'has part' some ('study design dependent variable' and ('is about' some %)) SPLIT=| C 'is concretized as' some ('realized in' some ('has part' some %)) SPLIT=| SC % SPLIT=| EC % SPLIT=| +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 objective independent variable dependent variable assay associated superclasses associated equivalent classes +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 C % C 'has part' some % SPLIT=| C 'has part' some ('study design independent variable' and ('is about' some %)) SPLIT=| C 'has part' some ('study design dependent variable' and ('is about' some %)) SPLIT=| C 'is concretized as' some ('realized in' some ('has part' some %)) SPLIT=| SC % SPLIT=| EC % SPLIT=| OBI:0000115 intervention design intervention design pending final vetting An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. OBI branch derived PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. Philppe Rocca-Serra equivalent study design study intervention OBI:0000951 compound treatment design compound treatment design metadata complete an intervention design in which the treatment is the administration of a compound MO_555 compound_treatment_design PERSON: Bjoern Peters This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. subclass study design ('study intervention' and 'administration of material to specimen') OBI:0000985 growth condition intervention design growth condition intervention design metadata complete A study design in which the independent variable is the environmental condition in which the specimen is growing MO_588 growth_condition_design PERSON: Bjoern Peters subclass intervention design study intervention|growth environment diff --git a/src/ontology/templates/value-specifications.tsv b/src/ontology/templates/value-specifications.tsv index adeeb7d4..3dd5092a 100644 --- a/src/ontology/templates/value-specifications.tsv +++ b/src/ontology/templates/value-specifications.tsv @@ -1,5 +1,5 @@ -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 parent class -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 TYPE 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 type parent class +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 TYPE C % OBI:0002199 reason for lack of data item An information content entity that provides an explanation why a data item is not provided. OBI cannot be assessed, not applicable, unknown Chris Stoeckert, Helena Ellis NCI BBRB subclass information content entity OBI:0002200 cannot be assessed determination cannot be assessed A reason for lack of data item that is the negative output of a determination if assay will provide reliable results. OBI Chris Stoeckert, Helena Ellis NCI BBRB subclass reason for lack of data item OBI:0002201 determination if assay will provide reliable results A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. OBI Chris Stoeckert, Helena Ellis NCI BBRB subclass planned process From 9ea9345b9a60aa012d4e8a87d22ac9455af91570 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 6 Aug 2024 15:55:06 -0500 Subject: [PATCH 07/38] Replace 'inheres in' and 'bearer of' with 'characteristic of' and 'has characteristic' in all templates --- src/ontology/templates/administration.tsv | 10 +++++----- src/ontology/templates/assays.tsv | 12 ++++++------ src/ontology/templates/devices.tsv | 2 +- src/ontology/templates/epitope-assays.tsv | 2 +- src/ontology/templates/physical-examination.tsv | 2 +- 5 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index aa085b77..9bdba9f1 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -1,14 +1,14 @@ 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: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 ('characteristic of' 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') -OBI:0000934 intramuscular injection intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe equivalent administering substance in vivo skeletal muscle tissue ('realizes' some ('function' and ('inheres in' some 'syringe'))) -OBI:0000942 intradermal injection intradermal injection is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo dermis ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0000934 intramuscular injection intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe equivalent administering substance in vivo skeletal muscle tissue ('realizes' some ('function' and ('characteristic of' some 'syringe'))) +OBI:0000942 intradermal injection intradermal injection is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo dermis ('realizes' some ('function' and ('characteristic of' some 'syringe'))) OBI:0000952 oral administration oral administration An administering substance in vivo into the mouth of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mouth -OBI:0000954 subcutaneous injection subcutaneous injection is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo hypodermis ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0000954 subcutaneous injection subcutaneous injection is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo hypodermis ('realizes' some ('function' and ('characteristic of' some 'syringe'))) OBI:0000983 intranasal mucosal administration intranasal mucosal administration The administration of a substance into the intranasal mucosis of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mucosa of nasopharynx -OBI:0000994 intravenous injection intravenous injection is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo vein ('realizes' some ('function' and ('inheres in' some 'syringe'))) +OBI:0000994 intravenous injection intravenous injection is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo vein ('realizes' some ('function' and ('characteristic of' some 'syringe'))) OBI:0001174 passive immunization passive immunization adoptive transfer The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum subclass administering substance in vivo adaptive immune receptor OBI:0003057 antibiotic administration process antibiotic administration process Administering substance in vivo where an antibiotic substance is administered to a living organism. Penn Group Chris Stoeckert|Cristian Cocos|Jie Zheng subclass administering substance in vivo antibacterial OBI:0003413 administering substance in vivo to cause disease An administration of substance in vivo with the intention to induce disease in the organism. IEDB IEDB subclass administering substance in vivo disease causation objective diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 40442d6d..4bee1c2d 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -1,13 +1,13 @@ 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)) +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 ('characteristic of' some %))) C (has_specified_input some %) and (realizes some ('analyte role' and ('characteristic of' some %))) C (has_specified_input some %) and (realizes some (function and ('characteristic of' some %))) SPLIT=| C (has_specified_input some %) and (realizes some ('reagent role' and ('characteristic of' some %))) C (has_specified_input some %) and (realizes some ('molecular label role' and ('characteristic of' 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 ('has characteristic' 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 CHMO:0000701 liquid chromatography-tandem mass spectrometry LC-MSMS|LC-MS-MS|LC-MS/MS|liquid chromatography tandem mass spectroscopy|LC-MS2|liquid chromatography-tandem mass spectroscopy|LCMSMS|liquid chromatography tandem mass spectrometry|LC/MS/MS A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. CHMO subclass tandem mass spectrometry assay liquid chromatography OBI:0000117 Bernoulli trial pending final vetting An assay where the output data is a datum with one of two values denoting success and failure. OBI branch derived PlanAndPlannedProcess Branch subclass assay OBI:0000182 NMR 3D molecular structure determination assay A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. IEDB Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013). PlanAndPlannedProcess Branch|IEDB equivalent 3D molecular structure determination assay NMR instrument 3D structural organization datum OBI:0000185 imaging assay pending final vetting An assay that produces a picture of an entity. OBI branch derived PlanAndPlannedProcess Branch subclass assay image -OBI:0000201 radioactivity detection An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. IEDB Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material. PlanAndPlannedProcess Branch|IEDB equivalent assay ('material entity' and ('bearer of' some radioactive)) ('material entity' and ('bearer of' some radioactive)) +OBI:0000201 radioactivity detection An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. IEDB Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material. PlanAndPlannedProcess Branch|IEDB equivalent assay ('material entity' and ('has characteristic' some radioactive)) ('material entity' and ('has characteristic' some radioactive)) OBI:0000288 protein-protein interaction detection assay metadata incomplete An assay that determines interactions between proteins, such as protein-protein binding. subclass assay OBI:0000291 transcription factor binding site assay metadata complete TF binding An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors OBI Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Philippe Rocca-Serra https://sourceforge.net/p/obi/obi-terms/767/ subclass binding assay information content entity TF_binding_site OBI:0000366 metabolite profiling assay metadata complete metabolite assay|metabolomic assay An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism OBI Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 Philippe Rocca-Serra subclass assay specimen @@ -68,7 +68,7 @@ OBI:0000893 real time polymerase chain reaction assay metadata complete Q-PCR|q OBI:0000897 DEPC structure mapping assay ready for release A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe RNA ontology PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28. Philippe Rocca-Serra subclass single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing ('deoxyribonucleic acid' or 'ribonucleic acid') measurement datum secondary structure of sequence macromolecule OBI:0000903 in vitro cell killing assay A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. IEDB Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. IEDB equivalent cell-cell killing assay cultured cell population OBI:0000904 reporter cell line analyte detection bioassay An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. IEDB CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant. IEDB subclass logical definition does not specify how the cell line is used as a reporter analyte assay maintaining cell culture cell line -OBI:0000910 radio immuno assay An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. IEDB To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay. IEDB subclass logical definition does not capture the interaction aspect assay ('material entity' and ('bearer of' some radioactive)) +OBI:0000910 radio immuno assay An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. IEDB To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay. IEDB subclass logical definition does not capture the interaction aspect assay ('material entity' and ('has characteristic' some radioactive)) OBI:0000911 real time reverse-transcription polymerase chain reaction assay metadata complete RRT-PCR|qRT-PCR|RT-rt PCR An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay. Melanie Courtot|Bjoern Peters subclass assay artificially induced reverse transcription real time polymerase chain reaction assay information content entity gene expression OBI:0000912 X-ray crystallography 3D molecular structure determination assay A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. IEDB Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes. IEDB subclass logical definition does not capture diffraction pattern 3D molecular structure determination assay X-ray source OBI:0000913 promoter activity detection by reporter gene assay An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. IEDB A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color. IEDB subclass logical definition does not capture gene insertion assay cell core promoter sequence-specific DNA binding @@ -141,7 +141,7 @@ OBI:0001476 phage display binding assay A binding assay in which a collection OBI:0001488 epitope tolerance induction experiment metadata complete tolerance induction An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response IEDB IEDB subclass efficacy of epitope intervention experiment OBI:0001491 binding assay using radioactivity detection metadata complete A binding assay that uses radioactivity detection as an indicator of binding. IEDB Bjoern Peters|Randi Vita equivalent binding assay radioactivity detection OBI:0001499 binding assay using fluorescence detection metadata complete A binding assay that uses fluorescence detection as an indicator of binding. IEDB Bjoern Peters|Randi Vita equivalent binding assay fluorescence detection assay -OBI:0001501 fluorescence detection assay An assay in which a material's fluorescence is determined. IEDB Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for. IEDB equivalent assay ('material entity' and ('bearer of' some fluorescence)) +OBI:0001501 fluorescence detection assay An assay in which a material's fluorescence is determined. IEDB Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for. IEDB equivalent assay ('material entity' and ('has characteristic' some fluorescence)) OBI:0001591 direct binding assay metadata complete A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. IEDB Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody._ Bjoern Peters|Randi Vita subclass binding assay OBI:0001593 competitive inhibition of binding assay A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. IEDB Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide._ IEDB subclass logical definition does not capture inhibition of binding binding assay ('material entity' and ('has role' some 'competitive binding reference ligand role')) OBI:0001624 organism species detection assay metadata complete organism identification assay An organism detection assay that identifies the organism species in a specimen. NIAID GSCID-BRC metadata working group Chris Stoeckert|Jie Zheng equivalent organism detection assay (achieves_planned_objective some 'organism species detection objective') @@ -656,7 +656,7 @@ OBI:0003599 single cell T cell receptor repertoire sequencing assay single cell OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay QCM An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. http://www.ncbi.nlm.nih.gov/pubmed/23504432|https://en.wikipedia.org/wiki/Quartz_crystal_microbalance Randi Vita|Bjoern Peters|Sebastian Duesing subclass assay OBI:0003604 multiplexed error-robust fluorescence in situ hybridization assay MERFISH A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1724 subclass fluorescence in-situ hybridization assay OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. https://doi.org/10.21769/BioProtoc.3070 Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1725 subclass fluorescence in-situ hybridization assay -OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus +OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('has characteristic' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course OBI:0600017 assay detecting a molecular label pending final vetting An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached OBI developer call, 3-12-12 Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present Matthew Brush subclass assay molecular-labeled material measurement datum molecular-labeled material diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index 8796211c..2a21fe95 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -309,7 +309,7 @@ OBI:0001204 SNP microarray SNP microarray metadata complete A DNA microarray us OBI:0001307 tiling microarray tiling microarray metadata complete genome tiling array A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. EFO_0002704: tiling array Person: Helen Parkinson DNA microarray OBI:0001865 assay array metadata complete A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg device solid support function OBI:0001869 Illumina BeadChip metadata complete An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. http://www.illumina.com/technology/beadarray_technology.ilmn PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi assay array Illumina -OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg equivalent Illumina BeadChip ('bearer of' some (function and ('realized in' only (assay and (has_specified_output some ('measurement datum' and ('is about' some 'DNA methylation'))))))) +OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg equivalent Illumina BeadChip ('has characteristic' some (function and ('realized in' only (assay and (has_specified_output some ('measurement datum' and ('is about' some 'DNA methylation'))))))) OBI:0001871 LSRFortessa X-20 metadata complete A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg Anna Maria Masci flow cytometer analyzer Becton Dickinson (BD Biosciences) OBI:0001971 Ion 316 Chip v2 Ion 316 Chip v2 Ion PGM 316 Chip|Ion 316 Chip|Ion PGM 316 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ ion semiconductor chip OBI:0001972 Ion 318 Chip v2 Ion 318 Chip v2 Ion 318 Chip|Ion PGM 318 Chip|Ion PGM 318 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ ion semiconductor chip diff --git a/src/ontology/templates/epitope-assays.tsv b/src/ontology/templates/epitope-assays.tsv index 8557f7ea..09eb0d05 100644 --- a/src/ontology/templates/epitope-assays.tsv +++ b/src/ontology/templates/epitope-assays.tsv @@ -1,5 +1,5 @@ Ontology ID label editor preferred term has curation status alternative label 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 label SPLIT=| A IEDB alternative term 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 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 label SPLIT=| A IEDB alternative term 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 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 ('characteristic of' 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')) diff --git a/src/ontology/templates/physical-examination.tsv b/src/ontology/templates/physical-examination.tsv index 4dbf9169..47d07326 100644 --- a/src/ontology/templates/physical-examination.tsv +++ b/src/ontology/templates/physical-examination.tsv @@ -1,5 +1,5 @@ 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 detection technique evaluant device input output anatomical site assessed biological trait -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 ( % 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 (function and ('inheres in' some %))) SPLIT=| C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is quality measurement of' some %) +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 ( % 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 (function and ('characteristic of' some %))) SPLIT=| C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is quality measurement of' some %) OBI:0003501 functional assessment of individual A physical examination of an organism's ability to perform functional activities. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass physical examination of an organism OBI:0003502 facial atrophy assessment An observational assessment of the loss of facial muscle tissue due to inactivity or disease. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass observational assessment of individual facial muscle facial muscle performance OBI:0003503 tongue atrophy assessment An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass observational assessment of individual tongue facial muscle performance From b3b54ad3150c8aa9248fb7d985f97a84fcfb863b Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 6 Aug 2024 16:23:38 -0500 Subject: [PATCH 08/38] Redirect references to CHEBI:atom to COB:atom --- src/ontology/OntoFox_inputs/ChEBI_input.txt | 11 +++--- .../OntoFox_outputs/ChEBI_imports.owl | 36 ++++++++----------- src/ontology/obi-edit.owl | 2 +- 3 files changed, 22 insertions(+), 27 deletions(-) diff --git a/src/ontology/OntoFox_inputs/ChEBI_input.txt b/src/ontology/OntoFox_inputs/ChEBI_input.txt index d0200298..bf8a1304 100755 --- a/src/ontology/OntoFox_inputs/ChEBI_input.txt +++ b/src/ontology/OntoFox_inputs/ChEBI_input.txt @@ -58,7 +58,6 @@ http://purl.obolibrary.org/obo/CHEBI_33697 http://purl.obolibrary.org/obo/CHEBI_16670 http://purl.obolibrary.org/obo/CHEBI_33696 http://purl.obolibrary.org/obo/CHEBI_32142 -http://purl.obolibrary.org/obo/CHEBI_33250 http://purl.obolibrary.org/obo/CHEBI_32142 http://purl.obolibrary.org/obo/CHEBI_472552 http://purl.obolibrary.org/obo/CHEBI_29237 # deuterium atom @@ -122,6 +121,10 @@ http://purl.obolibrary.org/obo/CHEBI_39124 # calcium ion [Top level source term URIs and target direct superclass URIs] +http://purl.obolibrary.org/obo/CHEBI_29237 # deuterium atom +subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom +http://purl.obolibrary.org/obo/CHEBI_33321 # rare earth metal atom +subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom http://purl.obolibrary.org/obo/CHEBI_23367 subClassOf http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/CHEBI_4705 @@ -226,12 +229,10 @@ http://purl.obolibrary.org/obo/CHEBI_32142 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 http://purl.obolibrary.org/obo/CHEBI_472552 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 -http://purl.obolibrary.org/obo/CHEBI_33250 -subClassOf http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/CHEBI_37972 -subClassOf http://purl.obolibrary.org/obo/CHEBI_33250 +subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom http://purl.obolibrary.org/obo/CHEBI_37973 -subClassOf http://purl.obolibrary.org/obo/CHEBI_33250 +subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom http://purl.obolibrary.org/obo/CHEBI_32142 subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 http://purl.obolibrary.org/obo/CHEBI_28358 # rac-lactic acid diff --git a/src/ontology/OntoFox_outputs/ChEBI_imports.owl b/src/ontology/OntoFox_outputs/ChEBI_imports.owl index 3b1dc17e..d652c8f1 100644 --- a/src/ontology/OntoFox_outputs/ChEBI_imports.owl +++ b/src/ontology/OntoFox_outputs/ChEBI_imports.owl @@ -86,7 +86,7 @@ water - An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. + An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms water @@ -352,7 +352,7 @@ cortisol - A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses + A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. cortisol @@ -660,8 +660,7 @@ - - + deuterium atom The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). @@ -754,18 +753,6 @@ - - - - - atom - A chemical entity constituting the smallest component of an element having the chemical properties of the element. - - atom - - - - @@ -780,7 +767,7 @@ - + rare earth metal atom rare earth metal atom @@ -955,7 +942,7 @@ - + phosphorus-32 atom The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days. @@ -967,7 +954,7 @@ - + phosphorus-33 atom The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. @@ -1097,9 +1084,10 @@ - ethylenediaminetetraacetic acid + EDTA(4-) + A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). - ethylenediaminetetraacetic acid + EDTA(4-) @@ -1409,6 +1397,12 @@ tris + + + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index b2139cf3..da909c9e 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -5502,7 +5502,7 @@ for now. - + From 05e16bd895bee2dfb4526b5871f9e5f696e56d30 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 6 Aug 2024 16:40:06 -0500 Subject: [PATCH 09/38] Redirect references to CHEBI:molecular entity to COB:molecular entity --- src/ontology/OntoFox_inputs/ChEBI_input.txt | 197 ++++++++++++---- .../OntoFox_outputs/ChEBI_imports.owl | 221 ++++++++---------- src/ontology/obi-edit.owl | 44 ++-- 3 files changed, 267 insertions(+), 195 deletions(-) diff --git a/src/ontology/OntoFox_inputs/ChEBI_input.txt b/src/ontology/OntoFox_inputs/ChEBI_input.txt index bf8a1304..67ec58ed 100755 --- a/src/ontology/OntoFox_inputs/ChEBI_input.txt +++ b/src/ontology/OntoFox_inputs/ChEBI_input.txt @@ -5,7 +5,6 @@ http://purl.obolibrary.org/obo/obi/dev/import/ChEBI_imports.owl CHEBI [Low level source term URIs] -http://purl.obolibrary.org/obo/CHEBI_23367 http://purl.obolibrary.org/obo/CHEBI_4705 http://purl.obolibrary.org/obo/CHEBI_15377 http://purl.obolibrary.org/obo/CHEBI_15956 @@ -121,102 +120,200 @@ http://purl.obolibrary.org/obo/CHEBI_39124 # calcium ion [Top level source term URIs and target direct superclass URIs] +http://purl.obolibrary.org/obo/CHEBI_86319 # 25-hydroxyvitamin D2 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_20067 # 3-hydroxybutyric acid +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_28774 # 3,3',5'-triiodothyronine +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_2637 # amikacin +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_16134 # ammonia +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_15422 # ATP (Adenosine triphosphate) +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_22868 # bile salt +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_16990 # bilirubin IXalpha +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_39123 # calcium cation +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_39124 # calcium ion +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_16526 # carbon dioxide +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_17996 # chloride +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_16113 # cholesterol +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_17650 # cortisol +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_16919 # creatine +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_16737 # creatinine +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_28689 # dehydroepiandrosterone +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_4551 # digoxin +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_33262 # elemental oxygen +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_23965 # estradiol +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_35366 # fatty acid +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_37445 # folic acids +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_81569 # Follicle stimulating hormone +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_166899 # globulin type +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_35143 # hemoglobin +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_47775 # high-density lipoprotein cholesterol +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_17230 # homocysteine +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_17544 # hydrogencarbonate +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_24875 # iron cation +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_6495 # lipoprotein +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_47774 # low-density lipoprotein cholesterol +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_81568 # Luteinizing hormone +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_39127 # magnesium cation +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_17423 # methemoglobin +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_168396 # mycophenolic acid +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_16301 # nitrite +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_61073 # oxygen radical +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_35780 # phosphate ion +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_16247 # phospholipid +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_29103 # potassium(1+) +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_17026 # progesterone +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_29101 # sodium(1+) +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_61057 # tacrolimus hydrate +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_17347 # testosterone +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_81567 # thyroid stimulating hormone +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_30660 # thyroxine +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_28864 # tobramycin +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_17855 # triglyceride +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_27226 # uric acid +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity +http://purl.obolibrary.org/obo/CHEBI_28001 # vancomycin +subClassOf http://purl.obolibrary.org/obo/COB_0000013 # molecular entity http://purl.obolibrary.org/obo/CHEBI_29237 # deuterium atom subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom http://purl.obolibrary.org/obo/CHEBI_33321 # rare earth metal atom subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom -http://purl.obolibrary.org/obo/CHEBI_23367 -subClassOf http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/CHEBI_4705 subClassOf http://purl.obolibrary.org/obo/CHEBI_16991 http://purl.obolibrary.org/obo/CHEBI_15377 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 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http://purl.obolibrary.org/obo/CHEBI_33376 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_33709 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_33839 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_35729 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_37333 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_37586 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_37987 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_37989 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_42098 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_42191 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_50076 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_51756 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_51760 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_52673 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_53526 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_59050 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_59051 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_59052 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_59053 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_59054 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_59055 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_59056 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_59424 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_9754 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_16991 subClassOf http://purl.obolibrary.org/obo/CHEBI_33696 http://purl.obolibrary.org/obo/CHEBI_33697 @@ -226,15 +323,15 @@ subClassOf http://purl.obolibrary.org/obo/CHEBI_33839 http://purl.obolibrary.org/obo/CHEBI_33696 subClassOf http://purl.obolibrary.org/obo/CHEBI_33839 http://purl.obolibrary.org/obo/CHEBI_32142 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_472552 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_37972 subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom http://purl.obolibrary.org/obo/CHEBI_37973 subClassOf http://purl.obolibrary.org/obo/COB_0000011 # atom http://purl.obolibrary.org/obo/CHEBI_32142 -subClassOf http://purl.obolibrary.org/obo/CHEBI_23367 +subClassOf http://purl.obolibrary.org/obo/COB_0000013 http://purl.obolibrary.org/obo/CHEBI_28358 # rac-lactic acid subClassOf http://purl.obolibrary.org/obo/BFO_0000040 # material entity (not a molecular entity) diff --git a/src/ontology/OntoFox_outputs/ChEBI_imports.owl b/src/ontology/OntoFox_outputs/ChEBI_imports.owl index d652c8f1..852fd320 100644 --- a/src/ontology/OntoFox_outputs/ChEBI_imports.owl +++ b/src/ontology/OntoFox_outputs/ChEBI_imports.owl @@ -84,7 +84,7 @@ - + water An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms @@ -96,7 +96,7 @@ - + ATP An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. @@ -108,7 +108,7 @@ - + biotin An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. @@ -120,7 +120,7 @@ - + cholesterol A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. @@ -132,7 +132,7 @@ - + ammonia An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. @@ -144,7 +144,7 @@ - + phospholipid A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. @@ -156,7 +156,7 @@ - + nitrite The nitrogen oxoanion formed by loss of a proton from nitrous acid. @@ -168,7 +168,7 @@ - + carbon dioxide A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. @@ -192,8 +192,7 @@ - - + globulin type One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma. @@ -205,7 +204,7 @@ - + creatinine A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. @@ -217,7 +216,7 @@ - + mycophenolic acid A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. @@ -229,7 +228,7 @@ - + creatine A glycine derivative having methyl and amidino groups attached to the nitrogen. @@ -241,7 +240,7 @@ - + bilirubin IXalpha A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. @@ -265,7 +264,7 @@ - + progesterone A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. @@ -277,7 +276,7 @@ - + hydrogensulfite hydrogensulfite @@ -288,8 +287,7 @@ - - + homocysteine A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. @@ -301,7 +299,7 @@ - + glucose An aldohexose used as a source of energy and metabolic intermediate. @@ -313,7 +311,7 @@ - + testosterone An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. @@ -325,8 +323,7 @@ - - + methemoglobin A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin. @@ -338,7 +335,7 @@ - + hydrogencarbonate The carbon oxoanion resulting from the removal of a proton from carbonic acid. @@ -350,7 +347,7 @@ - + cortisol A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. @@ -362,7 +359,7 @@ - + 5'-adenylyl sulfate An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. @@ -374,7 +371,7 @@ - + triglyceride Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. @@ -386,7 +383,7 @@ - + chloride A halide anion formed when chlorine picks up an electron to form an an anion. @@ -398,8 +395,7 @@ - - + 3-hydroxybutyric acid A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics. @@ -411,7 +407,7 @@ - + bile salt A sodium salt of the conjugate of any bile acid with either glycine or taurine. @@ -420,22 +416,10 @@ - - - - - molecular entity - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - - molecular entity - - - - - + cytochalasin cytochalasin @@ -446,7 +430,7 @@ - + estradiol A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. @@ -458,7 +442,7 @@ - + N-ethyl-N-nitrosourea A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. @@ -470,7 +454,7 @@ - + proton Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. @@ -482,7 +466,7 @@ - + iron cation iron cation @@ -493,7 +477,7 @@ - + luciferin A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. @@ -505,7 +489,7 @@ - + amikacin An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. @@ -517,7 +501,7 @@ - + sodium chloride An inorganic chloride salt having sodium(1+) as the counterion. @@ -529,7 +513,7 @@ - + uric acid An oxopurine that is the final oxidation product of purine metabolism. @@ -541,7 +525,7 @@ - + lead(0) lead(0) @@ -552,8 +536,7 @@ - - + vancomycin A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. @@ -577,7 +560,7 @@ - + acrylamide A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. @@ -589,7 +572,7 @@ - + dehydroepiandrosterone An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. @@ -601,8 +584,7 @@ - - + 3,3',5'-triiodothyronine 3,3',5'-triiodothyronine @@ -613,7 +595,7 @@ - + tobramycin A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. @@ -625,7 +607,7 @@ - + sodium(1+) A monoatomic monocation obtained from sodium. @@ -637,7 +619,7 @@ - + potassium(1+) A monoatomic monocation obtained from potassium. @@ -649,7 +631,7 @@ - + hydroxyl hydroxyl @@ -672,8 +654,7 @@ - - + thyroxine An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. @@ -685,7 +666,7 @@ - + ruthenium atom ruthenium atom @@ -696,7 +677,7 @@ - + fluorescein (lactone form) A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy. @@ -708,7 +689,7 @@ - + gadodiamide hydrate The hydrate of gadodiamide. @@ -720,7 +701,7 @@ - + gadoteridol A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -732,7 +713,7 @@ - + phenol red 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. @@ -744,7 +725,7 @@ - + sodium citrate dihydrate The dihydrate of trisodium citrate. @@ -756,7 +737,7 @@ - + elemental oxygen elemental oxygen @@ -778,7 +759,7 @@ - + rhodium atom A cobalt group element atom of atomic number 45. @@ -790,7 +771,7 @@ - + gadolinium atom gadolinium atom @@ -801,7 +782,7 @@ - + terbium atom terbium atom @@ -836,7 +817,7 @@ - + amino acid A carboxylic acid containing one or more amino groups. @@ -848,7 +829,7 @@ - + macromolecule 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. @@ -860,8 +841,7 @@ - - + hemoglobin hemoglobin @@ -872,7 +852,7 @@ - + fatty acid Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. @@ -884,7 +864,7 @@ - + gadolinium molecular entity gadolinium molecular entity @@ -895,7 +875,7 @@ - + phosphate ion A phosphorus oxoanion that is the conjugate base of phosphoric acid. @@ -907,7 +887,7 @@ - + gadodiamide A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -919,7 +899,7 @@ - + folic acids A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. @@ -931,7 +911,7 @@ - + sodium phosphate sodium phosphate @@ -966,7 +946,7 @@ - + Cy3 dye Cy3 dye @@ -977,7 +957,7 @@ - + Cy5 dye Cy5 dye @@ -1024,8 +1004,7 @@ - - + calcium cation calcium cation @@ -1036,7 +1015,7 @@ - + calcium ion calcium ion @@ -1047,7 +1026,7 @@ - + magnesium cation Any magnesium ion that is positively charged. @@ -1071,7 +1050,7 @@ - + digoxigenin A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. @@ -1083,7 +1062,7 @@ - + EDTA(4-) A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). @@ -1095,7 +1074,7 @@ - + digoxin A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. @@ -1118,7 +1097,7 @@ - + 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. @@ -1130,7 +1109,7 @@ - + low-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL). @@ -1142,7 +1121,7 @@ - + high-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). @@ -1154,7 +1133,7 @@ - + chromium-51 A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. @@ -1166,7 +1145,7 @@ - + Alexa Fluor 532 Alexa Fluor 532 @@ -1177,7 +1156,7 @@ - + Alexa Fluor 546 Alexa Fluor 546 @@ -1188,7 +1167,7 @@ - + Alexa Fluor 555 A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate. @@ -1200,7 +1179,7 @@ - + tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. @@ -1212,7 +1191,7 @@ - + dimethyl sulfate The dimethyl ester of sulfuric acid. @@ -1224,7 +1203,7 @@ - + diethyl pyrocarbonate The diethyl ester of dicarbonic acid. @@ -1236,7 +1215,7 @@ - + 1,1-dihydroxy-3-ethoxy-2-butanone A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. @@ -1248,7 +1227,7 @@ - + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. @@ -1260,7 +1239,7 @@ - + N-methylisatoic anhydride A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. @@ -1272,7 +1251,7 @@ - + (S)-1-(4-bromoacetamidobenzyl)EDTA A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. @@ -1284,7 +1263,7 @@ - + EDTA methidiumpropylamide A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. @@ -1296,7 +1275,7 @@ - + bromophenol blue 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. @@ -1308,7 +1287,7 @@ - + tacrolimus hydrate A hydrate that is the monohydrate form of tacrolimus. @@ -1320,7 +1299,7 @@ - + oxygen radical An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. @@ -1332,8 +1311,7 @@ - - + lipoprotein A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. @@ -1345,8 +1323,7 @@ - - + thyroid stimulating hormone thyroid stimulating hormone @@ -1357,7 +1334,7 @@ - + Luteinizing hormone Luteinizing hormone @@ -1368,7 +1345,7 @@ - + Follicle stimulating hormone Follicle stimulating hormone @@ -1379,7 +1356,7 @@ - + 25-hydroxyvitamin D2 A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group. @@ -1391,7 +1368,7 @@ - + tris A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. @@ -1403,6 +1380,12 @@ + + + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index da909c9e..043d17be 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -1660,14 +1660,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well - - - - @@ -3457,7 +3449,7 @@ objectives is a planned process. - + drug role @@ -3642,7 +3634,7 @@ objectives is a planned process. - + polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. @@ -5501,8 +5493,8 @@ for now. - + @@ -5589,7 +5581,7 @@ for now. - + @@ -7274,13 +7266,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + scattered molecular aggregate @@ -9251,7 +9243,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -9544,7 +9536,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + fucoidan Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). @@ -11115,7 +11107,7 @@ Added duirng Mar 1, 2010 dev call - + @@ -20112,7 +20104,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + @@ -26648,7 +26640,7 @@ determinations of compounds. - + @@ -26676,7 +26668,7 @@ determinations of compounds. - + @@ -27127,7 +27119,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -27321,7 +27313,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + intentional overdosing @@ -27430,7 +27422,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -28453,7 +28445,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -28889,13 +28881,13 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + From 5eca0d1a85eb6e23b073dbab8e93f256e92644c6 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 7 Aug 2024 11:38:29 -0500 Subject: [PATCH 10/38] Update device module --- src/ontology/modules/devices.owl | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl index 745ec45a..9aec9002 100644 --- a/src/ontology/modules/devices.owl +++ b/src/ontology/modules/devices.owl @@ -188,15 +188,15 @@ - + - + - + - + @@ -6227,7 +6227,7 @@ - + From b650131a7f6d3b2d920b588c36a2bbe90d3666bc Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 7 Aug 2024 11:49:10 -0500 Subject: [PATCH 11/38] Obsolete OBI:device --- src/ontology/modules/devices.owl | 382 ++++++++++++++-------------- src/ontology/modules/obsolete.owl | 18 ++ src/ontology/obi-edit.owl | 51 ---- src/ontology/templates/obsolete.tsv | 1 + 4 files changed, 210 insertions(+), 242 deletions(-) diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl index 9aec9002..a3ada02d 100644 --- a/src/ontology/modules/devices.owl +++ b/src/ontology/modules/devices.owl @@ -194,6 +194,12 @@ + + + + + + @@ -203,7 +209,7 @@ - + @@ -240,7 +246,7 @@ - + @@ -261,7 +267,7 @@ - + @@ -301,7 +307,7 @@ - + @@ -340,7 +346,7 @@ - + @@ -378,7 +384,7 @@ - + @@ -404,7 +410,7 @@ - + @@ -446,7 +452,7 @@ - + @@ -467,7 +473,7 @@ - + @@ -487,7 +493,7 @@ - + @@ -507,7 +513,7 @@ - + @@ -529,7 +535,7 @@ - + @@ -557,7 +563,7 @@ - + @@ -578,7 +584,7 @@ - + @@ -695,7 +701,7 @@ - + @@ -728,7 +734,7 @@ - + @@ -766,7 +772,7 @@ - + @@ -801,7 +807,7 @@ - + @@ -841,7 +847,7 @@ - + @@ -873,7 +879,7 @@ - + @@ -894,7 +900,7 @@ - + @@ -936,7 +942,7 @@ - + @@ -1224,7 +1230,7 @@ - + NMR sample holder An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. @@ -1240,7 +1246,7 @@ - + @@ -1356,7 +1362,7 @@ - + @@ -1438,7 +1444,7 @@ - + NMR tube washing system An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. @@ -1454,7 +1460,7 @@ - + NMR console A component of an NMR instrument that controls the activities of the other components. @@ -1485,7 +1491,7 @@ - + @@ -1539,7 +1545,7 @@ - + @@ -1701,7 +1707,7 @@ - + @@ -1729,7 +1735,7 @@ - + NMR magnet A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. @@ -1806,7 +1812,7 @@ - + @@ -2110,7 +2116,7 @@ - + @@ -2162,7 +2168,7 @@ - + @@ -2261,7 +2267,7 @@ - + autosampler An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. @@ -2385,7 +2391,7 @@ - + @@ -2422,7 +2428,7 @@ - + @@ -2443,7 +2449,7 @@ - + @@ -2678,7 +2684,7 @@ - + @@ -2839,7 +2845,7 @@ - + @@ -3691,7 +3697,7 @@ - + @@ -3714,7 +3720,7 @@ - + @@ -3739,7 +3745,7 @@ - + @@ -3783,7 +3789,7 @@ - + @@ -3810,7 +3816,7 @@ - + @@ -3834,7 +3840,7 @@ - + @@ -3854,7 +3860,7 @@ - + @@ -3875,7 +3881,7 @@ - + @@ -3908,7 +3914,7 @@ - + @@ -3934,7 +3940,7 @@ - + @@ -3954,7 +3960,7 @@ - + @@ -3974,7 +3980,7 @@ - + @@ -4018,7 +4024,7 @@ - + @@ -4036,16 +4042,10 @@ - - - - - - - + @@ -4103,7 +4103,7 @@ - + @@ -4128,7 +4128,7 @@ - + @@ -4153,7 +4153,7 @@ - + @@ -4180,7 +4180,7 @@ - + @@ -4222,7 +4222,7 @@ - + @@ -4248,7 +4248,7 @@ - + @@ -4268,7 +4268,7 @@ - + @@ -4294,7 +4294,7 @@ - + @@ -4314,7 +4314,7 @@ - + @@ -4334,7 +4334,7 @@ - + @@ -4382,7 +4382,7 @@ - + @@ -4402,7 +4402,7 @@ - + @@ -4470,7 +4470,7 @@ - + @@ -4504,7 +4504,7 @@ - + @@ -4524,7 +4524,7 @@ - + @@ -4550,7 +4550,7 @@ - + @@ -4570,7 +4570,7 @@ - + @@ -4596,7 +4596,7 @@ - + @@ -4656,7 +4656,7 @@ - + @@ -4676,7 +4676,7 @@ - + @@ -4702,7 +4702,7 @@ - + @@ -4742,7 +4742,7 @@ - + @@ -4774,7 +4774,7 @@ - + @@ -4794,7 +4794,7 @@ - + @@ -4840,7 +4840,7 @@ - + @@ -4872,7 +4872,7 @@ - + @@ -4898,7 +4898,7 @@ - + @@ -4944,7 +4944,7 @@ - + @@ -4964,7 +4964,7 @@ - + @@ -4990,7 +4990,7 @@ - + @@ -5024,7 +5024,7 @@ - + @@ -5044,7 +5044,7 @@ - + @@ -5070,7 +5070,7 @@ - + @@ -5096,7 +5096,7 @@ - + @@ -5136,7 +5136,7 @@ - + @@ -5198,7 +5198,7 @@ - + @@ -5218,7 +5218,7 @@ - + @@ -5238,7 +5238,7 @@ - + @@ -5298,7 +5298,7 @@ - + @@ -5324,7 +5324,7 @@ - + @@ -5392,7 +5392,7 @@ - + @@ -5460,7 +5460,7 @@ - + @@ -5480,7 +5480,7 @@ - + @@ -5500,7 +5500,7 @@ - + @@ -5540,7 +5540,7 @@ - + @@ -5572,7 +5572,7 @@ - + @@ -5604,7 +5604,7 @@ - + @@ -5624,7 +5624,7 @@ - + @@ -5658,7 +5658,7 @@ - + @@ -5692,7 +5692,7 @@ - + @@ -5718,7 +5718,7 @@ - + @@ -5766,7 +5766,7 @@ - + @@ -5786,7 +5786,7 @@ - + @@ -5806,7 +5806,7 @@ - + @@ -5866,7 +5866,7 @@ - + @@ -5892,7 +5892,7 @@ - + @@ -5918,7 +5918,7 @@ - + @@ -5938,7 +5938,7 @@ - + @@ -5970,7 +5970,7 @@ - + @@ -6004,7 +6004,7 @@ - + @@ -6038,7 +6038,7 @@ - + @@ -6064,7 +6064,7 @@ - + @@ -6084,7 +6084,7 @@ - + @@ -6104,7 +6104,7 @@ - + @@ -6168,7 +6168,7 @@ - + @@ -6751,7 +6751,7 @@ - + @@ -6988,7 +6988,7 @@ - + microtome blade A device that is the part of a microtome used to slice specimens to a desired thickness. @@ -7031,7 +7031,7 @@ - + pipette A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. Stephen A. Fisher, Junhyong Kim, Dan Berrios @@ -7064,7 +7064,7 @@ - + @@ -7270,7 +7270,7 @@ - + personal protective device Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. PPE is equipment worn by a worker to minimize exposure to specific hazards. @@ -7456,7 +7456,7 @@ - + apron A garment which is worn over other clothing and covers mainly the front of the body. @@ -7562,7 +7562,7 @@ - + transparent partition A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. @@ -7710,7 +7710,7 @@ - + specimen collection device A device used to collect a specimen. @@ -7779,7 +7779,7 @@ - + cotton swab A device which is a cotton pad mounted on one or both ends of a stick. @@ -7843,7 +7843,7 @@ - + catheter A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. @@ -7915,7 +7915,7 @@ - + A device designed to catch arthropods. John Judkins MIRO:30000011 @@ -7966,7 +7966,7 @@ - + @@ -8020,7 +8020,7 @@ - + A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. John Judkins dipper for immatures @@ -8269,7 +8269,7 @@ - + A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. John Judkins VSMO:0001355 @@ -8283,7 +8283,7 @@ - + A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. John Judkins https://github.com/obi-ontology/obi/issues/1302 @@ -8339,7 +8339,7 @@ - + @@ -8358,7 +8358,7 @@ - + A device that consists of a network of mesh and is designed to capture adult arthropods. VEuPathDB VSMO:0001522 @@ -8405,7 +8405,7 @@ - + A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. John Judkins VEuPathDB @@ -8418,7 +8418,7 @@ - + assay kit Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit. @@ -8892,7 +8892,7 @@ - + @@ -9183,7 +9183,7 @@ - + @@ -9401,7 +9401,7 @@ - + @@ -9593,7 +9593,7 @@ - + @@ -9746,7 +9746,7 @@ - + @@ -9819,7 +9819,7 @@ - + @@ -10072,7 +10072,7 @@ - + @@ -10241,7 +10241,7 @@ - + @@ -10263,7 +10263,7 @@ - + @@ -10284,7 +10284,7 @@ - + @@ -10318,7 +10318,7 @@ - + @@ -10354,7 +10354,7 @@ - + @@ -10387,7 +10387,7 @@ - + @@ -10469,7 +10469,7 @@ - + @@ -10601,7 +10601,7 @@ - + @@ -10628,7 +10628,7 @@ - + @@ -10650,7 +10650,7 @@ - + @@ -10671,7 +10671,7 @@ - + @@ -10692,7 +10692,7 @@ - + @@ -10719,7 +10719,7 @@ - + @@ -10740,7 +10740,7 @@ - + @@ -10789,7 +10789,7 @@ - + @@ -10811,7 +10811,7 @@ - + @@ -10832,7 +10832,7 @@ - + @@ -10854,7 +10854,7 @@ - + @@ -10881,7 +10881,7 @@ - + @@ -10908,7 +10908,7 @@ - + @@ -10931,7 +10931,7 @@ - + @@ -10958,7 +10958,7 @@ - + @@ -10979,7 +10979,7 @@ - + @@ -11001,7 +11001,7 @@ - + @@ -11033,7 +11033,7 @@ - + @@ -11066,7 +11066,7 @@ - + @@ -11089,7 +11089,7 @@ - + @@ -11110,7 +11110,7 @@ - + @@ -11140,7 +11140,7 @@ - + @@ -11169,7 +11169,7 @@ - + @@ -11208,7 +11208,7 @@ - + @@ -11246,7 +11246,7 @@ - + @@ -11276,7 +11276,7 @@ - + @@ -11320,7 +11320,7 @@ - + @@ -11401,7 +11401,7 @@ - + @@ -11451,7 +11451,7 @@ - + @@ -11472,7 +11472,7 @@ - + @@ -11499,7 +11499,7 @@ - + @@ -11526,7 +11526,7 @@ - + @@ -11547,7 +11547,7 @@ - + diff --git a/src/ontology/modules/obsolete.owl b/src/ontology/modules/obsolete.owl index 3aeb9954..bcced89c 100644 --- a/src/ontology/modules/obsolete.owl +++ b/src/ontology/modules/obsolete.owl @@ -597,6 +597,24 @@ + + + + + A voltmeter is a measurement device which is intended to perform some measure function. + An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. + + A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. + PERSON: Helen Parkinson + instrument + OBI development call 2012-12-17. + + obsolete_device + true + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 043d17be..5b01d8ce 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -11374,57 +11374,6 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - - - - - - - - - - - - - - - - - - - - - - - - - - - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device - - - - diff --git a/src/ontology/templates/obsolete.tsv b/src/ontology/templates/obsolete.tsv index fdaba18a..46d45302 100755 --- a/src/ontology/templates/obsolete.tsv +++ b/src/ontology/templates/obsolete.tsv @@ -32,6 +32,7 @@ OBI:0000929 obsolete_training service provider role metadata incomplete a ser OBI:0000936 obsolete_material access provider role metadata incomplete 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:0000968 obsolete_device ready for release instrument A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. OBI development call 2012-12-17. A voltmeter is a measurement device which is intended to perform some measure function.|An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. PERSON: Helen Parkinson subclass Obsolete Class true COB:0001300 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 metadata complete 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 From 0ced5d72e015ffbe881d59047973f2dc4e4bec10 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 11:41:21 -0500 Subject: [PATCH 12/38] Fix typo in RO import --- src/ontology/catalog-v001.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index cae333f8..8e86a305 100755 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -22,7 +22,7 @@ - + From d02c932b1a8e3acb40476f8c7a66db2fcea3a083 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 11:52:42 -0500 Subject: [PATCH 13/38] Remove mentions of CHEBI:molecular entity from assays.owl --- src/ontology/modules/assays.owl | 20 +++++++------------- 1 file changed, 7 insertions(+), 13 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 59254ba4..c532de1a 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -380,12 +380,6 @@ - - - - - - @@ -6000,7 +5994,7 @@ - + @@ -6017,7 +6011,7 @@ - + @@ -11917,7 +11911,7 @@ - + @@ -11925,7 +11919,7 @@ - + @@ -15728,7 +15722,7 @@ - + @@ -15739,7 +15733,7 @@ - + @@ -21668,7 +21662,7 @@ - + From fa7ddda776ed8b35f0c025a01b6f53b4b16aace0 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 13 Aug 2024 14:41:52 -0500 Subject: [PATCH 14/38] Remove BFO:0000028 --- src/ontology/obi-edit.owl | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 5b01d8ce..a6238ac7 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -1593,12 +1593,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - From 2a894e58bfe4fde4b78d74c350555d93d443426f Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 20 Aug 2024 12:42:21 -0500 Subject: [PATCH 15/38] Redirect references to IAO:measurement datum to COB:measurement datum --- src/ontology/OntoFox_inputs/IAO_input.txt | 1 - src/ontology/OntoFox_outputs/IAO_imports.owl | 14 +--- src/ontology/modules/assays.owl | 76 ++++++++++---------- src/ontology/modules/medical-history.owl | 12 ++-- src/ontology/obi-edit.owl | 61 +++++++--------- 5 files changed, 69 insertions(+), 95 deletions(-) diff --git a/src/ontology/OntoFox_inputs/IAO_input.txt b/src/ontology/OntoFox_inputs/IAO_input.txt index 99926b52..c95e7798 100644 --- a/src/ontology/OntoFox_inputs/IAO_input.txt +++ b/src/ontology/OntoFox_inputs/IAO_input.txt @@ -32,7 +32,6 @@ http://purl.obolibrary.org/obo/IAO_0000098 # data format specification http://purl.obolibrary.org/obo/IAO_0000100 # data set http://purl.obolibrary.org/obo/IAO_0000101 # image http://purl.obolibrary.org/obo/IAO_0000104 # plan specification -http://purl.obolibrary.org/obo/IAO_0000109 # measurement datum http://purl.obolibrary.org/obo/IAO_0000136 # is about http://purl.obolibrary.org/obo/IAO_0000144 # conclusion textual entity http://purl.obolibrary.org/obo/IAO_0000178 # material information bearer diff --git a/src/ontology/OntoFox_outputs/IAO_imports.owl b/src/ontology/OntoFox_outputs/IAO_imports.owl index 113517d4..a9a00772 100644 --- a/src/ontology/OntoFox_outputs/IAO_imports.owl +++ b/src/ontology/OntoFox_outputs/IAO_imports.owl @@ -342,7 +342,7 @@ interpreted by or directly executed by a processing unit. - + scalar measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. @@ -496,18 +496,6 @@ Example: The ISO document specifying what encompasses an XML document; The instr - - - - - measurement datum - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - - measurement datum - - - - diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index c532de1a..a25d091d 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -878,6 +878,12 @@ + + + + + + @@ -1262,12 +1268,6 @@ - - - - - - @@ -1824,7 +1824,7 @@ - + @@ -2013,7 +2013,7 @@ - + @@ -2045,7 +2045,7 @@ - + @@ -2309,7 +2309,7 @@ - + @@ -3554,7 +3554,7 @@ - + @@ -3666,7 +3666,7 @@ - + @@ -4120,7 +4120,7 @@ - + The level of actin mRNA levels in normal and diseased tiisue was measured using a northern blot assay. @@ -4219,7 +4219,7 @@ - + Determining the viral titer of a virus infected human by measuring the presence of hemagglutination when dilutions of serum samples are added to a known quantity of red blood cells. @@ -4661,7 +4661,7 @@ - + @@ -4737,7 +4737,7 @@ - + @@ -5205,7 +5205,7 @@ - + @@ -5556,7 +5556,7 @@ - + @@ -5594,7 +5594,7 @@ - + @@ -5645,7 +5645,7 @@ - + @@ -5769,7 +5769,7 @@ - + @@ -5864,7 +5864,7 @@ - + @@ -6062,7 +6062,7 @@ - + @@ -6191,7 +6191,7 @@ - + @@ -6326,7 +6326,7 @@ - + @@ -6470,7 +6470,7 @@ - + @@ -6509,7 +6509,7 @@ - + @@ -6554,7 +6554,7 @@ - + @@ -6769,7 +6769,7 @@ - + @@ -6806,7 +6806,7 @@ - + @@ -10732,7 +10732,7 @@ - + @@ -10855,7 +10855,7 @@ - + @@ -13805,7 +13805,7 @@ - + @@ -13835,7 +13835,7 @@ - + @@ -21219,7 +21219,7 @@ - + @@ -26903,7 +26903,7 @@ - + @@ -27034,7 +27034,7 @@ - + the detection of phycoerytherin by means of flow cytometry @@ -27349,7 +27349,7 @@ - + diff --git a/src/ontology/modules/medical-history.owl b/src/ontology/modules/medical-history.owl index a3f717cf..a6f8bf0c 100644 --- a/src/ontology/modules/medical-history.owl +++ b/src/ontology/modules/medical-history.owl @@ -69,15 +69,15 @@ - + - + - + - + @@ -437,7 +437,7 @@ - + A measurement datum of the total number of pregnancies a woman has had. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB @@ -450,7 +450,7 @@ - + A measurement datum of the total number of live births a female has had. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index a6238ac7..db94a0f5 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -2967,19 +2967,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - - - - - - @@ -3159,7 +3146,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + fluorescent reporter intensity A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. @@ -3532,7 +3519,7 @@ objectives is a planned process. - + ratio of collected to emitted light 10% @@ -4109,7 +4096,7 @@ editor = PRS - + measured expression level Examples are quantified data from an expression microarray experiment, PCR measurements, etc. @@ -4278,7 +4265,7 @@ specimen can later be subject. - + number of particles in subset 500, 200, 0 @@ -4293,7 +4280,7 @@ specimen can later be subject. - + number of lost events electronic 74, 0, 14 events lost due to data acquisition electronic coincidence. @@ -4597,7 +4584,7 @@ addition of has_role restriction - + parameter threshold 0.01, 0.03 @@ -5369,7 +5356,7 @@ for now. - + number of lost events computer 0, 125, 787 events lost due to computer busy. @@ -6935,7 +6922,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -9086,7 +9073,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + survival rate A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. @@ -9260,7 +9247,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + spike train datum Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog @@ -11020,7 +11007,7 @@ Added duirng Mar 1, 2010 dev call - + @@ -11384,7 +11371,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - + @@ -11433,7 +11420,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - + @@ -11561,7 +11548,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - + dose An organism has been injected 1ml of vaccine @@ -12303,7 +12290,7 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - + 3D structural organization datum The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. @@ -14672,7 +14659,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -15320,7 +15307,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + latitude coordinate measurement datum A measurement datum that is the measure of the latitude coordinate of a site. @@ -15337,7 +15324,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + longitude coordinate measurement datum A measurement datum that is the measure of the longitude coordinate of a site. @@ -17647,7 +17634,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -18804,7 +18791,7 @@ https://www.doi.org/ - + @@ -19360,7 +19347,7 @@ https://www.doi.org/ - + sequence read length measurement datum A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence. Stephen A. Fisher, Junhyong Kim, Dan Berrios @@ -19398,7 +19385,7 @@ https://www.doi.org/ - + specimen harvest quantity A scalar measurement datum that indicates the amount of specimen collected. Stephen A. Fisher, Junhyong Kim, Dan Berrios @@ -27460,13 +27447,13 @@ Manual editing of automatically recorded data in an anesthesia information manag - + - + prediction From 721f22a0985cce5af4560de574710d0ef7a9f478 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 20 Aug 2024 15:44:35 -0500 Subject: [PATCH 16/38] Remove references to BFO:entity --- src/ontology/modules/data-sets.owl | 12 ------ src/ontology/obi-edit.owl | 56 ++++++---------------------- src/ontology/templates/data-sets.tsv | 2 +- 3 files changed, 13 insertions(+), 57 deletions(-) diff --git a/src/ontology/modules/data-sets.owl b/src/ontology/modules/data-sets.owl index cab821ed..b97be9d9 100644 --- a/src/ontology/modules/data-sets.owl +++ b/src/ontology/modules/data-sets.owl @@ -92,12 +92,6 @@ - - - - - - @@ -114,12 +108,6 @@ - - - - - - The output produced by a digital imaging technique, such as microscopy, MRI, or CT. 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. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index db94a0f5..9975fad8 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -17623,50 +17623,18 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + A planned process in which predicted values for some thing are compared to measured values for that thing. comparing prediction to measurement diff --git a/src/ontology/templates/data-sets.tsv b/src/ontology/templates/data-sets.tsv index 95dc5f53..c39a9c4d 100644 --- a/src/ontology/templates/data-sets.tsv +++ b/src/ontology/templates/data-sets.tsv @@ -1,6 +1,6 @@ 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: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 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 OBI:0003333 computed image data set An image data set that is the output of an image data set analysis. The production of JPEG file by a digital camera. https://orcid.org/0000-0001-9625-1899 ""William D. Duncan"",https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik"",https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl"",https://orcid.org/0000-0002-1604-3078 ""Alan Ruttenberg"",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 image data set analysis From 71cf8114b7b69377807fe7efeabf699255451d47 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 20 Aug 2024 15:51:02 -0500 Subject: [PATCH 17/38] Remove reference to BFO:continuant --- src/ontology/obi-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 9975fad8..fd5ce925 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -5863,7 +5863,7 @@ Proposal is to obsolete. - + ionize process From b2a236940f91bc12fe37fa570aa639f57b7c77b3 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 20 Aug 2024 16:23:41 -0500 Subject: [PATCH 18/38] Remove references to BFO:quality --- src/ontology/OntoFox_inputs/OBA_input.txt | 2 +- src/ontology/OntoFox_inputs/OGMS_input.txt | 2 +- src/ontology/OntoFox_inputs/PATO_input.txt | 2 +- src/ontology/OntoFox_outputs/OBA_imports.owl | 20 ++++++++-- src/ontology/OntoFox_outputs/OGMS_imports.owl | 6 +-- src/ontology/OntoFox_outputs/PATO_imports.owl | 6 +-- src/ontology/obi-edit.owl | 38 ++++++------------- 7 files changed, 37 insertions(+), 39 deletions(-) diff --git a/src/ontology/OntoFox_inputs/OBA_input.txt b/src/ontology/OntoFox_inputs/OBA_input.txt index cf3cde0e..a75bc8b8 100755 --- a/src/ontology/OntoFox_inputs/OBA_input.txt +++ b/src/ontology/OntoFox_inputs/OBA_input.txt @@ -22,7 +22,7 @@ http://purl.obolibrary.org/obo/OBA_2060190 # brachioradialis functionality [Top level source term URIs and target direct superclass URIs] # WARN: OBA subclasses PATO:0000001 'quality' not BFO:0000019 'quality' http://purl.obolibrary.org/obo/OBA_0000001 # biological attribute -subClassOf http://purl.obolibrary.org/obo/BFO_0000019 # quality +subClassOf http://purl.obolibrary.org/obo/BFO_0000020 # characteristic [Source term retrieval setting] includeNoIntermediates diff --git a/src/ontology/OntoFox_inputs/OGMS_input.txt b/src/ontology/OntoFox_inputs/OGMS_input.txt index c39d9f03..e5279b4a 100644 --- a/src/ontology/OntoFox_inputs/OGMS_input.txt +++ b/src/ontology/OntoFox_inputs/OGMS_input.txt @@ -18,7 +18,7 @@ http://purl.obolibrary.org/obo/OGMS_0000123 # clinical data item http://purl.obolibrary.org/obo/OGMS_0000015 subClassOf http://purl.obolibrary.org/obo/IAO_0000030 http://purl.obolibrary.org/obo/OGMS_0000023 -subClassOf http://purl.obolibrary.org/obo/BFO_0000019 +subClassOf http://purl.obolibrary.org/obo/BFO_0000020 # characteristic http://purl.obolibrary.org/obo/OGMS_0000063 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/OGMS_0000090 diff --git a/src/ontology/OntoFox_inputs/PATO_input.txt b/src/ontology/OntoFox_inputs/PATO_input.txt index bb23fc9b..a10af868 100755 --- a/src/ontology/OntoFox_inputs/PATO_input.txt +++ b/src/ontology/OntoFox_inputs/PATO_input.txt @@ -58,7 +58,7 @@ http://purl.obolibrary.org/obo/PATO_0002027 # osmolality [Top level source term URIs and target direct superclass URIs] http://purl.obolibrary.org/obo/PATO_0001241 -subClassOf http://purl.obolibrary.org/obo/BFO_0000019 +subClassOf http://purl.obolibrary.org/obo/BFO_0000020 # characteristic [Source term retrieval setting] diff --git a/src/ontology/OntoFox_outputs/OBA_imports.owl b/src/ontology/OntoFox_outputs/OBA_imports.owl index 923f6bdd..ee3a537b 100644 --- a/src/ontology/OntoFox_outputs/OBA_imports.owl +++ b/src/ontology/OntoFox_outputs/OBA_imports.owl @@ -65,16 +65,22 @@ - + - + + characteristic + specifically dependent continuant + + characteristic + specifically dependent continuant + - + biological attribute biological attribute @@ -85,6 +91,7 @@ + limb coordination efficacy The process efficacy of a limb coordination. @@ -121,6 +128,7 @@ + whole organism stability The stability of a multicellular organism. @@ -133,6 +141,7 @@ + facial muscle performance The functionality of a facial muscle. @@ -145,6 +154,7 @@ + peripheral nervous system function The functionality of a peripheral nervous system. @@ -157,6 +167,7 @@ + knee joint functionality The functionality of a knee joint. @@ -169,6 +180,7 @@ + ankle joint functionality The functionality of a ankle joint. @@ -181,6 +193,7 @@ + tendon of biceps brachii functionality The functionality of a tendon of biceps brachii. @@ -193,6 +206,7 @@ + brachioradialis functionality The functionality of a brachioradialis. diff --git a/src/ontology/OntoFox_outputs/OGMS_imports.owl b/src/ontology/OntoFox_outputs/OGMS_imports.owl index 8f62c639..3099227b 100644 --- a/src/ontology/OntoFox_outputs/OGMS_imports.owl +++ b/src/ontology/OntoFox_outputs/OGMS_imports.owl @@ -67,9 +67,9 @@ - + - + @@ -123,7 +123,7 @@ - + phenotype A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. diff --git a/src/ontology/OntoFox_outputs/PATO_imports.owl b/src/ontology/OntoFox_outputs/PATO_imports.owl index c29b780f..581aa25e 100644 --- a/src/ontology/OntoFox_outputs/PATO_imports.owl +++ b/src/ontology/OntoFox_outputs/PATO_imports.owl @@ -62,9 +62,9 @@ - + - + @@ -383,7 +383,7 @@ - + physical object quality A quality which inheres in a continuant. diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index fd5ce925..ad084a8d 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -1575,12 +1575,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - @@ -7442,7 +7436,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -14689,30 +14683,20 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - + + + - - + + + + + - - - - - - - - - - - - - - - - + + From d4897e768481559413123990e0ed1ff227e8cde1 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 20 Aug 2024 16:35:00 -0500 Subject: [PATCH 19/38] Move IAO import of ICE out from under GDC --- src/ontology/OntoFox_inputs/IAO_input.txt | 2 +- src/ontology/OntoFox_outputs/IAO_imports.owl | 8 +------- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/src/ontology/OntoFox_inputs/IAO_input.txt b/src/ontology/OntoFox_inputs/IAO_input.txt index c95e7798..7673131d 100644 --- a/src/ontology/OntoFox_inputs/IAO_input.txt +++ b/src/ontology/OntoFox_inputs/IAO_input.txt @@ -64,7 +64,7 @@ http://purl.obolibrary.org/obo/IAO_0000594 # software application [Top level source term URIs and target direct superclass URIs] http://purl.obolibrary.org/obo/IAO_0000030 # information content entity -subClassOf http://purl.obolibrary.org/obo/BFO_0000031 # generically dependent continuant +subClassOf http://www.w3.org/2002/07/owl#Thing # owl:Thing http://purl.obolibrary.org/obo/IAO_0000178 # material information bearer subClassOf http://purl.obolibrary.org/obo/BFO_0000040 # material entity http://purl.obolibrary.org/obo/IAO_0000574 # assigning a centrally registered identifier diff --git a/src/ontology/OntoFox_outputs/IAO_imports.owl b/src/ontology/OntoFox_outputs/IAO_imports.owl index a9a00772..98298d88 100644 --- a/src/ontology/OntoFox_outputs/IAO_imports.owl +++ b/src/ontology/OntoFox_outputs/IAO_imports.owl @@ -194,12 +194,6 @@ - - - - - - @@ -330,7 +324,7 @@ interpreted by or directly executed by a processing unit. - + information content entity A generically dependent continuant that is about some thing. From be301b2f26e96b962c8f8840e0ecb063f0eccbc8 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 20 Aug 2024 16:48:18 -0500 Subject: [PATCH 20/38] Remove unused information carrier term --- src/ontology/OntoFox_inputs/IAO_input.txt | 1 - src/ontology/OntoFox_outputs/IAO_imports.owl | 12 ------------ 2 files changed, 13 deletions(-) diff --git a/src/ontology/OntoFox_inputs/IAO_input.txt b/src/ontology/OntoFox_inputs/IAO_input.txt index 7673131d..3f771140 100644 --- a/src/ontology/OntoFox_inputs/IAO_input.txt +++ b/src/ontology/OntoFox_inputs/IAO_input.txt @@ -14,7 +14,6 @@ http://purl.obolibrary.org/obo/IAO_0000006 # narrative object http://purl.obolibrary.org/obo/IAO_0000007 # action specification http://purl.obolibrary.org/obo/IAO_0000009 # datum label http://purl.obolibrary.org/obo/IAO_0000010 # software -http://purl.obolibrary.org/obo/IAO_0000015 # information carrier http://purl.obolibrary.org/obo/IAO_0000027 # data item http://purl.obolibrary.org/obo/IAO_0000028 # symbol http://purl.obolibrary.org/obo/IAO_0000030 # information content entity diff --git a/src/ontology/OntoFox_outputs/IAO_imports.owl b/src/ontology/OntoFox_outputs/IAO_imports.owl index 98298d88..8dff63f2 100644 --- a/src/ontology/OntoFox_outputs/IAO_imports.owl +++ b/src/ontology/OntoFox_outputs/IAO_imports.owl @@ -285,18 +285,6 @@ interpreted by or directly executed by a processing unit. - - - - - information carrier - A quality of an information bearer that imparts the information content - - information carrier - - - - From 64f93149eb537fa9b1e57cc4d8497bfb87e3767a Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 21 Aug 2024 12:58:26 -0500 Subject: [PATCH 21/38] Run make modules --- src/ontology/modules/administration.owl | 82 +- src/ontology/modules/assays.owl | 2046 ++++++++++++----------- src/ontology/modules/biopsy.owl | 14 +- src/ontology/modules/epitope-assays.owl | 6 +- src/ontology/modules/study-designs.owl | 30 +- 5 files changed, 1092 insertions(+), 1086 deletions(-) diff --git a/src/ontology/modules/administration.owl b/src/ontology/modules/administration.owl index 0ad3c632..10f4a06f 100644 --- a/src/ontology/modules/administration.owl +++ b/src/ontology/modules/administration.owl @@ -93,9 +93,9 @@ - + - + @@ -160,7 +160,7 @@ - + @@ -204,7 +204,7 @@ - + @@ -249,7 +249,7 @@ - + @@ -292,7 +292,7 @@ - + @@ -306,7 +306,7 @@ - + @@ -337,7 +337,7 @@ - + @@ -351,7 +351,7 @@ - + @@ -383,7 +383,7 @@ - + @@ -415,7 +415,7 @@ - + @@ -429,7 +429,7 @@ - + @@ -461,7 +461,7 @@ - + @@ -493,7 +493,7 @@ - + @@ -507,7 +507,7 @@ - + @@ -537,7 +537,7 @@ - + @@ -567,7 +567,7 @@ - + @@ -655,7 +655,7 @@ - + @@ -683,7 +683,7 @@ - + @@ -711,7 +711,7 @@ - + @@ -739,7 +739,7 @@ - + @@ -769,7 +769,7 @@ - + @@ -797,7 +797,7 @@ - + @@ -825,7 +825,7 @@ - + @@ -853,7 +853,7 @@ - + @@ -881,7 +881,7 @@ - + @@ -909,7 +909,7 @@ - + @@ -937,7 +937,7 @@ - + @@ -965,7 +965,7 @@ - + @@ -993,7 +993,7 @@ - + @@ -1026,7 +1026,7 @@ - + @@ -1054,7 +1054,7 @@ - + @@ -1088,7 +1088,7 @@ - + @@ -1116,7 +1116,7 @@ - + @@ -1144,7 +1144,7 @@ - + @@ -1174,7 +1174,7 @@ - + @@ -1202,7 +1202,7 @@ - + @@ -1230,7 +1230,7 @@ - + @@ -1258,7 +1258,7 @@ - + @@ -1292,7 +1292,7 @@ - + @@ -1349,7 +1349,7 @@ - + diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index a25d091d..9fc11458 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -105,9 +105,15 @@ - + - + + + + + + + @@ -171,12 +177,6 @@ - - - - - - @@ -230,6 +230,12 @@ + + + + + + @@ -872,6 +878,12 @@ + + + + + + @@ -1465,7 +1477,7 @@ - + @@ -1683,7 +1695,7 @@ - + @@ -1717,7 +1729,7 @@ - + @@ -1757,7 +1769,7 @@ - + @@ -1789,7 +1801,7 @@ - + @@ -1869,7 +1881,7 @@ - + @@ -1924,7 +1936,7 @@ - + @@ -2079,7 +2091,7 @@ - + @@ -2197,7 +2209,7 @@ - + @@ -2236,7 +2248,7 @@ - + @@ -2270,7 +2282,7 @@ - + @@ -2365,7 +2377,7 @@ - + @@ -2449,7 +2461,7 @@ - + @@ -2471,7 +2483,7 @@ - + @@ -2567,7 +2579,7 @@ - + @@ -2667,7 +2679,7 @@ - + @@ -2705,7 +2717,7 @@ - + @@ -2742,7 +2754,7 @@ - + @@ -2810,7 +2822,7 @@ - + @@ -2834,7 +2846,7 @@ - + @@ -2868,7 +2880,7 @@ - + @@ -2979,7 +2991,7 @@ - + @@ -3045,7 +3057,7 @@ - + @@ -3083,7 +3095,7 @@ - + @@ -3098,7 +3110,7 @@ - + @@ -3130,7 +3142,7 @@ - + @@ -3184,7 +3196,7 @@ - + @@ -3250,7 +3262,7 @@ - + @@ -3309,7 +3321,7 @@ - + @@ -3419,7 +3431,7 @@ - + @@ -3471,7 +3483,7 @@ - + @@ -3587,7 +3599,7 @@ - + @@ -3611,7 +3623,7 @@ - + @@ -3709,7 +3721,7 @@ - + @@ -3929,7 +3941,7 @@ - + @@ -4052,7 +4064,7 @@ - + @@ -4097,7 +4109,7 @@ - + @@ -4142,7 +4154,7 @@ - + @@ -4245,7 +4257,7 @@ - + @@ -4279,7 +4291,7 @@ - + @@ -4331,7 +4343,7 @@ - + @@ -4373,7 +4385,7 @@ - + @@ -4412,7 +4424,7 @@ - + @@ -4502,14 +4514,14 @@ - + - + @@ -4520,7 +4532,7 @@ - + @@ -4585,7 +4597,7 @@ - + @@ -4619,7 +4631,7 @@ - + @@ -4771,7 +4783,7 @@ - + @@ -4820,7 +4832,7 @@ - + @@ -4869,7 +4881,7 @@ - + @@ -4978,7 +4990,7 @@ - + @@ -5047,7 +5059,7 @@ - + @@ -5100,7 +5112,7 @@ - + @@ -5151,7 +5163,7 @@ - + @@ -5285,7 +5297,7 @@ - + @@ -5397,7 +5409,7 @@ - + @@ -5460,7 +5472,7 @@ - + @@ -5494,7 +5506,7 @@ - + @@ -5678,7 +5690,7 @@ - + @@ -5712,7 +5724,7 @@ - + @@ -5803,7 +5815,7 @@ - + @@ -5897,7 +5909,7 @@ - + @@ -5931,7 +5943,7 @@ - + @@ -5984,7 +5996,7 @@ - + @@ -6095,7 +6107,7 @@ - + @@ -6129,7 +6141,7 @@ - + @@ -6224,7 +6236,7 @@ - + @@ -6258,7 +6270,7 @@ - + @@ -6359,7 +6371,7 @@ - + @@ -6393,7 +6405,7 @@ - + @@ -6589,7 +6601,7 @@ - + @@ -6623,7 +6635,7 @@ - + @@ -6673,7 +6685,7 @@ - + @@ -6707,7 +6719,7 @@ - + @@ -6985,14 +6997,14 @@ - + - + @@ -7003,7 +7015,7 @@ - + @@ -7046,7 +7058,7 @@ - + @@ -7125,7 +7137,7 @@ - + @@ -7147,7 +7159,7 @@ - + @@ -7360,7 +7372,7 @@ - + @@ -7403,7 +7415,7 @@ - + @@ -7440,7 +7452,7 @@ - + @@ -7479,7 +7491,7 @@ - + @@ -7531,7 +7543,7 @@ - + @@ -7595,7 +7607,7 @@ - + @@ -7657,7 +7669,7 @@ - + @@ -7681,7 +7693,7 @@ - + @@ -7736,7 +7748,7 @@ - + @@ -7760,7 +7772,7 @@ - + @@ -7825,7 +7837,7 @@ - + @@ -7862,7 +7874,7 @@ - + @@ -7886,7 +7898,7 @@ - + @@ -7962,7 +7974,7 @@ - + @@ -8005,7 +8017,7 @@ - + @@ -8029,7 +8041,7 @@ - + @@ -8107,7 +8119,7 @@ - + @@ -8144,7 +8156,7 @@ - + @@ -8431,7 +8443,7 @@ - + @@ -8453,7 +8465,7 @@ - + @@ -8494,7 +8506,7 @@ - + @@ -8533,7 +8545,7 @@ - + @@ -8572,7 +8584,7 @@ - + @@ -8611,7 +8623,7 @@ - + @@ -8949,7 +8961,7 @@ - + @@ -9198,7 +9210,7 @@ - + @@ -9457,7 +9469,7 @@ - + @@ -9523,7 +9535,7 @@ - + @@ -9566,7 +9578,7 @@ - + @@ -9590,7 +9602,7 @@ - + @@ -9704,7 +9716,7 @@ - + @@ -9728,7 +9740,7 @@ - + @@ -9823,7 +9835,7 @@ - + @@ -9847,7 +9859,7 @@ - + @@ -9940,7 +9952,7 @@ - + @@ -9964,7 +9976,7 @@ - + @@ -9988,7 +10000,7 @@ - + @@ -10083,7 +10095,7 @@ - + @@ -10107,7 +10119,7 @@ - + @@ -10203,7 +10215,7 @@ - + @@ -10303,7 +10315,7 @@ - + @@ -10327,7 +10339,7 @@ - + @@ -10458,7 +10470,7 @@ - + @@ -10509,7 +10521,7 @@ - + @@ -10533,7 +10545,7 @@ - + @@ -10627,7 +10639,7 @@ - + @@ -10651,7 +10663,7 @@ - + @@ -10675,7 +10687,7 @@ - + @@ -10786,7 +10798,7 @@ - + @@ -10810,7 +10822,7 @@ - + @@ -10886,7 +10898,7 @@ - + @@ -10910,7 +10922,7 @@ - + @@ -11011,7 +11023,7 @@ - + @@ -11035,7 +11047,7 @@ - + @@ -11059,7 +11071,7 @@ - + @@ -11159,7 +11171,7 @@ - + @@ -11199,7 +11211,7 @@ - + @@ -11223,7 +11235,7 @@ - + @@ -11313,7 +11325,7 @@ - + @@ -11337,7 +11349,7 @@ - + @@ -11399,7 +11411,7 @@ - + @@ -11423,7 +11435,7 @@ - + @@ -11499,7 +11511,7 @@ - + @@ -11559,7 +11571,7 @@ - + @@ -11635,7 +11647,7 @@ - + @@ -11792,7 +11804,7 @@ - + @@ -11831,7 +11843,7 @@ - + @@ -11880,7 +11892,7 @@ - + @@ -11904,7 +11916,7 @@ - + @@ -11971,14 +11983,14 @@ - + - + @@ -11989,7 +12001,7 @@ - + @@ -12077,7 +12089,7 @@ - + @@ -12118,7 +12130,7 @@ - + @@ -12150,7 +12162,7 @@ - + @@ -12189,7 +12201,7 @@ - + @@ -12213,7 +12225,7 @@ - + @@ -12294,7 +12306,7 @@ - + @@ -12351,7 +12363,7 @@ - + @@ -12375,7 +12387,7 @@ - + @@ -12473,7 +12485,7 @@ - + @@ -12497,7 +12509,7 @@ - + @@ -12595,7 +12607,7 @@ - + @@ -12619,7 +12631,7 @@ - + @@ -12717,7 +12729,7 @@ - + @@ -12741,7 +12753,7 @@ - + @@ -12868,7 +12880,7 @@ - + @@ -12929,7 +12941,7 @@ - + @@ -12971,7 +12983,7 @@ - + @@ -13013,7 +13025,7 @@ - + @@ -13047,7 +13059,7 @@ - + @@ -13541,7 +13553,7 @@ - + @@ -13595,7 +13607,7 @@ - + @@ -13667,7 +13679,7 @@ - + @@ -13706,7 +13718,7 @@ - + @@ -13934,7 +13946,7 @@ - + @@ -14011,7 +14023,7 @@ - + @@ -14090,7 +14102,7 @@ - + @@ -14152,7 +14164,7 @@ - + @@ -14214,7 +14226,7 @@ - + @@ -14276,7 +14288,7 @@ - + @@ -14338,7 +14350,7 @@ - + @@ -14400,7 +14412,7 @@ - + @@ -14462,7 +14474,7 @@ - + @@ -14524,7 +14536,7 @@ - + @@ -14566,7 +14578,7 @@ - + @@ -14608,7 +14620,7 @@ - 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+ @@ -17409,7 +17421,7 @@ - + @@ -17499,7 +17511,7 @@ - + @@ -17567,7 +17579,7 @@ - + @@ -17631,7 +17643,7 @@ - + @@ -17702,7 +17714,7 @@ - + @@ -17764,7 +17776,7 @@ - + @@ -17825,7 +17837,7 @@ - + @@ -17888,7 +17900,7 @@ - + @@ -17952,7 +17964,7 @@ - + @@ -18013,7 +18025,7 @@ - + @@ -18088,7 +18100,7 @@ - + @@ -18345,7 +18357,7 @@ - + @@ -18714,7 +18726,7 @@ - + @@ -18797,7 +18809,7 @@ - + @@ -18821,7 +18833,7 @@ - + @@ -19530,7 +19542,7 @@ - + @@ -19552,10 +19564,10 @@ - + - + @@ -19596,7 +19608,7 @@ - + @@ -19636,7 +19648,7 @@ - + @@ -19762,7 +19774,7 @@ - + @@ -19802,7 +19814,7 @@ - + @@ -19842,7 +19854,7 @@ - + @@ -19882,7 +19894,7 @@ - + @@ -19922,7 +19934,7 @@ - + @@ -20368,7 +20380,7 @@ - + @@ -20402,7 +20414,7 @@ - + @@ -20441,7 +20453,7 @@ - + @@ -20475,7 +20487,7 @@ - + @@ -20514,7 +20526,7 @@ - + @@ -20548,7 +20560,7 @@ - + @@ -20586,7 +20598,7 @@ - + @@ -20620,14 +20632,14 @@ - + - + @@ -20635,7 +20647,7 @@ - + @@ -20660,7 +20672,7 @@ - + @@ -20709,7 +20721,7 @@ - + @@ -20756,7 +20768,7 @@ - + @@ -20805,7 +20817,7 @@ - + @@ -20913,14 +20925,14 @@ - + - + @@ -20931,7 +20943,7 @@ - + @@ -20979,7 +20991,7 @@ - + @@ -21146,7 +21158,7 @@ - + @@ -21180,7 +21192,7 @@ - + @@ -21691,7 +21703,7 @@ - + @@ -21731,7 +21743,7 @@ - + @@ -22296,7 +22308,7 @@ - + @@ -22342,7 +22354,7 @@ - + @@ -22388,7 +22400,7 @@ - + @@ -22445,7 +22457,7 @@ - + @@ -22491,7 +22503,7 @@ - + @@ -22537,7 +22549,7 @@ - + @@ -22572,7 +22584,7 @@ - + @@ -22607,7 +22619,7 @@ - + @@ -22642,7 +22654,7 @@ - + @@ -22677,7 +22689,7 @@ - + @@ -22712,7 +22724,7 @@ - + @@ -22747,7 +22759,7 @@ - + @@ -22793,7 +22805,7 @@ - + @@ -22828,7 +22840,7 @@ - + @@ -22863,7 +22875,7 @@ - + @@ -22898,7 +22910,7 @@ - + @@ -22933,7 +22945,7 @@ - + @@ -22979,7 +22991,7 @@ - + @@ -23025,7 +23037,7 @@ - + @@ -23071,7 +23083,7 @@ - + @@ -23117,7 +23129,7 @@ - + @@ -23163,7 +23175,7 @@ - + @@ -23209,7 +23221,7 @@ - + @@ -23255,7 +23267,7 @@ - + @@ -23301,7 +23313,7 @@ - + @@ -23433,7 +23445,7 @@ - + @@ -23484,7 +23496,7 @@ - + @@ -23535,7 +23547,7 @@ - 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+ @@ -47763,7 +47769,7 @@ - + @@ -47821,7 +47827,7 @@ - + @@ -47855,7 +47861,7 @@ - + @@ -47892,7 +47898,7 @@ - + @@ -47926,7 +47932,7 @@ - + @@ -47963,7 +47969,7 @@ - + @@ -47997,7 +48003,7 @@ - + @@ -48034,7 +48040,7 @@ - + @@ -48068,7 +48074,7 @@ - + @@ -48105,7 +48111,7 @@ - + @@ -48139,7 +48145,7 @@ - + @@ -48176,7 +48182,7 @@ - + @@ -48234,7 +48240,7 @@ - + @@ -48292,7 +48298,7 @@ - + @@ -48350,7 +48356,7 @@ - + @@ -48408,7 +48414,7 @@ - + @@ -48466,7 +48472,7 @@ - + @@ -48524,7 +48530,7 @@ - + @@ -48582,7 +48588,7 @@ - + @@ -48640,7 +48646,7 @@ - + @@ -48674,7 +48680,7 @@ - + @@ -48711,7 +48717,7 @@ - + @@ -48745,7 +48751,7 @@ - + @@ -48782,7 +48788,7 @@ - + @@ -48816,7 +48822,7 @@ - + @@ -48853,7 +48859,7 @@ - + @@ -48887,7 +48893,7 @@ - + @@ -48924,7 +48930,7 @@ - + @@ -48958,7 +48964,7 @@ - + @@ -48995,7 +49001,7 @@ - + @@ -49029,7 +49035,7 @@ - + @@ -49066,7 +49072,7 @@ - + @@ -49100,7 +49106,7 @@ - + @@ -49137,7 +49143,7 @@ - + @@ -49195,7 +49201,7 @@ - + @@ -49253,7 +49259,7 @@ - + @@ -49287,7 +49293,7 @@ - + @@ -49324,7 +49330,7 @@ - + @@ -49358,7 +49364,7 @@ - + @@ -49395,7 +49401,7 @@ - + @@ -49429,7 +49435,7 @@ - + @@ -49466,7 +49472,7 @@ - + @@ -49500,7 +49506,7 @@ - + @@ -49537,7 +49543,7 @@ - + @@ -49571,7 +49577,7 @@ - + @@ -49608,7 +49614,7 @@ - + @@ -49642,7 +49648,7 @@ - + @@ -49679,7 +49685,7 @@ - + @@ -49737,7 +49743,7 @@ - + @@ -49771,7 +49777,7 @@ - + @@ -49808,7 +49814,7 @@ - + @@ -49842,7 +49848,7 @@ - + @@ -49879,7 +49885,7 @@ - + @@ -49937,7 +49943,7 @@ - + @@ -49971,7 +49977,7 @@ - + @@ -50008,7 +50014,7 @@ - + @@ -50042,7 +50048,7 @@ - + @@ -50079,7 +50085,7 @@ - + @@ -50137,7 +50143,7 @@ - + @@ -50195,7 +50201,7 @@ - + @@ -50229,7 +50235,7 @@ - + @@ -50266,7 +50272,7 @@ - + @@ -50324,7 +50330,7 @@ - + @@ -50358,7 +50364,7 @@ - + @@ -50395,7 +50401,7 @@ - + @@ -50429,7 +50435,7 @@ - + @@ -50466,7 +50472,7 @@ - + @@ -50524,7 +50530,7 @@ - + @@ -50582,7 +50588,7 @@ - + @@ -50640,7 +50646,7 @@ - + @@ -50698,7 +50704,7 @@ - + @@ -50732,7 +50738,7 @@ - + @@ -50769,7 +50775,7 @@ - + @@ -50803,7 +50809,7 @@ - + @@ -50840,7 +50846,7 @@ - + @@ -50874,7 +50880,7 @@ - + @@ -50911,7 +50917,7 @@ - + @@ -50969,7 +50975,7 @@ - + @@ -51003,7 +51009,7 @@ - + @@ -51040,7 +51046,7 @@ - + @@ -51074,7 +51080,7 @@ - + @@ -51111,7 +51117,7 @@ - + @@ -51145,7 +51151,7 @@ - + @@ -51182,7 +51188,7 @@ - + @@ -51240,7 +51246,7 @@ - + @@ -51274,7 +51280,7 @@ - + @@ -51311,7 +51317,7 @@ - + @@ -51345,7 +51351,7 @@ - + @@ -51382,7 +51388,7 @@ - + @@ -51440,7 +51446,7 @@ - + @@ -51474,7 +51480,7 @@ - + @@ -51511,7 +51517,7 @@ - + @@ -51545,7 +51551,7 @@ - + @@ -51582,7 +51588,7 @@ - + @@ -51640,7 +51646,7 @@ - + @@ -51674,7 +51680,7 @@ - + @@ -51711,7 +51717,7 @@ - + @@ -51769,7 +51775,7 @@ - + @@ -51803,7 +51809,7 @@ - + @@ -51840,7 +51846,7 @@ - + @@ -51874,7 +51880,7 @@ - + @@ -51911,7 +51917,7 @@ - + @@ -51945,7 +51951,7 @@ - + @@ -51982,7 +51988,7 @@ - + @@ -52016,7 +52022,7 @@ - + @@ -52053,7 +52059,7 @@ - + @@ -52087,7 +52093,7 @@ - + @@ -52124,7 +52130,7 @@ - + @@ -52182,7 +52188,7 @@ - + @@ -52240,7 +52246,7 @@ - + @@ -52298,7 +52304,7 @@ - + @@ -52356,7 +52362,7 @@ - + @@ -52414,7 +52420,7 @@ - + @@ -52472,7 +52478,7 @@ - + @@ -52530,7 +52536,7 @@ - + @@ -52564,7 +52570,7 @@ - + @@ -52601,7 +52607,7 @@ - + @@ -52635,7 +52641,7 @@ - + @@ -52672,7 +52678,7 @@ - + @@ -52706,7 +52712,7 @@ - + @@ -52743,7 +52749,7 @@ - + @@ -52777,7 +52783,7 @@ - + @@ -52814,7 +52820,7 @@ - + @@ -52848,7 +52854,7 @@ - + @@ -52885,7 +52891,7 @@ - + @@ -52909,7 +52915,7 @@ - + @@ -52964,7 +52970,7 @@ - + diff --git a/src/ontology/modules/biopsy.owl b/src/ontology/modules/biopsy.owl index 48c01296..cfc4c15a 100644 --- a/src/ontology/modules/biopsy.owl +++ b/src/ontology/modules/biopsy.owl @@ -98,21 +98,21 @@ - + - + - + - + - + - + @@ -129,7 +129,7 @@ - + diff --git a/src/ontology/modules/epitope-assays.owl b/src/ontology/modules/epitope-assays.owl index 04366946..c25b1a12 100644 --- a/src/ontology/modules/epitope-assays.owl +++ b/src/ontology/modules/epitope-assays.owl @@ -87,9 +87,9 @@ - + - + @@ -24231,7 +24231,7 @@ - + diff --git a/src/ontology/modules/study-designs.owl b/src/ontology/modules/study-designs.owl index d5a544de..8827cc68 100644 --- a/src/ontology/modules/study-designs.owl +++ b/src/ontology/modules/study-designs.owl @@ -152,6 +152,12 @@ + + + + + + @@ -164,6 +170,12 @@ + + + + + + @@ -375,12 +387,6 @@ - - - - - - @@ -964,7 +970,7 @@ - + @@ -1040,7 +1046,7 @@ - + @@ -1992,7 +1998,7 @@ - + @@ -2285,12 +2291,6 @@ - - - - - - From af5572571967edb089b278166c599f5af1609748 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 21 Aug 2024 13:02:10 -0500 Subject: [PATCH 22/38] Remove references to BFO:0000055 (realizes) --- src/ontology/obi-edit.owl | 128 ++++++++++++++++++-------------------- 1 file changed, 61 insertions(+), 67 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index ad084a8d..59c87a0c 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -592,12 +592,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -880,7 +874,7 @@ process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm] - replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes' + replaced by http://purl.obolibrary.org/obo/COB_0000087: 'realizes' GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungal executes @@ -3157,7 +3151,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -3735,7 +3729,7 @@ editor = PRS - + @@ -5003,7 +4997,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -5062,7 +5056,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -5406,13 +5400,13 @@ for now. - + - + @@ -5844,7 +5838,7 @@ Proposal is to obsolete. - + @@ -6419,7 +6413,7 @@ Proposal is to obsolete. - + @@ -6553,11 +6547,11 @@ activity) - + - + @@ -6683,11 +6677,11 @@ that has_part some material entity is a material entity. If we add as equivalent - + - + @@ -6701,7 +6695,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -7040,7 +7034,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -8026,7 +8020,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -8151,7 +8145,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -8261,13 +8255,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + @@ -8293,7 +8287,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -8548,7 +8542,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -8564,7 +8558,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -8742,7 +8736,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -8758,7 +8752,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -10975,7 +10969,7 @@ Added duirng Mar 1, 2010 dev call - + @@ -11596,13 +11590,13 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - + - + @@ -11636,7 +11630,7 @@ A blood specimen that has been centrifuged to obtain the white blood cells. - + @@ -12514,11 +12508,11 @@ All subtype will be defined by textual definition now. - + - + @@ -14154,7 +14148,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -15615,7 +15609,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -16258,7 +16252,7 @@ Non-qualifying examples include a transiently transfected plasmid or siRNA oligo - + @@ -17521,7 +17515,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -17661,7 +17655,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -17872,7 +17866,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - + @@ -21502,7 +21496,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -21518,7 +21512,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -21766,7 +21760,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -22486,7 +22480,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - + @@ -27049,7 +27043,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -27268,7 +27262,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -27697,11 +27691,11 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -27760,7 +27754,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -27921,11 +27915,11 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -27997,7 +27991,7 @@ https://sourceforge.net/p/obi/obi-terms/738/ - + @@ -29199,7 +29193,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -29320,7 +29314,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -29741,7 +29735,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -29754,7 +29748,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -29805,7 +29799,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -29824,7 +29818,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -29850,7 +29844,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -30025,7 +30019,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -30199,7 +30193,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -30749,7 +30743,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -30779,7 +30773,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -31064,7 +31058,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + @@ -31770,7 +31764,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + From d2a24a0ba92cbca9987bb1a277440dffc4856a82 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Wed, 21 Aug 2024 13:07:23 -0500 Subject: [PATCH 23/38] Remove references to RO:0000059 (concretizes) --- src/ontology/obi-edit.owl | 36 +++++++++++++++--------------------- 1 file changed, 15 insertions(+), 21 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 59c87a0c..264c78a4 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -1363,12 +1363,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - @@ -3154,7 +3148,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -4724,7 +4718,7 @@ illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK200625 - + @@ -5059,7 +5053,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -7037,7 +7031,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -8148,7 +8142,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -8561,7 +8555,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -10972,7 +10966,7 @@ Added duirng Mar 1, 2010 dev call - + @@ -15888,7 +15882,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -16255,7 +16249,7 @@ Non-qualifying examples include a transiently transfected plasmid or siRNA oligo - + @@ -17518,7 +17512,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -17652,7 +17646,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -17869,7 +17863,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - + @@ -22483,7 +22477,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - + @@ -27757,7 +27751,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -27994,7 +27988,7 @@ https://sourceforge.net/p/obi/obi-terms/738/ - + From 96ba715e60e12966fc706c22eecb0668b073e79d Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Tue, 27 Aug 2024 15:19:41 -0400 Subject: [PATCH 24/38] Drop external-byhand.owl This file contain axioms about non-OBI terms: 10 object properties and 2 classes. The annotations about the 2 CLO classes are no longer needed. The 10 object properties should be imported from RO. I did not delete the external-byhand.owl file in case it's still used by something somewhere. --- src/ontology/OntoFox_inputs/RO_input.txt | 20 +++- src/ontology/OntoFox_outputs/RO_imports.owl | 109 ++++++++++++++++++++ src/ontology/obi-edit.owl | 1 - 3 files changed, 124 insertions(+), 6 deletions(-) diff --git a/src/ontology/OntoFox_inputs/RO_input.txt b/src/ontology/OntoFox_inputs/RO_input.txt index a80ba27d..7f677599 100644 --- a/src/ontology/OntoFox_inputs/RO_input.txt +++ b/src/ontology/OntoFox_inputs/RO_input.txt @@ -6,16 +6,26 @@ http://purl.obolibrary.org/obo/obi/dev/import/RO_imports.owl RO [Low level source term URIs] +http://purl.obolibrary.org/obo/BFO_0000062 # preceded by +http://purl.obolibrary.org/obo/BFO_0000063 # precedes +http://purl.obolibrary.org/obo/RO_0000079 # function of +http://purl.obolibrary.org/obo/RO_0000080 # quality of http://purl.obolibrary.org/obo/RO_0000081 # role of +http://purl.obolibrary.org/obo/RO_0000085 # has function +http://purl.obolibrary.org/obo/RO_0000086 # has quality http://purl.obolibrary.org/obo/RO_0000087 # has role http://purl.obolibrary.org/obo/RO_0000091 # has disposition http://purl.obolibrary.org/obo/RO_0000092 # disposition of -http://purl.obolibrary.org/obo/RO_0000085 # has function -http://purl.obolibrary.org/obo/RO_0000079 # function of -http://purl.obolibrary.org/obo/RO_0000086 # has quality -http://purl.obolibrary.org/obo/RO_0000080 # quality of -http://purl.obolibrary.org/obo/RO_0002351 # has member +http://purl.obolibrary.org/obo/RO_0001000 # derives from http://purl.obolibrary.org/obo/RO_0001025 # located in +http://purl.obolibrary.org/obo/RO_0002087 # immediately preceded by +http://purl.obolibrary.org/obo/RO_0002090 # immediately precedes +http://purl.obolibrary.org/obo/RO_0002180 # has component +http://purl.obolibrary.org/obo/RO_0002215 # capable of +http://purl.obolibrary.org/obo/RO_0002219 # surrounded by +http://purl.obolibrary.org/obo/RO_0002222 # temporal relation +http://purl.obolibrary.org/obo/RO_0002223 # starts +http://purl.obolibrary.org/obo/RO_0002351 # has member [Top level source term URIs and target direct superclass URIs] diff --git a/src/ontology/OntoFox_outputs/RO_imports.owl b/src/ontology/OntoFox_outputs/RO_imports.owl index 0d90f61d..b7a68003 100644 --- a/src/ontology/OntoFox_outputs/RO_imports.owl +++ b/src/ontology/OntoFox_outputs/RO_imports.owl @@ -69,6 +69,30 @@ + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + preceded by + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + @@ -157,6 +181,17 @@ + + + + derives from + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + + derives from + + + + @@ -169,6 +204,80 @@ + + + + immediately preceded by + + immediately preceded by + + + + + + + + immediately precedes + + immediately precedes + + + + + + + + has component + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + + has component + + + + + + + + capable of + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + capable of + + + + + + + + surrounded by + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x + + surrounded by + + + + + + + + temporally related to + + temporally related to + + + + + + + + starts + inverse of starts with + + starts + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 75f58ec9..4d9c6359 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -16,7 +16,6 @@ - From ec60b6314626667c6ec2650210e874d2e84c592e Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 27 Aug 2024 16:01:18 -0500 Subject: [PATCH 25/38] Fix almost all unsatisfiability issues --- src/ontology/OntoFox_inputs/GO_input.txt | 7 ++-- src/ontology/OntoFox_outputs/GO_imports.owl | 35 ++++++++--------- src/ontology/modules/assays.owl | 18 ++++----- src/ontology/modules/obsolete.owl | 24 ++++++++++++ src/ontology/obi-edit.owl | 42 +++++++-------------- src/ontology/templates/obsolete.tsv | 1 + 6 files changed, 66 insertions(+), 61 deletions(-) diff --git a/src/ontology/OntoFox_inputs/GO_input.txt b/src/ontology/OntoFox_inputs/GO_input.txt index 8a413b0a..829ce0e5 100755 --- a/src/ontology/OntoFox_inputs/GO_input.txt +++ b/src/ontology/OntoFox_inputs/GO_input.txt @@ -41,6 +41,7 @@ http://purl.obolibrary.org/obo/GO_0004448 # isocitrate dehydrogenase [NAD(P)+] a http://purl.obolibrary.org/obo/GO_0004457 # lactate dehydrogenase activity http://purl.obolibrary.org/obo/GO_0004540 # ribonuclease activity http://purl.obolibrary.org/obo/GO_0005216 +http://purl.obolibrary.org/obo/GO_0005488 # binding http://purl.obolibrary.org/obo/GO_0005575 http://purl.obolibrary.org/obo/GO_0005577 # fibrinogen complex http://purl.obolibrary.org/obo/GO_0005694 @@ -179,8 +180,6 @@ http://purl.obolibrary.org/obo/GO_0140730 # amphiregulin production http://purl.obolibrary.org/obo/GO_0140779 # XCL1 production [Top level source term URIs and target direct superclass URIs] -http://purl.obolibrary.org/obo/GO_0001047 # core promoter binding -subClassOf http://purl.obolibrary.org/obo/OBI_0001588 # binding http://purl.obolibrary.org/obo/GO_0001788 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0001806 @@ -264,7 +263,7 @@ subClassOf http://purl.obolibrary.org/obo/GO_0032991 http://purl.obolibrary.org/obo/GO_0019882 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0019904 -subClassOf http://purl.obolibrary.org/obo/OBI_0001588 +subClassOf http://purl.obolibrary.org/obo/GO_0005488 http://purl.obolibrary.org/obo/GO_0030041 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0030097 @@ -394,7 +393,7 @@ subClassOf http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/GO_0043316 subClassOf http://purl.obolibrary.org/obo/GO_0001906 http://purl.obolibrary.org/obo/GO_0043565 -subClassOf http://purl.obolibrary.org/obo/OBI_0001588 +subClassOf http://purl.obolibrary.org/obo/GO_0005488 http://purl.obolibrary.org/obo/GO_0048869 subClassOf http://purl.obolibrary.org/obo/GO_0008150 http://purl.obolibrary.org/obo/GO_0050896 diff --git a/src/ontology/OntoFox_outputs/GO_imports.owl b/src/ontology/OntoFox_outputs/GO_imports.owl index 014e607f..7e04ef73 100644 --- a/src/ontology/OntoFox_outputs/GO_imports.owl +++ b/src/ontology/OntoFox_outputs/GO_imports.owl @@ -89,7 +89,7 @@ - + core promoter sequence-specific DNA binding Binding to a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon. @@ -99,15 +99,6 @@ - - - - - - - - - @@ -313,7 +304,7 @@ - + antigen binding Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. Antigen binding by an MHC protein complex allows the antigen to be displayed to a T cell or NK cell. @@ -514,6 +505,18 @@ + + + + + binding + The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. + + binding + + + + @@ -853,7 +856,7 @@ - + protein domain specific binding Binding to a specific domain of a protein. @@ -1657,7 +1660,7 @@ - + sequence-specific DNA binding Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. @@ -2143,12 +2146,6 @@ XCL1 production - - - - - - diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 729ca80d..f02130ed 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -1040,6 +1040,12 @@ + + + + + + @@ -5443,7 +5449,7 @@ - + @@ -7055,7 +7061,7 @@ - + @@ -8445,12 +8451,6 @@ - - - - - - @@ -8765,7 +8765,7 @@ - + diff --git a/src/ontology/modules/obsolete.owl b/src/ontology/modules/obsolete.owl index bcced89c..46ce6ac3 100644 --- a/src/ontology/modules/obsolete.owl +++ b/src/ontology/modules/obsolete.owl @@ -40,6 +40,12 @@ + + + + + + @@ -834,6 +840,24 @@ + + + + + A peptide binding to an MHC molecule to form a complex. + + The process of material entities forming complexes. + 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. + PERSON: Bjoern Peters, Randi Vita + IEDB + + + obsolete_binding + true + + + + diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 4d9c6359..598b8f6c 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -12581,7 +12581,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -14118,11 +14118,11 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + - + @@ -14840,7 +14840,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -14932,7 +14932,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -14961,7 +14961,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -14979,22 +14979,6 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - binding - A peptide binding to an MHC molecule to form a complex. - - The process of material entities forming complexes. - 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. - PERSON: Bjoern Peters, Randi Vita - IEDB - binding - - - - @@ -15044,7 +15028,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -15073,7 +15057,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + @@ -15582,7 +15566,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - + @@ -21100,7 +21084,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -21128,7 +21112,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -29844,7 +29828,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + epitope binding by adaptive immune receptor is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding. @@ -30716,7 +30700,7 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + diff --git a/src/ontology/templates/obsolete.tsv b/src/ontology/templates/obsolete.tsv index 46d45302..60fdfb0e 100755 --- a/src/ontology/templates/obsolete.tsv +++ b/src/ontology/templates/obsolete.tsv @@ -48,6 +48,7 @@ OBI:0001572 obsolete cell bound MHC binding constant determination assay metada OBI:0001574 obsolete cell lysate MHC competitive binding assay using radioactivity detection ready for release 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 metadata complete 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 ready for release 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:0001588 obsolete_binding metadata complete The process of material entities forming complexes. IEDB A peptide binding to an MHC molecule to form a complex. PERSON: Bjoern Peters, Randi Vita 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. subclass Obsolete Class true IAO:0000228 GO:0005488 OBI:0001611 obsolete purified MHC direct binding assay ready for release 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 ready for release 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 ready for release 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 From 09166e74b28c1de214ff1cbf898322ebbd890c51 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Thu, 29 Aug 2024 17:59:05 -0500 Subject: [PATCH 26/38] Remove unused unsatisfiable class --- src/ontology/obi-edit.owl | 22 ---------------------- 1 file changed, 22 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 598b8f6c..c6a62040 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -15741,28 +15741,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891 - - - - - - - - - - - - B cell epitope specific immune complex formation - - immune complex formation resulting from antibody binding to epitope - PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters - IEDB (QTT) - Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl - B cell epitope specific immune complex formation - - - - From a58f92c4652787ce1597c82ac797be7778225896 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Fri, 30 Aug 2024 10:22:36 -0500 Subject: [PATCH 27/38] Obsolete OBI:0001720 --- src/ontology/modules/obsolete.owl | 17 +++++++++++++++++ src/ontology/templates/obsolete.tsv | 1 + 2 files changed, 18 insertions(+) diff --git a/src/ontology/modules/obsolete.owl b/src/ontology/modules/obsolete.owl index 46ce6ac3..9bbbc61c 100644 --- a/src/ontology/modules/obsolete.owl +++ b/src/ontology/modules/obsolete.owl @@ -906,6 +906,23 @@ + + + + + + immune complex formation resulting from antibody binding to epitope + PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters + IEDB (QTT) + + Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl + B cell epitope specific immune complex formation + obsolete B cell epitope specific immune complex formation + true + + + + diff --git a/src/ontology/templates/obsolete.tsv b/src/ontology/templates/obsolete.tsv index 60fdfb0e..155a9a71 100755 --- a/src/ontology/templates/obsolete.tsv +++ b/src/ontology/templates/obsolete.tsv @@ -52,6 +52,7 @@ OBI:0001588 obsolete_binding metadata complete The process of material entiti OBI:0001611 obsolete purified MHC direct binding assay ready for release 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 ready for release 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 ready for release 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:0001720 obsolete B cell epitope specific immune complex formation ready for release B cell epitope specific immune complex formation immune complex formation resulting from antibody binding to epitope IEDB (QTT) PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl subclass Obsolete Class true IAO:0000103 OBI:0001737 obsolete B cell epitope specific X-ray crystallography assay ready for release 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 organizational term 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 metadata complete 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 From 3f8b57ec4f018985321ecbc843fc7c6859fdcaf4 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Fri, 30 Aug 2024 11:28:24 -0500 Subject: [PATCH 28/38] Remove usage of BFO_0000001 --- src/ontology/obi-edit.owl | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 3b1b9875..b58c02ca 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -1518,14 +1518,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - From cd6485ee6e4c6e9e0c9628d8095459beddf23404 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Fri, 30 Aug 2024 11:29:08 -0500 Subject: [PATCH 29/38] Remove usage of BFO_0000002 --- src/ontology/obi-edit.owl | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index b58c02ca..f09d4950 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -950,8 +950,6 @@ instance level relation [GOC:cjm] - - is_proxy_for position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. @@ -1518,12 +1516,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - From d3ebf2448cc097f777def866c61ba9c11cf3ac1e Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Fri, 30 Aug 2024 11:29:59 -0500 Subject: [PATCH 30/38] Remove usage of BFO_0000003 --- src/ontology/obi-edit.owl | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index f09d4950..80a1c1ec 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -1293,8 +1293,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - process is result of The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR is a relationship between a process and a preceding occurrent that directly caused the later one to occur @@ -1516,12 +1514,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - From 934cb5ab2003065512d58b9c2f93a0f47d02d574 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Fri, 30 Aug 2024 11:31:44 -0500 Subject: [PATCH 31/38] Remove usage of BFO_0000004 --- src/ontology/obi-edit.owl | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 80a1c1ec..ae4aa9e4 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -1385,8 +1385,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - @@ -1514,12 +1512,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - From 781304474f0077b34c0226fa47ccad86ed0f9aab Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Fri, 30 Aug 2024 12:03:09 -0500 Subject: [PATCH 32/38] Remove usage of BFO_0000035 It's unclear to me why making this change in Protege resulted in that change to RO_0001000. --- src/ontology/obi-edit.owl | 22 +++++----------------- 1 file changed, 5 insertions(+), 17 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index ae4aa9e4..c2245df1 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -1384,8 +1384,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + @@ -1554,12 +1553,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - @@ -15190,15 +15183,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - - - - - - - - + + + + From 5d13bb269bb94d5e8ffee3edaa9cb789988bbb5b Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 3 Sep 2024 10:55:32 -0500 Subject: [PATCH 33/38] Fix multiple-definition conflict --- src/ontology/obi-edit.owl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index c2245df1..e093fd0a 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -3433,7 +3433,6 @@ objectives is a planned process. processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material From dccf1f46fbcd21f25c865997cb8261a25e9fc55a Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 3 Sep 2024 10:59:26 -0500 Subject: [PATCH 34/38] Fix multiple-label conflicts --- src/ontology/obi-edit.owl | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index e093fd0a..5f2f2856 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -682,7 +682,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot - has_specified_input @@ -708,7 +707,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. @@ -767,7 +765,6 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot - has_specified_output @@ -927,7 +924,6 @@ instance level relation [GOC:cjm] A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - is_specified_output_of @@ -3108,7 +3104,6 @@ objectives is a planned process. branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process @@ -3434,7 +3429,6 @@ objectives is a planned process. Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples PERSON: Alan Ruttenberg - processed material From 492a5bf7d60ad01f143a770b29b787360b493188 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 3 Sep 2024 11:55:18 -0500 Subject: [PATCH 35/38] Relabel templates --- src/ontology/templates/administration.tsv | 2 +- .../templates/antibody-purification.tsv | 2 +- src/ontology/templates/assays.tsv | 6 +-- src/ontology/templates/biobank-specimens.tsv | 2 +- src/ontology/templates/biopsy.tsv | 2 +- src/ontology/templates/data-sets.tsv | 2 +- .../templates/data-transformations.tsv | 8 +-- src/ontology/templates/devices.tsv | 2 +- src/ontology/templates/epitope-assays.tsv | 2 +- src/ontology/templates/medical-history.tsv | 2 +- .../templates/physical-examination.tsv | 2 +- src/ontology/templates/sample-collection.tsv | 2 +- src/ontology/templates/sequence-analysis.tsv | 2 +- .../templates/specimen-assay-data.tsv | 50 +++++++++---------- src/ontology/templates/study-designs.tsv | 2 +- .../templates/value-specifications.tsv | 2 +- 16 files changed, 45 insertions(+), 45 deletions(-) diff --git a/src/ontology/templates/administration.tsv b/src/ontology/templates/administration.tsv index 9bdba9f1..39ad0dfb 100644 --- a/src/ontology/templates/administration.tsv +++ b/src/ontology/templates/administration.tsv @@ -2,7 +2,7 @@ ontology ID label editor preferred term has curation status alternative label de 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 ('characteristic of' 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') +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') OBI:0000934 intramuscular injection intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe equivalent administering substance in vivo skeletal muscle tissue ('realizes' some ('function' and ('characteristic of' some 'syringe'))) OBI:0000942 intradermal injection intradermal injection is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot equivalent administering substance in vivo dermis ('realizes' some ('function' and ('characteristic of' some 'syringe'))) OBI:0000952 oral administration oral administration An administering substance in vivo into the mouth of an organism PERSON: Melanie Courtot equivalent administering substance in vivo mouth diff --git a/src/ontology/templates/antibody-purification.tsv b/src/ontology/templates/antibody-purification.tsv index ca6b2148..1279f84b 100644 --- a/src/ontology/templates/antibody-purification.tsv +++ b/src/ontology/templates/antibody-purification.tsv @@ -1,5 +1,5 @@ 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 % +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 diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 6ac34517..c71d669e 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -1,5 +1,5 @@ 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 ('characteristic of' some %))) C (has_specified_input some %) and (realizes some ('analyte role' and ('characteristic of' some %))) C (has_specified_input some %) and (realizes some (function and ('characteristic of' some %))) SPLIT=| C (has_specified_input some %) and (realizes some ('reagent role' and ('characteristic of' some %))) C (has_specified_input some %) and (realizes some ('molecular label role' and ('characteristic of' 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 % +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 ('characteristic of' some %))) C ('has specified input' some %) and (realizes some ('analyte role' and ('characteristic of' some %))) C ('has specified input' some %) and (realizes some (function and ('characteristic of' some %))) SPLIT=| C ('has specified input' some %) and (realizes some ('reagent role' and ('characteristic of' some %))) C ('has specified input' some %) and (realizes some ('molecular label role' and ('characteristic of' 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 ('has characteristic' 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 @@ -47,7 +47,7 @@ OBI:0000743 immune response assay metadata incomplete An assay that determines OBI:0000748 bisulfite sequencing assay metadata complete A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. url:https://en.wikipedia.org/wiki/Bisulfite_sequencing PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. Philippe Rocca-Serra|Sagar Jain subclass DNA meth profiling is a epigenetic mod assay, does not need inference DNA methylation profiling assay DNA sequencing assay DNA extract ('deoxyribonucleotide' and ('has part' some 'methyl group')) DNA sequencer DNA extract ('measurement datum' and 'DNA sequence data') epigenetic modification identification objective OBI:0000787 human antithrombin-III in blood assay ready for release AT-III assay An assay that measures the amount of antithrombin III in blood. url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. Alan Ruttenberg subclass analyte assay ('scattered molecular aggregate' and ('has grain' some antithrombin-III)) scalar measurement datum blood coagulation OBI:0000802 prothrombin time assay metadata complete An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). Alan Ruttenberg subclass assay scalar measurement datum blood coagulation -OBI:0000805 antithrombin-III berichrome assay metadata complete AT-III assay An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 subclass human antithrombin-III in blood assay (has_specified_output some 'scalar measurement datum') and ('has participant' some 'Berichrom(r) Antithrombin III (A) Kit') and (has_specified_output exactly 1 Thing) +OBI:0000805 antithrombin-III berichrome assay metadata complete AT-III assay An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 subclass human antithrombin-III in blood assay ('has specified output' some 'scalar measurement datum') and ('has participant' some 'Berichrom(r) Antithrombin III (A) Kit') and ('has specified output' exactly 1 Thing) OBI:0000808 spectrolyse heparin antifactor-Xa assay metadata complete An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration. url:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). Alan Ruttenberg subclass assay scalar measurement datum blood coagulation OBI:0000812 measuring neural activity in the caudate nucleus assay metadata complete An assay that measures neural activity in the caudate nucleus Jessica Turner, NIF|Dirk Derom, OBI An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus Helen Parkinson subclass extracellular electrophysiology recording assay OBI:0000820 activated partial thromboplastin time assay metadata complete aPTT assay An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy. url:http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0004310 The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660) Alan Ruttenberg|OBI call There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant). subclass assay ('blood specimen' or 'blood plasma specimen') time measurement datum blood coagulation @@ -81,7 +81,7 @@ OBI:0000964 in live cell assay metadata incomplete An assay in which a measure OBI:0000966 in live organism assay metadata complete in vivo assay An assay in which a measurement is made by observing entities located in an organism. Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. Bjoern Peters subclass assay ('has participant' some ('material entity' and ('located in' some (organism and ('has quality' some alive))))) OBI:0000975 cell-cell binding detection by flow cytometry assay A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. IEDB Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates. IEDB equivalent cytometry assay flow cytometry assay binding OBI:0000978 in container assay metadata incomplete An assay in which a measurement is made by observing entities located in a container. subclass assay -OBI:0001001 Edinburgh handedness assay metadata complete An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory|PMID:5146491 Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: ""Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)"" Alan Ruttenberg|Jessica Turner|Gully Burns (orcid:0000-0003-1493-865X) subclass handedness assay Homo sapiens Edinburgh score (has_specified_input value 'Edingburgh handedness inventory') +OBI:0001001 Edinburgh handedness assay metadata complete An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory|PMID:5146491 Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: ""Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)"" Alan Ruttenberg|Jessica Turner|Gully Burns (orcid:0000-0003-1493-865X) subclass handedness assay Homo sapiens Edinburgh score ('has specified input' value 'Edingburgh handedness inventory') OBI:0001005 RNASE CL3 structure mapping assay ready for release single nucleotide resolution mapping assay using RNAse CL3 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. RNA ontology PMID:16453415 Philippe Rocca-Serra subclass single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing RNA extract ribonuclease CL3 (chicken) secondary structure of RNA molecule OBI:0001006 CMCT structure mapping assay ready for release single nucleotide resolution mapping assay using CMCT probe A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure RNA ontology PMID:2422386 and PMID:2446263 Philippe Rocca-Serra subclass single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing ('deoxyribonucleic acid' or 'ribonucleic acid') measurement datum secondary structure of sequence macromolecule OBI:0001008 MPE-Fe(II) structure mapping assay ready for release single nucleotide resolution mapping assay using Fe-MP probe A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. RNA ontology PMID:6209709 Philippe Rocca-Serra subclass single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing RNA extract measurement datum secondary structure of RNA molecule diff --git a/src/ontology/templates/biobank-specimens.tsv b/src/ontology/templates/biobank-specimens.tsv index b0ce5268..818b1bd0 100644 --- a/src/ontology/templates/biobank-specimens.tsv +++ b/src/ontology/templates/biobank-specimens.tsv @@ -1,5 +1,5 @@ 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 specimen collection process gross anatomical part collection process input URI -ID A rdfs: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 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 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 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 diff --git a/src/ontology/templates/biopsy.tsv b/src/ontology/templates/biopsy.tsv index 3aa976ba..9d1c616a 100644 --- a/src/ontology/templates/biopsy.tsv +++ b/src/ontology/templates/biopsy.tsv @@ -1,5 +1,5 @@ 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 % +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 diff --git a/src/ontology/templates/data-sets.tsv b/src/ontology/templates/data-sets.tsv index c39a9c4d..73adafd5 100644 --- a/src/ontology/templates/data-sets.tsv +++ b/src/ontology/templates/data-sets.tsv @@ -1,5 +1,5 @@ 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 % +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 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 diff --git a/src/ontology/templates/data-transformations.tsv b/src/ontology/templates/data-transformations.tsv index bb2f1947..e9b522b1 100644 --- a/src/ontology/templates/data-transformations.tsv +++ b/src/ontology/templates/data-transformations.tsv @@ -1,7 +1,7 @@ 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 % +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') -OBI:0003648 liquid chromatrography mass spectrometry analysis liquid chromatography mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography 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 'liquid chromatography mass spectrometry assay') -OBI:0003649 liquid chromatography-tandem mass spectrometry analysis liquid chromatography tandem mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography 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 'liquid chromatography-tandem mass spectrometry') +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') +OBI:0003648 liquid chromatrography mass spectrometry analysis liquid chromatography mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography 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 'liquid chromatography mass spectrometry assay') +OBI:0003649 liquid chromatography-tandem mass spectrometry analysis liquid chromatography tandem mass spectrometry analysis A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography 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 'liquid chromatography-tandem mass spectrometry') diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv index cbcefb10..3b7a3c9e 100644 --- a/src/ontology/templates/devices.tsv +++ b/src/ontology/templates/devices.tsv @@ -309,7 +309,7 @@ OBI:0001204 SNP microarray SNP microarray metadata complete A DNA microarray us OBI:0001307 tiling microarray tiling microarray metadata complete genome tiling array A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. EFO_0002704: tiling array Person: Helen Parkinson DNA microarray OBI:0001865 assay array metadata complete A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg device solid support function OBI:0001869 Illumina BeadChip metadata complete An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. http://www.illumina.com/technology/beadarray_technology.ilmn PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi assay array Illumina -OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip ('has characteristic' some (function and ('realized in' only (assay and (has_specified_output some ('measurement datum' and ('is about' some (deoxyribonucleotide and ('has part' some 'methyl group'))))))))) +OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip ('has characteristic' some (function and ('realized in' only (assay and ('has specified output' some ('measurement datum' and ('is about' some (deoxyribonucleotide and ('has part' some 'methyl group'))))))))) OBI:0001871 LSRFortessa X-20 metadata complete A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg Anna Maria Masci flow cytometer analyzer Becton Dickinson (BD Biosciences) OBI:0001971 Ion 316 Chip v2 Ion 316 Chip v2 Ion PGM 316 Chip|Ion 316 Chip|Ion PGM 316 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ ion semiconductor chip OBI:0001972 Ion 318 Chip v2 Ion 318 Chip v2 Ion 318 Chip|Ion PGM 318 Chip|Ion PGM 318 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ ion semiconductor chip diff --git a/src/ontology/templates/epitope-assays.tsv b/src/ontology/templates/epitope-assays.tsv index 7ea5a792..da3ee3b5 100644 --- a/src/ontology/templates/epitope-assays.tsv +++ b/src/ontology/templates/epitope-assays.tsv @@ -1,5 +1,5 @@ Ontology ID label editor preferred term has curation status alternative label 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 label SPLIT=| A IEDB alternative term 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 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 ('characteristic of' 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 label SPLIT=| A IEDB alternative term 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 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 ('characteristic of' 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')) diff --git a/src/ontology/templates/medical-history.tsv b/src/ontology/templates/medical-history.tsv index c1ccb4d3..7b8912cb 100644 --- a/src/ontology/templates/medical-history.tsv +++ b/src/ontology/templates/medical-history.tsv @@ -38,7 +38,7 @@ OBI:0002402 hormonal birth control former use history A hormonal birth contro OBI:0002403 hormonal birth control current use history A hormonal birth control use history that indicates an individual is currently a hormonal birth control user. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass hormonal birth control use history OBI:0002404 no hormonal birth control use history A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass hormonal birth control use history OBI:0002405 hormonal replacement therapy history A clinical history in which an individual has had hormonal replacement therapy in the past. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass clinical history -OBI:0002406 delivery form for hormonal replacement therapy form of hormone replacement therapy A processed material used for delivery of hormones in hormone replacement therapy. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass processed material +OBI:0002406 delivery form for hormonal replacement therapy form of hormone replacement therapy A processed material used for delivery of hormones in hormone replacement therapy. NCI BBRB, OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass processed material entity OBI:0002407 pill delivery form for hormonal replacement therapy A delivery form for hormonal replacement therapy that is a pill for oral administration. OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass delivery form for hormonal replacement therapy OBI:0002408 patch delivery form for hormonal replacement therapy A delivery form for hormonal replacement therapy that is a patch for transdermal administration. OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass delivery form for hormonal replacement therapy OBI:0002409 cream delivery form for hormonal replacement therapy A delivery form for hormonal replacement therapy that is a cream for transdermal administration. OBIB Chris Stoeckert, Helena Ellis NCI BBRB subclass delivery form for hormonal replacement therapy diff --git a/src/ontology/templates/physical-examination.tsv b/src/ontology/templates/physical-examination.tsv index 47d07326..d6380b55 100644 --- a/src/ontology/templates/physical-examination.tsv +++ b/src/ontology/templates/physical-examination.tsv @@ -1,5 +1,5 @@ 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 detection technique evaluant device input output anatomical site assessed biological trait -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 ( % 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 (function and ('characteristic of' some %))) SPLIT=| C has_specified_input some % C has_specified_output some % C has_specified_output some ('is about' some %) C has_specified_output some ('is quality measurement of' some %) +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 ( % 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 (function and ('characteristic of' some %))) SPLIT=| C 'has specified input' some % C 'has specified output' some % C 'has specified output' some ('is about' some %) C 'has specified output' some ('is quality measurement of' some %) OBI:0003501 functional assessment of individual A physical examination of an organism's ability to perform functional activities. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass physical examination of an organism OBI:0003502 facial atrophy assessment An observational assessment of the loss of facial muscle tissue due to inactivity or disease. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass observational assessment of individual facial muscle facial muscle performance OBI:0003503 tongue atrophy assessment An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease. Critical Path Institute Daniel Olson, ORCID: 0000-0002-8134-1207 https://github.com/obi-ontology/obi/issues/1637 subclass observational assessment of individual tongue facial muscle performance diff --git a/src/ontology/templates/sample-collection.tsv b/src/ontology/templates/sample-collection.tsv index 0319846f..834b94a1 100644 --- a/src/ontology/templates/sample-collection.tsv +++ b/src/ontology/templates/sample-collection.tsv @@ -1,5 +1,5 @@ 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 specimen type -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 C % C has_specified_output some (% and 'has role' some 'specimen role') +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 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 diff --git a/src/ontology/templates/sequence-analysis.tsv b/src/ontology/templates/sequence-analysis.tsv index 7c43a66c..8b4ce88c 100644 --- a/src/ontology/templates/sequence-analysis.tsv +++ b/src/ontology/templates/sequence-analysis.tsv @@ -1,5 +1,5 @@ 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 output input input of output of objective -ID A rdfs:label A editor preferred term AL 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_specified_output' some % C 'has_specified_input' some % C is_specified_input_of some % C is_specified_output_of some % C achieves_planned_objective some % +ID A rdfs:label A editor preferred term AL 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 specified output' some % C 'has specified input' some % C 'is specified input of' some % C 'is specified output of' some % C achieves_planned_objective some % OBI:0002565 adapter-sequence trimming A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). Dan Berrios Dan Berrios subclass sequence trimming adapter-trimmed sequence data 'adapter sequence data' OBI:0002566 file merge A data transformation in which data contained in 2 or more files are merged into a single file. Dan Berrios Dan Berrios subclass data transformation OBI:0002567 sequence alignment A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. Dan Berrios Dan Berrios subclass sequence analysis data transformation aligned sequence data sequence data diff --git a/src/ontology/templates/specimen-assay-data.tsv b/src/ontology/templates/specimen-assay-data.tsv index ea6871dc..452c6861 100644 --- a/src/ontology/templates/specimen-assay-data.tsv +++ b/src/ontology/templates/specimen-assay-data.tsv @@ -1,22 +1,22 @@ 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 axiom 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 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') -OBI:0003246 feces microbiology datum An organism detection datum that is the specified output of a feces microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'feces microbiology assay') -OBI:0003247 urine assay datum A data item that is the specified output of a urine assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'urine assay') -OBI:0003248 urine microbiology datum An organism detection datum that is the specified output of a urine microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'urine microbiology assay') -OBI:0003249 induced sputum assay datum A data item that is the specified output of a induced sputum assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'induced sputum assay') -OBI:0003251 induced sputum microbiology datum An organism detection datum that is the specified output of an induced sputum microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'induced sputum microbiology assay') -OBI:0003252 cerebrospinal fluid assay datum A data item that is the specified output of a cerebrospinal fluid assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'cerebrospinal fluid assay') -OBI:0003253 cerebrospinal fluid microbiology datum An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'cerebrospinal fluid microbiology assay') -OBI:0003254 endotracheal aspirate assay datum An organism detection datum that is the specified output of an endotracheal aspirate assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'endotracheal aspirate assay') -OBI:0003255 endotracheal tube aspirate microbiology datum An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'endotracheal tube aspirate microbiology assay') -OBI:0003256 lung microbiology datum An organism detection datum that is the specified output of a lung microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'lung microbiology assay') -OBI:0003257 nasopharyngeal or oropharyngeal swab microbiology datum An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'nasopharyngeal or oropharyngeal swab microbiology assay') -OBI:0003258 pleural fluid microbiology datum An organism detection datum that is the specified output of a pleural fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'pleural fluid microbiology assay') -OBI:0003259 umbilical cord blood assay datum A data item that is the specified output of an umbilical cord blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and is_specified_output_of some 'umbilical cord blood assay') -OBI:0003260 umbilical cord blood microbiology datum An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and is_specified_output_of some 'umbilical cord blood microbiology assay') +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') +OBI:0003246 feces microbiology datum An organism detection datum that is the specified output of a feces microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'feces microbiology assay') +OBI:0003247 urine assay datum A data item that is the specified output of a urine assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'urine assay') +OBI:0003248 urine microbiology datum An organism detection datum that is the specified output of a urine microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'urine microbiology assay') +OBI:0003249 induced sputum assay datum A data item that is the specified output of a induced sputum assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'induced sputum assay') +OBI:0003251 induced sputum microbiology datum An organism detection datum that is the specified output of an induced sputum microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'induced sputum microbiology assay') +OBI:0003252 cerebrospinal fluid assay datum A data item that is the specified output of a cerebrospinal fluid assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'cerebrospinal fluid assay') +OBI:0003253 cerebrospinal fluid microbiology datum An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'cerebrospinal fluid microbiology assay') +OBI:0003254 endotracheal aspirate assay datum An organism detection datum that is the specified output of an endotracheal aspirate assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'endotracheal aspirate assay') +OBI:0003255 endotracheal tube aspirate microbiology datum An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'endotracheal tube aspirate microbiology assay') +OBI:0003256 lung microbiology datum An organism detection datum that is the specified output of a lung microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'lung microbiology assay') +OBI:0003257 nasopharyngeal or oropharyngeal swab microbiology datum An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'nasopharyngeal or oropharyngeal swab microbiology assay') +OBI:0003258 pleural fluid microbiology datum An organism detection datum that is the specified output of a pleural fluid microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'pleural fluid microbiology assay') +OBI:0003259 umbilical cord blood assay datum A data item that is the specified output of an umbilical cord blood assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('data item' and 'is specified output of' some 'umbilical cord blood assay') +OBI:0003260 umbilical cord blood microbiology datum An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('organism detection datum' and 'is specified output of' some 'umbilical cord blood microbiology assay') OBI:0003261 bacteria in blood datum A blood microbiology datum that is about bacteria. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Bacteria) OBI:0003262 virus in blood datum A blood microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Viruses) OBI:0003263 eukaryota in blood datum A blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('blood microbiology datum' and 'is about' some Eukaryota) @@ -38,12 +38,12 @@ OBI:0003278 bacteria in pleural fluid datum A pleural fluid microbiology datu OBI:0003279 eukaryota in pleural fluid datum A pleural fluid microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('pleural fluid microbiology datum' and 'is about' some Eukaryota) OBI:0003280 virus in pleural fluid datum A pleural fluid microbiology datum that is about a virus. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('pleural fluid microbiology datum' and 'is about' some Viruses) OBI:0003281 eukaryota in umbilical cord blood datum An umbilical cord blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1428 ('umbilical cord blood microbiology datum' and 'is about' some Eukaryota) -OBI:0003365 milk assay datum A data item that is the specified output of a milk assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1515 ('data item' and is_specified_output_of some 'milk assay') -OBI:0003382 placental blood microbiology datum An organism detection datum that is the specified output of a placental blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1297 ('organism detection datum' and is_specified_output_of some 'placental blood microbiology assay') +OBI:0003365 milk assay datum A data item that is the specified output of a milk assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1515 ('data item' and 'is specified output of' some 'milk assay') +OBI:0003382 placental blood microbiology datum An organism detection datum that is the specified output of a placental blood microbiology assay. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1297 ('organism detection datum' and 'is specified output of' some 'placental blood microbiology assay') OBI:0003383 eukaryota in placental blood datum A placental blood microbiology datum that is about eukaryota. VEuPathDB John Judkins https://github.com/obi-ontology/obi/issues/1297 ('placental blood microbiology datum' and 'is about' some Eukaryota) -OBI:0003417 antigen specific antibodies assay datum A data item that is the specified output of an antigen specific antibodies assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('data item' and is_specified_output_of some 'antigen specific antibodies assay') -OBI:0003420 antigen specific antibodies in blood assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and is_specified_output_of some 'blood assay') -OBI:0003421 antigen specific antibodies in milk assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and is_specified_output_of some 'milk assay') -OBI:0003577 skin of body microbiology datum An organism detection datum that is the specified output of a skin of body microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'skin of body microbiology assay') -OBI:0003579 bone marrow microbiology datum An organism detection datum that is the specified output of a bone marrow microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'bone marrow microbiology assay') -OBI:0003581 nasal aspirate microbiology datum An organism detection datum that is the specified output of a nasal aspirate microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and is_specified_output_of some 'nasal aspirate microbiology assay') +OBI:0003417 antigen specific antibodies assay datum A data item that is the specified output of an antigen specific antibodies assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('data item' and 'is specified output of' some 'antigen specific antibodies assay') +OBI:0003420 antigen specific antibodies in blood assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and 'is specified output of' some 'blood assay') +OBI:0003421 antigen specific antibodies in milk assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1526 ('antigen specific antibodies assay datum' and 'is specified output of' some 'milk assay') +OBI:0003577 skin of body microbiology datum An organism detection datum that is the specified output of a skin of body microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and 'is specified output of' some 'skin of body microbiology assay') +OBI:0003579 bone marrow microbiology datum An organism detection datum that is the specified output of a bone marrow microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and 'is specified output of' some 'bone marrow microbiology assay') +OBI:0003581 nasal aspirate microbiology datum An organism detection datum that is the specified output of a nasal aspirate microbiology assay. VEuPathDB John Judkins ORCID:0000-0001-6595-0902 https://github.com/obi-ontology/obi/issues/1680 ('organism detection datum' and 'is specified output of' some 'nasal aspirate microbiology assay') diff --git a/src/ontology/templates/study-designs.tsv b/src/ontology/templates/study-designs.tsv index b0c2389d..f56b5ab2 100644 --- a/src/ontology/templates/study-designs.tsv +++ b/src/ontology/templates/study-designs.tsv @@ -34,7 +34,7 @@ OBI:0001337 clinical history design clinical history design metadata complete A OBI:0001358 post-transcriptional modification design post-transcriptional modification design metadata complete A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. MO_392 cellular_modification_design Person: Chris Stoeckert, Jie Zheng post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases subclass intervention design biological feature identification objective study intervention OBI:0001365 cellular process design cellular process design metadata complete A study design that aims to study the 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. MO_810 cellular_process_design Person: Chris Stoeckert, Jie Zheng subclass study design ('cellular feature identification objective' and ('is about' some 'cellular process')) OBI:0001374 injury design injury design metadata complete A study design in which the response of an organism(s) to injury or damage is studied. MO_726 injury_design Person: Chris Stoeckert, Jie Zheng subclass study design organism feature identification objective -OBI:0001377 organism status comparison design organism status comparison design metadata complete A study design that compares samples from live and dead organisms. MO_841 organism_status_design Person: Chris Stoeckert, Jie Zheng subclass study design biological feature identification objective ('is concretized as' some ('realized in' some (assay and (has_specified_input some ('pre-mortem specimen' or 'post mortem specimen'))))) +OBI:0001377 organism status comparison design organism status comparison design metadata complete A study design that compares samples from live and dead organisms. MO_841 organism_status_design Person: Chris Stoeckert, Jie Zheng subclass study design biological feature identification objective ('is concretized as' some ('realized in' some (assay and ('has specified input' some ('pre-mortem specimen' or 'post mortem specimen'))))) OBI:0001387 genotyping by array design genotyping by array design metadata complete A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. MO_560 genotyping_design Person: Chris Stoeckert, Jie Zheng subclass genotyping design OBI:0001396 stimulus or stress design stimulus or stress design metadata complete A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. MO_568 stimulus_or_stress_design Person: Chris Stoeckert, Jie Zheng subclass intervention design ('organism feature identification objective' and ('is about' some 'response to stimulus')) study intervention OBI:0001401 protocol optimization design protocol optimization design metadata complete A study design where different protocols or protocol parameters are compared aims to find an optimized protocol MO_934 optimization_design Person: Chris Stoeckert, Jie Zheng subclass study design protocol optimization objective diff --git a/src/ontology/templates/value-specifications.tsv b/src/ontology/templates/value-specifications.tsv index 3dd5092a..5e951172 100644 --- a/src/ontology/templates/value-specifications.tsv +++ b/src/ontology/templates/value-specifications.tsv @@ -2,7 +2,7 @@ ontology ID label editor preferred term has curation status alternative label de 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 TYPE C % OBI:0002199 reason for lack of data item An information content entity that provides an explanation why a data item is not provided. OBI cannot be assessed, not applicable, unknown Chris Stoeckert, Helena Ellis NCI BBRB subclass information content entity OBI:0002200 cannot be assessed determination cannot be assessed A reason for lack of data item that is the negative output of a determination if assay will provide reliable results. OBI Chris Stoeckert, Helena Ellis NCI BBRB subclass reason for lack of data item -OBI:0002201 determination if assay will provide reliable results A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. OBI Chris Stoeckert, Helena Ellis NCI BBRB subclass planned process +OBI:0002201 determination if assay will provide reliable results A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. OBI Chris Stoeckert, Helena Ellis NCI BBRB subclass completely executed planned process OBI:0002202 GX A cannot be assessed determination for histologic tumor grade. OBI AJCC 7th edition GX: cannot be assessed. Chris Stoeckert, Helena Ellis NCI BBRB subclass cannot be assessed determination OBI:0002203 pTX A cannot be assessed determination for pathologic primary tumor staging. OBI AJCC 7th edition pTX: cannot be assessed. Chris Stoeckert, Helena Ellis NCI BBRB subclass cannot be assessed determination OBI:0002204 pNX A cannot be assessed determination of pathologic staging of lymph nodes. OBI AJCC 7th edition pNX: cannot be assessed. Chris Stoeckert, Helena Ellis NCI BBRB subclass cannot be assessed determination From bac8d742274b187ebf875dfc35943085dd14bcc1 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 3 Sep 2024 12:23:52 -0500 Subject: [PATCH 36/38] Remove one missed label --- src/ontology/obi-edit.owl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index 5f2f2856..e29f3138 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -712,7 +712,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - is_specified_input_of From fd040dacace244dc392316edae6659998aecc692 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 3 Sep 2024 12:54:45 -0500 Subject: [PATCH 37/38] Move 'region' out from under GDC --- src/ontology/OntoFox_inputs/SO_input.txt | 4 ++-- src/ontology/OntoFox_outputs/SO_imports.owl | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/ontology/OntoFox_inputs/SO_input.txt b/src/ontology/OntoFox_inputs/SO_input.txt index e3e11709..fc9d998f 100755 --- a/src/ontology/OntoFox_inputs/SO_input.txt +++ b/src/ontology/OntoFox_inputs/SO_input.txt @@ -19,7 +19,7 @@ http://purl.obolibrary.org/obo/SO_0000235 # TF_binding_site [Top level source term URIs and target direct superclass URIs] http://purl.obolibrary.org/obo/SO_0000001 -subClassOf http://purl.obolibrary.org/obo/BFO_0000031 +subClassOf http://purl.obolibrary.org/obo/BFO_0000040 # material entity http://purl.obolibrary.org/obo/SO_0000104 subClassOf http://purl.obolibrary.org/obo/SO_0000001 http://purl.obolibrary.org/obo/SO_0000276 @@ -49,4 +49,4 @@ includeNoIntermediates [Source annotation URIs] http://www.w3.org/2000/01/rdf-schema#label copyTo http://purl.obolibrary.org/obo/IAO_0000111 -http://purl.obolibrary.org/obo/IAO_0000115 \ No newline at end of file +http://purl.obolibrary.org/obo/IAO_0000115 diff --git a/src/ontology/OntoFox_outputs/SO_imports.owl b/src/ontology/OntoFox_outputs/SO_imports.owl index 95034541..e51e038b 100644 --- a/src/ontology/OntoFox_outputs/SO_imports.owl +++ b/src/ontology/OntoFox_outputs/SO_imports.owl @@ -62,9 +62,9 @@ - + - + @@ -77,7 +77,7 @@ - + region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. From dff4b025dcc5f3bffd6059c486fefeabd0c1ca70 Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Thu, 5 Sep 2024 13:25:22 -0400 Subject: [PATCH 38/38] Restore labels for six OBI terms used in COB --- src/ontology/obi-edit.owl | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl index e29f3138..d004c99a 100644 --- a/src/ontology/obi-edit.owl +++ b/src/ontology/obi-edit.owl @@ -682,6 +682,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot + has specified input @@ -712,6 +713,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters + is specified input of @@ -764,6 +766,7 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot + has specified output @@ -923,6 +926,7 @@ instance level relation [GOC:cjm] A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters + is specified output of @@ -3103,6 +3107,7 @@ objectives is a planned process. branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + completely executed planned process @@ -3428,6 +3433,7 @@ objectives is a planned process. Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples PERSON: Alan Ruttenberg + processed material entity