diff --git a/.gitignore b/.gitignore index 7add119..27bf703 100644 --- a/.gitignore +++ b/.gitignore @@ -46,3 +46,4 @@ src/patterns/all_pattern_terms.txt .idea/vcs.xml .idea/workspace.xml .idea/misc.xml +/.idea diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 681030e..2782394 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -19,6 +19,8 @@ These are the current imports in NMRCV | bfo | http://purl.obolibrary.org/obo/bfo.owl | mirror | | ro | http://purl.obolibrary.org/obo/ro.owl | None | | omo | http://purl.obolibrary.org/obo/omo.owl | mirror | +| iao | http://purl.obolibrary.org/obo/iao.owl | None | +| obi | http://purl.obolibrary.org/obo/obi.owl | custom | | chebi | http://purl.obolibrary.org/obo/chebi.owl | None | ## Components diff --git a/src/mappings/obi-mapping.tsv b/src/mappings/obi-mapping.tsv new file mode 100644 index 0000000..2e79e0e --- /dev/null +++ b/src/mappings/obi-mapping.tsv @@ -0,0 +1,65 @@ +subject_id subject_label predicate_id object_id object_label mapping_justification comment mapping_date author_id subject_source subject_source_version object_source object_source_version confidence +http://nmrML.org/nmrCV#NMR:1400014 NMR probe skos:exactMatch OBI:0000516 NMR probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400231 Bruker NMR probe skos:exactMatch OBI:0000561 Bruker NMR probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400194 Bruker 1mm MicroProbe skos:exactMatch OBI:0000590 Bruker 1mm MicroProbe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400191 Bruker CryoProbe skos:exactMatch OBI:0000531 Bruker CryoProbe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400223 high resolution probe skos:exactMatch OBI:0000480 Bruker high resolution probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400195 flow high resolution probe skos:exactMatch OBI:0000527 flow high resolution probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400192 high resolution magic angle spin probe skos:exactMatch OBI:0000607 high resolution magic angle spin probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400224 high resolution probe with ATM skos:exactMatch OBI:0000616 high resolution probe with automatic tuning and matching semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400225 micro imaging probe skos:exactMatch OBI:0000620 Bruker micro imaging probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400193 solid magic angle spinning probe skos:exactMatch OBI:0000629 Bruker solid magic angle spinning probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400280 direct detection probe skos:exactMatch OBI:0000491 direct detection NMR probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400131 flow probe skos:exactMatch OBI:0000519 flow probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400244 NMR imaging probe "skos:exactMatch " OBI:0000539 imaging NMR probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400281 indirect detection probe skos:exactMatch OBI:0000640 indirect detection probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400232 JEOL NMR probe skos:exactMatch OBI:0000529 JEOL NMR probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400233 CapNMR probe skos:exactMatch OBI:0000635 JEOL CapNMR probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400242 liquid NMR probe skos:exactMatch OBI:0000559 liquid NMR probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400243 solid NMR probe skos:exactMatch OBI:0000479 solid NMR probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400248 tecmag EAGLE probe skos:exactMatch OBI:0000564 tecmag EAGLE probe semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400059 NMR instrument skos:exactMatch OBI:0000566 NMR instrument semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400198 Bruker NMR instrument skos:exactMatch OBI:0000596 Bruker NMR instrument semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400197 AVANCE II spectrometer skos:exactMatch OBI:0000580 AVANCE II spectrometer semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400241 AC instrument skos:exactMatch OBI:0000541 Bruker AC series NMR instrument semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400240 AMX instrument skos:exactMatch OBI:0000514 Bruker AMX series NMR instrument semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400201 Capillary LC-NMR skos:exactMatch OBI:0000553 Bruker Capillary LC-NMR platform semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1000376 LC-NMR instrument skos:exactMatch OBI:0000503 Bruker LC-NMR platform semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1000377 LC-NMR/MS instrument skos:exactMatch OBI:0000582 Bruker LC-NMR/MS platform semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400199 Metabolic Profiler instrument skos:exactMatch OBI:0000632 Bruker Metabolic Profiler semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +NA NA skos:exactMatch OBI:0000613 Bruker SPE-NMR platform semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400283 continuous wave NMR instrument skos:exactMatch OBI:0000486 continuous wave NMR instrument semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400284 fourier transformation NMR instrument skos:exactMatch OBI:0000487 fourier transformation NMR instrument semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400226 JEOL NMR instrument skos:exactMatch OBI:0000600 JEOL NMR instrument semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400228 JNM-ECA Series FT NMR instrument skos:exactMatch OBI:0000641 JEOL ECA NMR spectrometer semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400227 JNM-ECX Series FT NMR instrument skos:exactMatch OBI:0000625 JEOL ECX NMR spectrometer semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400250 tecmag NMR instrument skos:exactMatch OBI:0000534 tecmag NMR instrument semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400234 Varian NMR instrument skos:exactMatch OBI:0000611 Varian NMR instrument semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400239 Varian GEMINI skos:exactMatch OBI:0000477 Varian GEMINI spectrometer semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400235 Varian MERCURY skos:exactMatch OBI:0000631 Varian MERCURY spectrometer semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1000397 Varian UnityInova instrument skos:exactMatch OBI:0000558 Varian UNITY INOVA spectrometer semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400237 Varian UNITY skos:exactMatch OBI:0000579 Varian UNITY spectrometer semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400238 Varian VXR skos:exactMatch OBI:0000524 Varian VXR spectrometer semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400130 magic angle spinning rotor skos:exactMatch OBI:0000523 magic angle spinning rotor semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400132 NMR sample tube skos:exactMatch OBI:0000578 NMR sample tube semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400015 NMR console skos:exactMatch OBI:0000499 NMR console semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400246 tecmag console skos:exactMatch OBI:0000599 tecmag NMR console semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400249 APOLLO console skos:exactMatch OBI:0000483 APOLLO console semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400247 DISCOVERY console skos:exactMatch OBI:0000513 DISCOVERY console semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400185 NMR magnet skos:exactMatch OBI:0000517 NMR magnet semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400186 Bruker NMR magnet skos:exactMatch OBI:0000597 Bruker NMR magnet semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400187 UltraShield skos:exactMatch OBI:0000567 Bruker UltraShield NMR magnet semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400190 UltraShield Plus skos:exactMatch OBI:0000530 Bruker UltraShield Plus NMR magnet semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400188 Ultrastabilized skos:exactMatch OBI:0000575 Bruker Ultrastabilized NMR magnet semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400189 US 2 skos:exactMatch OBI:0000467 Bruker US 2 NMR magnet semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400212 NMR sample holder skos:exactMatch OBI:0000484 NMR sample holder semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400211 Bruker MATCH skos:exactMatch OBI:0000612 Bruker MATCH tube holder system semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400204 NMR tube washing system skos:exactMatch OBI:0000498 NMR tube washing system semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400205 Bruker AutoClean skos:exactMatch OBI:0000475 Bruker AutoClean system semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400002 NMR autosampler skos:exactMatch OBI:0000555 autosampler semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400209 Bruker autosampler skos:exactMatch OBI:0000464 Bruker autosampler semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400210 B-ACS skos:exactMatch OBI:0000492 Bruker B-ACS system semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400206 Bruker BEST NMR skos:exactMatch OBI:0000591 Bruker BEST NMR system semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400203 NMR Case skos:exactMatch OBI:0000473 Bruker NMR Case sample changer semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400208 SampleJet skos:exactMatch OBI:0000624 Bruker SampleJet system semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 +http://nmrML.org/nmrCV#NMR:1400013 NMR acquisition computer skos:exactMatch OBI:0000636 acquisition computer semapv:ManualMappingCuration The mapping is based on lexical matching, introspection of OBI and detective work on issue trackers. Main reason for asserting skos:exactMatch is the fact that an author of nmrCV, Daniel Schober, is listed as the term editor of the OBI equivalents (see also: https://sourceforge.net/p/obi/mailman/message/20507660/ & https://sourceforge.net/p/obi/mailman/message/20621928/). 2024-08-29 orcid:0000-0002-1595-3213 http://nmrML.org/nmrCV 2.0 http://purl.obolibrary.org/obo/obi.owl http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl 0.95 \ No newline at end of file diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 381b01a..2dfeac5 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= a4c0ac9d9d7ac7b03403ce94c3d1d76c44d412b433490d312ed763a12e8e19f6 +CONFIG_HASH= 1ba644404ead28f12b159a84d638daf10791c394ce2f9060998152d134df9dcc # ---------------------------------------- @@ -159,7 +159,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = bfo ro omo chebi +IMPORTS = bfo ro omo iao obi chebi IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -376,6 +376,10 @@ $(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_terms_combine if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ $(ANNOTATE_CONVERT_FILE); fi +## Module for ontology: obi + +$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl + echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in nmrCV.Makefile!" && false ## Module for ontology: chebi $(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/chebi.owl $(IMPORTDIR)/chebi_terms_combined.txt @@ -427,7 +431,7 @@ mirror-bfo: | $(TMPDIR) .PHONY: mirror-ro .PRECIOUS: $(MIRRORDIR)/ro.owl mirror-ro: | $(TMPDIR) - curl -L $(OBOBASE)/ro.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \ + curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \ $(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl @@ -439,6 +443,22 @@ mirror-omo: | $(TMPDIR) $(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl +## ONTOLOGY: iao +.PHONY: mirror-iao +.PRECIOUS: $(MIRRORDIR)/iao.owl +mirror-iao: | $(TMPDIR) + curl -L $(OBOBASE)/iao.owl --create-dirs -o $(TMPDIR)/iao-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/iao-download.owl --base-iri $(OBOBASE)/IAO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: obi +.PHONY: mirror-obi +.PRECIOUS: $(MIRRORDIR)/obi.owl +mirror-obi: | $(TMPDIR) + curl -L $(OBOBASE)/obi.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(TMPDIR)/obi-download.owl --base-iri $(OBOBASE)/OBI --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl + + ## ONTOLOGY: chebi .PHONY: mirror-chebi .PRECIOUS: $(MIRRORDIR)/chebi.owl diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index c30f804..d1cd16c 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -6,6 +6,8 @@ + + \ No newline at end of file diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl new file mode 100644 index 0000000..28f7772 --- /dev/null +++ b/src/ontology/imports/iao_import.owl @@ -0,0 +1,466 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-08-21") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (definition) + +AnnotationAssertion( "definition"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition"@en) + +# Annotation Property: (editor note) + +AnnotationAssertion( "editor note"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "editor note"@en) + +# Annotation Property: (term editor) + +AnnotationAssertion( "term editor"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) +AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "term editor"@en) + +# Annotation Property: (definition source) + +AnnotationAssertion( "definition source"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition source"@en) + +# Annotation Property: (has obsolescence reason) + +AnnotationAssertion( "has obsolescence reason"@en) +AnnotationAssertion( "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification."@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "has obsolescence reason"@en) + +# Annotation Property: (term replaced by) + +AnnotationAssertion( "term replaced by"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) +AnnotationAssertion(rdfs:label "term replaced by"@en) + + +############################ +# Object Properties +############################ + +# Object Property: (is about) + +AnnotationAssertion( "This document is about information artifacts and their representations"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A (currently) primitive relation that relates an information artifact to an entity."@en) +AnnotationAssertion( "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic."@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) +AnnotationAssertion(rdfs:label "is about"@en) +ObjectPropertyDomain( ) + + + +############################ +# Classes +############################ + +# Class: (objective specification) + +AnnotationAssertion( "objective specification"@en) +AnnotationAssertion( "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved."@en) +AnnotationAssertion( "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\""@en) +AnnotationAssertion( "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that."@en) +AnnotationAssertion( "Answers the question, why did you do this experiment?"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Barry Smith"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Jennifer Fostel"@en) +AnnotationAssertion( "goal specification"@en) +AnnotationAssertion( "OBI Plan and Planned Process/Roles Branch"@en) +AnnotationAssertion( "OBI_0000217"@en) +AnnotationAssertion(rdfs:label "objective specification"@en) +SubClassOf( ) + +# Class: (action specification) + +AnnotationAssertion( "Pour the contents of flask 1 into flask 2"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity that describes an action the bearer will take."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "OBI Plan and Planned Process branch"@en) +AnnotationAssertion(rdfs:label "action specification"@en) +SubClassOf( ) + +# Class: (data item) + +AnnotationAssertion( "data item"@en) +AnnotationAssertion( "Data items include counts of things, analyte concentrations, and statistical summaries."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) +AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) +AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) +AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief"@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Jonathan Rees"@en) +AnnotationAssertion( "data"@en) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: (information content entity) + +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion( "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A generically dependent continuant that is about some thing."@en) +AnnotationAssertion( "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)."@en) +AnnotationAssertion( "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity."@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000142"@en) +AnnotationAssertion(rdfs:label "information content entity"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (directive information entity) + +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en) +AnnotationAssertion( "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) +AnnotationAssertion( "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it."@en) +AnnotationAssertion( "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO"@en) +AnnotationAssertion( "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion(rdfs:label "directive information entity"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "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."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (data about an ontology part) + +AnnotationAssertion( "data about an ontology part"@en) +AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "data about an ontology part"@en) +SubClassOf( ) + +# Class: (plan specification) + +AnnotationAssertion( "plan specification"@en) +AnnotationAssertion( "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en) +AnnotationAssertion( "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) +AnnotationAssertion( "2014-03-31: A plan specification can have other parts, such as conditional specifications."@en) +AnnotationAssertion( "2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231."@en) +AnnotationAssertion( "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Clint Dowland"@en) +AnnotationAssertion( "OBI Plan and Planned Process branch"@en) +AnnotationAssertion( "OBI_0000344"@en) +AnnotationAssertion(rdfs:comment "2/3/2009 Comment from OBI review. + +Action specification not well enough specified. +Conditional specification not well enough specified. +Question whether all plan specifications have objective specifications. + +Request that IAO either clarify these or change definitions not to use them"@en) +AnnotationAssertion(rdfs:label "plan specification"@en) +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (obsolescence reason specification) + +AnnotationAssertion( "obsolescence reason specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The reason for which a term has been deprecated. 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."@en) +AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (denotator type) + +AnnotationAssertion( "denotator type"@en) +AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) +AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) +AnnotationAssertion(rdfs:label "denotator type"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + + +############################ +# Named Individuals +############################ + +# Individual: (example to be eventually removed) + +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) +ClassAssertion( ) + +# Individual: (failed exploratory term) + +AnnotationAssertion( "failed exploratory term"@en) +AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "failed exploratory term"@en) +ClassAssertion( ) + +# Individual: (metadata complete) + +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) +ClassAssertion( ) + +# Individual: (organizational term) + +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion(rdfs:label "organizational term"@en) +ClassAssertion( ) + +# Individual: (ready for release) + +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) +ClassAssertion( ) + +# Individual: (metadata incomplete) + +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) +ClassAssertion( ) + +# Individual: (uncurated) + +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) +ClassAssertion( ) + +# Individual: (pending final vetting) + +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) +ClassAssertion( ) + +# Individual: (placeholder removed) + +AnnotationAssertion( "placeholder removed"@en) +AnnotationAssertion(rdfs:label "placeholder removed"@en) +ClassAssertion( ) + +# Individual: (terms merged) + +AnnotationAssertion( "terms merged"@en) +AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(rdfs:label "terms merged"@en) +ClassAssertion( ) + +# Individual: (term imported) + +AnnotationAssertion( "term imported"@en) +AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(rdfs:label "term imported"@en) +ClassAssertion( ) + +# Individual: (term split) + +AnnotationAssertion( "term split"@en) +AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(rdfs:label "term split"@en) +ClassAssertion( ) + +# Individual: (universal) + +AnnotationAssertion( "universal"@en) +AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) +AnnotationAssertion(rdfs:label "universal"@en) +ClassAssertion( ) + +# Individual: (defined class) + +AnnotationAssertion( "defined class"@en) +AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) +AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "defined class"@en) +ClassAssertion( ) + +# Individual: (named class expression) + +AnnotationAssertion( "named class expression"@en) +AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) +AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "named class expression"@en) +ClassAssertion( ) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) +ClassAssertion( ) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) +ClassAssertion( ) + + +) \ No newline at end of file diff --git a/src/ontology/imports/iao_terms.txt b/src/ontology/imports/iao_terms.txt new file mode 100644 index 0000000..fe0378b --- /dev/null +++ b/src/ontology/imports/iao_terms.txt @@ -0,0 +1,3 @@ +IAO:0000033 # 'directive information entity' + IAO:0000005 # 'objective specification' + IAO:0000104 # 'plan specification' \ No newline at end of file diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl new file mode 100644 index 0000000..6afe9f9 --- /dev/null +++ b/src/ontology/imports/obi_import.owl @@ -0,0 +1,497 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-08-29") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(Datatype(xsd:date)) + +############################ +# Object Properties +############################ + +# Object Property: (has_specified_input) + +AnnotationAssertion( "has_specified_input") +AnnotationAssertion( "see is_input_of example_of_usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is_specified_input_of"@en) +AnnotationAssertion( "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Coutot") +AnnotationAssertion(rdfs:label "has_specified_input"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (is_specified_input_of) + +AnnotationAssertion( "is_specified_input_of") +AnnotationAssertion( "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"@en) +AnnotationAssertion( ) +AnnotationAssertion( "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."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "is_specified_input_of"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has_specified_output) + +AnnotationAssertion( "has_specified_output") +AnnotationAssertion( ) +AnnotationAssertion( "The inverse property of is_specified_output_of"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Larry Hunter") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion(rdfs:label "has_specified_output"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (is_manufactured_by) + +AnnotationAssertion( "is_manufactured_by"@en) +AnnotationAssertion( "http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)"@en) +AnnotationAssertion( ) +AnnotationAssertion( "c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the \"Manufacturer Role\", and those people/and or machines were members or of directed by the organization to do this."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Liju Fan"@en) +AnnotationAssertion( "has_make"@en) +AnnotationAssertion( "has_manufacturer"@en) +AnnotationAssertion(rdfs:label "is_manufactured_by"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is_specified_output_of) + +AnnotationAssertion( "is_specified_output_of") +AnnotationAssertion( ) +AnnotationAssertion( "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."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Bjoern Peters") +AnnotationAssertion(rdfs:label "is_specified_output_of"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (achieves_planned_objective) + +AnnotationAssertion( "achieves_planned_objective") +AnnotationAssertion( "A cell sorting process achieves the objective specification 'material separation objective'") +AnnotationAssertion( ) +AnnotationAssertion( "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.") +AnnotationAssertion( "BP, AR, PPPB branch") +AnnotationAssertion( "PPPB branch derived") +AnnotationAssertion( "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch") +AnnotationAssertion(rdfs:label "achieves_planned_objective") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (objective_achieved_by) + +AnnotationAssertion( "objective_achieved_by") +AnnotationAssertion( ) +AnnotationAssertion( "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.") +AnnotationAssertion( "OBI") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "objective_achieved_by") +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + + + +############################ +# Classes +############################ + +# Class: (planned process) + +AnnotationAssertion( "planned process") +AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") +AnnotationAssertion( ) +AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) +AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") +AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "branch derived") +AnnotationAssertion( "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)"@en) +AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") +AnnotationAssertion(rdfs:label "planned process"@en) +EquivalentClasses( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (processed material) + +AnnotationAssertion( "processed material"@en) +AnnotationAssertion( "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Is a material entity that is created or changed during material processing."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "processed material"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (material processing) + +AnnotationAssertion( "material processing") +AnnotationAssertion( "A cell lysis, production of a cloning vector, creating a buffer.") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process which results in physical changes in a specified input material"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca Serra") +AnnotationAssertion( "material transformation"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion(rdfs:label "material processing"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (organization) + +AnnotationAssertion( "organization"@en) +AnnotationAssertion( "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members."@en) +AnnotationAssertion( "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: + +1) there are organization_member_roles (president, treasurer, branch +editor), with individual persons as bearers + +2) there are organization_roles (employer, owner, vendor, patent holder) + +3) an organization has a charter / rules / bylaws, which specify what roles +there are, how they should be realized, and how to modify the +charter/rules/bylaws themselves. + +It is debatable what the organization itself is (some kind of dependent +continuant or an aggregate of people). This also determines who/what the +bearer of organization_roles' are. My personal favorite is still to define +organization as a kind of 'legal entity', but thinking it through leads to +all kinds of questions that are clearly outside the scope of OBI. + +Interestingly enough, it does not seem to matter much where we place +organization itself, as long as we can subclass it (University, Corporation, +Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, +W3C, University of Oklahoma), and have it play roles. + +This leads to my proposal: We define organization through the statements 1 - +3 above, but without an 'is a' statement for now. We can leave it in its +current place in the is_a hierarchy (material entity) or move it up to +'continuant'. We leave further clarifications to BFO, and close this issue +for now."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg") +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "PERSON: Susanna Sansone") +AnnotationAssertion( "GROUP: OBI") +AnnotationAssertion(rdfs:label "organization"@en) +SubClassOf( ) + +# Class: (contain function) + +AnnotationAssertion( "contain function"@en) +AnnotationAssertion( "A syringe, a beaker") +AnnotationAssertion( ) +AnnotationAssertion( "A contain function is a function to constrain a material entities location in space"@en) +AnnotationAssertion( "Bill Bug") +AnnotationAssertion( "Daniel Schober") +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "Melanie Courtot") +AnnotationAssertion(rdfs:label "contain function"@en) +SubClassOf( ) + +# Class: (information processor function) + +AnnotationAssertion( "information processor function"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process."@en) +AnnotationAssertion( "Frank Gibson") +AnnotationAssertion( "data processor function"@en) +AnnotationAssertion(rdfs:label "information processor function"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (measure function) + +AnnotationAssertion( "measure function"@en) +AnnotationAssertion( "A glucometer measures blood glucose concentration, the glucometer has a measure function.") +AnnotationAssertion( ) +AnnotationAssertion( "Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference."@en) +AnnotationAssertion( "PERSON: Daniel Schober") +AnnotationAssertion( "PERSON: Helen Parkinson") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON:Frank Gibson") +AnnotationAssertion(rdfs:label "measure function"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (consume data function) + +AnnotationAssertion( "consume data function"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data."@en) +AnnotationAssertion( "PERSON: Daniel Schober") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion(rdfs:label "consume data function"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (material transformation objective) + +AnnotationAssertion( "material transformation objective") +AnnotationAssertion( "The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.") +AnnotationAssertion( ) +AnnotationAssertion( "an objective specifiction that creates an specific output object from input materials."@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "artifact creation objective"@en) +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "material transformation objective"@en) +SubClassOf( ) + +# Class: (manufacturing) + +AnnotationAssertion( "manufacturing") +AnnotationAssertion( ) +AnnotationAssertion( "A planned process with the objective to produce a processed material which will have a function for future use."@en) +AnnotationAssertion( "This includes a single scientist making a processed material for personal use."@en) +AnnotationAssertion( "A person or organization (having manufacturer role) is a participant in this process") +AnnotationAssertion( "Manufacturing implies reproducibility and responsibility AR") +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "manufacturing"@en) +EquivalentClasses( ObjectSomeValuesFrom( )) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (manufacturing objective) + +AnnotationAssertion( "manufacturing objective") +AnnotationAssertion( ) +AnnotationAssertion( "is the objective to manufacture a material of a certain function (device)"@en) +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion( "PERSON: Frank Gibson") +AnnotationAssertion( "PERSON: Jennifer Fostel") +AnnotationAssertion( "PERSON: Melanie Courtot") +AnnotationAssertion( "PERSON: Philippe Rocca-Serra") +AnnotationAssertion( "GROUP: OBI PlanAndPlannedProcess Branch") +AnnotationAssertion(rdfs:label "manufacturing objective"@en) +SubClassOf( ) + +# Class: (vial) + +AnnotationAssertion( "vial") +AnnotationAssertion( ) +AnnotationAssertion( "A container made from solid material and primarily used for holding liquid.") +AnnotationAssertion( "https://orcid.org/0000-0002-8844-9165") +AnnotationAssertion( "https://en.wikipedia.org/wiki/Vial") +AnnotationAssertion(rdfs:label "vial") +SubClassOf( ) + +# Class: (manufacturer role) + +AnnotationAssertion( "manufacturer role") +AnnotationAssertion( "With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.") +AnnotationAssertion( ) +AnnotationAssertion( "Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.") +AnnotationAssertion( "GROUP: Role Branch") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "manufacturer role") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) + +# Class: (measurement device) + +AnnotationAssertion( "measurement device") +AnnotationAssertion( "A ruler, a microarray scanner, a Geiger counter.") +AnnotationAssertion( ) +AnnotationAssertion( "A device in which a measure function inheres.") +AnnotationAssertion( "GROUP:OBI Philly workshop") +AnnotationAssertion( "OBI") +AnnotationAssertion(rdfs:label "measurement device") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (manufacturer) + +AnnotationAssertion( "manufacturer") +AnnotationAssertion( ) +AnnotationAssertion( "A person or organization that has a manufacturer role.") +AnnotationAssertion(rdfs:label "manufacturer") +EquivalentClasses( ObjectIntersectionOf(ObjectUnionOf( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (test tube) + +AnnotationAssertion( "test tube") +AnnotationAssertion( ) +AnnotationAssertion( "A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "collection tube") +AnnotationAssertion( "sample tube") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Test_tube") +AnnotationAssertion(rdfs:label "test tube") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (container) + +AnnotationAssertion( "container") +AnnotationAssertion( ) +AnnotationAssertion( "A device that can be used to restrict the location of material entities over time") +AnnotationAssertion( "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)") +AnnotationAssertion( "PERSON: Bjoern Peters") +AnnotationAssertion(rdfs:label "container") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (device) + +AnnotationAssertion( "device") +AnnotationAssertion( "A voltmeter is a measurement device which is intended to perform some measure function.") +AnnotationAssertion( "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.") +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.") +AnnotationAssertion( "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.") +AnnotationAssertion( "PERSON: Helen Parkinson") +AnnotationAssertion( "instrument") +AnnotationAssertion( "OBI development call 2012-12-17.") +AnnotationAssertion(rdfs:label "device") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (organism) + +AnnotationAssertion( "organism"@en) +AnnotationAssertion( "animal"@en) +AnnotationAssertion( "fungus"@en) +AnnotationAssertion( "plant"@en) +AnnotationAssertion( "virus"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) +AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") +AnnotationAssertion( "13-02-2009: +OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. +This issue is outside the scope of OBI.") +AnnotationAssertion( "GROUP: OBI Biomaterial Branch") +AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) +AnnotationAssertion(rdfs:label "organism"@en) +SubClassOf( ) + +# Class: (computer) + +AnnotationAssertion( "computer") +AnnotationAssertion( "Apple PowerBook, Dell OptiPlex") +AnnotationAssertion( ) +AnnotationAssertion( "A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.") +AnnotationAssertion( "Melanie Courtot") +AnnotationAssertion( "Trish Whetzel") +AnnotationAssertion( "http://en.wikipedia.org/wiki/Computer") +AnnotationAssertion(rdfs:label "computer") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + + +) \ No newline at end of file diff --git a/src/ontology/imports/obi_remove_list.txt b/src/ontology/imports/obi_remove_list.txt new file mode 100644 index 0000000..65bc2db --- /dev/null +++ b/src/ontology/imports/obi_remove_list.txt @@ -0,0 +1,34 @@ +OBI:0200000 # 'data transformation' +OBI:0200166 # 'data transformation objective' +OBI:0200111 # 'data visualization' +OBI:0000659 # 'specimen collection process' +OBI:0100051 # specimen +OBI:0000953 # 'processed specimen' +OBI:0000112 # 'specimen role' +OBI:0002076 # 'collection of specimens' +OBI:0000684 # 'specimen collection objective' +OBI:0001933 # 'value specification' +OBI:0000017 # 'regulatory role' +OBI:0000947 # 'service provider role' +OBI:0002989 # 'material supplier' +OBI:0000450 # 'regulatory agency' +IAO:0000009 +IAO:0000010 +IAO:0000027 +IAO:0000030 +IAO:0000037 +IAO:0000038 +IAO:0000064 +IAO:0000078 +IAO:0000098 +IAO:0000100 +IAO:0000101 +IAO:0000179 +IAO:0000180 +IAO:0000183 +IAO:0000184 +IAO:0000310 +NCBITaxon:10239 +NCBITaxon:2 +NCBITaxon:2157 +NCBITaxon:2759 \ No newline at end of file diff --git a/src/ontology/imports/obi_terms.txt b/src/ontology/imports/obi_terms.txt new file mode 100644 index 0000000..0d58211 --- /dev/null +++ b/src/ontology/imports/obi_terms.txt @@ -0,0 +1,11 @@ +OBI:0000835 # manufacturer +OBI:0100026 # organism +NCBITaxon:9606 # Homo sapiens +OBI:0000245 # organization +OBI:0000571 # 'manufacturer role' +OBI:0000011 # planned process +OBI:0000457 # manufacturing +OBI:0000832 # 'measurement device' +OBI:0400107 # computer +OBI:0000836 # test tube +OBI:0000304 # is_manufactured_by \ No newline at end of file diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 4b26ca5..6902244 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,15 +7,14 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-02-20") + +Annotation( ) +Annotation(owl:versionInfo "2024-08-26") Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -23,124 +22,28 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -150,113 +53,35 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty(rdfs:comment)) -Declaration(AnnotationProperty(rdfs:label)) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) ############################ # Annotation Properties ############################ -# Annotation Property: (definition) - -AnnotationAssertion( "definition"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) -AnnotationAssertion( "2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "definition"@en) -AnnotationAssertion(rdfs:label "definition") - -# Annotation Property: (term editor) - -AnnotationAssertion( "term editor"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) -AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "term editor"@en) - -# Annotation Property: (definition source) - -AnnotationAssertion( "definition source"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "definition source"@en) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: (is a defining property chain axiom) - -AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL") -AnnotationAssertion(rdfs:label "is a defining property chain axiom") - # Annotation Property: (is a defining property chain axiom where second argument is reflexive) AnnotationAssertion( "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.") @@ -282,32 +107,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (has_broad_synonym) - -AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") -AnnotationAssertion(rdfs:label "has broad synonym"@en) -AnnotationAssertion(rdfs:label "has_broad_synonym") -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") - -# Annotation Property: (database_cross_reference) - -AnnotationAssertion(rdfs:label "database_cross_reference") - -# Annotation Property: (has exact synonym) - -AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") -AnnotationAssertion(rdfs:label "has exact synonym"@en) -AnnotationAssertion(rdfs:label "has_exact_synonym") -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") - -# Annotation Property: (has_obo_format_version) - -AnnotationAssertion(rdfs:label "has_obo_format_version") - ############################ # Object Properties @@ -339,7 +138,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "part of"@en) -AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) @@ -366,36 +164,37 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has part"@en) -AnnotationAssertion(rdfs:label "has part") SubObjectPropertyOf( ) TransitiveObjectProperty() -# Object Property: (preceded by) - -AnnotationAssertion( "preceded by"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."@en) -AnnotationAssertion( "is preceded by"@en) -AnnotationAssertion( "preceded_by"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "preceded by"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (precedes) - -AnnotationAssertion( "precedes"@en) -AnnotationAssertion( "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."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "precedes"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) +# Object Property: (realized in) + +AnnotationAssertion( "realized in"@en) +AnnotationAssertion( "this disease is realized in this disease course"@en) +AnnotationAssertion( "this fragility is realized in this shattering"@en) +AnnotationAssertion( "this investigator role is realized in this investigation"@en) +AnnotationAssertion( "is realized by"@en) +AnnotationAssertion( "realized_in"@en) +AnnotationAssertion( "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) +AnnotationAssertion(rdfs:comment "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realized in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (realizes) + +AnnotationAssertion( "realizes"@en) +AnnotationAssertion( "this disease course realizes this disease"@en) +AnnotationAssertion( "this investigation realizes this investigator role"@en) +AnnotationAssertion( "this shattering realizes this fragility"@en) +AnnotationAssertion( "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) +AnnotationAssertion(rdfs:comment "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) # Object Property: (characteristic of) @@ -422,8 +221,6 @@ AnnotationAssertion( "is bearer of"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has characteristic"@en) -AnnotationAssertion(rdfs:label "has characteristic") -AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -451,11 +248,28 @@ AnnotationAssertion( "has_participant"@en) AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label "has participant"@en) -AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) -ObjectPropertyDomain( ) ObjectPropertyRange( ) +# Object Property: (is concretized as) + +AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) +AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) +AnnotationAssertion( "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) +AnnotationAssertion(rdfs:label "is concretized as"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (concretizes) + +AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) +AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) +AnnotationAssertion( "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) +AnnotationAssertion(rdfs:label "concretizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (function of) AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) @@ -469,18 +283,6 @@ SubObjectPropertyOf( ) ObjectPropertyDomain( ) -# Object Property: (quality of) - -AnnotationAssertion( "this red color is a quality of this apple"@en) -AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) -AnnotationAssertion( "is quality of"@en) -AnnotationAssertion( "quality_of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "quality of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - # Object Property: (role of) AnnotationAssertion( "this investigator role is a role of this person"@en) @@ -504,16 +306,6 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (has quality) - -AnnotationAssertion( "this apple has quality this red color"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) -AnnotationAssertion( "has_quality"@en) -AnnotationAssertion(rdfs:label "has quality"@en) -SubObjectPropertyOf( ) -ObjectPropertyRange( ) - # Object Property: (has role) AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) @@ -525,137 +317,6 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (has disposition) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has disposition"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (disposition of) - -AnnotationAssertion( "inverse of has disposition") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "disposition of"@en) -SubObjectPropertyOf( ) - -# Object Property: (has regulatory component activity) - -AnnotationAssertion( "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has negative regulatory component activity) - -AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") -AnnotationAssertion(rdfs:label "has negative regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has positive regulatory component activity) - -AnnotationAssertion( "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:31:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.") -AnnotationAssertion(rdfs:label "has positive regulatory component activity") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has component activity) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:44:33Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.") -AnnotationAssertion(rdfs:label "has component activity") -SubObjectPropertyOf( ) - -# Object Property: (has component process) - -AnnotationAssertion( "w 'has process component' p if p and w are processes, 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.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-05-24T09:49:21Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "has component process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulated by) - -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:24Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( ) rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.") -AnnotationAssertion(rdfs:label "directly regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly negatively regulated by) - -AnnotationAssertion(Annotation( ) "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:38Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly negatively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (directly positively regulated by) - -AnnotationAssertion(Annotation( ) "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-17T13:52:47Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "directly positively regulated by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has effector activity) - -AnnotationAssertion(Annotation( ) "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-09-22T14:14:36Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:comment "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.") -AnnotationAssertion(rdfs:label "has effector activity") -SubObjectPropertyOf( ) -FunctionalObjectProperty() - -# Object Property: (ends after) - -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) -AnnotationAssertion(rdfs:label "ends after"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately preceded by) - -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "starts_at_end_of") -AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately preceded by"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately precedes) - -AnnotationAssertion( ) -AnnotationAssertion( "David Osumi-Sutherland") -AnnotationAssertion( "ends_at_start_of") -AnnotationAssertion( "meets") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately precedes"@en) -SubObjectPropertyOf( ) - # Object Property: (overlaps) AnnotationAssertion( ) @@ -669,169 +330,6 @@ AnnotationAssertion(rdfs:label "over SubObjectPropertyOf( ) SymmetricObjectProperty() -# Object Property: (has component) - -AnnotationAssertion( ) -AnnotationAssertion( "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.") -AnnotationAssertion( "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.") -AnnotationAssertion( "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit."@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has component"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (regulates) - -AnnotationAssertion( "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "GO") -AnnotationAssertion( "Regulation precludes parthood; the regulatory process may not be within the regulated process.") -AnnotationAssertion( "regulates (processual)") -AnnotationAssertion( "false"^^xsd:boolean) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulates) - -AnnotationAssertion( "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "negatively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (positively regulates) - -AnnotationAssertion( "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "positively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (capable of) - -AnnotationAssertion( "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)") -AnnotationAssertion( "osteoclast SubClassOf 'capable of' some 'bone resorption'") -AnnotationAssertion( "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. ") -AnnotationAssertion( ) -AnnotationAssertion( "has function realized in") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable of part of) - -AnnotationAssertion( "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.") -AnnotationAssertion( ) -AnnotationAssertion( "has function in") -AnnotationAssertion(rdfs:label "capable of part of"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (temporally related to) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.") -AnnotationAssertion( "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^xsd:anyURI) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.") -AnnotationAssertion(rdfs:label "temporally related to"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has input) - -AnnotationAssertion( ) -AnnotationAssertion( "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.") -AnnotationAssertion( ) -AnnotationAssertion( "consumes") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has input"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (acts upstream of) - -AnnotationAssertion( "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") -AnnotationAssertion( "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within) - -AnnotationAssertion( "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.") -AnnotationAssertion( "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.") -AnnotationAssertion( "affects") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of, positive effect) - -AnnotationAssertion( "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y") -AnnotationAssertion(rdfs:label "causally upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of, negative effect) - -AnnotationAssertion( "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - # Object Property: (characteristic of part of) AnnotationAssertion( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") @@ -852,346 +350,25 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mereotopologically related to"@en) -# Object Property: (enables) - -AnnotationAssertion( "a particular instances of akt-2 enables some instance of protein kinase activity") -AnnotationAssertion( "c enables p iff c is capable of p and c acts to execute p.") -AnnotationAssertion( ) -AnnotationAssertion( "catalyzes") -AnnotationAssertion( "executes") -AnnotationAssertion( "has") -AnnotationAssertion( "is catalyzing") -AnnotationAssertion( "is executing") -AnnotationAssertion( "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enables"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enables"^^xsd:anyURI) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (functionally related to) - -AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") -AnnotationAssertion( ) -AnnotationAssertion( "This is a grouping relation that collects relations used for the purpose of connecting structure and function") -AnnotationAssertion(rdfs:label "functionally related to"@en) - -# Object Property: (part of structure that is capable of) - -AnnotationAssertion( "this relation holds between c and p when c is part of some c', and c' is capable of p.") -AnnotationAssertion( ) -AnnotationAssertion( "false"^^xsd:boolean) -AnnotationAssertion(rdfs:label "part of structure that is capable of"@en) -SubObjectPropertyOf( ) - -# Object Property: (involved in) - -AnnotationAssertion( "c involved_in p if and only if c enables some process p', and p' is part of p") -AnnotationAssertion( ) -AnnotationAssertion( "actively involved in") -AnnotationAssertion( "enables part of") -AnnotationAssertion(rdfs:label "involved in"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Involved_in"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (enabled by) - -AnnotationAssertion( "inverse of enables") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enabled by"@en) -AnnotationAssertion(rdfs:label "enabled by") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (regulated by) - -AnnotationAssertion( "inverse of regulates") -AnnotationAssertion( ) -AnnotationAssertion( "regulated by (processual)") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulated by"@en) -SubObjectPropertyOf( ) -TransitiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (negatively regulated by) - -AnnotationAssertion( "inverse of negatively regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulated by"@en) -SubObjectPropertyOf( ) - -# Object Property: (positively regulated by) - -AnnotationAssertion( "inverse of positively regulates") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulated by"@en) -SubObjectPropertyOf( ) - -# Object Property: (input of) - -AnnotationAssertion( "inverse of has input") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "input of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally downstream of) - -AnnotationAssertion( ) -AnnotationAssertion( "inverse of upstream of") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (immediately causally downstream of) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (indirectly positively regulates) - -AnnotationAssertion( "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly activates") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "indirectly positively regulates"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (indirectly negatively regulates) - -AnnotationAssertion( "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "indirectly inhibits") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "indirectly negatively regulates"@en) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (causally related to) - -AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Causality") "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.") -AnnotationAssertion( "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. - -To define causal relations in an activity-flow type network, we make use of 3 primitives: - - * Temporal: how do the intervals of the two occurrents relate? - * Is the causal relation regulatory? - * Is the influence positive or negative? - -The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. - -For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. - -For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. - -Each of these 3 primitives can be composed to yield a cross-product of different relation types.") -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label "causally related to"@en) - -# Object Property: (causally upstream of) - -AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (immediately causally upstream of) - -AnnotationAssertion( "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within) - -AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") -AnnotationAssertion( "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2") -AnnotationAssertion( ) -AnnotationAssertion( "influences (processual)") -AnnotationAssertion( "affects") -AnnotationAssertion(rdfs:label "causally upstream of or within") -SubObjectPropertyOf( ) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (causally downstream of or within) - -AnnotationAssertion( "inverse of causally upstream of or within") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causally downstream of or within") -SubObjectPropertyOf( ) -TransitiveObjectProperty() - -# Object Property: (involved in regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' regulates some p") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (involved in positive regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' positively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in positive regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in negative regulation of) - -AnnotationAssertion( "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "involved in negative regulation of") -SubObjectPropertyOf( ) - -# Object Property: (involved in or involved in regulation of) - -AnnotationAssertion( "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p") -AnnotationAssertion( "OWL does not allow defining object properties via a Union") -AnnotationAssertion( ) -AnnotationAssertion( "involved in or reguates") -AnnotationAssertion(rdfs:label "involved in or involved in regulation of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (interacts with) - -AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) -AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") -AnnotationAssertion( ) -AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") -AnnotationAssertion( "in pairwise interaction with") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "interacts with") -AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0914"^^xsd:anyURI) -SymmetricObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (molecularly interacts with) - -AnnotationAssertion( "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.") -AnnotationAssertion( ) -AnnotationAssertion( "binds") -AnnotationAssertion( "molecularly binds with") -AnnotationAssertion(rdfs:label "molecularly interacts with") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion( "http://purl.obolibrary.org/obo/MI_0915"^^xsd:anyURI) -SubObjectPropertyOf( ) -SymmetricObjectProperty() - -# Object Property: (phosphorylates) - -AnnotationAssertion( "Axiomatization to GO to be added later") -AnnotationAssertion( ) -AnnotationAssertion( "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.") -AnnotationAssertion(rdfs:label "phosphorylates") -SubObjectPropertyOf( ) - -# Object Property: (directly regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "molecularly controls") -AnnotationAssertion(rdfs:label "directly regulates activity of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly negatively regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly inhibits") -AnnotationAssertion( "molecularly decreases activity of") -AnnotationAssertion(rdfs:label "directly negatively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly positively regulates activity of) - -AnnotationAssertion( "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly activates") -AnnotationAssertion( "molecularly increases activity of") -AnnotationAssertion(rdfs:label "directly positively regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (helper property (not for use in curation)) - -AnnotationAssertion( ) -AnnotationAssertion( "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.") -AnnotationAssertion(rdfs:label "helper property (not for use in curation)") - -# Object Property: (is kinase activity) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "is kinase activity") -SubObjectPropertyOf( ) - -# Object Property: (causal agent in process) - -AnnotationAssertion( "A relationship between a material entity and a process where the material entity has some causal role that influences the process") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causal agent in process") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (causal relation between processes) - -AnnotationAssertion( "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label "causal relation between processes") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) +# Object Property: (member of) + +AnnotationAssertion( "An organism that is a member of a population of organisms") +AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") +AnnotationAssertion( "is member of") +AnnotationAssertion( "member part of") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "member of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has member) + +AnnotationAssertion( "has member is a mereological relation between a collection and an item.") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has member"@en) +SubObjectPropertyOf( ) # Object Property: (depends on) @@ -1199,581 +376,55 @@ AnnotationAssertion( "depends on") AnnotationAssertion(rdfs:seeAlso ) -# Object Property: (causal relation between entities) - -AnnotationAssertion( "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion(rdfs:label "causal relation between entities") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (causally influenced by) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influenced by (entity-centric)") -AnnotationAssertion(rdfs:label "causally influenced by") -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (interaction relation helper property) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "interaction relation helper property") -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (molecular interaction relation helper property) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "molecular interaction relation helper property") -SubObjectPropertyOf( ) - -# Object Property: (causally influences) - -AnnotationAssertion( "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "causally influences (entity-centric)") -AnnotationAssertion(rdfs:label "causally influences") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (directly regulates) - -AnnotationAssertion( "p directly regulates q iff p is immediately causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "directly regulates (processual)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly regulates") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (has part structure that is capable of) - -AnnotationAssertion( "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'") -AnnotationAssertion( "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has part structure that is capable of") -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causal relation between material entity and a process) - -AnnotationAssertion( "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.") -AnnotationAssertion( "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "causal relation between material entity and a process") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (capable of regulating) - -AnnotationAssertion( "pyrethroid -> growth") -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a regulates p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of negatively regulating) - -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of negatively regulating") -SubObjectPropertyOf( ) - -# Object Property: (capable of positively regulating) - -AnnotationAssertion( "renin -> arteriolar smooth muscle contraction") -AnnotationAssertion( "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "capable of positively regulating") -SubObjectPropertyOf( ) - -# Object Property: (process has causal agent) - -AnnotationAssertion( "Inverse of 'causal agent in process'") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "process has causal agent") -SubObjectPropertyOf( ) - -# Object Property: (directly positively regulates) - -AnnotationAssertion( "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly positively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly positively regulates") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_positively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (directly negatively regulates) - -AnnotationAssertion( "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "directly negatively regulates (process to process)") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "directly negatively regulates") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (enables subfunction) - -AnnotationAssertion( "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.") -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-25T23:20:13Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "enables subfunction") -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:30Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:49:51Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of or within, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, positive effect) - -AnnotationAssertion( "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:14Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, positive effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (acts upstream of, negative effect) - -AnnotationAssertion( "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-01-26T23:53:22Z"^^xsd:dateTime) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acts upstream of, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, negative effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:05Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "causally upstream of or within, negative effect") -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect"^^xsd:anyURI) -SubObjectPropertyOf( ) - -# Object Property: (causally upstream of or within, positive effect) - -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2018-03-13T23:55:19Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") -AnnotationAssertion(rdfs:seeAlso ) -SubObjectPropertyOf( ) - -# Object Property: (regulates activity of) - -AnnotationAssertion( "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates activity of") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (indirectly causally upstream of) - -AnnotationAssertion( "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:07:17Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly causally upstream of"@en) -SubObjectPropertyOf( ) - -# Object Property: (indirectly regulates) - -AnnotationAssertion( "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.") -AnnotationAssertion( ) -AnnotationAssertion( "2022-09-26T06:08:01Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "indirectly regulates"@en) -SubObjectPropertyOf( ) -SubObjectPropertyOf( ) - -# Object Property: (device utilizes material) - -AnnotationAssertion( "A diagnostic testing device utilizes a specimen.") -AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") -AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") -AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) -AnnotationAssertion( "utilizes") -AnnotationAssertion(rdfs:label "device utilizes material"@en) - -# Object Property: (regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "regulates characteristic") -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (positively regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "positively regulates characteristic") -SubObjectPropertyOf( ) - -# Object Property: (negatively regulates characteristic) - -AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "negatively regulates characteristic") -SubObjectPropertyOf( ) +# Object Property: (generically depends on) +AnnotationAssertion( "Genetic information generically depend on molecules of DNA.") +AnnotationAssertion( "The novel *War and Peace* generically depends on this copy of the novel.") +AnnotationAssertion( "The pattern shared by chess boards generically depends on any chess board.") +AnnotationAssertion( "The score of a symphony g-depends on a copy of the score.") +AnnotationAssertion( "This pdf file generically depends on this server.") +AnnotationAssertion( "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.") +AnnotationAssertion( "[072-ISO]") +AnnotationAssertion( "g-depends on") +AnnotationAssertion(rdfs:label "generically depends on") +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) +# Object Property: (is carrier of) -############################ -# Classes -############################ - -# Class: (continuant) - -AnnotationAssertion( "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."@en) -AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) +AnnotationAssertion( "Molecules of DNA are carriers of genetic information.") +AnnotationAssertion( "This copy of *War and Peace* is carrier of the novel written by Tolstoy.") +AnnotationAssertion( "This hard drive is carrier of these data items.") +AnnotationAssertion( "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*") +AnnotationAssertion( "[072-ISO]") +AnnotationAssertion(rdfs:label "is carrier of"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) -# Class: (occurrent) - -AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) -AnnotationAssertion(rdfs:label "occurrent"@en) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (independent continuant) - -AnnotationAssertion( "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) -AnnotationAssertion(rdfs:comment "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) -AnnotationAssertion(rdfs:label "independent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (process) - -AnnotationAssertion( "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) -AnnotationAssertion(rdfs:comment "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) -AnnotationAssertion(rdfs:label "process"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (disposition) - -AnnotationAssertion(rdfs:label "disposition"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (realizable entity) - -AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) -AnnotationAssertion(rdfs:label "realizable"@en) -AnnotationAssertion(rdfs:label "realizable entity"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (quality) - -AnnotationAssertion(rdfs:label "quality"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (characteristic) - -AnnotationAssertion( "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])"@en) -AnnotationAssertion(rdfs:comment "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) -AnnotationAssertion(rdfs:label "characteristic"@en) -AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) -AnnotationAssertion(rdfs:seeAlso "https://github.com/OBOFoundry/COB/issues/65") -AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) -DisjointClasses( ) - -# Class: (role) - -AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) -AnnotationAssertion(rdfs:label "role"@en) -SubClassOf( ) - -# Class: (generically dependent continuant) - -AnnotationAssertion( "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) -AnnotationAssertion(rdfs:comment "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) -AnnotationAssertion(rdfs:label "generically dependent continuant"@en) -SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (function) - -AnnotationAssertion(rdfs:label "function"@en) -SubClassOf( ) - -# Class: (material entity) - -AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) -AnnotationAssertion(rdfs:label "material entity"@en) -SubClassOf( ) - -# Class: (molecular_function) - -AnnotationAssertion(Annotation( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") -AnnotationAssertion( "molecular function") -AnnotationAssertion( "GO:0003674") -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") -AnnotationAssertion(rdfs:comment "This is the same as GO molecular function") -AnnotationAssertion(rdfs:label "gene product or complex activity"@en) -AnnotationAssertion(rdfs:label "molecular_function") -SubClassOf( ) -DisjointClasses( ) - -# Class: (biological_process) - -AnnotationAssertion(Annotation( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") -AnnotationAssertion( "A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2012-09-19T15:05:24Z") -AnnotationAssertion( "Wikipedia:Biological_process") -AnnotationAssertion( "biological process") -AnnotationAssertion( "physiological process") -AnnotationAssertion( "single organism process") -AnnotationAssertion( "single-organism process") -AnnotationAssertion( "GO:0008150") -AnnotationAssertion(rdfs:comment "A biological process is an evolved process") -AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") -AnnotationAssertion(rdfs:label "biological process"@en) -AnnotationAssertion(rdfs:label "biological_process") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (kinase activity) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") -AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") -AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") -AnnotationAssertion( "phosphokinase activity") -AnnotationAssertion( "GO:0016301") -AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") -AnnotationAssertion(rdfs:label "kinase activity") -SubClassOf( ) -SubClassOf( ObjectHasSelf()) - -# Class: (curation status specification) - -AnnotationAssertion( "curation status specification"@en) -AnnotationAssertion( ) -AnnotationAssertion( "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."@en) -AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) -AnnotationAssertion( "PERSON:Bill Bug"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion( "OBI_0000266"@en) -AnnotationAssertion(rdfs:label "curation status specification"@en) -EquivalentClasses( ObjectOneOf( )) - -# Class: (quality) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") -AnnotationAssertion( "PATO:0000001") -AnnotationAssertion(rdfs:label "quality") -SubClassOf( ) ############################ -# Named Individuals +# Classes ############################ -# Individual: (example to be eventually removed) +# Class: () -AnnotationAssertion( "example to be eventually removed"@en) -AnnotationAssertion(rdfs:label "example to be eventually removed"@en) - -# Individual: (metadata complete) - -AnnotationAssertion( "metadata complete"@en) -AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) -AnnotationAssertion(rdfs:label "metadata complete"@en) - -# Individual: (organizational term) - -AnnotationAssertion( "organizational term"@en) -AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) -AnnotationAssertion(rdfs:label "organizational term"@en) - -# Individual: (ready for release) - -AnnotationAssertion( "ready for release"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) -AnnotationAssertion(rdfs:label "ready for release"@en) - -# Individual: (metadata incomplete) - -AnnotationAssertion( "metadata incomplete"@en) -AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) -AnnotationAssertion(rdfs:label "metadata incomplete"@en) - -# Individual: (uncurated) - -AnnotationAssertion( "uncurated"@en) -AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) -AnnotationAssertion(rdfs:label "uncurated"@en) - -# Individual: (pending final vetting) - -AnnotationAssertion( "pending final vetting"@en) -AnnotationAssertion( ) -AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) -AnnotationAssertion(rdfs:label "pending final vetting"@en) -ClassAssertion( ) - -# Individual: (to be replaced with external ontology term) - -AnnotationAssertion( "to be replaced with external ontology term"@en) -AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) +DisjointClasses( ObjectSomeValuesFrom( )) -# Individual: (requires discussion) +# Class: () -AnnotationAssertion( "requires discussion"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "requires discussion"@en) -ClassAssertion( ) +DisjointClasses( ObjectSomeValuesFrom( )) -SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) -DifferentIndividuals( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(Annotation( "true"^^xsd:boolean) ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'") Annotation(rdfs:label "involved in BP") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/ro_terms.txt b/src/ontology/imports/ro_terms.txt index 8b13789..c2d2454 100644 --- a/src/ontology/imports/ro_terms.txt +++ b/src/ontology/imports/ro_terms.txt @@ -1 +1,12 @@ - +RO:0000052 # 'characteristic of' +RO:0000053 # 'has characteristic' +BFO_0000050 # 'part of' +BFO_0000051 # 'has part' +BFO:0000054 # realized in +BFO:0000055 # realizes +RO:0000056 # is participant +RO:0000057 # has participant +RO:0000058 # is concretized as +RO:0000059 # concretizes +RO:0000079 # function of +RO:0002351 # has member \ No newline at end of file diff --git a/src/ontology/nmrCV-edit.owl b/src/ontology/nmrCV-edit.owl index 6cf13eb..7de827b 100644 --- a/src/ontology/nmrCV-edit.owl +++ b/src/ontology/nmrCV-edit.owl @@ -16,6 +16,8 @@ Prefix(oboInOwl:=) Ontology( Import() Import() +Import() +Import() Import() Import() Annotation(dce:contributor "Annick Moing") @@ -445,12 +447,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -777,17 +773,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -815,27 +802,52 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class(oboInOwl:ObsoleteClass)) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(AnnotationProperty(obo:IAO_0000115)) Declaration(AnnotationProperty(dce:coverage)) +Declaration(AnnotationProperty(dcterms:date)) Declaration(AnnotationProperty(dcterms:description)) +Declaration(AnnotationProperty(dcterms:identifier)) Declaration(AnnotationProperty(dcterms:license)) Declaration(AnnotationProperty(dcterms:title)) Declaration(AnnotationProperty(doap:audience)) @@ -973,10 +985,14 @@ SubClassOf( "data file attribute"@en) SubClassOf( obo:BFO_0000031) -# Class: (NMR instrument type) +# Class: (obsolete_NMR instrument type) -AnnotationAssertion(rdfs:label "NMR instrument type"@en) -SubClassOf( ) +AnnotationAssertion(obo:IAO_0000116 "The concept represented by this class is already present ('NMR instrument') and ontologically more correct.") +AnnotationAssertion(obo:IAO_0000231 obo:IAO_0000227) +AnnotationAssertion(obo:IAO_0100001 ) +AnnotationAssertion(rdfs:label "obsolete_NMR instrument type"@en) +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) +SubClassOf( oboInOwl:ObsoleteClass) # Class: (1D spectrum coordinate system descriptor) @@ -2117,12 +2133,12 @@ AnnotationAssertion(rdfs:comment "used to b AnnotationAssertion(rdfs:label "data simulation"@en) SubClassOf( ) -# Class: (dynamic nuclear polarization NMR) +# Class: (dynamic nuclear polarization NMR instrument) AnnotationAssertion(oboInOwl:hasExactSynonym "DNP NMR") AnnotationAssertion(oboInOwl:hasExactSynonym "dynamic nuclear polarization enhanced NMR system") -AnnotationAssertion(rdfs:label "dynamic nuclear polarization NMR"@en) -SubClassOf( ) +AnnotationAssertion(rdfs:label "dynamic nuclear polarization NMR instrument"@en) +SubClassOf( ) # Class: (chemical shift) @@ -2183,6 +2199,7 @@ SubClassOf( "Varian autosampler"@en) SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (Varian SMS 50) @@ -2193,6 +2210,7 @@ SubClassOf( "Varian probe"@en) SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (5mm HCN probe) @@ -2397,12 +2415,14 @@ SubClassOf( "Bruker tube"@en) SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (JEOL magnet) AnnotationAssertion(rdfs:label "JEOL magnet"@en) AnnotationAssertion(foaf:homepage "http://www.jeolusa.com/PRODUCTS/Nuclear-Magnetic-Resonance/Magnets") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (JEOL ECS magnet) @@ -2433,6 +2453,7 @@ SubClassOf( "Wilmad tube"@en) SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (4mm Match tube) @@ -2508,6 +2529,7 @@ SubClassOf( "Norell tube"@en) SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (JEOL FID file) @@ -2545,6 +2567,7 @@ SubClassOf( "Agilent magnet") AnnotationAssertion(rdfs:label "Varian magnet"@en) SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (premium compact narrow bore magnet) @@ -2930,10 +2953,14 @@ SubClassOf( "bucket fusioning"@en) SubClassOf( ) -# Class: (JNM-ECX Series FT NMR instrument) +# Class: (obsolete_JNM-ECX Series FT NMR instrument) -AnnotationAssertion(rdfs:label "JNM-ECX Series FT NMR instrument"@en) -SubClassOf( ) +AnnotationAssertion(obo:IAO_0000116 "duplicate of http://nmrML.org/nmrCV#NMR:1400227") +AnnotationAssertion(obo:IAO_0000231 obo:IAO_0000227) +AnnotationAssertion(obo:IAO_0100001 ) +AnnotationAssertion(rdfs:label "obsolete_JNM-ECX Series FT NMR instrument"@en) +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) +SubClassOf( oboInOwl:ObsoleteClass) # Class: (JNM-ECZR Series FT NMR instrument) @@ -3034,36 +3061,6 @@ SubClassOf( "Avance I spectrometer"@en) SubClassOf( ) -# Class: (Oxford Instruments) - -AnnotationAssertion(rdfs:label "Oxford Instruments"@en) -SubClassOf( ) - -# Class: (Spinlock SRL) - -AnnotationAssertion(rdfs:label "Spinlock SRL"@en) -SubClassOf( ) - -# Class: (General Electric) - -AnnotationAssertion(rdfs:label "General Electric"@en) -SubClassOf( ) - -# Class: (Kimble Chase) - -AnnotationAssertion(rdfs:label "Kimble Chase"@en) -SubClassOf( ) - -# Class: (Phillips) - -AnnotationAssertion(rdfs:label "Phillips"@en) -SubClassOf( ) - -# Class: (Siemens AG) - -AnnotationAssertion(rdfs:label "Siemens AG"@en) -SubClassOf( ) - # Class: (Varian Inova 500) AnnotationAssertion(rdfs:label "Varian Inova 500"@en) @@ -3098,6 +3095,7 @@ SubClassOf( "Agilent NMR instrument"@en) SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (Agilent 400-MR NMR instrument) @@ -3325,14 +3323,18 @@ AnnotationAssertion(oboInOwl:id "NMR:100045 AnnotationAssertion(rdfs:label "sample") SubClassOf( obo:BFO_0000030) -# Class: (instrument) +# Class: (obsolete_instrument) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MSI:NMR") obo:IAO_0000115 "Description of the instrument or the mass spectrometer.") +AnnotationAssertion(obo:IAO_0000116 "not needed as OBI has better equivalent") +AnnotationAssertion(obo:IAO_0000231 obo:IAO_0000228) +AnnotationAssertion(obo:IAO_0100001 obo:OBI_0000968) AnnotationAssertion(oboInOwl:hasExactSynonym "instrument configuration") AnnotationAssertion(oboInOwl:hasOBONamespace "NMR") AnnotationAssertion(oboInOwl:id "NMR:1000463") -AnnotationAssertion(rdfs:label "instrument") -SubClassOf( obo:BFO_0000030) +AnnotationAssertion(rdfs:label "obsolete_instrument") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) +SubClassOf( oboInOwl:ObsoleteClass) # Class: (Varian/Agilent instrument model) @@ -4164,19 +4166,23 @@ SubClassOf( (optional part of NMR instrument) +AnnotationAssertion(obo:IAO_0000116 "This defined class is a grouping class whose children are inferred based on its logical definition and are materialized by the reasoning step in the creation of the release artefact."@en) +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(rdfs:comment "def: Part of an NMR instrument which is not cardinally important and hence optional / facultative for the proper intended function of the instrument. synonym: optional part of NMR instrument clsdel: ontologically there is no such universal which characteristic is a possible (!) state of being a part of something...") AnnotationAssertion(rdfs:label "optional part of NMR instrument") AnnotationAssertion(owl:versionInfo "TODO: Discuss \"obligatory_part_of\".") -SubClassOf( ) +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( obo:OBI_0000968) -# Class: (autosampler) +# Class: (NMR autosampler) +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(rdfs:comment "def: 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. altdef: The autosampler is an automatic sample changer.") -AnnotationAssertion(rdfs:label "autosampler") -SubClassOf( ) +AnnotationAssertion(rdfs:label "NMR autosampler") +SubClassOf( obo:OBI_0000968) # Class: (multiplicity feature) @@ -4209,30 +4215,39 @@ SubClassOf( (cardinal part of NMR instrument) +AnnotationAssertion(obo:IAO_0000116 "This defined class is a grouping class whose children are inferred based on its logical definition and are materialized by the reasoning step in the creation of the release artefact."@en) +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(rdfs:comment "def: A part of an NMR instrument which is cardinally important and hence obligatory and compulsatory for the proper intended function of the instrument. synonym: cardinal part of NMR instrument") AnnotationAssertion(rdfs:label "cardinal part of NMR instrument") -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf(obo:OBI_0000968 ObjectSomeValuesFrom(obo:BFO_0000050 ))) +SubClassOf( obo:OBI_0000968) -# Class: (acquisition computer) +# Class: (NMR acquisition computer) +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(rdfs:comment "def: A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.") -AnnotationAssertion(rdfs:label "acquisition computer") -SubClassOf( ) +AnnotationAssertion(rdfs:label "NMR acquisition computer") +SubClassOf( obo:OBI_0400107) +SubClassOf( ObjectSomeValuesFrom(obo:BFO_0000050 )) # Class: (NMR probe) +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(rdfs:comment "def: Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile “single point of failure” that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency. altdef: The instrument that transmits and recieves radiofrequency to and from the NMR sample.") AnnotationAssertion(rdfs:label "NMR probe") -SubClassOf( ) +SubClassOf( obo:OBI_0000832) +SubClassOf( ObjectSomeValuesFrom(obo:BFO_0000050 )) -# Class: (console) +# Class: (NMR console) +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(rdfs:comment "def: A component of an NMR instrument that controls the activities of the other components.") -AnnotationAssertion(rdfs:label "console") +AnnotationAssertion(rdfs:label "NMR console") AnnotationAssertion(owl:versionInfo "TODO: same as or part of acquisition computer?") -SubClassOf( ) +SubClassOf( obo:OBI_0000968) +SubClassOf( ObjectSomeValuesFrom(obo:BFO_0000050 )) # Class: (number of acquisition data points) @@ -4425,10 +4440,11 @@ SubClassOf( (NMR instrument) +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(rdfs:comment "def: An Instrument which is used to carry out a NMR analysis of some sample. synonym: NMR instrument") AnnotationAssertion(rdfs:label "NMR instrument") -SubClassOf( ) +SubClassOf( obo:OBI_0000832) # Class: (NMR instrument acquisition parameter set) @@ -4822,12 +4838,14 @@ SubClassOf( (NMR sample tube) AnnotationAssertion(obo:IAO_0000115 "The sample-tube holds the NMR sample and sits in the NMR probe. It is usually a glass tube of 5-20mm diameter.") +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(dce:source "http://en.wikipedia.org/wiki/NMR_tube") AnnotationAssertion(doap:bug-database "https://github.com/nmrML/nmrML/issues/54") AnnotationAssertion(oboInOwl:hasExactSynonym "sample tube") AnnotationAssertion(rdfs:comment "sortal dimensions are Vendor, Size (Diameter, length), Material (glass, quarz, pyrex ...), Frequency, Concentricity, OD and ID") AnnotationAssertion(rdfs:label "NMR sample tube") -SubClassOf( ) +SubClassOf( obo:OBI_0000836) +SubClassOf( ObjectSomeValuesFrom(obo:BFO_0000050 )) # Class: (spectrum pre-processing software) @@ -4996,16 +5014,19 @@ SubClassOf( (NMR magnet) +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(rdfs:comment "def: A magnet which induces a certain frequency (MHz) and which has a certain bore diameter. altdef: 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.") AnnotationAssertion(rdfs:label "NMR magnet") -SubClassOf( ) +SubClassOf( obo:OBI_0000968) +SubClassOf( ObjectSomeValuesFrom(obo:BFO_0000050 )) # Class: (Bruker NMR magnet) AnnotationAssertion(rdfs:comment "defneed") AnnotationAssertion(rdfs:label "Bruker NMR magnet") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (UltraShield) @@ -5101,6 +5122,7 @@ AnnotationAssertion(rdfs:comment "defneed") AnnotationAssertion(rdfs:label "Bruker NMR instrument") AnnotationAssertion(foaf:homepage "https://www.bruker.com/de/products/mr/nmr.html") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (Metabolic Profiler instrument) @@ -5112,7 +5134,7 @@ SubClassOf( "NMR Instruments using hyphenated analytical techniques combining mass spectrometry and chromatograph.") AnnotationAssertion(rdfs:label "Hyphenated NMR instrument") -SubClassOf( ) +SubClassOf( ) # Class: (Capillary LC-NMR) @@ -5128,9 +5150,10 @@ SubClassOf( (NMR tube washing system) +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(rdfs:comment "defneed") AnnotationAssertion(rdfs:label "NMR tube washing system") -SubClassOf( ) +SubClassOf( obo:OBI_0000968) # Class: (Bruker AutoClean) @@ -5138,6 +5161,7 @@ AnnotationAssertion(rdfs:comment "def: In t defprov: Bruker website") AnnotationAssertion(rdfs:label "Bruker AutoClean") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (Bruker BEST NMR) @@ -5168,6 +5192,7 @@ SubClassOf( "defneed") AnnotationAssertion(rdfs:label "Bruker autosampler") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (B-ACS) @@ -5184,12 +5209,15 @@ AnnotationAssertion(rdfs:comment "def: The synonym: Bruker Multiple Adjustable Tube Clamp Holder") AnnotationAssertion(rdfs:label "Bruker MATCH") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (NMR sample holder) +AnnotationAssertion(obo:IAO_0000233 ) AnnotationAssertion(rdfs:comment "def: A NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the NMR sample.") AnnotationAssertion(rdfs:label "NMR sample holder") -SubClassOf( ) +SubClassOf( obo:OBI_0000968) +SubClassOf( ObjectSomeValuesFrom(obo:BFO_0000050 )) # Class: (NMR software) @@ -5261,6 +5289,7 @@ SubClassOf( "JEOL NMR instrument") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (JNM-ECX Series FT NMR instrument) @@ -5289,12 +5318,14 @@ SubClassOf( "https://www.bruker.com/products/mr/nmr/probes/probes.html") AnnotationAssertion(rdfs:label "Bruker NMR probe") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (JEOL NMR probe) AnnotationAssertion(rdfs:comment "defneed") AnnotationAssertion(rdfs:label "JEOL NMR probe") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (CapNMR probe) @@ -5305,6 +5336,7 @@ SubClassOf( "Varian NMR instrument") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (Varian MERCURY) @@ -5362,6 +5394,7 @@ SubClassOf( "tecmag console") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (DISCOVERY console) @@ -5387,6 +5420,7 @@ SubClassOf( "tecmag NMR instrument") SubClassOf( ) +SubClassOf( ObjectHasValue(obo:OBI_0000304 )) # Class: (CAT) @@ -5406,38 +5440,12 @@ AnnotationAssertion(rdfs:label "vendor") AnnotationAssertion(owl:versionInfo "TODO: Belongs in Ref Ontol.") SubClassOf( ) -# Class: (NMR instrument manufacturer) - -AnnotationAssertion(rdfs:comment "A manufacturer that produces (and eventually sells) NMR instruments.") -AnnotationAssertion(rdfs:label "NMR instrument manufacturer") -SubClassOf( ) - -# Class: (Bruker) - -AnnotationAssertion(rdfs:comment "defneed") -AnnotationAssertion(rdfs:label "Bruker") -AnnotationAssertion(owl:versionInfo "TODO: May not need definition due to its instance character.") -SubClassOf( ) +# Class: (NMR device manufacturer) -# Class: (Varian) - -AnnotationAssertion(rdfs:label "Varian") -SubClassOf( ) - -# Class: (JEOL) - -AnnotationAssertion(rdfs:label "JEOL") -SubClassOf( ) - -# Class: (MR Resources) - -AnnotationAssertion(rdfs:label "MR Resources") -SubClassOf( ) - -# Class: (tecmag) - -AnnotationAssertion(rdfs:label "tecmag") -SubClassOf( ) +AnnotationAssertion(obo:IAO_0000115 "A manufacturer that produces NMR instruments and/or their parts"@en) +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(rdfs:label "NMR device manufacturer"@en) +EquivalentClasses( ObjectIntersectionOf(obo:OBI_0000835 ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))))) # Class: (sample temperature information) @@ -5445,21 +5453,6 @@ AnnotationAssertion(rdfs:comment "def: In s AnnotationAssertion(rdfs:label "sample temperature information") SubClassOf( ) -# Class: (Doty Scientific) - -AnnotationAssertion(rdfs:label "Doty Scientific") -SubClassOf( ) - -# Class: (Wilmad) - -AnnotationAssertion(rdfs:label "Wilmad") -SubClassOf( ) - -# Class: (JS Research) - -AnnotationAssertion(rdfs:label "JS Research") -SubClassOf( ) - # Class: (data file) AnnotationAssertion(rdfs:label "data file") @@ -5470,34 +5463,29 @@ AnnotationAssertion(skos:example "an FID ra AnnotationAssertion(skos:scopeNote "In the NMR case a file generated by an NMR acquisition computer, console or NMR processing software.") SubClassOf( obo:BFO_0000031) -# Class: (Acorn NMR Inc) - -AnnotationAssertion(rdfs:label "Acorn NMR Inc") -SubClassOf( ) - -# Class: (liquid chromatography NMR) +# Class: (liquid chromatography NMR instrument) AnnotationAssertion(oboInOwl:hasExactSynonym "LC NMR") -AnnotationAssertion(rdfs:label "liquid chromatography NMR") +AnnotationAssertion(rdfs:label "liquid chromatography NMR instrument") SubClassOf( ) -# Class: (LC MS NMR) +# Class: (LC MS NMR instrument) AnnotationAssertion(rdfs:comment "Includes the connection to a high-resolution TOF-LC-MS system.") -AnnotationAssertion(rdfs:label "LC MS NMR") +AnnotationAssertion(rdfs:label "LC MS NMR instrument") SubClassOf( ) -# Class: (solid phase extraction NMR) +# Class: (solid phase extraction NMR instrument) AnnotationAssertion(oboInOwl:hasExactSynonym "SPE NMR") AnnotationAssertion(rdfs:comment "A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE™ NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra.") -AnnotationAssertion(rdfs:label "solid phase extraction NMR") -SubClassOf( ) +AnnotationAssertion(rdfs:label "solid phase extraction NMR instrument") +SubClassOf( ) -# Class: (Capillary LC-NMR) +# Class: (Capillary LC-NMR instrument) AnnotationAssertion(rdfs:comment "Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume.") -AnnotationAssertion(rdfs:label "Capillary LC-NMR") +AnnotationAssertion(rdfs:label "Capillary LC-NMR instrument") SubClassOf( ) # Class: (direct detection probe) @@ -5510,19 +5498,19 @@ SubClassOf( "indirect detection probe") SubClassOf( ) -# Class: (continuous wave NMR) +# Class: (continuous wave NMR instrument) AnnotationAssertion(rdfs:comment "Continuous wave NMR spectrometers are similar in principle to optical spectrometers. The sample is held in a strong magnetic field, and the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm") -AnnotationAssertion(rdfs:label "continuous wave NMR") -SubClassOf( ) +AnnotationAssertion(rdfs:label "continuous wave NMR instrument") +SubClassOf( ) # Class: (fourier transformation NMR instrument) AnnotationAssertion(rdfs:comment "In FT-NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm") AnnotationAssertion(rdfs:label "fourier transformation NMR instrument") -SubClassOf( ) +SubClassOf( ) # Class: (NMR software data format) @@ -5621,66 +5609,6 @@ AnnotationAssertion(rdfs:comment "J-coupler AnnotationAssertion(rdfs:label "multiplet feature") SubClassOf( ) -# Class: (ThermoMattson) - -AnnotationAssertion(rdfs:label "ThermoMattson") -SubClassOf( ) - -# Class: (FOSS) - -AnnotationAssertion(rdfs:label "FOSS") -SubClassOf( ) - -# Class: (Jasco) - -AnnotationAssertion(rdfs:label "Jasco") -SubClassOf( ) - -# Class: (Agilent Technologies) - -AnnotationAssertion(rdfs:label "Agilent Technologies") -SubClassOf( ) - -# Class: (micromass) - -AnnotationAssertion(rdfs:label "micromass") -SubClassOf( ) - -# Class: (Waters) - -AnnotationAssertion(rdfs:label "Waters") -SubClassOf( ) - -# Class: (ThermoNicolet) - -AnnotationAssertion(rdfs:label "ThermoNicolet") -SubClassOf( ) - -# Class: (Perkin Elmer) - -AnnotationAssertion(rdfs:label "Perkin Elmer") -SubClassOf( ) - -# Class: (OceanOptics) - -AnnotationAssertion(rdfs:label "OceanOptics") -SubClassOf( ) - -# Class: (ThermoFinnigan) - -AnnotationAssertion(rdfs:label "ThermoFinnigan") -SubClassOf( ) - -# Class: (Applied Biosystems) - -AnnotationAssertion(rdfs:label "Applied Biosystems") -SubClassOf( ) - -# Class: (TX) - -AnnotationAssertion(rdfs:label "TX") -SubClassOf( ) - # Class: (Net CDF format) AnnotationAssertion(rdfs:label "Net CDF format") @@ -5701,11 +5629,6 @@ SubClassOf( "Bruker WIN NMR format") SubClassOf( ) -# Class: (acdlabs) - -AnnotationAssertion(rdfs:label "acdlabs") -SubClassOf( ) - # Class: obo:BFO_0000023 (role) EquivalentClasses(obo:BFO_0000023 obo:CHEBI_50906) @@ -5834,7 +5757,7 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CHEBI_229456 ) -# Class: obo:CHEBI_229458 (titan(III)-nitrate) +# Class: obo:CHEBI_229458 (thallium(III) nitrate) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CHEBI_229458 ) @@ -6027,5 +5950,281 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CHEBI_85487 ) +############################ +# Named Individuals +############################ + +# Individual: (Thermo Fischer) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion(dcterms:date "2024-08-26T13:28:30Z"^^xsd:dateTime) +AnnotationAssertion(dcterms:source "https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific") +AnnotationAssertion(rdfs:label "Thermo Fischer") +AnnotationAssertion(skos:altLabel "Thermo FIsher Scientific") +AnnotationAssertion(skos:altLabel "Thermo Fisher Scientific Inc.") +AnnotationAssertion(skos:altLabel "Thermo Scientific™") +AnnotationAssertion(foaf:homepage "https://thermofisher.com") +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Magritek) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion(dcterms:date "2024-08-26T14:26:12Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "Magritek") +AnnotationAssertion(foaf:homepage "https://magritek.com/"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Nanalysis) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion(dcterms:date "2024-08-26T14:30:14Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "Nanalysis") +AnnotationAssertion(foaf:homepage "https://www.nanalysis.com/"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (NMR Service) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion(dcterms:date "2024-08-26T14:32:08Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "NMR Service") +AnnotationAssertion(skos:altLabel "NMR Service GmbH") +AnnotationAssertion(foaf:homepage "https://nmr-service.de/"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Deutero) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion(dcterms:date "2024-08-26T14:33:47Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "Deutero") +AnnotationAssertion(foaf:homepage "https://www.deutero.de/"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Norell®) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion(dcterms:date "2024-08-26T14:36:15Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "Norell®") +AnnotationAssertion(foaf:homepage "https://secure.nmrtubes.com/"^^xsd:anyURI) + +# Individual: (Chemagnetics) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion(dcterms:date "2024-08-26T14:40:56Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "Chemagnetics") +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Nalorac) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:contributor ) +AnnotationAssertion(dcterms:date "2024-08-26T14:42:26Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:label "Nalorac") +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Oxford Instruments) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:identifier "GB0006650450") +AnnotationAssertion(dcterms:source "https://en.wikipedia.org/wiki/Oxford_Instruments"^^xsd:anyURI) +AnnotationAssertion(rdfs:label "Oxford Instruments"@en) +AnnotationAssertion(foaf:homepage "https://www.oxinst.com"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Spinlock SRL) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(rdfs:label "Spinlock SRL"@en) +AnnotationAssertion(skos:altLabel "Spinlock") +AnnotationAssertion(foaf:homepage "https://spinlock.com.ar"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (General Electric) + +AnnotationAssertion(rdfs:label "General Electric"@en) +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (Kimble Chase) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(rdfs:label "Kimble Chase"@en) +AnnotationAssertion(skos:altLabel "Kimble Chase Life Science and Research Products LLC") +AnnotationAssertion(foaf:homepage "https://www.dwk.com/about-us"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Phillips) + +AnnotationAssertion(rdfs:label "Phillips"@en) +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (Siemens AG) + +AnnotationAssertion(rdfs:label "Siemens AG"@en) + +# Individual: (Bruker) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:source "https://en.wikipedia.org/wiki/Bruker"^^xsd:anyURI) +AnnotationAssertion(rdfs:label "Bruker") +AnnotationAssertion(skos:altLabel "Bruker Corporation") +AnnotationAssertion(foaf:homepage "https://www.bruker.com"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Varian) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:source "https://en.wikipedia.org/wiki/Varian,_Inc."^^xsd:anyURI) +AnnotationAssertion(rdfs:label "Varian") +AnnotationAssertion(skos:altLabel "Varian, Inc.") +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (JEOL) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:source "https://en.wikipedia.org/wiki/JEOL"^^xsd:anyURI) +AnnotationAssertion(rdfs:label "JEOL") +AnnotationAssertion(skos:altLabel "Nihon Denshi Kabushiki-kaisha"@ja) +AnnotationAssertion(skos:altLabel "日本電子"@ja) +AnnotationAssertion(foaf:homepage "https://www.jeol.co.jp") +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (MR Resources) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(rdfs:label "MR Resources") +AnnotationAssertion(foaf:homepage "https://www.mrr.com/"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (tecmag) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(rdfs:label "tecmag") +AnnotationAssertion(skos:altLabel "Tecmag") +AnnotationAssertion(foaf:homepage "https://tecmag.com/"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Doty Scientific) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(rdfs:label "Doty Scientific") +AnnotationAssertion(skos:altLabel "Doty Scientific, Inc.") +AnnotationAssertion(foaf:homepage "https://dotynmr.com"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Wilmad) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(rdfs:label "Wilmad") +AnnotationAssertion(foaf:homepage "https://sp-wilmadlabglass.com/"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (JS Research) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(rdfs:label "JS Research") +AnnotationAssertion(skos:altLabel "J S RESEARCH INC.") +AnnotationAssertion(skos:altLabel "JSR") +AnnotationAssertion(foaf:homepage "https://www.jsresearch.com/"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (Acorn NMR Inc) + +AnnotationAssertion(rdfs:label "Acorn NMR Inc") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (ThermoMattson) + +AnnotationAssertion(rdfs:label "ThermoMattson") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (FOSS) + +AnnotationAssertion(rdfs:label "FOSS") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (Jasco) + +AnnotationAssertion(rdfs:label "Jasco") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (Agilent Technologies) + +AnnotationAssertion(obo:IAO_0000233 ) +AnnotationAssertion(dcterms:source "https://en.wikipedia.org/wiki/Agilent_Technologies"^^xsd:anyURI) +AnnotationAssertion(rdfs:label "Agilent Technologies") +AnnotationAssertion(foaf:homepage "https://www.agilent.com/"^^xsd:anyURI) +ClassAssertion(obo:OBI_0000245 ) +ClassAssertion(ObjectSomeValuesFrom(obo:RO_0000087 ObjectIntersectionOf(obo:OBI_0000571 ObjectSomeValuesFrom(obo:BFO_0000054 ObjectIntersectionOf(obo:OBI_0000457 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectSomeValuesFrom(obo:BFO_0000050 )))))) ) + +# Individual: (micromass) + +AnnotationAssertion(rdfs:label "micromass") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (Waters) + +AnnotationAssertion(rdfs:label "Waters") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (ThermoNicolet) + +AnnotationAssertion(rdfs:label "ThermoNicolet") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (Perkin Elmer) + +AnnotationAssertion(rdfs:label "Perkin Elmer") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (OceanOptics) + +AnnotationAssertion(rdfs:label "OceanOptics") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (ThermoFinnigan) + +AnnotationAssertion(rdfs:label "ThermoFinnigan") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (Applied Biosystems) + +AnnotationAssertion(rdfs:label "Applied Biosystems") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (TX) + +AnnotationAssertion(rdfs:label "TX") +ClassAssertion(obo:OBI_0000245 ) + +# Individual: (acdlabs) + +AnnotationAssertion(rdfs:label "acdlabs") +ClassAssertion(obo:OBI_0000245 ) + + SubClassOf(ObjectIntersectionOf(obo:CHEBI_23367 ObjectSomeValuesFrom(obo:RO_0000087 obo:CHEBI_228364)) ) ) \ No newline at end of file diff --git a/src/ontology/nmrCV-odk.yaml b/src/ontology/nmrCV-odk.yaml index 55856b4..72511ac 100644 --- a/src/ontology/nmrCV-odk.yaml +++ b/src/ontology/nmrCV-odk.yaml @@ -39,12 +39,16 @@ import_group: - id: bfo module_type: mirror - id: ro + use_base: true - id: omo module_type: mirror - #- id: iao + - id: iao + make_base: true #- id: chmo #- id: pato - #- id: obi + - id: obi + make_base: true + module_type: custom - id: chebi is_large: true use_gzipped: true diff --git a/src/ontology/nmrCV.Makefile b/src/ontology/nmrCV.Makefile index 3e779f0..007fbae 100644 --- a/src/ontology/nmrCV.Makefile +++ b/src/ontology/nmrCV.Makefile @@ -4,3 +4,13 @@ ## changes here rather than in the main Makefile +## Module for ontology: obi +## Since the default extract BOT method imports too many unneeded terms, we customize the import module build process by +## using ROBOT "remove" to remove the terms specified here and in the "obi_remove_list.txt" + +$(IMPORTDIR)/obi_import.owl: $(MIRRORDIR)/obi.owl $(IMPORTDIR)/obi_terms.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/obi_terms.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ + remove -T $(IMPORTDIR)/obi_remove_list.txt --select "self descendants instances" --signature true \ + $(ANNOTATE_CONVERT_FILE); fi \ No newline at end of file