Import chebi dependencies #18
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Add CHEBI terms with a 'NMR chemical shift reference compound' role
`sh run.sh robot reason --reasoner ELK -i nmrcv-edit.owl --exclude-duplicate-axioms true --exclude-tautologies structural --annotate-inferred-axioms True convert -f ofn -o nmrcv-edit.owl`
…ecular entities which bear a CHEBI:'NMR chemical shift reference compound' role using: `sh run.sh robot reason --reasoner ELK -i nmrcv-edit.owl --exclude-duplicate-axioms true --exclude-tautologies structural --annotate-inferred-axioms True convert -f ofn -o nmrcv-edit.owl`
StroemPhi
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Feb 18, 2025
| AnnotationAssertion(oboInOwl:hasExactSynonym <http://nmrML.org/nmrCV#NMR:1000086> "JRES spectrum") | ||
| AnnotationAssertion(rdfs:label <http://nmrML.org/nmrCV#NMR:1000086> "2D J-resolved spectrum"@en) | ||
| SubClassOf(<http://nmrML.org/nmrCV#NMR:1000086> <http://nmrML.org/nmrCV#NMR:1002007>) |
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This should have been checked in seperately and better also not in this PR, but it is fine. '2D J-resolved spectrum' was declared a subclassOf 'NMR spectrum' as well as of '2D spectrum'. Since the latter is more precise and itself an decendant of 'NMR spectrum', deleting this axiom is removing a redundancy that "messed up" the hierarchy.
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Mar 21, 2025
This PR makes a new release for nmrCV to reflect the current changes made by NFDI4Chem. Changes summary: * **ATTENTION: This might introduce breaking changes with regard to using nmrCV in conjunction with nmrML! We therefore advise to keep using nmrCV version 1.1.0 with nmrML!** * The maintenance & development of nmrCV was migrated to an [Ontology Development Kit based workflow](https://github.com/INCATools/ontology-development-kit/tree/master), see also: #1, #8, #14 & #30. Due to that nmrCV: * is now also published in the form of `full` and `base` [release artefacts](https://oboacademy.github.io/obook/reference/release-artefacts/) in .obo, .ttl as well as .owl serialization. * now imports terms from exisiting ontologies, such as CHEBI, BFO, RO, OBI & IAO, instead of redefining them anew, * most importantly it imports chemical entites from CHEBI as was initially planned and its nmrCV placeholder terms where thus properly deprecated, see also #13, #18, #26, #29. #53, #54 & #55, * is now using a date based versioning scheme instead of a [semantic versioning scheme](https://semver.org/), starting with the 2025-03-19 release, which can be interpreted as a 2.0_alpha version. * In the present PR the ontology annotations where updated to include the new NFDI4Chem contributors and to reflect the reviving of nmrCV and its new scope. * Annotations specific to the contributors of the previous version where adjusted, in that contributors are now consistently listed individually using `dc:contributor` where no ORCID could be identified and `dcterms.contributor` where corresponding ORCIDs could be identified. * The textual definition of `NMR sample` was made more general in #2. * The NMR manufacturer pattern was harmonized with OBI in #40 * The calibration compound branch was improved in #45. * The class `characterized compound` was added in #37 A complete list of changes was created with `robot diff`: * [diff_nmrCV1.1-nmrCV2.0alpha.md](https://github.com/nmrML/nmrCV/blob/main/diff_nmrCV1.1-nmrCV_2025-03-20.md) * [diff_nmrCV1.1-nmrCV2.0alpha.html](https://github.com/nmrML/nmrCV/blob/main/diff_nmrCV1.1-nmrCV_2025-03-20.html)
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This PR closes #6, by importing the chemical entities that either have a NMR solvent role or a NMR shift reference compound role. The exact changes are documented in #6 (comment) and #6 (comment).