Assign reference compounds #48 #55
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StroemPhi
approved these changes
Feb 17, 2025
add more compounds to import from CHEBI
accidentally checked in 2fe119c
more fine-grained NMR related roles into ChEBI
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StroemPhi
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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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In this PR chemical shift reference compounds were manually assigned to their corresponding IUPAC grouping classes, which are children of "chemical shift reference compound".
For this, missing compounds were also imported from ChEBI. The subsumption of these compounds under the "chemical shift reference compound" class was done via inferencing using
robot reasonwith the ELK reasoner in the nmrCV-edit.owl.