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Merged
StroemPhi merged 21 commits into from
Mar 21, 2025
Merged

Make 2.0_alpha release #60

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0465103
Call ODK's `make prepare-release`
StroemPhi Feb 18, 2025
519f45d
Create ROBOT diff between current v1.1 & new nmrCV.owl
StroemPhi Feb 18, 2025
e316741
Add Noura's and my ranges
StroemPhi Mar 17, 2025
28cc42d
Update ontology metadata
StroemPhi Mar 17, 2025
c3d31e0
Use version IRI and file ending to point to previous version
StroemPhi Mar 17, 2025
520cc37
Check in regenerated release files
StroemPhi Mar 17, 2025
6fcca0d
Using "nmrCV" as preferred prefix
StroemPhi Mar 19, 2025
790f718
Update robot diff output
StroemPhi Mar 19, 2025
70f0950
Fix error in IRI of "87Sr spectrum chemical shift reference compound"
StroemPhi Mar 19, 2025
649e0dc
Fix alphabetical order by saving as via Protege
StroemPhi Mar 19, 2025
3e1b016
Use correct verionIRI of previous version
StroemPhi Mar 19, 2025
d680c92
Fix typo in http://nmrML.org/nmrCV#NMR:0002000
StroemPhi Mar 19, 2025
3c37d61
Use nmrCV specific versionIRI pattern and add creation date automatic…
StroemPhi Mar 19, 2025
f8f0cbf
Change ontology description to reflect nmrCV reboot
StroemPhi Mar 20, 2025
b72b335
Regenerate release artefacts and import modules
StroemPhi Mar 20, 2025
a51346c
Updated ROBOT diff output
StroemPhi Mar 20, 2025
5441082
Revert "Regenerate release artefacts and import modules"
StroemPhi Mar 20, 2025
f3abe32
Fix OBI importing unused Uberon classes and no label for Homo Sapiens
StroemPhi Mar 20, 2025
e5d2182
Deactivate reasoning step when refreshing ChEBI
StroemPhi Mar 20, 2025
dace401
Regenerate all artefacts
StroemPhi Mar 21, 2025
fee3a1a
Update diff files
StroemPhi Mar 21, 2025
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15,694 changes: 15,694 additions & 0 deletions diff_nmrCV1.1-nmrCV_2025-03-20.html
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20,891 changes: 20,891 additions & 0 deletions diff_nmrCV1.1-nmrCV_2025-03-20.md
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54 changes: 43 additions & 11 deletions nmrCV-base.obo
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Original file line number Diff line number Diff line change
@@ -1,13 +1,45 @@
format-version: 1.2
data-version: nmrCV/releases/2023-11-23/nmrCV-base.owl
ontology: nmrCV/nmrCV-base
property_value: http://purl.org/dc/elements/1.1/type IAO:8000001
property_value: http://purl.org/dc/terms/description "This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model." xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/mark/1.0/
property_value: http://purl.org/dc/terms/title "nuclear magnetic resonance CV" xsd:string
property_value: owl:versionInfo "2023-11-23" xsd:string

[Term]
id: NMRCV:0000000
name: root node
data-version: http://nmrml.org/cv/2025-03-20/nmrCV-base.owl
idspace: dce http://purl.org/dc/elements/1.1/
idspace: dcterms http://purl.org/dc/terms/
idspace: doap http://usefulinc.com/ns/doap#
idspace: foaf http://xmlns.com/foaf/0.1/
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
idspace: skos http://www.w3.org/2004/02/skos/core#
idspace: vann http://purl.org/vocab/vann/
ontology: http://nmrML.org/nmrCV/nmrCV-base.owl
property_value: dce:contributor "Chris Taylor" xsd:string
property_value: dce:contributor "Dennis Rubtsov" xsd:string
property_value: dce:contributor "Helen Jenkins" xsd:string
property_value: dce:contributor "Irena Spasic" xsd:string
property_value: dce:contributor "Joseph Cruz" xsd:string
property_value: dce:contributor "Larissa Soldatova" xsd:string
property_value: dce:contributor "Michael Wilson" xsd:string
property_value: dce:coverage "Nuclear magnetic resonance (NMR) data annotation as required by the msi sanctioned open\naccess nmrML XML format developed by the COSMOS EU project." xsd:string
property_value: dce:creator "COSMOS - COordination Of Standards In MetabOlomicS Project - WP2 team" xsd:string
property_value: dce:type IAO:8000001
property_value: dcterms:abstract "With this artifact, the Nuclear Magnetic Resonance Controlled Vocabulary (nmrCV) is undergoing a significant evolution to become an ontology designed to describe NMR spectroscopy experiments and their outputs in detail, supporting FAIR research data management. Initially, nmrCV v1.1.0 was deliberately designed as a controlled vocabulary, not a formal ontology with Description Logic (DL) semantics. It was approved by th Metabolomics Standards Initiative (MSI) and serves to provide descriptors for the nuclear magnetic resonance markup language (nmrML), enabling vendor-agnostic NMR data sharing, particularly within NMR metabolomics. Since version 1.1.0, nmrCV had not been updated nor actively maintained.\n\nRecognizing the need for a DL-enabled NMR spectroscopy ontology suitable for use independently of nmrML within a larger ontology framework, and addressing the limitations of the original controlled vocabulary, Germany's National Research Data Infrastructure project for Chemistry (NFDI4Chem) took on the responsibility for nmrCV's further development and maintenance. This decision was made after a discussion about its optimal integration within the broader ontology landscape at the third Ontologies4Chem workshop in fall 2023.\n\nThe decision to build upon nmrCV v1.1.0 was based on its existing definition of essential concepts, its BFO alignment, and its planned integration with ontologies like the Ontology for Biomedical Investigations (OBI) and the Chemical Entities of Biological Interest (ChEBI). Improvements in the present version include replacing out-of-scope and placeholder terms with more suitable equivalents from established ontologies like OBI and ChEBI, adhering to the OBO Foundry principles, corrections regarding the BFO subsumption and other established ontology design patterns, as well as the introduction of DL semantics.\n\n⚠️ Compatibility Note: Due to these significant changes, which prioritize ontology rigor over nmrML alignment, this and future versions of nmrCV may introduce breaking changes for nmrML users. Therefore, nmrML users are strongly advised to thoroughly test new nmrCV versions before production deployment. Alternatively, users may choose to continue using nmrCV v1.1.0, which was specifically designed for nmrML compatibility." xsd:string
property_value: dcterms:contributor https://orcid.org/0000-0001-5306-5690
property_value: dcterms:contributor https://orcid.org/0000-0001-5687-9059
property_value: dcterms:contributor https://orcid.org/0000-0001-8604-1732
property_value: dcterms:contributor https://orcid.org/0000-0002-1595-3213
property_value: dcterms:contributor https://orcid.org/0000-0002-3207-2434
property_value: dcterms:contributor https://orcid.org/0000-0002-6687-7169
property_value: dcterms:contributor https://orcid.org/0000-0002-7899-7192
property_value: dcterms:contributor https://orcid.org/0000-0002-8148-6895
property_value: dcterms:contributor https://orcid.org/0000-0003-1144-3600
property_value: dcterms:contributor https://orcid.org/0009-0001-5998-5030
property_value: dcterms:created "2025-03-20" xsd:string
property_value: dcterms:license https://creativecommons.org/publicdomain/mark/1.0/
property_value: dcterms:references "https://doi.org/10.1021/acs.analchem.7b02795" xsd:string
property_value: dcterms:title "nuclear magnetic resonance CV" xsd:string
property_value: doap:audience "This CV is to be used by metabolomics researchers, or basically any chenomics or proteomics researchers who apply the nmrML xml to store their NMRraw data in a vendor agnostic manner. But nmrML can also be used to capture experimental results and (limited) basic metadata like molecule to spectral feature assignments." xsd:string
property_value: doap:bug-database "https://github.com/nmrML/nmrCV/issues" xsd:string
property_value: doap:implements "https://github.com/nmrML/nmrML" xsd:string
property_value: doap:location "https://github.com/nmrML/nmrCV" xsd:string
property_value: doap:maintainer https://www.wikidata.org/wiki/Q96678459
property_value: owl:priorVersion https://nmrml.org/cv/v1.1.0/nmrCV.owl
property_value: owl:versionInfo "2.0_alpha" xsd:string
property_value: owl:versionInfo "2025-03-20" xsd:string
property_value: vann:preferredNamespacePrefix "nmrCV" xsd:string

147 changes: 118 additions & 29 deletions nmrCV-base.owl
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Original file line number Diff line number Diff line change
@@ -1,20 +1,62 @@
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/nmrCV/nmrCV-base.owl#"
xml:base="http://purl.obolibrary.org/obo/nmrCV/nmrCV-base.owl"
<rdf:RDF xmlns="http://nmrML.org/nmrCV/nmrCV-base.owl#"
xml:base="http://nmrML.org/nmrCV/nmrCV-base.owl"
xmlns:dce="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:doap="http://usefulinc.com/ns/doap#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:dcterms="http://purl.org/dc/terms/">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/nmrCV/nmrCV-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmrCV/releases/2023-11-23/nmrCV-base.owl"/>
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:vann="http://purl.org/vocab/vann/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://nmrML.org/nmrCV/nmrCV-base.owl">
<owl:versionIRI rdf:resource="http://nmrml.org/cv/2025-03-20/nmrCV-base.owl"/>
<dce:contributor>Chris Taylor</dce:contributor>
<dce:contributor>Dennis Rubtsov</dce:contributor>
<dce:contributor>Helen Jenkins</dce:contributor>
<dce:contributor>Irena Spasic</dce:contributor>
<dce:contributor>Joseph Cruz</dce:contributor>
<dce:contributor>Larissa Soldatova</dce:contributor>
<dce:contributor>Michael Wilson</dce:contributor>
<dce:coverage>Nuclear magnetic resonance (NMR) data annotation as required by the msi sanctioned open
access nmrML XML format developed by the COSMOS EU project.</dce:coverage>
<dce:creator>COSMOS - COordination Of Standards In MetabOlomicS Project - WP2 team</dce:creator>
<dce:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<dcterms:description>This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model.</dcterms:description>
<dcterms:abstract xml:lang="en">With this artifact, the Nuclear Magnetic Resonance Controlled Vocabulary (nmrCV) is undergoing a significant evolution to become an ontology designed to describe NMR spectroscopy experiments and their outputs in detail, supporting FAIR research data management. Initially, nmrCV v1.1.0 was deliberately designed as a controlled vocabulary, not a formal ontology with Description Logic (DL) semantics. It was approved by th Metabolomics Standards Initiative (MSI) and serves to provide descriptors for the nuclear magnetic resonance markup language (nmrML), enabling vendor-agnostic NMR data sharing, particularly within NMR metabolomics. Since version 1.1.0, nmrCV had not been updated nor actively maintained.

Recognizing the need for a DL-enabled NMR spectroscopy ontology suitable for use independently of nmrML within a larger ontology framework, and addressing the limitations of the original controlled vocabulary, Germany&apos;s National Research Data Infrastructure project for Chemistry (NFDI4Chem) took on the responsibility for nmrCV&apos;s further development and maintenance. This decision was made after a discussion about its optimal integration within the broader ontology landscape at the third Ontologies4Chem workshop in fall 2023.

The decision to build upon nmrCV v1.1.0 was based on its existing definition of essential concepts, its BFO alignment, and its planned integration with ontologies like the Ontology for Biomedical Investigations (OBI) and the Chemical Entities of Biological Interest (ChEBI). Improvements in the present version include replacing out-of-scope and placeholder terms with more suitable equivalents from established ontologies like OBI and ChEBI, adhering to the OBO Foundry principles, corrections regarding the BFO subsumption and other established ontology design patterns, as well as the introduction of DL semantics.

⚠️ Compatibility Note: Due to these significant changes, which prioritize ontology rigor over nmrML alignment, this and future versions of nmrCV may introduce breaking changes for nmrML users. Therefore, nmrML users are strongly advised to thoroughly test new nmrCV versions before production deployment. Alternatively, users may choose to continue using nmrCV v1.1.0, which was specifically designed for nmrML compatibility.</dcterms:abstract>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0001-5306-5690"/>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0001-5687-9059"/>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0001-8604-1732"/>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0002-1595-3213"/>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0002-3207-2434"/>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0002-6687-7169"/>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0002-7899-7192"/>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0002-8148-6895"/>
<dcterms:contributor rdf:resource="https://orcid.org/0000-0003-1144-3600"/>
<dcterms:contributor rdf:resource="https://orcid.org/0009-0001-5998-5030"/>
<dcterms:created>2025-03-20</dcterms:created>
<dcterms:license rdf:resource="https://creativecommons.org/publicdomain/mark/1.0/"/>
<dcterms:references>https://doi.org/10.1021/acs.analchem.7b02795</dcterms:references>
<dcterms:title>nuclear magnetic resonance CV</dcterms:title>
<owl:versionInfo>2023-11-23</owl:versionInfo>
<vann:preferredNamespacePrefix>nmrCV</vann:preferredNamespacePrefix>
<doap:audience>This CV is to be used by metabolomics researchers, or basically any chenomics or proteomics researchers who apply the nmrML xml to store their NMRraw data in a vendor agnostic manner. But nmrML can also be used to capture experimental results and (limited) basic metadata like molecule to spectral feature assignments.</doap:audience>
<doap:bug-database>https://github.com/nmrML/nmrCV/issues</doap:bug-database>
<doap:implements>https://github.com/nmrML/nmrML</doap:implements>
<doap:location>https://github.com/nmrML/nmrCV</doap:location>
<doap:maintainer rdf:resource="https://www.wikidata.org/wiki/Q96678459"/>
<owl:priorVersion rdf:resource="https://nmrml.org/cv/v1.1.0/nmrCV.owl"/>
<owl:versionInfo>2.0_alpha</owl:versionInfo>
<owl:versionInfo>2025-03-20</owl:versionInfo>
</owl:Ontology>


Expand All @@ -30,55 +72,102 @@



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<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/title">
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<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
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<owl:AnnotationProperty rdf:about="http://purl.org/vocab/vann/preferredNamespacePrefix"/>



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