From 1b2a63589a946229d0e63879424f6aab1ffbd1c9 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Tue, 2 Dec 2025 09:09:16 +0100 Subject: [PATCH 1/3] Links --- docs/20_role/40_data_steward.mdx | 2 +- docs/50_data_publication/10_repositories.mdx | 2 +- .../20_choose_repository/50_nmrxiv.mdx | 2 +- .../20_ontology.mdx | 50 +++++++++---------- 4 files changed, 28 insertions(+), 28 deletions(-) diff --git a/docs/20_role/40_data_steward.mdx b/docs/20_role/40_data_steward.mdx index eda3685a..597c52c2 100644 --- a/docs/20_role/40_data_steward.mdx +++ b/docs/20_role/40_data_steward.mdx @@ -24,7 +24,7 @@ Data stewards may work directly at an institute, but, in Germany, many are part To efficiently manage data and maintain an overview, data stewards can use a [Data Management Plan](/docs/dmp) as a supporting tool. -Recently, a [BMBF](https://www.bmbf.de/bmbf/de/home/home_node.html)-funded project titled [DataStew](https://www.ub.uni-koeln.de/forschen_publizieren/forschen/forschungsdaten_managen/datastew/index_ger.html) has been analyzing the concept of data stewardship in the German academic landscape and identifying various stakeholder requirements to be able to provide recommendations for education and training for the role. Similar to the above-mentioned Dutch project, the first [results](https://doi.org/10.5281/zenodo.7327371) here show the multi-faceted task areas assigned to data stewards. From consultating on general RDM services, development or expansion of IT-tools and infrastructure for RDM in research, discipline-specific consulting, conducting their own data-focused research for specific disciplines, to occupying coordinative roles, one data steward position is rarely like the next. +Recently, a [BMBF](https://www.bmbf.de/bmbf/de/home/home_node.html)-funded project titled [DataStew](https://doi.org/10.4126/FRL01-006441397) has been analyzing the concept of data stewardship in the German academic landscape and identifying various stakeholder requirements to be able to provide recommendations for education and training for the role. Similar to the above-mentioned Dutch project, the first [results](https://doi.org/10.5281/zenodo.7327371) here show the multi-faceted task areas assigned to data stewards. From consultating on general RDM services, development or expansion of IT-tools and infrastructure for RDM in research, discipline-specific consulting, conducting their own data-focused research for specific disciplines, to occupying coordinative roles, one data steward position is rarely like the next. ### Data Stewards in Chemistry diff --git a/docs/50_data_publication/10_repositories.mdx b/docs/50_data_publication/10_repositories.mdx index 7b441f80..331b0e67 100644 --- a/docs/50_data_publication/10_repositories.mdx +++ b/docs/50_data_publication/10_repositories.mdx @@ -41,7 +41,7 @@ To ease the selection of a suitable research data repository for chemistry resea ## Sources and further information -- [Repository Platforms for Research Data IG](https://www.rd-alliance.org/groups/repository-platforms-research-data.html) +- [Repository Platforms for Research Data IG](https://www.rd-alliance.org/groups/repository-platforms-research-data/activity/) - [FAIRsFAIR Repository Support Series: Using registries to improve the visibility of your repository service](https://www.dcc.ac.uk/events/fairsfair-repository-support-series-using-registries-improve-visibility-your-repository) - [The Repository Chemotion: infrastructure for sustainable research in chemistry](https://doi.org/10.1002/anie.202007702) - [Chemotion ELN: an open source electronic lab notebook for chemists in academia](https://doi.org/10.1186/s13321-017-0240-0) diff --git a/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx b/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx index e88cf886..f82ab197 100644 --- a/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx +++ b/docs/50_data_publication/20_choose_repository/50_nmrxiv.mdx @@ -44,7 +44,7 @@ More details about the platform architecture and related topics – [here](https Enable the FAIR sharing of raw NMR data to enhance the quality of chemical research and dissemination. Also, to develop non-prescriptivist curation and analysis standards for data and metadata. Build standards with input and contributions from the community and make them compatible with existing and potential newly developed formats and approaches. -More details about the data standards and related topics – [here](https://docs.nmrxiv.org/category/data.html) +More details about the data standards and related topics – here: [project](https://docs.nmrxiv.org/submission-guides/data-model/project.html), [sample](https://docs.nmrxiv.org/submission-guides/data-model/sample.html), [spectra](https://docs.nmrxiv.org/submission-guides/data-model/spectra.html) ### Workshops and Training diff --git a/docs/60_topics/63_data_description_annotation/20_ontology.mdx b/docs/60_topics/63_data_description_annotation/20_ontology.mdx index 741656c9..d25b4e6e 100644 --- a/docs/60_topics/63_data_description_annotation/20_ontology.mdx +++ b/docs/60_topics/63_data_description_annotation/20_ontology.mdx @@ -53,30 +53,30 @@ This tabular overview lists the suitable ontologies with regard to: - the possibility of reusing them in a modular way (whereas a BFO alignment and OBO compatibility indicates an increased possibility), - and, their use in known applications. -| Ontology | Domain | Licence | Modularity | Used in | -| ------------------------------------------------------------------------------ | ------------------------------- | -------------------------------------------------------------------------------- | ---------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------- | -| [ChEBI](https://www.ebi.ac.uk/ols/ontologies/chebi) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB | -| [CHIRO](https://terminology.nfdi4chem.de/ts/ontologies/chiro) | chemistry | [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/) | BFO & OBO based | unknown | -| [ChemOnt](http://classyfire.wishartlab.com/downloads) | chemistry | custom OA licence | subsumable under BFO's _material entity_ | YMDB, HMDB, T3DB, ECMDB, DrugBank,PubChem, ChEBI, LIPID MAPS, MoNA | -| [CHEMINF](https://terminology.nfdi4chem.de/ts/ontologies/cheminf) | chemistry | [CC-BY 3.0](https://creativecommons.org/licenses/by/3.0/) | BFO & OBO based | PubChem, Open PHACTS | -| [CHMO](https://terminology.nfdi4chem.de/ts/ontologies/chmo) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | Chemotion, Allotrope™ | -| [MOP](https://terminology.nfdi4chem.de/ts/ontologies/mop) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | RXNO | -| [RXNO](https://terminology.nfdi4chem.de/ts/ontologies/rxno) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | NameRXN, Wikipedia, Chemotion | -| [OntoKin](http://www.theworldavatar.com/kb/ontokin/ontokin.owl) | chemistry | unknown | OntoCAPE upper level & modules | J-Park Simulator | -| [AFO](https://www.ebi.ac.uk/ols/ontologies/afo) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO classes & relations, many AFO- some custom OBO-modules | Allotrope™ | -| [PROCO](https://raw.githubusercontent.com/proco-ontology/PROCO/main/proco.owl) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO/AFO & OBO based | Allotrope™ | -| [MS](https://terminology.nfdi4chem.de/ontologies/ms) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO mapping possible | mzML | -| [nmrCV](https://terminology.nfdi4chem.de/ontologies/nmrcv) | chemistry | [Public Domain Mark 1.0](https://creativecommons.org/publicdomain/mark/1.0/deed) | BFO & OBO mapping possible | MetaboLights, HMDB | -| [BFO](https://terminology.nfdi4chem.de/ontologies/bfo) | upper level (classes only) | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | OBO backbone | >300 ontologies & >50 organizations, PubChem | -| [RO](https://terminology.nfdi4chem.de/ts/ontologies/ro) | upper level (relations) | CC0 1.0 | BFO & OBO based | Monarch Initiative, OBO Foundry, Gene Ontology, PubChem | -| [IAO](https://terminology.nfdi4chem.de/ts/ontologies/iao) | information artefacts | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | OBO Foundry, Allotrope™, PubChem, ISA tools | -| [OBI](https://terminology.nfdi4chem.de/ts/ontologies/obi) | biomedicine | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | OBO Foundry, Allotrope™, PubChem | -| [UO](https://terminology.nfdi4chem.de/ts/ontologies/uo) | scientific units | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | OBO Foundry, UOM, PubChem | -| [QUDT](http://www.qudt.org/pages/QUDToverviewPage.html) | scientific units | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based mapping possible | openPHACTS | -| [PATO](https://terminology.nfdi4chem.de/ts/ontologies/pato) | phenotypic & physical qualities | [CC-BY 3.0](https://creativecommons.org/licenses/by/3.0/) | BFO & OBO based | OBO Foundry, Allotrope™ | -| [SIO](https://terminology.nfdi4chem.de/ts/ontologies/sio) | upper level | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO alignment | PubChemRDF, Bio2RDF, SADI Semantic Web Services, DisGeNET, EBI's Gene Expression Atlas, Graph4Code project | -| [EDAM](https://terminology.nfdi4chem.de/ts/ontologies/edam) | life-sciences & data management | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO mapping possible | EMBOSS, Bio-jETI | -| [OntoCAPE](http://www.theworldavatar.com/ontology/ontocape/) | upper level & engineering | [GNU GPLv2](https://www.gnu.org/licenses/old-licenses/gpl-2.0) | provides upper level concepts | J-Park Simulator | +| Ontology | Domain | Licence | Modularity | Used in | +| ----------------------------------------------------------------------- | ------------------------------- | -------------------------------------------------------------------------------- | ---------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------- | +| [ChEBI](https://www.ebi.ac.uk/ols/ontologies/chebi) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB | +| [CHIRO](https://terminology.nfdi4chem.de/ts/ontologies/chiro) | chemistry | [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/) | BFO & OBO based | unknown | +| [ChemOnt](http://classyfire.wishartlab.com/downloads) | chemistry | custom OA licence | subsumable under BFO's _material entity_ | YMDB, HMDB, T3DB, ECMDB, DrugBank,PubChem, ChEBI, LIPID MAPS, MoNA | +| [CHEMINF](https://terminology.nfdi4chem.de/ts/ontologies/cheminf) | chemistry | [CC-BY 3.0](https://creativecommons.org/licenses/by/3.0/) | BFO & OBO based | PubChem, Open PHACTS | +| [CHMO](https://terminology.nfdi4chem.de/ts/ontologies/chmo) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | Chemotion, Allotrope™ | +| [MOP](https://terminology.nfdi4chem.de/ts/ontologies/mop) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | RXNO | +| [RXNO](https://terminology.nfdi4chem.de/ts/ontologies/rxno) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | NameRXN, Wikipedia, Chemotion | +| [OntoKin](http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl) | chemistry | [MIT](https://github.com/TheWorldAvatar/ontology/blob/main/LICENSE.txt) | OntoCAPE upper level & modules | J-Park Simulator | +| [AFO](https://www.ebi.ac.uk/ols/ontologies/afo) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO classes & relations, many AFO- some custom OBO-modules | Allotrope™ | +| [PROCO](http://purl.obolibrary.org/obo/proco.owl) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO/AFO & OBO based | Allotrope™ | +| [MS](https://terminology.nfdi4chem.de/ontologies/ms) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO mapping possible | mzML | +| [nmrCV](https://terminology.nfdi4chem.de/ontologies/nmrcv) | chemistry | [Public Domain Mark 1.0](https://creativecommons.org/publicdomain/mark/1.0/deed) | BFO & OBO mapping possible | MetaboLights, HMDB | +| [BFO](https://terminology.nfdi4chem.de/ontologies/bfo) | upper level (classes only) | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | OBO backbone | >300 ontologies & >50 organizations, PubChem | +| [RO](https://terminology.nfdi4chem.de/ts/ontologies/ro) | upper level (relations) | CC0 1.0 | BFO & OBO based | Monarch Initiative, OBO Foundry, Gene Ontology, PubChem | +| [IAO](https://terminology.nfdi4chem.de/ts/ontologies/iao) | information artefacts | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | OBO Foundry, Allotrope™, PubChem, ISA tools | +| [OBI](https://terminology.nfdi4chem.de/ts/ontologies/obi) | biomedicine | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | OBO Foundry, Allotrope™, PubChem | +| [UO](https://terminology.nfdi4chem.de/ts/ontologies/uo) | scientific units | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | OBO Foundry, UOM, PubChem | +| [QUDT](http://www.qudt.org/pages/QUDToverviewPage.html) | scientific units | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based mapping possible | openPHACTS | +| [PATO](https://terminology.nfdi4chem.de/ts/ontologies/pato) | phenotypic & physical qualities | [CC-BY 3.0](https://creativecommons.org/licenses/by/3.0/) | BFO & OBO based | OBO Foundry, Allotrope™ | +| [SIO](https://terminology.nfdi4chem.de/ts/ontologies/sio) | upper level | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO alignment | PubChemRDF, Bio2RDF, SADI Semantic Web Services, DisGeNET, EBI's Gene Expression Atlas, Graph4Code project | +| [EDAM](https://terminology.nfdi4chem.de/ts/ontologies/edam) | life-sciences & data management | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO mapping possible | EMBOSS, Bio-jETI | +| [OntoCAPE](http://www.theworldavatar.com/ontology/ontocape/OntoCAPE.owl)| upper level & engineering | [GNU GPLv2](https://www.gnu.org/licenses/old-licenses/gpl-2.0) | provides upper level concepts | J-Park Simulator | ## General Scientific Ontologies @@ -86,7 +86,7 @@ The second version of the **Basic Formal Ontology ([BFO 2.0](https://terminology ### SIO -The **Semanticscience Integrated Ontology ([SIO](https://terminology.nfdi4chem.de/ts/ontologies/sio))** is another upper level ontology that provides basic concepts (e.g. objects, information and processes) as well as their associated basic characteristics (e.g. functions, qualities and roles). It also contains many basic relations (e.g. _part of_, _has participant_ or _is about_) needed in the description of real objects, processes and information. It has been used in [Bio2RDF](http://bio2rdf.org/), [SADI Semantic Web Services](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212890/), [DisGeNET](https://www.disgenet.org/rdf), [PubChemRDF](http://pubchem.ncbi.nlm.nih.gov/rdf/), [EBI's Gene Expression Atlas](https://www.ebi.ac.uk/gxa/home) and the [Graph4Code project](https://wala.github.io/graph4code/). To foster semantic interoperability, SIO is mapped to BFO and RO for important core classes and relations. +The **Semanticscience Integrated Ontology ([SIO](https://terminology.nfdi4chem.de/ts/ontologies/sio))** is another upper level ontology that provides basic concepts (e.g. objects, information and processes) as well as their associated basic characteristics (e.g. functions, qualities and roles). It also contains many basic relations (e.g. _part of_, _has participant_ or _is about_) needed in the description of real objects, processes and information. It has been used in [Bio2RDF](http://bio2rdf.org/), [SADI Semantic Web Services](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212890/), [DisGeNET](https://www.disgenet.org/rdf), [PubChemRDF](https://pubchem.ncbi.nlm.nih.gov/docs/rdf), [EBI's Gene Expression Atlas](https://www.ebi.ac.uk/gxa/home) and the [Graph4Code project](https://wala.github.io/graph4code/). To foster semantic interoperability, SIO is mapped to BFO and RO for important core classes and relations. ### OntoCape From bfe0966814099d58b1c15a345ec1b23543a16211 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Tue, 2 Dec 2025 09:27:59 +0100 Subject: [PATCH 2/3] outsource links --- .../20_ontology.mdx | 78 +++++++++++++------ 1 file changed, 54 insertions(+), 24 deletions(-) diff --git a/docs/60_topics/63_data_description_annotation/20_ontology.mdx b/docs/60_topics/63_data_description_annotation/20_ontology.mdx index d25b4e6e..d13ee2ae 100644 --- a/docs/60_topics/63_data_description_annotation/20_ontology.mdx +++ b/docs/60_topics/63_data_description_annotation/20_ontology.mdx @@ -53,30 +53,60 @@ This tabular overview lists the suitable ontologies with regard to: - the possibility of reusing them in a modular way (whereas a BFO alignment and OBO compatibility indicates an increased possibility), - and, their use in known applications. -| Ontology | Domain | Licence | Modularity | Used in | -| ----------------------------------------------------------------------- | ------------------------------- | -------------------------------------------------------------------------------- | ---------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------- | -| [ChEBI](https://www.ebi.ac.uk/ols/ontologies/chebi) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB | -| [CHIRO](https://terminology.nfdi4chem.de/ts/ontologies/chiro) | chemistry | [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/) | BFO & OBO based | unknown | -| [ChemOnt](http://classyfire.wishartlab.com/downloads) | chemistry | custom OA licence | subsumable under BFO's _material entity_ | YMDB, HMDB, T3DB, ECMDB, DrugBank,PubChem, ChEBI, LIPID MAPS, MoNA | -| [CHEMINF](https://terminology.nfdi4chem.de/ts/ontologies/cheminf) | chemistry | [CC-BY 3.0](https://creativecommons.org/licenses/by/3.0/) | BFO & OBO based | PubChem, Open PHACTS | -| [CHMO](https://terminology.nfdi4chem.de/ts/ontologies/chmo) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | Chemotion, Allotrope™ | -| [MOP](https://terminology.nfdi4chem.de/ts/ontologies/mop) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | RXNO | -| [RXNO](https://terminology.nfdi4chem.de/ts/ontologies/rxno) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | NameRXN, Wikipedia, Chemotion | -| [OntoKin](http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl) | chemistry | [MIT](https://github.com/TheWorldAvatar/ontology/blob/main/LICENSE.txt) | OntoCAPE upper level & modules | J-Park Simulator | -| [AFO](https://www.ebi.ac.uk/ols/ontologies/afo) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO classes & relations, many AFO- some custom OBO-modules | Allotrope™ | -| [PROCO](http://purl.obolibrary.org/obo/proco.owl) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO/AFO & OBO based | Allotrope™ | -| [MS](https://terminology.nfdi4chem.de/ontologies/ms) | chemistry | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO mapping possible | mzML | -| [nmrCV](https://terminology.nfdi4chem.de/ontologies/nmrcv) | chemistry | [Public Domain Mark 1.0](https://creativecommons.org/publicdomain/mark/1.0/deed) | BFO & OBO mapping possible | MetaboLights, HMDB | -| [BFO](https://terminology.nfdi4chem.de/ontologies/bfo) | upper level (classes only) | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | OBO backbone | >300 ontologies & >50 organizations, PubChem | -| [RO](https://terminology.nfdi4chem.de/ts/ontologies/ro) | upper level (relations) | CC0 1.0 | BFO & OBO based | Monarch Initiative, OBO Foundry, Gene Ontology, PubChem | -| [IAO](https://terminology.nfdi4chem.de/ts/ontologies/iao) | information artefacts | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | OBO Foundry, Allotrope™, PubChem, ISA tools | -| [OBI](https://terminology.nfdi4chem.de/ts/ontologies/obi) | biomedicine | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | OBO Foundry, Allotrope™, PubChem | -| [UO](https://terminology.nfdi4chem.de/ts/ontologies/uo) | scientific units | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based | OBO Foundry, UOM, PubChem | -| [QUDT](http://www.qudt.org/pages/QUDToverviewPage.html) | scientific units | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO based mapping possible | openPHACTS | -| [PATO](https://terminology.nfdi4chem.de/ts/ontologies/pato) | phenotypic & physical qualities | [CC-BY 3.0](https://creativecommons.org/licenses/by/3.0/) | BFO & OBO based | OBO Foundry, Allotrope™ | -| [SIO](https://terminology.nfdi4chem.de/ts/ontologies/sio) | upper level | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO alignment | PubChemRDF, Bio2RDF, SADI Semantic Web Services, DisGeNET, EBI's Gene Expression Atlas, Graph4Code project | -| [EDAM](https://terminology.nfdi4chem.de/ts/ontologies/edam) | life-sciences & data management | [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) | BFO & OBO mapping possible | EMBOSS, Bio-jETI | -| [OntoCAPE](http://www.theworldavatar.com/ontology/ontocape/OntoCAPE.owl)| upper level & engineering | [GNU GPLv2](https://www.gnu.org/licenses/old-licenses/gpl-2.0) | provides upper level concepts | J-Park Simulator | +|Ontology |Domain |Licence |Modularity |Used in | +|----------|-------------------------------|------------------------|----------------------------------------------------------|----------------------------------------------------------------------------------------------------------| +|[ChEBI] |chemistry |[CC-BY 4.0] |BFO & OBO based |YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB | +|[CHIRO] |chemistry |[CC0 1.0] |BFO & OBO based |unknown | +|[ChemOnt] |chemistry |custom OA licence |subsumable under BFO's _material entity_ |YMDB, HMDB, T3DB, ECMDB, DrugBank,PubChem, ChEBI, LIPID MAPS, MoNA | +|[CHEMINF] |chemistry |[CC-BY 3.0] |BFO & OBO based |PubChem, Open PHACTS | +|[CHMO] |chemistry |[CC-BY 4.0] |BFO & OBO based |Chemotion, Allotrope™ | +|[MOP] |chemistry |[CC-BY 4.0] |BFO & OBO based |RXNO | +|[RXNO] |chemistry |[CC-BY 4.0] |BFO & OBO based |NameRXN, Wikipedia, Chemotion | +|[OntoKin] |chemistry |[MIT] |OntoCAPE upper level & modules |J-Park Simulator | +|[AFO] |chemistry |[CC-BY 4.0] |BFO classes & relations, many AFO- some custom OBO-modules|Allotrope™ | +|[PROCO] |chemistry |[CC-BY 4.0] |BFO/AFO & OBO based |Allotrope™ | +|[MS] |chemistry |[CC-BY 4.0] |BFO & OBO mapping possible |mzML | +|[nmrCV] |chemistry |[Public Domain Mark 1.0]|BFO & OBO mapping possible |MetaboLights, HMDB | +|[BFO] |upper level (classes only) |[CC-BY 4.0] |OBO backbone |>300 ontologies & >50 organizations, PubChem | +|[RO] |upper level (relations) |[CC0 1.0] |BFO & OBO based |Monarch Initiative, OBO Foundry, Gene Ontology, PubChem | +|[IAO] |information artefacts |[CC-BY 4.0] |BFO & OBO based |OBO Foundry, Allotrope™, PubChem, ISA tools | +|[OBI] |biomedicine |[CC-BY 4.0] |BFO & OBO based |OBO Foundry, Allotrope™, PubChem | +|[UO] |scientific units |[CC-BY 4.0] |BFO & OBO based |OBO Foundry, UOM, PubChem | +|[QUDT] |scientific units |[CC-BY 4.0] |BFO & OBO based mapping possible |openPHACTS | +|[PATO] |phenotypic & physical qualities|[CC-BY 3.0] |BFO & OBO based |OBO Foundry, Allotrope™ | +|[SIO] |upper level |[CC-BY 4.0] |BFO alignment |PubChemRDF, Bio2RDF, SADI Semantic Web Services, DisGeNET, EBI's Gene Expression Atlas, Graph4Code project| +|[EDAM] |life-sciences & data management|[CC-BY 4.0] |BFO & OBO mapping possible |EMBOSS, Bio-jETI | +|[OntoCAPE]|upper level & engineering |[GNU GPLv2] |provides upper level concepts |J-Park Simulator | + +[ChEBI]: https://www.ebi.ac.uk/ols/ontologies/chebi +[CHIRO]: https://terminology.nfdi4chem.de/ts/ontologies/chiro +[ChemOnt]: http://classyfire.wishartlab.com/downloads +[CHEMINF]: https://terminology.nfdi4chem.de/ts/ontologies/cheminf +[CHMO]: https://terminology.nfdi4chem.de/ts/ontologies/chmo +[MOP]: https://terminology.nfdi4chem.de/ts/ontologies/mop +[RXNO]: https://terminology.nfdi4chem.de/ts/ontologies/rxno +[OntoKin]: http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl +[AFO]: https://www.ebi.ac.uk/ols/ontologies/afo +[PROCO]: http://purl.obolibrary.org/obo/proco.owl +[MS]: https://terminology.nfdi4chem.de/ontologies/ms +[nmrCV]: https://terminology.nfdi4chem.de/ontologies/nmrcv +[BFO]: https://terminology.nfdi4chem.de/ontologies/bfo +[RO]: https://terminology.nfdi4chem.de/ts/ontologies/ro +[IAO]: https://terminology.nfdi4chem.de/ts/ontologies/iao +[OBI]: https://terminology.nfdi4chem.de/ts/ontologies/obi +[UO]: https://terminology.nfdi4chem.de/ts/ontologies/uo +[QUDT]: http://www.qudt.org/pages/QUDToverviewPage.html +[PATO]: https://terminology.nfdi4chem.de/ts/ontologies/pato +[SIO]: https://terminology.nfdi4chem.de/ts/ontologies/sio +[EDAM]: https://terminology.nfdi4chem.de/ts/ontologies/edam +[OntoCAPE]: http://www.theworldavatar.com/ontology/ontocape/OntoCAPE.owl + +[CC-BY 3.0]: https://creativecommons.org/licenses/by/3.0/ +[CC-BY 4.0]: https://creativecommons.org/licenses/by/4.0/ +[CC0 1.0]: https://creativecommons.org/publicdomain/zero/1.0/ +[Public Domain Mark 1.0]: https://creativecommons.org/publicdomain/mark/1.0/deed +[GNU GPLv2]: https://www.gnu.org/licenses/old-licenses/gpl-2.0 +[MIT]: https://github.com/TheWorldAvatar/ontology/blob/main/LICENSE.txt ## General Scientific Ontologies From 88fb035b6ac77ca4967681c24725aa8462a7bfb1 Mon Sep 17 00:00:00 2001 From: Johannes Liermann Date: Tue, 2 Dec 2025 10:06:22 +0100 Subject: [PATCH 3/3] chore: remove unused dependency --- package.json | 1 - 1 file changed, 1 deletion(-) diff --git a/package.json b/package.json index 3227a004..0348944d 100644 --- a/package.json +++ b/package.json @@ -20,7 +20,6 @@ "@docusaurus/faster": "^3.9.2", "@docusaurus/plugin-sitemap": "^3.9.2", "@docusaurus/preset-classic": "^3.9.2", - "@easyops-cn/docusaurus-search-local": "^0.52.1", "@fontsource/ibm-plex-sans": "^5.2.8", "@mdx-js/react": "^3.1.1", "clsx": "^2.1.1",