NFDI4Chem
The review The current landscape of author guidelines in chemistry through the lens of research data sharing provides an overview and usage guidance for ontologies in chemistry.
The table below is from the WG Ontology collection spreadsheet.
Source: /files/meta/Used_Ontologies_at_NFDI.xlsx (sheet: NFDI4Chem)
| Ontology ID | Domain | License | Modularity | Format | Used in | Comments | developed / reused / only indexed / only evaluated | NFDI4Chem contributions |
|---|---|---|---|---|---|---|---|---|
| AFO | Chemistry - all chemical domains | CC BY 4.0 | BFO 2020, questionable OBO alignment, imports: DCTERMS, CARO, SKOS, DC, OWL, RDFS, NCIT, OBI, NCBITAXON, IAO, PATO, ENVO, BFO, RO, CHEBI, CHMO | owl | Allotrope™ | reused | ||
| ChEBI | Chemistry - chemical entities | CC BY 4.0 | OBO_based, BFO_mappable, imports: RO, IAO, RDFS, OWL, OIO | owl | YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB | reused | ||
| ChemOnt | Chemistry - chemical entities | Custom OA license | BFO_mappable, ChEBI_mappable, OBO_mappable | owl | YMDB, HMDB, T3DB, ECMDB, DrugBank, PubChem, ChEBI, LIPID MAPS, MoNA | only evaluated | ||
| CHMO | Chemistry - chemical methods | CC BY 4.0 | OBO_based, extends OBI, maps_to: "FIX, REX", imports: CHEBI, OIO, DC, IAO, DCTERMS, OBI, MS, RDFS, BFO, OWL, RO, OBCS | owl | Chemotion, Allotrope™ | reused | on GitHub | |
| CHEMINF | Chemistry - cheminformatics | CC0 1.0 | OBO_based, extends IAO, imports: OIO, DC, OBI, RDFS, OWL, IAO, PR, DCTERMS, OMO, PATO, BFO, RO, CHEBI, APOLLO_SV, GO, UO, SKOS | owl | PubChem, Open PHACTS | reused | on GitHub | |
| MS | Chemistry - mass spectrometry | CC BY 4.0 | OBO_mappable, imports: CARO, CHEBI, RO, GO, NCBITAXON, DC, NCIT, PATO, UBERON, OBI, RDFS, OIO, DCTERMS, PR, IAO, SKOS, SO, NBO, OWL, OGMS, PCO, CL, ENVO, BFO, UO, BSPO, STATO | owl | mzML | reused | ||
| MOP | Chemistry - molecular reactions | CC BY 4.0 | BFO aligned, OBO based, imports: CHEBI, OIO, DC, IAO, DCTERMS, RDFS, BFO, RXNO, RO | owl | RXNO | reused | on GitHub | |
| nmrCV | Chemistry - NMR spectroscopy | Public Domain Mark 1.0 | BFO aligned, OBO_mappable, imports: DC, RDFS, OIO, DCTERMS, SKOS, IAO, BFO | owl | MetaboLights, HMDB | reused | on GitHub | |
| FIX | Chemistry - physico-chemical methods and properties | unkown | orphaned, use discouraged | owl | OUTDATED/ORPHANED; not encurraged for reuse | only indexed | ||
| REX | Chemistry - physico-chemical processes | unkown | orphaned, use discouraged | owl | OUTDATED/ORPHANED; not encurraged for reuse | only indexed | ||
| BFO | Upper level (classes only) | CC BY 4.0 | BFO version 2.0 classes only, OBO backbone | owl | ~300 ontologies & ~50 organizations, PubChem | reused | ||
| IAO | Information artifacts | CC BY 4.0 | BFO aligned, OBO based, imports: DC, OBI, RDFS, DCTERMS, OMO, OIO, PATO, BFO, RO, APOLLO_SV, UO | owl | OBO Foundry, Allotrope™, PubChem, ISA tools | reused | on GitHub | |
| OBI | Biomedicine | CC BY 4.0 | BFO aligned, OBO based, imports: CHEBI, GO, DC, NCBITAXON, OWL, OMRSE, UBERON, VO, RDFS, IAO, SO, PR, DCTERMS, CLO, OGMS, HP, IDO, OPL, OBA, PATO, CL, OIO, BFO, RO, COB, APOLLO_SV, ENVO, UO, CHMO | owl | OBO Foundry, Allotrope™, PubChem | reused | on GitHub | |
| UO | Scientific units | CC BY 3.0 | OBO_based | owl | OBO Foundry, UOM, PubChem | reused | on GitHub | |
| OM | Scientific units | CC BY 4.0 | no mapping/alignment to others known | owl | alignment probably not needed for use case of reusing for units | reused | ||
| QUDT | Scientific units | CC BY 4.0 | OBO_mappable | owl | Open PHACTS | reused | ||
| PATO | Phenotypic & physical qualities | CC BY 3.0 | OBO_based | owl | OBO Foundry, Allotrope™ | reused | on GitHub | |
| SEPIO | Scientific Evidence and Provenance | CC BY 3.0 | BFO aligned, OBO based (imports from OBI, RO, IAO, COB, PATO, STATO), partial PROV-O alignement (e.g. Agent & Activity) | owl | Ga4GH Variant Annotation Model | reused | ||
| ENVO | environments,environmental processes, ecosystems, habitats, and related entities | CC0 1.0 | OBO_based, BFO_aligned | owl | reused | |||
| PROV-O | general scientific and provenance | W3C License | W3C_based | owl | reused | |||
| SWO | software domain | CC BY 4.0 | BFO aligned | owl | reused | |||
| SIO | Upper level | CC BY 4.0 | BFO aligned | owl | PubChem, Bio2RDF, SADI Semantic Web Services, DisGeNET’s gene-disease associations, EBI’s Gene Expression Atlas, Graph4Code | reused | ||
| EDAM | Life-sciences & data management | CC BY 4.0 | OBO_mappable | owl | EMBOSS, Bio-jETI | reused | ||
| EFO | experimental variables | Apache License 2.0 | BFO aligned | owl | EBI databases, core ontology for OpenTargets.org, NHGRI GWAS catalogue | reused | on GitHub | |
| RO | General science w/focus on life sciences | CC0 1.0 | OBO_based, BFO_aligned, DC, OIO, DCTERMS, IAO, SKOS, OBI, OGMS, OMO, UBERON, RDFS, PATO, ENVO, BFO, GO, CL, CHEBI | owl | all OBO ontologies and many others | reused | on GitHub | |
| DUO | data use conditions | CC BY 4.0 | OBO_based, BFO_aligned | owl | reused | |||
| TIME | Time | CC BY 4.0 | no mapping/alignment to others known, W3C_based | owl | reused | |||
| PROCO | Chemistry - process chemistry | CC BY 4.0 | AFO & OBO based, BFO_aligned | owl | Allotrope™ | reused | ||
| SOSA | general scientific domain (Sensor, Observation, Sample, and Actuator) | W3C License | W3C_based (imports FOAF & TIME) | owl | only indexed | |||
| SSN | general scientific domain (Sensor, Observation, Sample, and Actuator) | W3C License | W3C_based (imports SOSA, FOAF & TIME) | owl | only indexed | |||
| SSN-SYSTEM | SSN extention | W3C License | W3C_based | owl | only indexed | |||
| OBOE | general scientific domain (scientific observation and measurement) | CC BY 3.0 | owl | only indexed | ||||
| BTO | Biology - enzyme comprising tissues, cell lines, cell types and cell cultures | CC BY 4.0 | no mapping/alignment to others known, slim ontological commitment allows for broad modular reuse | owl | OBO ontology; indexed in NFDI4Chem due to NMRxiv's need for annotating biosogicalsamples | only indexed | ||
| OntoKin | Chemistry - reaction kinetics | Unknown | based on OntoCAPE upper level & modules, OBO_incompatible | owl | J-Park Simulator | only indexed | ||
| CHIRO | Chemistry - roles of chemical entities | CC0 1.0 | OBO_based, extends ChEBI's role branch, BFO_aligned | owl | Unknown | reused | ||
| MI | Biology - structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions | CC BY 4.0 | no mapping/alignment to others known | owl | unsure why indexed | only indexed | ||
| NCIT | Biology - reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities | CC BY 4.0 | OBO_based | owl | unsure why indexed, not BFO aligned but OBO Edition | only indexed | ||
| MOD | Biology - protein chemical modifications | CC BY 4.0 | no mapping/alignment to others known | owl | unsure why indexed | only indexed | ||
| REPRODUCEME | General science | CC BY-NC-SA 2.0 | P-PLAN & PROV-O extention | owl | only indexed | |||
| OntoCAPE | Upper level & engineering | GNU GPLv2 | no mapping/alignment to others known | owl | J-Park Simulator | only evaluated | ||
| RXNO | Chemistry - synthetic reactions | CC BY 4.0 | OBO_based, extends MOP & OBI, BFO_aligned | owl | NameRXN, Wikipedia, Chemotion | reused | on GitHub | |
| VIBSO | Chemistry - vibrational spectroscopy | CC BY 4.0 | OBO_based, extends CHMO & OBI, BFO_aligned | owl | NFDI4Chem | developed | on GitHub | |
| DCTERMS | General | CC BY 4.0 | used as module for annotation properties | rdf | used for ontology annotations, e.g contributor, license etc. | reused | ||
| DCAT | General | W3C License | W3C_based | owl | NFDI4Chem Search service | reused | ||
| BIOSCHEMA | Biology, Chemistry | CC BY 4.0 | SCHEMA_aligned | rdf | NFDI4Chem Search service, and possibly others | reused | yes by TA2 & TA4 |