NFDI4Chem
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| FIX | Chemistry - physico-chemical methods and properties | unkown | orphaned, use discouraged | owl | OUTDATED/ORPHANED; not encurraged for reuse | only indexed | ||
| REX | Chemistry - physico-chemical processes | unkown | orphaned, use discouraged | owl | OUTDATED/ORPHANED; not encurraged for reuse | only indexed | ||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 |