Table 1.
Domains and subdomains covered by NIF, along with the vocabularies imported from external sources for each, and the corresponding NIF OWL module
| Domain | External sources | Import or adapt to OWL | NIF module | Unique classes (as of 4/28/08) | Comment |
|---|---|---|---|---|---|
| Organism taxonomy | NCBI Taxonomy, GBIF, ITIS, IMSR, Jackson Labs mouse catalog | adapt | http://purl.org/nbirn/birnlex/ontology/BIRNLex-OrganismalTaxonomy.owl | 760 | Specifically the taxonomy of model organisms in common use by neuroscientists |
| Molecules | IUPHAR ion channels and receptors, Sequence Ontology (SO); pending: NCBI Entrez Gene, NCBI Entrez Protein, NCBI RefSeq, NCBI Homologene; NIDA drug lists, PDSP Ki, ChEBI, and Protein Ontology | Adapt IUPHAR; import SO | http://purl.org/nif/ontology/NIF-Molecule.owl | 3,883 | Tested OWL representation techniques on this limited number of molecules (~750). See below for more detail on how molecules in general are to be addressed in NIFSTD |
| Sub-cellular anatomy | Sub-cellular Anatomy Ontology (SAO) | Import | http://ccdb.ucsd.edu/SAO/1.2.8/SAO.owl | 827 | SAO covers general cellular structure—referencing the Gene Ontology Cellular Component taxonomy—and more nerve cell-specific structures needed to characterize ultrastructural studies of the nervous system |
| Cell | CCDB, NeuronDB, NeuroMorpho.org terminologies; pending: OBO Cell Ontology | Adapt | http://purl.org/nif/ontology/NIF-Cell.owl | 128 | |
| Multi-scale representation of Nervous System Mac Macroscopic anatomy | NeuroNames extended by including terms from BIRN, SumsDB, BrainMap.org, etc | Adapt | http://purl.org/nbirn/birnlex/ontology/BIRNLex-Anatomy.owl | 1,398 | |
| Nervous system function | Sensory, Behavior, Cognition terms from NIF, BIRN, BrainMap.org, MeSH, and UMLS | Adapt | http://purl.org/nbirn/birnlex/ontology/BIRNLex-SenseCogBehavior.owl | 152 | |
| Nervous system dysfunction | Nervous system disease from MeSH, NINDS terminology; pending: OMIM | Adapt | http://purl.org/nbirn/birnlex/ontology/BIRNLex-Disease.owl | 333 | |
| Phenotypic qualities | PATO | Import | http://purl.org/nbirn/birnlex/ontology/BIRNLex-OBO-UBO.owl | 1949 | Imported as part of the OBO foundary core |
| Investigation: reagents | Overlaps with molecules above, especially RefSeq for mRNA, ChEBI, Sequence ontology; pending: Protein Ontology | Adapt and import | http://purl.org/nbirn/birnlex/ontology/BIRNLex-Investigation.owl | n.a. | |
| Investigation: instruments | Import | http://purl.org/nbirn/birnlex/ontology/BIRNLex-Investigation.owl | 566 | BIRNLex-Investigation imports a BIRNLex-OBI-Proxy file being assembled in parallel with the Ontology of Biomedical Investigation (OBI) This proxy will be replaced by OBI itself, once there is a full production release of OBI | |
| Investigation: protocols and plans | Biomaterial transformations, assays, data collection, data transformation | Import | http://purl.org/nbirn/birnlex/ontology/BIRNLex-Investigation.owl | (Included in 566 above) | same as above—i.e., ultimately derived from OBI |
| Investigation: resource type | NIF, OBI, IATR/NITRC, NCBC Resourceome ontology (BRO) | Mostly adapt, except for OBI | http://purl.org/nbirn/birnlex/ontology/BIRNLex-Investigation.owl | (Included in 566 above) | Will ultimately be a single ontology shared by NITRC, Resourceome, OBI, and NIF |
Also indicated is whether the source was in OWL or needed to be adapted, the number of unique classes (concepts) under each domain/subdomain and any comments about the import