Table 1.
The NIFSTD OWL modules and corresponding community sources from which they were built.
| NIFSTD modules | External source | Import/adapt |
|---|---|---|
| Organismal taxonomy | NCBI Taxonomy, GBIF, ITIS, IMSR, Jackson Labs mouse catalog; the model organisms in common use by neuroscientists are extracted from NCBI taxonomy and kept in a separate module with mappings | Adapt |
| Molecules, chemicals | IUPHAR ion channels and receptors, sequence ontology (SO); NIDA drug lists from ChEBI, and imported protein ontology (PRO) | Adapt/import |
| Sub-cellular anatomy | Sub-cellular anatomy ontology (SAO). Extracted cell parts and sub-cellular structures from SAO-CORE. Imported GO cellular component with mapping | Adapt/import |
| Cell | CCDB, NeuronDB, NeuroMorpho.org. Terminologies; OBO cell ontology was not considered as it did not contain region specific cell types | Adapt |
| Gross anatomy | NeuroNames extended by including terms from BIRNLex, SumsDB, BrainMap.org, etc.; multi-scale representation of nervous system, macroscopic anatomy | Adapt |
| Nervous system function | Sensory, behavior, cognition terms from NIF, BIRN, BrainMap.org, MeSH, and UMLS | Adapt |
| Nervous system dysfunction | Nervous system disease from MeSH, NINDS terminology; Imported Disease Ontology (DO) with mapping | Adapt/import |
| Phenotypic qualities | Phenotypic quality ontology (PATO); imported as part of the OBO foundry core | Import |
| Investigation: reagents | Overlaps with molecules above from ChEBI, SO, and PRO | Adapt/import |
| Investigation: instruments, protocols, plans | Based on the ontology for biomedical investigation (OBI) to include entities for biomaterial transformations, assays, data collection, data transformations. OBI-Proxi class still remains. See discussion below | Adapt |
| Investigation: resource type | NIF, OBI, NITRC, biomedical resource ontology (BRO) | Adapt |
| Investigation: cognitive paradigm | Cognitive paradigm ontology (CogPO) was extended from NIF-investigation module | Import |
| Biological process | Gene ontology (GO) biological process | Import |
This table reports the updates of the external sources that were previously used in Bug et al. (2008) paper.