Bundles
The Neurocommons RDF distribution is organized into modules or "bundles". Following is list of what's provided. Each has its own page of documentation.
In most cases bundle B corresponds to named graph http://purl.org/science/graph/B.
| Bundle | Description | Documentation |
|---|---|---|
| Derived from MeSH: | ||
| mesh/mesh-skos | MeSH polyhierarchy represented using SKOS courtesy van Assem et al. | /mesh/mesh-skos |
| mesh/qualified-headings | MeSH qualified headings - defines one URI for each valid major/minor heading combination | /mesh/qualified-headings |
| Derived from Medline: | ||
| medline/subject-headings | Medline: NLM MeSH subject headings for all articles | /medline/subject-headings |
| medline/titles-years | Medline: title and year of publication for each article | /medline/titles-years |
| Derived from NCBI: | ||
| ncbi/goa | NCBI Gene Ontology annotations | /ncbi/goa |
| ncbi/homologene | NCBI Homologene selection | /ncbi/homologene |
| ncbi/gene-info | NCBI Gene gene synonyms extraction | /ncbi/gene-info |
| ncbi/gene-pubmed | Links from NCBI Gene to Medline | /ncbi/gene-pubmed |
| Ontologies: | ||
| bams | BAMS (Brain Architecture Management System) | /bams |
| galen | Galen ontology | /galen |
| obo/all | All OBO ontologies | /obo/all |
| mesh-eswc06 | Supporting ontology for conversion of MeSH polyhierarchy to RDF | /mesh-eswc06 |
| nci-thesaurus | NCI thesaurus | /nci-thesaurus |
| sciencecommons | Ad hoc Science Commons ontology | /sciencecommons |
| senselab | Senselab | /senselab |
| skos | W3C SKOS (Simple Knowledge Organization System) ontology | /skos |
| pdspki | PDSP Ki | /pdspki |
| Other: | ||
| addgene | Addgene plasmid catalog | /addgene |
| neurocommons-text | Neurocommons text processing pilot | /neurocommons-text |
| aba | ABA (Allen Brain Atlas) | /aba |
| reactome | Reactome records (direct from RDB) | /reactome |
| inferred-relations | Transitive closure of subclass and part_of | /inferred-relations |
| New in version 2 (forthcoming): | ||
| amino-acid | Amino acid ontology | /amino-acid |
| bfo | Basic Formal Ontology | /bfo |
| hla | IMGT/HLA | /hla |
| hpo | Human Phenotype Ontology | /hpo |
| iao | Information Artifact Ontology | /iao |
| mahco | Stemnet MaHCO | /mahco |
| medline/abstracts | Medline abstracts | /medline/abstracts |
| medline/alleles | Mentions of HLA alleles in Medline abstracts | /medline/alleles |
| medline/backbone | Medline 'backbone' | /medline/backbone |
| ncbi/gene-backbone | Entrez Gene 'backbone' | /ncbi/gene-backbone |
| ncbi/gene-names | Entrez Gene gene names | /ncbi/gene-names |
| nif | Neuroscience Information Framework (NIF) ontology | /nif |
| omim | OMIM links to Pubmed and to HLA allele mentions | /omim |
The best way to get bundles is via the RDF installer (RDFherd), but they are also available via HTTP at [1].
