Bundles

(Redirected from Graph contents)

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].