Bundles/omim

Bundle: omim
Graph: <http://purl.org/science/graph/omim>

Home page: http://www.ncbi.nlm.nih.gov/omim/

OMIM records, named with pseudo-common-naming-system URIs e.g. <http://purl.org/common/record/omim/126200>, have type sc:omim_record .

OMIM / HLA

The bundle captures a small amount of the information available in the OMIM flat file - only the HLA associations at this point. There were 236 of these as of August 2009, as found via regular expression match.

In this bundle OMIM records are related to allele classes (e.g. <http://purl.org/stemnet/HLA#DRB_1501>, see Bundles/mahco-hla) via the IAO "mentions" relation <http://purl.obolibrary.org/obo/IAO_0000142>.

<http://purl.org/common/record/omim/126200>
  <http://purl.obolibrary.org/obo/IAO_0000142>
  <http://purl.org/stemnet/HLA#DRB_1501>.

OMIM / Pubmed

Each OMIM record has multiple references to the literature. NCBI provides a flat file giving pubmed ids for these references. The OMIM record is related to the journal article via the IAO 'mentions' relation (the OMIM record mentions the article). (If we had 'cites' this would feel nicer.)

Some OMIM citations of articles

PREFIX foaf: <http://xmlns.com/foaf/0.1/>
prefix sc: <http://purl.org/science/owl/sciencecommons/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix mentions: <http://purl.obolibrary.org/obo/IAO_0000142>

select ?label ?pmid
where 
 {
  ?omim rdf:type sc:omim_record . 
  ?omim mentions: ?article . 
  ?omim rdfs:label ?label .
  ?pubmed foaf:primaryTopic ?article .
  ?pubmed sc:has_id_in_databank ?pmid .
 }
limit 20

See also ImmPort