Re: [hcls] ISMB Bioontologies SIG Poster

Matthias Samwald wrote:
> * Add connections between RDF/OWL resources that I have overlooked so
> far, based on the criteria described on the wiki page: "Only make
> connections where there really are substantial connections on the RDF
> level, i.e. relations spanning the two ontologies. As a counter-example,
> several ontologies have some kind of mapping or annotation with Uniprot
> entries, but since Uniprot RDF and these ontologies do not use the same
> URIs, these are not shown as connections. If two ontologies are mapped
> in a separate mapping file, there should be a direct connection between
> both ontologies and the mapping file should not be depicted. Connections
> should also be omitted if the number of actual relations is minimal
> (e.g. only one or two). If in doubt, do not introduce a connection."
> (

Two suggestions:

1. UniProt is not one database, but several (some of which may be 
"duplicated" elsewhere in your map, and some are "duplicates" themselves).

It may therefore be worth adding these relationships to your map:

UniProtKB (UniProt) -- UniRef (UniProt)
UniProtKB (UniProt) -- UniParc (UniProt)
UniProtKB (UniProt) -- Taxonomy (UniProt)
UniProtKB (UniProt) -- Keywords (UniProt)
UniProtKB (UniProt) -- Pathways (UniProt)
UniProtKB (UniProt) -- GO (UniProt)
Keywords (UniProt) -- GO (UniProt)
UniRef (UniProt) -- Taxonomy (UniProt)
UniParc (UniProt) -- Taxonomy (UniProt)
UniProtKB (UniProt) -- Citations (UniProt)
UniProtKB (UniProt) -- Enzyme (UniProt)

2. I've created some mappings between the UniProt RDF distribution and 
several RDFified databases hosted by bio2rdf:


This would allow us to add the following connections:

UniProtKB (UniProt) -- OMIM (bio2rdf)
UniProtKB (UniProt) -- PDB (bio2rdf)
UniProtKB (UniProt) -- MGI (bio2rdf)
UniProtKB (UniProt) -- GenBank (bio2rdf)

Also, these, but they seem to be broken on the bio2rdf server right now:

Citations (UniProt) -- PubMed (bio2rdf)
UniProtKB (UniProt) -- InterPro (bio2rdf)
UniProtKB (UniProt) -- Ensembl (bio2rdf)

What do you think?

Received on Monday, 16 July 2007 16:42:15 UTC