20140520

RDF model (Ensembl/DDBJ/RefSeq)

• INSDC to RDF

SIO or SO

• ?gene sio:is-transcribed-into or so:so_transcribed_to ?transcript
• ?transcript sio:has-ordered-part ?exon, ?exon, ?exon ...
• ?exon sio:has-value, sio:refers-to ?exon_stable_uri
• Ask SO group (OBO foundry) to add descriptions and mappings to SIO?
• If they won't do it, we'll keep using SIO.

Sequence IDs

• To be precisely identify the reference sequence in FALDO, conceptual URI for chromosome can be ambiguous.
• Each data provider will use their own URIs for reference sequences.
• Still, we can design common URI patterns for reference sequence URIs, hopefully
• http://example.org/prefix/taxonomy_id/landmark_id
• taxonomy_id: NCBI Taxonomy ID or BioSamples ID or ...?
• landmark_id: Chromosomes, plasmids, contigs ...
• How to specify builds (assembly), versions?
• http://identifiers.org/insdc/XXX012345
• http://identifiers.org/refseq/NC_000001.10 (human chromosome 1, GRCh38)
• Or, Third party (e.g., Bio2RDF) can provide links to compatible sequence URIs

Ensembl

• Need to speak to EBI guys to proceed more...

Identifiers.org

• Going to make virtual SPARQL endpoint visible from outside
• Filter some parts of graph so that you can select just the active URIs
  • e.g.

       SELECT ?go ?protein {
	SERVICE <htttp://identifiers.org/mappingsparql>{ # just an example for now
      SELECT ?go
      WHERE {
        GRAPH <id:active> {
             <http://identifiers.org/go/GO:0000001> owl:sameAs ?go .
          }
      }
    }  
    ?protein up:classsifiedWith ?go.
}

And

SELECT ?go {
WHERE {
       <http://identifiers.org/go/GO:0000001> owl:sameAs ?go .
       FILTER(contains(str(?go), "bio2rdf")
}

GFVO

• Updated GFVO to convert GFF, GVF; no exceptions produced in Ruby code now.

• Coding VCF converter with SIO

• After Joachim releasing updated shell tool, Soichi will try to run it on his VCF files.

• Wrote converter RDF to JSON-LD to use NoSQL database as SPARQL endpoint; minimize JSON.

• RDF SPARQL On The Fly

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Low priority issues for this time

• Phenotype