20140519

RDF model

• Refactored to use feature, region, position URI fragments instead of UUIDs
• Introdueced SIO for gene/exons

Ensembl

• Fixed some stuff.
• Started to model bits of Ensembl variations
• Started writing scripts to populate the model.

Identifiers

Made a virtual SPARQL endpoint that can be used to auto map identifiers from one database to an other. You can check it out from github. Currently it is hard coded to Camille's laptop IP and needs to be brought to production standard. However today the script works correctly.

./sparql-identifiers.sh "PREFIX owl: <http://www.w3.org/2002/07/owl#> 
SELECT ?target ?type  
WHERE {
    <http://identifiers.org/go/GO:0006915> owl:sameAs ?target 
    SERVICE<http://beta.sparql.uniprot.org/sparql/>
        {?target a ?type}}"

• Discussed generic URIs for chromosomes
• Chromosome ontology to subtype Human chromosome 1 concept?
• or create new "genome" database to register at http://identifiers.org/genome ?