civic_sample.ttl review

[JervenBolleman]

Hi all,

Great work on getting started with translating this data set into RDF!
I spotted some minor issues in the sample and thought to open an issue.

civicv:299
    civico:variantName "D473H"^^xsd:string ;
    m2r:evidence civice:745,civice:755,civice:1099 ;
    faldo:location [ 
    a faldo:Region ;
        faldo:begin [
            a faldo:ExactPosition ;
            faldo:position "128849189"^^xsd:integer ;
            faldo:reference "7"^^xsd:integer
        ];
	    faldo:end [
            a faldo:ExactPosition ;
            faldo:position "128849189"^^xsd:integer ;
            faldo:reference "7"^^xsd:integer
        ]
    ] ;
    m2r:reference_allele "G"^^xsd:string ;
    m2r:alternative_allele "C"^^xsd:string ;
    civico:referenceBuild "GRCh37"^^xsd:string ;
    civico:transcript "ENST00000249373.3"^^xsd:string ;
    civico:ensemblVersion "75"^^xsd:string ;
    civico:variantOrigin "Somatic Mutation"^^xsd:string ;
    m2r:disease civic:disease_0060105,civic:disease_2513 ;
    civico:variantID "299"^^xsd:string ;
    a obo:SO_0001583, m2r:Variation .

Here there is SNP described with a faldo:location (great !) I think this can be better modelled as in the example on SNP added by @ktym to the FALDO repository.

The faldo:reference is right now '7' but should be an IRI pointing to a chromsome, i.e. as in the Ensembl RDF it could be <http://rdf.ebi.ac.uk/resource/ensembl/75/homo_sapiens/GRCh38/7>

A great first effort!

[ktym]

Hi Jerven, thank you for your quick review. We'll update the use of FALDO for SNPs and the Ensembl reference URIs. May we assume that the reference chromosome URI will be the form of <http://rdf.ebi.ac.uk/resource/ensembl/75/homo_sapiens/GRCh38/7> as it seems that the use of URIs is somewhat inconsistent in the Ensembl RDF for now?