Change identifiers.org URLs to have https instead of http

marvinm2 commented 3 years ago

In the RDF, the identifiers of chemicals and genes/proteins are with IRIs that start with 'http://'. These should be updated to 'https://'

egonw commented 3 years ago

Example WPRDF:

<http://identifiers.org/ncbigene/7337>
        a                   wp:Protein , wp:DataNode ;

Where others use https://identifiers.org/ncbigene/7337.

egonw commented 3 years ago

Typical example of SPARQL queries that need updating but often simplify:

BIND(IRI(CONCAT("http://identifiers.org/aop/",?_aopfilter_integer)) AS ?AOPf )

and

BIND ( iri(concat("https://identifiers.org/", ?Hgnc_id)) AS ?hgncUri )

egonw commented 3 years ago

Updates needed:

[x] update unit tests (where http://identifiers.org is hardcoded)
[ ] https://www.wikipathways.org/index.php/Help:WikiPathways_Sparql_queries

egonw commented 3 years ago

New RDF:

<https://identifiers.org/ncbigene/4548>
        a                              wp:Protein , wp:DataNode ;
        rdfs:label                     "MTR*"^^xsd:string ;
        dc:identifier                  <https://identifiers.org/ncbigene/4548> ;
        dc:source                      "Entrez Gene"^^xsd:string ;
        dcterms:bibliographicCitation  <https://identifiers.org/pubmed/17163662> , <https://identifiers.org/pubmed/6107306> , <https://identifiers.org/pubmed/10377254> , <https://identifiers.org/pubmed/10833329> , <https://identifiers.org/pubmed/19450180> ;
        dcterms:identifier             "4548"^^xsd:string ;
        dcterms:isPartOf               <http://rdf.wikipathways.org/Pathway/WP1533_r107121/WP/Interaction/af0e5> , <http://rdf.wikipathways.org/Pathway/WP1533_r107121/WP/Interaction/id808612a1> , <https://identifiers.org/wikipathways/WP1533_r107121> , <http://rdf.wikipathways.org/Pathway/WP1533_r107121/WP/Interaction/id2d5f4bfa> , <http://rdf.wikipathways.org/Pathway/WP1533_r107121/WP/Interaction/e1d06> ;
        wp:bdbEnsembl                  <https://identifiers.org/ensembl/ENSG00000116984> ;
        wp:bdbEntrezGene               <https://identifiers.org/ncbigene/4548> ;
        wp:bdbHgncSymbol               <https://identifiers.org/hgnc.symbol/MTR> ;
        wp:bdbUniprot                  <https://identifiers.org/uniprot/Q99707> , <https://identifiers.org/uniprot/B1ANE3> ;
        wp:isAbout                     <http://rdf.wikipathways.org/Pathway/WP1533_r107121/DataNode/c34ed> ;
        foaf:page                      <http://www.ncbi.nlm.nih.gov/gene/4548> .

wikipathways / GPML2RDF

Change identifiers.org URLs to have https instead of http #98