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diff --git a/issues/rdf/expose-rdf-to-web.gmi b/issues/rdf/expose-rdf-to-web.gmi new file mode 100644 index 0000000..e5da94a --- /dev/null +++ b/issues/rdf/expose-rdf-to-web.gmi @@ -0,0 +1,85 @@ +# Expose Versioned "rdf.genenetwork.org" Namespaces + +* assigned: bonfacem +* status: in-progress + +## Description + +We have switched all RDF namespaces from "genenetwork.org" to the versioned base "rdf.genenetwork.org/v1." These endpoints don't resolve yet. + +## What changed + +Replaced + +* "http://genenetwork.org/id/" -> "http://rdf.genenetwork.org/v1/id/" +* "http://genenetwork.org/category/" -> "http://rdf.genenetwork.org/v1/category/" +* "http://genenetwork.org/term/" -> "http://rdf.genenetwork.org/v1/term/" + +## Current Problem + +New "rdf.genenetwork.org/v1/*" URIs return a 5XX/4XX which blocks validation, dereferencing and external re-use + +## Expected Behaviour + +All rdf.genenetwork.org/v1/* namespaces resolve over HTTP. At minimum: + +* Human-readable HTML in a browser. +* RDF (Turtle or RDF/XML) via content negotiation. + +## Notes + +(Example) Queries for all terms/categories/ids: + +``` +PREFIX gn: <http://rdf.genenetwork.org/v1/id/> +PREFIX gnc: <http://rdf.genenetwork.org/v1/category/> +PREFIX gnt: <http://rdf.genenetwork.org/v1/term/> + +CONSTRUCT { + gn:Arabidopsis_thaliana ?p ?o . +} FROM <http://rdf.genenetwork.org/v1> +WHERE { + gn:Arabidopsis_thaliana ?p ?o . + ?s ?p ?o . +} + +CONSTRUCT { + gnc:phenotype ?p ?o . +} FROM <http://rdf.genenetwork.org/v1> +WHERE { + gnc:phenotype ?p ?o . + ?s ?p ?o . +} + +CONSTRUCT { + gnt:shortName ?p ?o . +} FROM <http://rdf.genenetwork.org/v1> +WHERE { + gnt:shortName ?p ?o . + ?s ?p ?o . +} + +``` + +Some terms/categories/ids descriptions will have to be manually updated since querying them as a subject return nothing. + +When serving, all supported formats based off Virtuoso's content negotiation: + +=> https://docs.openlinksw.com/virtuoso/rdfsparqlprotocolendpoint/ + +Location of all files (tux02): /export/data/genenetwork-virtuoso/ + +For current gn3, old data is maintained in this named graph: "http://genenetwork.org" while new data is being uploaded to this named graph: "http://rdf.genenetwork.org/v1" + +## Tasks + +* [X] Set up new named graph for the rdf endpoint. Maintain old named graph for gn3 stability. +* [X] Serve: "/v1/id/<id>"; "/v1/category/<category>"; and "/v1/term/<term>" under "rdf.genenetwork.org" as "text/microdata+html" +* [X] Verify: `curl -H "Accept: text/html" http://rdf.genenetwork.org/v1/term/...` +* [X] Configure DNS (rdf.genenetwork.org) to point to gn-guile server. + +## Resolution + +=> https://git.genenetwork.org/gn-guile/commit/?id=45662839565f6482e7f034a07ae373bbeaeb9713 + +* closed |
