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openphacts / GLOBAL

Global project issues [private for now. owner lee harland]
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RDF validation error for compound information output #372

Open danidi opened 7 years ago

danidi commented 7 years ago

For the default example of compound information, using rdf output format retrieves elements like ns1:drugbank_vocabulary:text for drugbank. The second : will cause parsing problems and give validation errors e.g. on http://openphacts.cs.man.ac.uk:9090/OPS-IMS/validate and https://www.w3.org/RDF/Validator/.

The same might be true for the ttl output.

stain commented 7 years ago

Confirmed, this is for both RDF/XML and Turtle

<http://bio2rdf.org/drugbank_resource:DB00398_DB00755> void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> ;
  ns1:interactingDrug <http://bio2rdf.org/drugbank:DB00755> ;
  ns2:drugbank_vocabulary:text "DDI between Sorafenib and Tretinoin - The strong CYP2C8 inhibitor, Sorafenib, may decrease the metabolism and clearance of oral Tretinoin. Consider alternate therapy or monitor for changes in Tretinoin effectiveness and adverse/toxic effects if Sorafenib is initiated, discontinued to dose changed."@en .

The prefix should be something like

@prefix drugbank: <http://bio2rdf.org/drugbank_vocabulary:> .

but I guess the last : there breaks something in Puelia, even if : is a valid URI path character