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PathVisio / pathvisio

PathVisio - pathway editor, visualization and analysis software
http://www.pathvisio.org
Apache License 2.0
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Pathvisio 4 vs 3.3.0 DOI ref wrong address #204

Open ondrej-kuda opened 8 months ago

ondrej-kuda commented 8 months ago

Hi, I edited a pathway in PV4 and inserted refs as DOIs. When I open it in PV3 and upload it to web, the link is broken - an extra prefix https://doi.org/ is used. Best regards, Ondrej

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khanspers commented 8 months ago

@mkutmon @egonw : I assume these references need to be adjusted in PV3 to upload correctly?

egonw commented 8 months ago

I can fix that

egonw commented 8 months ago

hi @ondrej-kuda, the DOI is in some way not clearly defined and the display guidelines often write something like "the DOI should be displayed as https://doi.org/10....", but in GPML it is just the unique part:

    <bp:PublicationXref xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:id="dc64d">
      <bp:ID rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.1074/jbc.M403484200</bp:ID>
      <bp:DB rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DOI</bp:DB>
      <bp:TITLE rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></bp:TITLE>
      <bp:SOURCE rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></bp:SOURCE>
      <bp:YEAR rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></bp:YEAR>
    </bp:PublicationXref>

Mind you, on the classic website, the title, authors, year, source, will not show up, but on the new website it will look up that info and still display it.

ondrej-kuda commented 8 months ago

Hi Egon, thank you for your help. I used the GUI tool to insert the refs: Citation > New citation > identifier in DOI database > Query > Done. Best regards, Ondrej

egonw commented 8 months ago

Yes, that is the right way. The DOI support is still under development, and while it only provides limited support, I'm happy we support them in the first place, because not all literature is indexed in PubMed.