BioPAX instance xml:base and URIs

[Igor Rodchenkov]

It bothered me recently - once again I found that using '#' as part of URI is not a good idea for BioPAX instance data. (It's ok for the ontology itself to define uris starting with "http://www.biopax.org/release/biopax-level3.owl#" though).

Look: http://www.w3.org/wiki/HashVsSlash

Using "slash URIs" is more flexible way to go if we care about all URIs be dereferenceable URIs, Linked Data, etc..

So, I wish providers use like:

• xml:base="http://biocyc.org/biopax/biopax-level3/" instead of xml:base="http://biocyc.org/biopax/biopax-level3#" or xml:base="http://biocyc.org/biopax/biopax-level3" (the latter will make URI look somewhat ugly);
  
• xml:base="http://www.pantherdb.org/pathways/biopax/" instead xml:base="http://www.pantherdb.org/pathways/biopax#";
  
• xml:base="http://www.phosphosite.org/phosphosite.owl/" instead xml:base="http://www.phosphosite.org/phosphosite.owl#";
  
• xml:base="http://www.reactome.org/biopax/48887/" instead xml:base="http://www.reactome.org/biopax/48887#"
  

('#' in RDF/XML expressions like rdf:about="#..." and rdf:resource="#..." means a different thing - it means for readers to replace '#' with xml:base there to get full URI; '#' in web URLs before query parameters is a special thing too. '#' is evil ;))

(PC2 uses, e.g., xml:base="http://purl.org/pc2/2/")

IR.

[Andrea Splendiani]

Hi,

The short answer is: you are right.

/ Uris are more linked-data/web friendly for instance data.

We should perhaps resurrect the Sem web docs we were working on long time ago and wrap some recommendation?

Ciao,

Andrea

Apologies for typos, Sent from an iPhone

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[Andrea Splendiani]

Hi,

on a related subject. Is there a chance for a remote contact at Harmony ?

ciao,

Andrea