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[bioontology-support] EDAM - PURLs

Trish Whetzel whetzel at stanford.edu
Mon Sep 27 17:01:49 PDT 2010


Hi Jon, 

Yes, the re-directs below will be possible. For the time being, we can re-direct all forms of the URLs below to EBI and when the new PURL software is released that supports suffix matching we can update PURLs of the form "http://purl.bioontology.org/ontology/EDAM/EDAM_0000613" to point to BioPortal, with the other PURLs still resolving to EBI. What is the target URL at EBI? 

We do maintain a PURL server, http://purl.bioontology.org. Feel free to sign-up for an account.  

Trish 

PS - cc'ing our support mailing list for tracking. 


On Sep 21, 2010, at 8:33 AM, Jon Ison wrote:

> Hi Trish
> 
> Hope all is well and thanks for the efforts with the NBCO BioPortal.
> 
> I must now revisit the issue of purls for the EDAM terms.  We talked in our previous emails about
> suffixes to purls and redirects to term end-points.
> 
> You mentioned that I could have
> (1) purls based on http://purl.bioontology.org/ that redirect to NCBO browser and
> (2) purls based on http://purl.obolibrary.org/ that redirect to EBI.
> 
> This sadly is not viable, as I need to recommend a single style of purl that'll be used e.g. for
> annotation purposes.
> 
> What I really need is support for suffixes that redirect to term endpoints in different formats e.g.:
> http://purl.bioontology.org/ontology/EDAM/EDAM_0000613 (default, NCBO browser)
> http://purl.bioontology.org/ontology/EDAM/EDAM_0000613?style=xml
> http://purl.bioontology.org/ontology/EDAM/EDAM_0000613?style=html
> http://purl.bioontology.org/ontology/EDAM/EDAM_0000613?style=txt
> http://purl.bioontology.org/ontology/EDAM/EDAM_0000613?style=json
> 
> Is this possible yet (somehow) with purls based on http://purl.bioontology.org/ ?
> 
> If not, I might have to use http://purl.obolibrary.org/ (which supports the suffixes) and set up a
> redirect at EBI, e.g. for suffix "?style=ncbo" and/or default (no suffix), which redirects to you.
> 
> One last question, I guess you're not responsible for http://purl.obolibrary.org/ - but do you run
> such a server?
> 
> Cheers
> 
> Jon
> 
> 
> 
> 
>>> So, if NCBO could add support for the "style=format" approach then
>>> that would be ideal, e.g.:
>>> http://purl.obolibrary.org/obo/EDAM_0000006?style=html
>>> http://purl.obolibrary.org/obo/EDAM_0000006?style=xml
>>> etc
>>> 
>>> Could you let me know please if that might be possible, and if so,
>>> when it might happen?
>> 
>> The PURL software currently supports the format '?style=<format>'.
>> More information can be found at: http://purl.org/docs/help.html,
>> section 2.2.  Therefore, you can have http://purl.bioontology.org/ontology/EDAM/EDAM_0000613
>>  resolve to the term in BioPortal and then http://purl.obolibrary.org/obo/EDAM_0000006?style=html
>>  resolve to EBI (note the PURLS in this example are set-up on two
>> different PURL servers). If the partial PURL on the obolibrary server
>> is set up to resolve to EBI then both http://purl.obolibrary.org/obo/EDAM_0000006?style=html
>>  and http://purl.obolibrary.org/obo/EDAM_0000006 will resolve to EBI
>> and the purl.bioontology.org PURL will resolve to BioPortal page.
>> 
>> 
>>> I'm happy for the default term end-points (when an URL is specified
>>> without a suffix) to be the
>>> NCBO browser, as is currently the case.
>>> 
>>> However, where a style is given, the URLs will need to resolve to EBI:
>>> http://wwwdev.ebi.ac.uk/Tools/dbfetch/dbfetch/edam/
>>> 
>>> and eventually (in some months time) to:
>>> http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/edam/
>>> 
>>> Will this be possible, is so, where do I set the basic end-point for
>>> my terms?
>> 
>> Yes, the target URL can be modified after the PURL is created.
>> 
>> 
>>> It might be that the URLs (including the default/without suffix)
>>> first to redirect to EBI, then
>>> (if no suffix is given) redirect back to the appropriate term in
>>> NCBO browser.
>> 
>> See example scenarios above.
>> 
>>> Depending on what can be done, I might not need your basic PURL
>>> server; the "OBO-foundry
>>> compliant" URLs as shown above are preferable.
>> 
>> All PURL servers have the same functionality. One of the additional
>> features we can provide for the community at large is a target for the
>> PURL to resolve to that is the HTML or RDF view of the term.
>> 
>> 
>> Best regards,
>> Trish
>> 
>> 
> 
> 




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