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[bioontology-support] [Obo-unit] Proposal to change UO to a representation of instances
whetzel at stanford.edu
Fri Dec 25 15:49:41 PST 2009
The request for the change to the BioPortal Term Web service output related
to the ID field has been added to the tracker.
>From: Alan Ruttenberg [mailto:alanruttenberg at gmail.com]
>Sent: Thursday, December 24, 2009 2:14 PM
>To: Trish Whetzel
>Cc: Philippe Rocca-Serra; George Gkoutos; Chris Mungall; obo-unit;
>Subject: Re: [Obo-unit] Proposal to change UO to a representation of
>On Thursday, December 24, 2009, Trish Whetzel <whetzel at stanford.edu>
>> Yes, that is a known issue. Just to clarify, is presenting the value
>for the id field as OBI_000046, without the prefix ok?
>No, I don't think so. There is one ID OBI defines for the term, and
>that is the URI. Abbreviations for it are acceptable as long as the
>abbreviation mechanism is well defined, as is the case in all the RDF
>serializations. There are also abbreviation mechanisms available in
>XML. For OBO format there is a policy and documentation being drafted
>it, but this isn't OBO format.
>Why don't you use XML entities if you want to abbreviate?
>> On Dec 24, 2009, at 7:45 AM, Alan Ruttenberg wrote:
>> I miswrote "obi:" instead of "obo:". Substance of the comment still
>> On Thu, Dec 24, 2009 at 10:37 AM, Alan Ruttenberg
>> <alanruttenberg at gmail.com> wrote:
>> Hi Trish,
>> That returns:
>> <accessDate>2009-12-24 07:32:59.258 PST</accessDate>
>> The ID field should either be removed, or another field in which
>> prefixes are defined be added. A prefix like "obi:" standing in
>> isolation is meaningless, and the string obi:OBI_0000462 similarly has
>> no meaning (nor should it) in any system that I am aware of.
>> On Thu, Dec 24, 2009 at 5:23 AM, Trish Whetzel <whetzel at stanford.edu>
>> Regarding access to instance terms via BioPortal web services, this is
>> possible using the Term
>> For example, using the service to access a term from the latest
>> version from OBI for the term "Affymetrix" the web service signature
>> There is a tracker item to modify the output of the Term service for
>> Individuals so that more information about the term is returned. I'll
>> on the timeframe for this when everyone is back from the Winter break.
>> On Dec 21, 2009, at 8:27 AM, Alan Ruttenberg wrote:
>> On Mon, Dec 21, 2009 at 10:26 AM, Philippe Rocca-Serra
><rocca at ebi.ac.uk>
>> On a side note, switching to instances would disrupt access/visibility
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