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[bioontology-support] [Obo-unit] Proposal to change UO to a representation of instances

Trish Whetzel 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.

Trish


>-----Original Message-----
>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;
>support
>Subject: Re: [Obo-unit] Proposal to change UO to a representation of
>instances
>
>On Thursday, December 24, 2009, Trish Whetzel <whetzel at stanford.edu>
>wrote:
>> 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?
>
>-Alan
>
>
>> Trish
>>
>> On Dec 24, 2009, at 7:45 AM, Alan Ruttenberg wrote:
>> I miswrote "obi:" instead of "obo:". Substance of the comment still
>stands.
>> -Alan
>>
>> On Thu, Dec 24, 2009 at 10:37 AM, Alan Ruttenberg
>> <alanruttenberg at gmail.com> wrote:
>> Hi Trish,
>>
>> That returns:
>>
>> <success>
>>
> <accessedResource>/bioportal/virtual/ontology/1123/obo:OBI_0000462</acc
>essedResource>
>>  <accessDate>2009-12-24 07:32:59.258 PST</accessDate>
>>  <data>
>>    <classBean>
>>      <id>obo:OBI_0000462</id>
>>      <fullId>http://purl.obolibrary.org/obo/OBI_0000462</fullId>
>>      <label>Affymetrix</label>
>>      <type>Individual</type>
>>      <relations/>
>>    </classBean>
>>  </data>
>> </success>
>>
>> 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.
>>
>>
>> -Alan
>>
>> On Thu, Dec 24, 2009 at 5:23 AM, Trish Whetzel <whetzel at stanford.edu>
>wrote:
>> Regarding access to instance terms via BioPortal web services, this is
>> possible using the Term
>>
>services: http://www.bioontology.org/wiki/index.php/BioPortal_REST_servi
>ces#Term_services.
>> For example, using the service to access a term from the latest
>ontology
>> version from OBI for the term "Affymetrix" the web service signature
>is:
>>
>http://rest.bioontology.org/bioportal/virtual/ontology/1123/obo:OBI_0000
>462.
>>  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
>check
>> on the timeframe for this when everyone is back from the Winter break.
>> Trish
>>
>> 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>
>> wrote:
>>
>> On a side note, switching to instances would disrupt access/visibility
>>




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