Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Trish Whetzel whetzel at
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.


>-----Original Message-----
>From: Alan Ruttenberg [mailto:alanruttenberg at]
>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>
>> 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?
>> Trish
>> On Dec 24, 2009, at 7:45 AM, Alan Ruttenberg wrote:
>> I miswrote "obi:" instead of "obo:". Substance of the comment still
>> -Alan
>> On Thu, Dec 24, 2009 at 10:37 AM, Alan Ruttenberg
>> <alanruttenberg at> wrote:
>> Hi Trish,
>> That returns:
>> <success>
> <accessedResource>/bioportal/virtual/ontology/1123/obo:OBI_0000462</acc
>>  <accessDate>2009-12-24 07:32:59.258 PST</accessDate>
>>  <data>
>>    <classBean>
>>      <id>obo:OBI_0000462</id>
>>      <fullId></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>
>> 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.
>> 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>
>> wrote:
>> On a side note, switching to instances would disrupt access/visibility

More information about the bioontology-support mailing list