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

Alan Ruttenberg alanruttenberg at
Thu Dec 24 14:13:39 PST 2009

On Thursday, December 24, 2009, Trish Whetzel <whetzel at> 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?


> 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> wrote:
> Hi Trish,
> That returns:
> <success>
>  <accessedResource>/bioportal/virtual/ontology/1123/obo:OBI_0000462</accessedResource>
>  <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> wrote:
> Regarding access to instance terms via BioPortal web services, this is
> possible using the 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:
>  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>
> wrote:
> On a side note, switching to instances would disrupt access/visibility

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