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

Alan Ruttenberg alanruttenberg at gmail.com
Thu Dec 24 07:45:09 PST 2009


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</accessedResource>
>  <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_services#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_0000462.
>>  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
>>
>> from resource browsers such as NCBO Bioportal or EBI's OLS.
>>
>> I have just checked with Bioportal (looking for 'Affymetrix' which is
>>
>> represented as an instance, or individual, in OBI) .
>>
>> Bioportal web interface finds the entry but tells the following: "Sorry,
>>
>> Affymetrix is not browsable because it is a individual".
>>
>> It may be that the web service returns a different message though.
>>
>> In our case, this would have a negative impact .
>>
>> Our tool, ISAcreator (http://isatab.sourceforge.net/isacreator.html)
>>
>> accesses both Bioportal and OLS and allows users to select ontology
>>
>> classes (e.g Units from UO) to annotate experiments.
>>
>> We can file a feature request to Bioportal in order to gauge how long it
>>
>> may take before instance terms can served and browsed.
>>
>> Yes, I suggest you do. And OLS.
>> ccing Trish so that it is on her radar.
>>
>> -Alan
>>
>>
>>
>> Cheers
>>
>> Philippe
>>
>>
>>
>> George Gkoutos wrote:
>>
>> On 19 Dec 2009, at 00:53, Chris Mungall wrote:
>>
>>
>> On Dec 18, 2009, at 12:20 PM, Alan Ruttenberg wrote:
>>
>>
>> On 12/17/09, Chris Mungall <cjm at berkeleybop.org> wrote:
>>
>> On Dec 17, 2009, at 3:55 AM, Robert Hoehndorf wrote:
>>
>>
>>  CM> I'm neutral, I don't use UO in any application. I'm not
>>
>>  CM> actually sure if there are any users of UO out there?
>>
>> Me, potentially, though I am not sure what you consider to be a
>>
>> "use". Formalization of categories in other ontologies using the
>>
>> unit-categories would be my goal, not sure if this is considered
>>
>> "use".
>>
>> potential use is different from current actual use. I was attempting
>>
>> to solicit feedback from actual users to make sure anything we do
>>
>> doesn't break systems in production. For example, it's typical
>>
>> practice to announce obsoletions a few weeks in advance to give
>>
>> people
>>
>> time to prepare. If you're a potential user then your fairly
>>
>> insulated
>>
>> from the damaging effects of any changes.
>>
>>
>> As it happens, I remember UO *is* in active use by one fairly large
>>
>> and important project I'm involved with, so we should proceed
>>
>> carefully with any changes. If we do switch to instances we may have
>>
>> to have some hack whereby the current .obo file keeps using classes,
>>
>> which would be an unfortunate mismatch.
>>
>> Could we get some examples of use in this project?
>>
>> It *would* be an unfortunate mismatch. I might suggest that OBO edit
>>
>> needs to be adjusted so it can handle instances if it is to remain a
>>
>> viable option for use for developing foundry ontologies.
>>
>> I don't like the idea of keeping something a certain way just because
>>
>> the tooling isn't up to snuff. It's reasonable to have a transition
>>
>> period.
>>
>> I agree that it's an unacceptable reason for keeping the ontology a
>>
>> certain way and I'm happy to switch to using Protege to edit UO. My
>>
>> point was that there are downstream users who may be affected by
>>
>> switching the underlying representation. We could insulate them by
>>
>> having a system in place whereby the .obo file that people are using
>>
>> remains fundamentally unchanged. I don't think this is the best
>>
>> solution, I'm just trying to lay out some of the options and costs.
>>
>> Another option is the transition period - we announce that the
>>
>> representation will change to instances and give people a reasonably
>>
>> amount of time to insulate themselves from any changes. I presume you
>>
>> want to go with the less radical solution on overriding OBO policy and
>>
>> not obsoleting existing IDs despite the fact that we are changing the
>>
>> meaning. I don't think this is a good way to earning popularity,
>>
>> breaking production systems for what people perceive to be meaningless
>>
>> philosophical distinctions, but if this is required for compatibility
>>
>> with OBI, then we should do it.
>>
>> Personally I'm not enthusiastic about the change - at the PATO meeting
>>
>> in Cambridge in 2006 we decided the units were classes, so for
>>
>> example, "kg" is instantiated whenever there is a 1-kg weighing
>>
>> entity. This seems at least to me to be simple, intuitive,
>>
>> unproblematic and avoids the extra indirection of information content
>>
>> entities.
>>
>>
>>
>> that was my understanding as well. We should obviously try to
>>
>> accommodate the usage of UO within the OBI community and I am happy to
>>
>> edit in Protege although I wonder whether we could have a conversion
>>
>> script or something like that. In any case, I think we should not be
>>
>> obsoleting existing IDs.
>>
>>
>> My current feeling is that if IAO/OBI wish to use unit instances the
>>
>> safest thing may be to use different IDs - perhaps we could have a
>>
>> system whereby the numeric local part of the ID is synchronized.
>>
>> Useless. The numeric local part has no status in any of our systems
>>
>> and I would chastise a programmer that assumed it did.
>>
>> I was just suggesting some kind of skolemization mechanism to auto-
>>
>> generate the ID and having the relationship formally captured.
>>
>>
>> If we go this route we will have duplicated effort, IMO. I don't want
>>
>> to see that happen cause I think that fundamentally the unit
>>
>> representatins are used in the same way.
>>
>> I agree it's not perfect but it seems the best solution to me.
>>
>>
>> -Alan
>>
>>
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>>
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>>
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>>
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>>
>>
>>
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>>
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>>
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>>
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>>
>>
>>
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>> Take advantage of Verizon's best-in-class app development support
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>> _______________________________________________
>>
>> Obo-unit mailing list
>>
>> Obo-unit at lists.sourceforge.net
>>
>> https://lists.sourceforge.net/lists/listinfo/obo-unit
>>
>>
>> Trish Whetzel, PhD
>> Outreach Coordinator
>> The National Center for Biomedical Ontology
>> Ph: 650-721-2378
>> whetzel at stanford.edu
>> http://www.bioontology.org
>>
>>
>



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