Re: [OBO-Edit Working Group] synonym categories

[Melissa H. <mha...@uo...>]

Hi Chris,
thanks for the info. I agree, a plural synonym category should be 
promoted to an official synonym type. 

When I make the changes as you suggested, I get a load error:
/Found unexpected scope identifier plural /(etc)

John, is this because of the synonym category manager misbehaving?  (see 
my bug report # 1591612)
If I add a category "plural" with ID "PLURAL" and scope exact, then it 
doesn't save it.
Trying a second time with scope related, it does, but doesn't put the 
scope on the synonymtypedef in the header.

melissa

Chris Mungall wrote:
> I can tell you how to do it in obo format, but not in oboedit
>
> 1. add a new synonymtypedef to the header
>
> synonymtypedef: plural "plural" RELATED
>
> Then on a per term basis
>
> name: tooth
> synonym: "teeth" plural RELATED []
>
> We're doing something similar for PATO-UNITS, for unit symbols 
> (George, have you added these yet). CHEBI want something similar.
>
> I don't think teeth is an exact synonym for tooth though. I think an 
> instance of teeth is an instance of a collection-of-the-type-tooth, 
> and deserves a different term. But for practical purposes it's fine to 
> have the plural token as a related non-exact synonym for the singular 
> form.
>
> we should share the same synonymtypedef over all ontologies so I 
> suggest we promote "plural" (or "PLURAL" if we use capitals as in the 
> obo format spec) as an official synonymtype
>
> On Nov 6, 2006, at 3:38 PM, Melissa Haendel wrote:
>
>> Hi Jane,
>> thanks for the help!
>>
>> We currently have them as exact/related synonyms also.  The problem for
>> us is that for a good portion of our ontology, the old name was plural.
>> Keeping them as regular synonyms overpopulates our pull-downs with terms
>> that only differ in an 's' at the end. We'd like to maintain searches on
>> these, but not give them the same status as the other synonyms. We're
>> considering using a different synonym type and allowing searches for
>> these terms, but not putting them in our pulldowns where we do want to
>> put our regular synonyms.
>>
>> melissa
>>
>> ja...@eb... wrote:
>>> Hi Melissa - in GO I think we just have the plural as an exact synonym,
>>> because terms are classes e.g. mitochondria would be an exact 
>>> synonym for
>>> mitochondrion...
>>>
>>> jane
>>>
>>>
>>>> Hi all,
>>>> I was wondering if any of you had advice on how to deal with plural
>>>> synonyms.  We've recently cleaned up our ontology to remove plural
>>>> terms, but need to keep some as plural synonyms.  In our database, 
>>>> we'll
>>>> have a synonym type plural, but how this gets presented in OBO-Edit 
>>>> is a
>>>> bit up in the air (especially given that I am having some problems 
>>>> with
>>>> the synonym category manager).  Also, do any of your databases return
>>>> searches on plural terms?  Any help is appreciated!
>>>> Thanks, Melissa
>>>> -- 
>>>>
>>>> Melissa Haendel, Ph.D.
>>>>
>>>>
>>>>
>>>> ZFIN Scientific Curator
>>>>
>>>> Zebrafish Information Network
>>>>
>>>> 5291 University of Oregon
>>>>
>>>> Eugene, OR 97403-5291
>>>>
>>>> Phone: (541) 346-5108
>>>>
>>>>
>>>> ------------------------------------------------------------------------- 
>>>>
>>>> Using Tomcat but need to do more? Need to support web services, 
>>>> security?
>>>> Get stuff done quickly with pre-integrated technology to make your job
>>>> easier
>>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache 
>>>> Geronimo
>>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 
>>>>
>>>> _______________________________________________
>>>> Geneontology-oboedit-working-group mailing list
>>>> Gen...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group 
>>>>
>>>>
>>>>
>>>
>>>
>>
>> -- 
>> Melissa Haendel, Ph.D.
>>
>>
>>
>> ZFIN Scientific Curator
>>
>> Zebrafish Information Network
>>
>> 5291 University of Oregon
>>
>> Eugene, OR 97403-5291
>>
>> Phone: (541) 346-5108
>>
>>
>> ------------------------------------------------------------------------- 
>>
>> Using Tomcat but need to do more? Need to support web services, 
>> security?
>> Get stuff done quickly with pre-integrated technology to make your 
>> job easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache 
>> Geronimo
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>> _______________________________________________
>> Geneontology-oboedit-working-group mailing list
>> Gen...@li...
>> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group 
>>
>>

-- 

Melissa Haendel, Ph.D.

 

ZFIN Scientific Curator

Zebrafish Information Network

5291 University of Oregon

Eugene, OR 97403-5291

Phone: (541) 346-5108