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[bioontology-support] NEMO BioPortal mappings

Natasha Noy noy at stanford.edu
Thu May 6 16:38:52 PDT 2010


Yes, we got the same from Maryann today as well. We'll see what we can  
do.

Natasha


On May 6, 2010, at 3:25 PM, Gwen Frishkoff wrote:

>
> Not at all! I'm just trying to be a good BioPortal citizen. :)
>
> We were just talking with Paea earlier and with Maryann Martone this  
> afternoon about this, too. I think everyone agrees it would be  
> useful to see who is  working on similar "branches" from BFO, OBO,  
> or whatever.
>
> Thanks much for your advice and support.
> Gwen
>
> Gwen Frishkoff, Ph.D.
> Assistant Professor, Department of Psychology
> Associate Member, Neuroscience Institute
> 140 Decatur Street
> Urban Life, Rm 712
> Georgia State University
> Atlanta, Georgia  30303-3083
>
> Email: gfrishkoff at gsu.edu
> Phone: 404-413-6303
> Fax:   404-413-6218
>
> "A speaker is like a lousy auto mechanic: every time he fixes  
> something in the language, he screws up something else." -- Joseph  
> H. Greenberg
>
> Natasha Noy wrote:
>> Gwen,
>> This makes a lot of sense, and these terms should appear shortly :)  
>> We are just updating all our mappings and we will include the  
>> mappings between the terms with identical IDs. Bear with us,  
>> please...
>> Natasha
>> On May 5, 2010, at 7:25 PM, Gwen Frishkoff wrote:
>>> Thanks. Yes. I've attached a screenshot of the mappings between  
>>> NEMO terms and terms in other BioPortal ontologies. The only  
>>> mappings that appear are the ones I entered manually. Terms that  
>>> are re-used in NEMO (with the same URI as in the source ontology)  
>>> do not appear.
>>>
>>> Maybe I'm missing the point of the BioPortal mappings. If the  
>>> purpose is only to show mappings between terms with different URI,  
>>> then there's nothing to add for NEMO. We have tried whenever  
>>> possible to re-use existing terms from other ontologies. But it  
>>> might be helpful to see which ontologies in BioPortal are re-using  
>>> terms, without redefining them (i.e., attaching new URI to terms  
>>> with the same label).
>>>
>>> Does this make any sense? :)
>>>
>>> Thanks,
>>> Gwen
>>>
>>> Gwen Frishkoff, Ph.D.
>>> Assistant Professor, Department of Psychology
>>> Associate Member, Neuroscience Institute
>>> 140 Decatur Street
>>> Urban Life, Rm 712
>>> Georgia State University
>>> Atlanta, Georgia  30303-3083
>>>
>>> Email: gfrishkoff at gsu.edu
>>> Phone: 404-413-6303
>>> Fax:   404-413-6218
>>>
>>> "A speaker is like a lousy auto mechanic: every time he fixes  
>>> something in the language, he screws up something else." -- Joseph  
>>> H. Greenberg
>>>
>>> Trish Whetzel wrote:
>>>> Thanks for the update to the file. Can you expand on "the  
>>>> mappings do not appear automatically in BioPortal"?
>>>> Trish
>>>> On May 5, 2010, at 6:46 PM, Gwen Frishkoff wrote:
>>>>>
>>>>> Sorry, Trish. I've labeled the source and target terms and URI  
>>>>> more clearly (I hope). See attached.
>>>>>
>>>>> Notice that the URI for the term in NEMO and the URI for the  
>>>>> term that it maps to are the same. In one sense, this makes the  
>>>>> mapping absolutely trivial -- except that the mappings do not  
>>>>> appear automatically in BioPortal.
>>>>>
>>>>> Thanks,
>>>>> Gwen
>>>>>
>>>>> Gwen Frishkoff, Ph.D.
>>>>> Assistant Professor, Department of Psychology
>>>>> Associate Member, Neuroscience Institute
>>>>> 140 Decatur Street
>>>>> Urban Life, Rm 712
>>>>> Georgia State University
>>>>> Atlanta, Georgia  30303-3083
>>>>>
>>>>> Email: gfrishkoff at gsu.edu
>>>>> Phone: 404-413-6303
>>>>> Fax:   404-413-6218
>>>>>
>>>>> "A speaker is like a lousy auto mechanic: every time he fixes  
>>>>> something in the language, he screws up something else." --  
>>>>> Joseph H. Greenberg
>>>>>
>>>>> Trish Whetzel wrote:
>>>>>> Hi Gwen,
>>>>>> We can upload the mappings so they are available via the  
>>>>>> mapping Web service and BioPortal UI. However, the file format  
>>>>>> is not entirely clear to me. For the term,  
>>>>>> ConnectedSpatiotemporalRegion, what term is it mapped to?
>>>>>> Trish
>>>>>> On May 5, 2010, at 3:40 PM, Gwen Frishkoff wrote:
>>>>>>>
>>>>>>> Dear Trish,
>>>>>>>
>>>>>>> Attached is a list of mappings for NEMO. I manually entered  
>>>>>>> mappings for a handful of concepts with NEMO URI (~35 of  
>>>>>>> these). The reason these have NEMO URI is because the mapping  
>>>>>>> is probably not an identity mapping , so we redefined the  
>>>>>>> concepts in a way that made sense for our specific applications.
>>>>>>>
>>>>>>> Thanks so much for your assistance with this. I hope you don't  
>>>>>>> literally mean that you need to enter these manually. If so,  
>>>>>>> NEMO does have an ontology curator, and I can ask her to do  
>>>>>>> this through BioPortal. But if you have a back-end way to do  
>>>>>>> it more quickly, that would be great.
>>>>>>>
>>>>>>> Thanks again,
>>>>>>> Gwen
>>>>>>>
>>>>>>> Gwen Frishkoff, Ph.D.
>>>>>>> Assistant Professor, Department of Psychology
>>>>>>> Associate Member, Neuroscience Institute
>>>>>>> 140 Decatur Street
>>>>>>> Urban Life, Rm 712
>>>>>>> Georgia State University
>>>>>>> Atlanta, Georgia  30303-3083
>>>>>>>
>>>>>>> Email: gfrishkoff at gsu.edu
>>>>>>> Phone: 404-413-6303
>>>>>>> Fax:   404-413-6218
>>>>>>>
>>>>>>> "A speaker is like a lousy auto mechanic: every time he fixes  
>>>>>>> something in the language, he screws up something else." --  
>>>>>>> Joseph H. Greenberg
>>>>>>>
>>>>>>> <NEMO_BioPortalMappings_2010May5.xls>
>>>>>> Trish Whetzel, PhD
>>>>>> Outreach Coordinator
>>>>>> The National Center for Biomedical Ontology
>>>>>> Ph: 650-721-2378
>>>>>> whetzel at stanford.edu
>>>>>> http://www.bioontology.org
>>>>> <NEMO_BioPortalMappings_2010May5v2.xls>
>>> <Picture 1.png>_______________________________________________
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>>> bioontology-support at lists.stanford.edu
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