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[bioontology-support] NEMO BioPortal mappings

Gwen Frishkoff gfrishkoff at gsu.edu
Thu May 6 16:54:23 PDT 2010


Super. Thanks!
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:
> 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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> 



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