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[bioontology-support] NEMO BioPortal mappings

Gwen Frishkoff gfrishkoff at gsu.edu
Thu May 20 19:26:34 PDT 2010


Hello! I don't think it does. Thanks for noting this. I think Natasha 
pointed this out as well.

Best,
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,
> 
> Sorry for the delay. I'm not quite clear on the issue. For the search, 
> the screenshot shows the Resource Index page rather than the Ontology 
> Search page: http://bioportal.bioontology.org/search.  Does the ontology 
> search page have the issue you mention?
> 
> Trish
> 
> 
> On May 6, 2010, at 5:07 PM, Gwen Frishkoff wrote:
> 
>> Hi again.
>>
>> On a related note, when I search on a term in BioPortal, it only finds 
>> it does not seem to recognize the the term is being used (built on) if 
>> it is directly imported to an ontology (rather than newly declared 
>> with a new ID).
>>
>> So if I wanted to see which ontologies are specifying subclasses of 
>> "quality" I might be missing quite a few -- namely those that are 
>> built on BFO. The same thing is true for terms that have been 
>> (manually, not literally) "mireoted" in. Forgive me if you're already 
>> aware of these issues. I just wanted to weigh in as one enthusiastic 
>> user of BioPortal, to let you know what kind of changes might be 
>> useful for us as onto developers.
>>
>> 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:
>>> 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>_______________________________________________
>>>>>> bioontology-support mailing list
>>>>>> bioontology-support at lists.stanford.edu
>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> <Picture 1.png>
> 



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