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[bioontology-support] NEMO BioPortal mappings

Gwen Frishkoff gfrishkoff at gsu.edu
Wed May 5 19:25:06 PDT 2010


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>
> 
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