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[bioontology-support] NEMO BioPortal mappings

Natasha Noy noy at stanford.edu
Thu May 6 14:18:15 PDT 2010


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>
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