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[bioontology-support] Extracting a portion of an ontology

Trish Whetzel whetzel at stanford.edu
Sun Dec 5 16:55:41 PST 2010


Hi Fahim, 

Can you send the URL you are using with the View Extraction web service?

Thanks,
Trish


On Dec 3, 2010, at 4:51 PM, Fahim Imam wrote:

> Hi Paul,
> Hope you are doing well. Seems like the extractor web service is not returning the list of synonyms from NCBI Taxonomy. I just extracted 'Breast Carcinoma' sub-tree and that is the case along with other subtrees from the Taxonomy. Can you take a look? 
> 
> Thanks,
> Fahim
> 
> On Tue, Aug 17, 2010 at 4:14 PM, Fahim Imam <smtifahim at gmail.com> wrote:
> Thanks so much Paul! That makes sense. None of us have 5GB of  free RAM. 
> 
> Regards,
> Fahim
> 
> 
> On Tue, Aug 17, 2010 at 3:04 PM, Paul R Alexander <palexander at stanford.edu> wrote:
> Fahim,
> 
> I was able to open the ontology using Protege 4.1, but it took a little over 5GB of RAM to do so. You can definitely extract branches from ontologies using the BioPortal REST services. It will return an OWL file that contains the concepts in that branch. See here for more documentation:
> http://www.bioontology.org/wiki/index.php/View_Extraction
> 
> Paul
> 
> 
> On 8/17/10 12:13 PM, Fahim Imam wrote:
>> 
>> Hi Trish,
>> We were wondering if there is any way to extract a subclass of certain class e.g., Primate from NCBI Taxonomy (in any format like csv/spredsheet). I remember you told me about a way to extract certain view from an ontology within Bioportal. Jonathan Cachat, our summer intern in NIF is working on Organisms and we failed to load the taxonomy file through ptotege due to some memory issue. Increasing the heap space did not help.
>> 
>> Paul, are you able to load the ncbi taxonomy owl file in protege? Here is the owl link  http://purl.org/obo/owl/NCBITaxon
>> 
>> 
>> Thanks,
>> Fahim
>> 
>> 
>> -- 
>> __________________________________
>> Fahim T. Imam
>> NIF Ontological Engineer & Programmer Analyst
>> Neuroscience Information Framework      
>> University of California, San Diego
>> 9500 Gilman Drive, M/C 0446
>> La Jolla, CA 92093-0446
>> 
>> work: (858) 534-5356
>> web: http://neuinfo.org
> 
> 
> 
> 
> 
> 
> -- 
> __________________________________
> Fahim T. Imam
> NIF Ontological Engineer & Programmer Analyst
> Neuroscience Information Framework      
> University of California, San Diego
> 9500 Gilman Drive, M/C 0446
> La Jolla, CA 92093-0446
> 
> work: (858) 534-5356
> web: http://neuinfo.org

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