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[bioontology-support] Extracting a portion of an ontology

Fahim Imam smtifahim at gmail.com
Mon Dec 6 12:12:55 PST 2010


Hi Trish,
Here is the URL that I tried to extract the subclasses of 'Breast Cancer'
from NCBI Taxonomy:
http://rest.bioontology.org/bioportal/viewextractor/42693/?conceptid=Breast_Carcinoma&ontologyname=http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl&delay=10

Thanks,
Fahim

On Sun, Dec 5, 2010 at 4:55 PM, Trish Whetzel <whetzel at stanford.edu> wrote:

> 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
>
>
>


-- 
__________________________________
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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