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[bioontology-support] extraction of subtree of ontology

Trish Whetzel whetzel at stanford.edu
Thu Mar 18 18:35:38 PDT 2010


Hi Eugene,

I have passed this back to the developers to review further.  I did  
notice one difference in the ontology name parameter in that the  
documentation has been updated to include "http" in the ontology name,  
e.g.
http://rest.bioontology.org/bioportal/viewextractor/42142/?conceptid=D009358&ontologyname=http://Congenital-Disorder.owl&delay=2000 
.

Trish


On Mar 18, 2010, at 5:24 PM, Eugene wrote:

> Could you please to check what's wrong with the URL?
>
> http://rest.bioontology.org/bioportal/viewextractor/42142/?conceptid=D009358&ontologyname=Congenital-Disorder.owl&delay=20000
>
> I get Proxy Error.
>
> Thanks
>
> Eugene
>
> -----Original Message-----
> From: Natasha Noy [mailto:noy at stanford.edu]
> Sent: Wednesday, March 17, 2010 2:33 PM
> To: Eugene
> Cc: support at bioontology.org
> Subject: Re: [bioontology-support] extraction of subtree of ontology
>
> Of you use a different value for the ontologyname parameter for
> different ontologies, you will be fine: that parameter is part of the
> id.
>
> Natasha
>
>
> On Mar 16, 2010, at 5:36 PM, Eugene wrote:
>
>> By the way, I forgot to ask one more thing:
>>
>> UMLS contains multiple ontologies. How can I guarantee the ID of
>> each term (for the same type, such as disease) is unique across all
>> ontologies in UMLS? Is there a way for me to ensure that?
>>
>> Thanks
>>
>> Eugene
>>
>> From: Eugene
>> Sent: Tuesday, March 16, 2010 5:33 PM
>> To: 'support at bioontology.org'
>> Subject: extraction of subtree of ontology
>>
>> Dear Sir/Madam,
>>
>> Is there a way to download the whole disease or compound category by
>> just one command?
>>
>> The example said in the email needs to specify the concept id.
>> However, under disease category, for example, it has more than 10
>> top-level concepts. So I need to call more than 10 times. Then I
>> need to merge those 10+ files into one file. It is not pretty
>> straightforward.
>>
>> Thanks
>>
>> Eugene
>>
>> From: drnigam at gmail.com [mailto:drnigam at gmail.com] On Behalf Of
>> Nigam Shah
>> Sent: Tuesday, March 16, 2010 3:46 PM
>> To: Eugene; Satnam Alag
>> Subject: Re: Introductions
>>
>> BTW, for questions like this emailing support at bioontology.org is
>> best. It will go to people who respond to users regularly. I merely
>> end up reading the documentation and replying to you.
>>
>> Regards,
>> Nigam.
>>
>> On Tue, Mar 16, 2010 at 3:36 PM, Nigam Shah <nigam at stanford.edu>
>> wrote:
>> Yes it is. You are not using a conceptid ("Peptides" is not a
>> concept id in MSH). See: http://bioportal.bioontology.org/visualize/42142
>> to find a valid ID for "Peptides" .. use the search box above the
>> tree view.
>>
>> For example, for "Melanoma", the ID is D008545. And if I use that, I
>> will get an OWL file from: http://rest.bioontology.org/bioportal/viewextractor/42142/?conceptid=D008545&ontologyname=testing.owl&delay=2000
>> . I just tested it. So the URL is correct, you need to use the right
>> parameters.
>>
>> --Nigam.
>>
>> On Tue, Mar 16, 2010 at 3:29 PM, Eugene <eugene at nextbio.com> wrote:
>> Nigam,
>>
>> Is the URL right?
>>
>> http://rest.bioontology.org/bioportal/viewextractor/42142/?conceptid=Peptides&ontologyname=testing.owl&delay=2000
>>
>> Should ontology name have prefix "http"? I use above URL, but I
>> cannot get it.
>>
>> 42142 is MeSH ID (according to the link http://rest.bioontology.org/bioportal/ontologies/download/42142?email=example@example.org
>> ).
>>
>> I have followed the instruction: http://www.bioontology.org/wiki/index.php/View_Extraction
>>
>> Any idea?
>>
>> Thanks
>>
>> Eugene
>>
>>
>> From: drnigam at gmail.com [mailto:drnigam at gmail.com] On Behalf Of
>> Nigam Shah
>> Sent: Tuesday, March 16, 2010 2:31 PM
>> To: Eugene
>> Subject: Fwd: Introductions
>>
>> Might be useful for you to know the options too .. sorry for the
>> short onliners .. trying to multi task at a meeting.
>>
>> Cheers!
>> Nigam.
>>
>> ---------- Forwarded message ----------
>> From: Nigam Shah <nigam at stanford.edu>
>> Date: Tue, Mar 16, 2010 at 2:27 PM
>> Subject: Re: Introductions
>> To: Satnam Alag <satnam at nextbio.com>
>>
>>
>> I am in Seattle right now at a meeting .. so can't get on the phone.
>> Overall, here are the options:
>>
>> 1) The simple, extraction of a sub-tree of an ontology (say the
>> 'disease branch' or MeSH .. or the subtree under 'Melanoma'). That
>> can be done using our production services .. for example the one  
>> at: http://www.bioontology.org/wiki/index.php/View_Extraction
>>
>> 2) A bit detailed extraction that give more "knobs" beyond just the
>> the sub-tree .. i.e. allow you to 'exclude' terms that are not the
>> right semantic type, that have a high freq in medline, that have the
>> wrong syntactic type on average (say not noun-phrase). That can be
>> done using our prototype Lexicon Builder .. the one at: http://www.bioontology.org/wiki/index.php/Lexicon_Builder
>>
>> 3) Getting the compound and diseases sections of multiple (or all)
>> UMLS ontologies; the 13% actually used in medline (per Rong Xu's
>> paper). This data is in mysql tables that are not open to the
>> public. Someone (i.e. me or my student) would have to work with you
>> to figure out the exact query you want to run and then run it.
>>
>> My guess is the number (2) WILL get you what you are after. However,
>> in order to do that, you (or probably Eugene) need to:
>>
>> - identify what UMLS ontologies you want (MSH, SNOMEDCT, NCIT,
>> ICD9 .. what else?). You can't do all "UMLS" in the Lexicon Builder.
>> - make a few trial runs (say with MSH) ... trying different
>> parameters for the semantic types, the syntactic types and the
>> frequency cutoffs; try including, excluding synoyms, using or not
>> using "mappings" to terms from other ontologies. Basically read the
>> Lexicon Builder paper and try out different parameter combinations
>> - if it gets you what you need, great .. if not, we can iterate to
>> define the right parameter set for you.
>>
>> If you are convinced that (2) will not work, or you don't want to
>> (or can't) spend time digging into this, we can explore option (3).
>> But that requires my time, which I don't have much right now.
>>
>> Regards,
>> Nigam.
>>
>> On Tue, Mar 16, 2010 at 1:51 PM, Satnam Alag <satnam at nextbio.com>
>> wrote:
>> Is there an easy way for us to get the compound and diseases
>> sections of the UMLS ontology that has been processed by you. We are
>> particularly interested in the 13% of the ontology that is actually
>> used in medline. Is there a good phone number I can call you at? Thx
>>
>>
>> Satnam Alag
>> V.P. of Engineering
>> NextBio
>> Ph: 408 582 4160 (C)
>> www.nextbio.com
>>
>>
>>
>> _______________________________________________
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>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
> _______________________________________________
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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org



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