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[bioontology-support] extraction of subtree of ontology

Natasha Noy noy at stanford.edu
Wed Mar 17 14:25:05 PDT 2010


Unfortunately, there is no single-shot way to get it, in part because  
we need to limit the amount of data that we are returning, otherwise  
our response times become really slow. Some of these ontologies are  
very large, and if you ask for a "branch" that's almost the whole  
ontology, we'll need to generate an XML that is in tens of megabytes  
-- we simply don't have the capacity for that at the moment. We are  
working on figuring out a way to get this supported better, but it  
will be a little while before we get there.

You will have to right a script to iterate over all concepts to get  
the information that you need.

Natasha


On Mar 16, 2010, at 5:32 PM, Eugene wrote:

> 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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