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[bioontology-support] extraction of subtree of ontology

Natasha Noy noy at stanford.edu
Wed Mar 17 14:33:01 PDT 2010


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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