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[bioontology-support] extract "description" in Bio Portal

Trish Whetzel whetzel at stanford.edu
Tue Sep 21 18:09:50 PDT 2010


Hi Eugene,

To clarify the information on the wiki, the concept id should be used  
with the Get term web service, with the concept id referring to the  
value of the ID field.  However it should be uri-encoded since there  
are cases where the concept id is a URL itself. For the SNOMED CT term  
"Disorder characterized by pain", the concept id is 373673007 and then  
the Get term web service call is:
http://rest.bioontology.org/bioportal/concepts/42789?conceptid=373673007&email=example@example.org
As Nigam noted, there is a bug in using the value of the field Full Id.

As for definitions, SNOMED CT does not have definitions. For  
ontologies/terminologies that do contain definitions, they are  
returned within the attribute <definitions> from the Get term web  
service, e.g. http://rest.bioontology.org/bioportal/concepts/44450/BRO:Resource?email=example@example.org

Trish


On Sep 21, 2010, at 2:37 PM, Eugene wrote:

> Send again. CC to Pralabh.
>
> From: Eugene
> Sent: Tuesday, September 21, 2010 2:37 PM
> To: 'Nigam Shah'
> Cc: support at bioontology.org
> Subject: RE: extract "description" in Bio Portal
>
> Nigam,
>
> Thanks.
>
> We have tried that. But it doesn’t work. Perhaps, something is  
> wrong. Here is what we do:
>
> 1.       We get ontology version ID for SnoMed CT, which is 42789
> 2.       We get encoded concept idhttp%3A%2F%2Fpurl.bioontology.org 
> %2Fontology%2FSNOMEDCT%2F373673007
>
> Now apply above parameter to the url: http://rest.bioontology.org/bioportal/concepts/42789?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F373673007&email=example@example.org
>
> Just cannot get the data back.
>
> Eugene
>
> From: Nigam Shah [mailto:nigam at stanford.edu]
> Sent: Tuesday, September 21, 2010 11:17 AM
> To: Eugene
> Cc: support at bioontology.org
> Subject: Re: extract "description" in Bio Portal
>
> Please see: http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_term
>
> -Nigam.
>
> On Tue, Sep 21, 2010 at 11:12 AM, Eugene <eugene at nextbio.com> wrote:
> Dear Sir or Madam,
>
> I have a question in downloading ontology terms. Is there a way to  
> download description/glossy information along with the terms?
>
> Thanks
>
> Eugene
>
> > -----Original Message-----
> > From: Natasha Noy [mailto:noy at stanford.edu]
> > Sent: Thursday, March 18, 2010 8:55 PM
> > To: Eugene
> > Cc: support at bioontology.org
> > Subject: Re: [bioontology-support] extraction of subtree of ontology
> >
> > I just tried it --using a delay of 20 rather than 20000 and got the
> > OWL file back. Perhaps the delay was too long and it was timing out.
> >
> > Please note that due to heavy load on the server, we had to limit  
> the
> > size of the result to 5000 classes. So, if you are trying to get a
> > branch that has more than 5000 classes, you won't be able to get all
> > of it.
> >
> > Natasha
> >
> >
> > 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
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> bioontology-support mailing list
> >>> bioontology-support at lists.stanford.edu
> >>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> >>
> >
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
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