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

Nigam Shah nigam at stanford.edu
Tue Sep 21 11:16:34 PDT 2010


Please see:
http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_term

<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
> >>
> >
>
>
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