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

Eugene eugene at nextbio.com
Tue Sep 21 11:12:59 PDT 2010


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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