Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] extraction of subtree of ontology

Eugene eugene at nextbio.com
Thu Mar 18 21:40:00 PDT 2010


Thanks. Is the URL correct?

http://rest.bioontology.org/bioportal/concepts/42142/all?pagesize=1000&email=eugene@nextbio.com

I don't specify pagenum because I need all pages returned.

What's the returned format? What we like is OWL format. Is there a way to get that format?

Eugene


-----Original Message-----
From: Natasha Noy [mailto:noy at stanford.edu] 
Sent: Thursday, March 18, 2010 9:06 PM
To: Eugene
Cc: support at bioontology.org
Subject: Re: [bioontology-support] extraction of subtree of ontology

Unfortunately, at the moment, no: the limit was an emergency fixed  
yesterday after BioPortal started crashing any time someone tries to  
get a large view. We are working on figuring out a way to deal with  
this increased load and also on the best way to provide the  
information on where the service left off in the view extractor  
results (paging in tree traversal is less trivial than in a list).

I would suggest that you use the getAllTerms service [1] instead of  
the view extractor: that service implements paging and so you can  
reliably get all the concepts that you need in chunks. You can then  
filter them on your end. That's probably the best thing that can be  
done at this point.

Natasha

[1] http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Get_all_terms_using_the_specific_ontology_version_id

On Mar 18, 2010, at 9:00 PM, Eugene wrote:

> Thanks. Is there a way for us to know which branch has over 5000  
> classes an which doesn't have?
>
> For each download, we need to get complete items. We are building  
> the commercial product. We couldn't build a product that only has  
> partial information.
>
> 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
>>
>




More information about the bioontology-support mailing list