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[bioontology-support] extraction of subtree of ontology

Trish Whetzel whetzel at stanford.edu
Thu Mar 18 23:06:57 PDT 2010


That URL works for me. The output is XML. There are tags in the XML  
that include the <pageSize>, which will have as a value your input  
parameter and also <pageNum> and <numPages>. The pageNum value will  
indicate which 'page' is being accessed and numPages will contain the  
total number of 'pages'.

Is your end goal to have a complete version of MeSH that is in OWL or  
only certain branches?

Trish


On Mar 18, 2010, at 9:40 PM, Eugene wrote:

> 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
>>>
>>
>
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