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[bioontology-support] issues with rootpath

Trish Whetzel whetzel at stanford.edu
Tue Jul 10 18:32:57 PDT 2012


Hi Darcy, 

The "rootpath" call is now working with the virtual ontology id.

Trish 



On Jul 5, 2012, at 2:54 PM, Darcy Davis wrote:

> Hi Ray,
> 
> Thanks for helping out with this issue. The call below still failed for me, called through a perl script. Also fails in google chrome browser, which does not undo the uri encoding.
> 
> http://rest.bioontology.org/bioportal/virtual/rootpath/1341/ADDISON%20CRISIS?apikey=5df9c983-2602-4152-b8f6-e8ebf9fa5674&delim=*
> 
> Darcy Davis
> ________________________________________
> From: Ray Fergerson [ray.fergerson at stanford.edu]
> Sent: Thursday, July 05, 2012 2:18 PM
> To: 'Trish Whetzel'; Darcy Davis
> Cc: support at bioontology.org; Alex Skrenchuk; Michael Dorf
> Subject: RE: [bioontology-support] issues with rootpath
> 
> We believe that we have fixed this now. The call will work
> programmatically if you replace the space in a conceptid with a '%20'.
> Unfortunately browsers (at least some) do not handle this correctly (they
> unreplace the %20 with a space causing a bad URL). Thus you cannot try out
> the fix in a browser. Please let us know if you cannot get this to work
> programmatically.
> 
> Ray
> 
> -----Original Message-----
> From: bioontology-support-bounces at lists.stanford.edu
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Trish
> Whetzel
> Sent: Monday, July 02, 2012 9:16 PM
> To: Darcy Davis
> Cc: support at bioontology.org Support
> Subject: Re: [bioontology-support] issues with rootpath
> 
> Hi Darcy,
> 
> I was able to confirm this term is in the database used by the "rootpath"
> call and was able to use the "Get Term" call with the '+' sign URI-encoded
> as one of your examples below used this format:
> http://rest.bioontology.org/bioportal/virtual/ontology/1341?conceptid=ADDI
> SON%2BCRISIS&apikey=YourAPIKey
> However, I have not been able to identify an error in the format of the
> "rootpath" call for this term. Perhaps one of the developers can chime in
> from here on whether there is an error in the format of the call or if
> there is a bug?
> 
> Trish
> 
> 
> On Jul 2, 2012, at 7:10 PM, Trish Whetzel wrote:
> 
>> Hi Darcy,
>> 
>> On first pass, there seems to be an issue with the COSTART data used for
> the "rootpath" web service call, I'll review further. I believe the call
> using %20 instead of a space should be the proper format.
>> 
>> Trish
>> 
>> 
>> On Jul 2, 2012, at 6:14 PM, Darcy Davis wrote:
>> 
>>> Hi Trish,
>>> 
>>> I'm sorry to bother you again. I've resolved the earlier problem I had
> with period-delimited output by simply changing the delimiter. However, I
> have a new problem. Using the rootpath service, I cannot find a way to get
> results for concept ids that contain spaces or other protected characters.
> Uri encoding does not seem to work, although it does work for other
> services. An example is below.
>>> 
>>> Ontology ID: 1341 (COSTART)
>>> Concept ID: ADDISON CRISIS
>>> 
>>> all of the following do not work for me:
>>> http://rest.bioontology.org/bioportal/virtual/rootpath/1341/ADDISON
>>> CRISIS?apikey=<my api key>
>>> http://rest.bioontology.org/bioportal/virtual/rootpath/1341/ADDISON+C
>>> RISIS?apikey=<my api key>
>>> http://rest.bioontology.org/bioportal/virtual/rootpath/1341/ADDISON%2
>>> BCRISIS?apikey=<my api key>
>>> http://rest.bioontology.org/bioportal/virtual/rootpath/1341/http%3A%2
>>> F%2Fpurl.bioontology.org%2Fontology%2FCST%2FADDISON%2BCRISIS?apikey=<
>>> my api key>
>>> 
>>> What is the correct way to find this concept with the rootpath service.
> Thanks!
>>> 
>>> Darcy Davis
>>> ________________________________________
>>> From: Trish Whetzel [whetzel at stanford.edu]
>>> Sent: Friday, June 29, 2012 2:08 PM
>>> To: Darcy Davis
>>> Subject: Re: [bioontology-support] issues with versioning in rootpath
>>> 
>>> Can you send a few concepts from each ontology that contain periods in
> the concept id?
>>> 
>>> Thanks!
>>> Trish
>>> 
>>> 
>>> On Jun 29, 2012, at 2:01 PM, Darcy Davis wrote:
>>> 
>>> Hi Trish,
>>> 
>>> Thank you for explaining the versioning to me. I've also noticed that
> the hierarchy services (rootpath, etc) delimit the paths with a period,
> but this symbol is also in many concept ids (for example NCI Thesaurus and
> ICD-9 ids). This makes parsing correctly very difficult, and I wondered if
> there is a known solution. Thanks again!
>>> 
>>> Darcy
>>> ________________________________________
>>> From: Trish Whetzel [whetzel at stanford.edu]
>>> Sent: Friday, June 22, 2012 3:33 PM
>>> To: Darcy Davis
>>> Cc: support at bioontology.org<mailto:support at bioontology.org>
>>> Subject: Re: [bioontology-support] issues with versioning in rootpath
>>> 
>>> Hi Darcy,
>>> 
>>> The Hierarchy web services return content from the Hierarchy database,
> which has only 1 version of a given ontology. This was noted in the
> general section for the Hierarchy Web services, but not the individual web
> services within this section of the documentation. This has now been
> updated for each specific hierarchy web service [1] and does include
> details on how to find out which version of an ontology is populated in
> the Hierarchy database. As for updates of ontology content for the
> hierarchy database, this is work in progress and when updated will be
> announced.
>>> 
>>> Trish
>>> 
>>> [1]
>>> http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Hie
>>> rarchy_Services
>>> 
>>> 
>>> On Jun 21, 2012, at 1:25 PM, Darcy Davis wrote:
>>> 
>>> Hi Trish,
>>> 
>>> I have some comments/questions about the ontology versions in various
> REST services.  The /version/rootpath/ service documentation indicates
> that this should "returns parents from the latest version of that
> ontology", which is not necessarily true. It is operating on an older
> version of CHEBI, for example (46336 vs. new version 47284). When is this
> likely to be updated? Also, where can I find out which ontology versions
> are being used by the annotator? Thank you for your time!
>>> 
>>> Darcy Davis
>>> ddavis at buckinstitute.org<mailto:ddavis at buckinstitute.org>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu<mailto:bioontology-support at lis
>>> ts.stanford.edu>
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> 
>>> 
>>> 
>>> Trish Whetzel, PhD
>>> Outreach Coordinator
>>> The National Center for Biomedical Ontology
>>> Ph: 650-721-2378
>>> http://www.bioontology.org
>>> 
>>> "Like" NCBO on Facebook: http://on.fb.me/bioontology
>>> 
>>> Follow NCBO on Twitter: http://twitter.com/#!/bioontology
>>> 
>>> Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
>>> 
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
>> 
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>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> 
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