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[bioontology-support] issues with rootpath

Darcy Davis DDavis at buckinstitute.org
Thu Jul 5 14:54:16 PDT 2012


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
>>
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>>
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>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> _______________________________________________
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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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