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[bioontology-support] issues with rootpath

Trish Whetzel whetzel at stanford.edu
Mon Jul 2 21:16:26 PDT 2012


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=ADDISON%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+CRISIS?apikey=<my api key>
>> http://rest.bioontology.org/bioportal/virtual/rootpath/1341/ADDISON%2BCRISIS?apikey=<my api key>
>> http://rest.bioontology.org/bioportal/virtual/rootpath/1341/http%3A%2F%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#Hierarchy_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 lists.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
>> 
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>> 
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> 
> 
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