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[bioontology-support] issues with rootpath

Darcy Davis DDavis at buckinstitute.org
Mon Jul 2 18:14:38 PDT 2012


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>
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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
http://www.bioontology.org

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