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[bioontology-support] [BioPortal] Feedback from Rob Taylor

Taylor, Rob rob.taylor at Vanderbilt.Edu
Wed Dec 9 03:51:01 PST 2015


It’s indeed working. Thanks so much. We greatly appreciate it.

Rob Taylor
REDCap Development Team - Senior Developer (http://projectredcap.org<http://projectredcap.org/>)
Vanderbilt Institute for Clinical and Translational Research (VICTR)

From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: Tuesday, December 08, 2015 7:20 PM
To: Taylor, Rob <rob.taylor at Vanderbilt.Edu>
Cc: support at bioontology.org; Jennifer Leigh Vendetti <vendetti at stanford.edu>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Rob Taylor

Hi Rob,

We've recently rebuilt our entire search index to add a new data field. Some ontologies may not have indexed properly, which caused the problem you reported. I've re-indexed the ICD10CM ontology, and the terms you reported as missing appear to be back.

Let me know if you run into any further issues.

Thanks!

Michael Dorf


On Dec 4, 2015, at 14:45, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Rob,


On Dec 4, 2015, at 10:50 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Rob Taylor
Email: rob.taylor at vanderbilt.edu<mailto:rob.taylor at vanderbilt.edu>
Location: http://bioportal.bioontology.org/ontologies/ICD10CM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10CM%2FJ98

Feedback:
Is the list of ICD-10CM codes complete in the BioPortal service database? We utilize the BioPortal service in our application REDCap, and users are complaining that lots of valid ICD-10 codes cannot be found when searching the BioPortal service, such as the two ICD-10CM codes below. Could you please tell me if the BioPortal only provides an abridged listing of these codes or if perhaps there is a bug that is preventing it from finding such items. THANKS!
J96.92 - Respiratory failure, unspecified with hypercapnia
J98.11 – Atelectasis



This looks to be a problem with our search index.  Making a call to the REST API to retrieve the classes by their IDs succeeds, e.g. (Atelectasis):

http://data.bioontology.org/ontologies/ICD10CM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FICD10CM%2FJ98.11<http://data.bioontology.org/ontologies/ICD10CM/classes/http:/purl.bioontology.org/ontology/ICD10CM/J98.11>

… but using the search endpoint on the same class returns an empty collection:

http://data.bioontology.org/search?q=Atelectasis&ontologies=ICD10CM

Another user reported a similar problem yesterday.  Our search expert is back in the office on Monday and will have a look at reindexing.

Apologies for the trouble.

Best,
Jennifer


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