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[bioontology-support] appliance V1.0

Madani,Sina AHMadani at
Tue Aug 21 07:55:16 PDT 2012

Thank you Paul,

I did another upload for ICD9. Parsing went ok as well as adding the terminology to the annotation services. However I noticed two things

1.       If I search in the normal mode for a term like diabetes, appliance does not generate any result. But if I select advanced option and select a target terminology like ICD9, it returns results. It seems the blank default to run search against all terminologies is not working

2.       For annotation services, I started with loaderBigConcepts process but the appliance automatically processed loaderBigPaths as well after it finished loading concepts and reached status 14. The annotation is working for ICD9 now.

Quick question on mapping: is there any process available on the current version of appliance to do automatic mapping (CUI based) if I add another RRF or OWL terminology like SNOMED or NCI?

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From: Paul R Alexander [mailto:palexander at]
Sent: Monday, August 20, 2012 7:40 PM
To: Madani,Sina
Cc: 'support at'
Subject: Re: [bioontology-support] appliance V1.0


If anything, the parsing process should be more reliable in the 1.0 version as we added some code to ensure minor errors did not cause parsing failures. There have been no new post-processing steps added recently.

The UI will still cache data, so doing an 'ncborestart' might resolve that.


On 8/17/12 9:06 AM, Madani,Sina wrote:

I installed the new version of appliance in our local environment. The first terminology inject, SNOMED, was successful according to Lexgrid log file. However, when I manually flushed memcashed the status showed that SNOMED is parsing. This status is being shown since last night after Lexgrid load was successfully finished.

Before uploading SNOMED, I changed parser schedule to False and rebuilt file. Also, in submit new ontology form I used a very small zip file for SNOMED (per previous instructions). Then I did FTP to upload the complete SNOMED zip file (400Mb) to the upload folder, unzipped it, and manually (from Admin menu) parsed ontology 10001. In previous versions, after successful parsing I was able to browse and searched immediately.

Are new automatic processing(s) added after parsing in Version 1.0?



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