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[bioontology-support] SNOMED and ICD10

Madani,Sina AHMadani at mdanderson.org
Fri Dec 10 13:11:16 PST 2010


Thank you Pradip
I found three lexbig jar file in the ncbo instance, added ICD10 OID (I got it from HL7 OID registry website). It loaded quickly and it working!
Need to work on SNOMED owl and RRF version now.

Thanks for all your help and prompt response!

Sina

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From: Kanjamala, Pradip P. [mailto:Kanjamala.Pradip at mayo.edu]
Sent: Friday, December 10, 2010 10:54 AM
To: Madani,Sina
Subject: RE: SNOMED and ICD10

Hi Sina,
For NCBO, we break apart the jar files into their individual jar components to avoid conflicts with jar files that Protégé and the NCBO codebase uses. The LexEVS classes are bundled in the lexbig.jar file. The lbRuntime.jar file is actually the lexbig.jar file + all dependent 3rd party jar files. For NCBO the 3rd party jar are bundled individually.

Pradip

________________________________
From: Madani,Sina [mailto:AHMadani at mdanderson.org]
Sent: Friday, December 10, 2010 10:48 AM
To: Kanjamala, Pradip P.
Subject: RE: SNOMED and ICD10
Hi Pradip,
do you happen to know where lbRuntime.jar file exist in ncbo? I basically list all jar files in any directory but there is non for lbRuntime

Thanks
Sina

From: Kanjamala, Pradip P. [mailto:Kanjamala.Pradip at mayo.edu]
Sent: Thursday, December 09, 2010 1:36 PM
To: Madani,Sina
Cc: Paul R Alexander
Subject: RE: SNOMED and ICD10

Hi Sina,
The difficulty loading ICD10CM is caused by a missing OID in the lexbig.jar file. A new lexbig.jar file has been checked into the BioPortal SVN trunk that could be checked out and used instead of the lexbig.jar file you have in your BioPortal instance. The other option would be to add the missing OID like you did with the lbRuntime.jar file.

For RRF SNOMED, I would suggest you use a small zipped RRF file to make the initial submission and then transfer the correct set of RRF files into the appropriate file location. Reparse the ontology and and load should work fine.

The LexEVS_UMLS_Mapper was a program that we used to create inter-cui mappings between different RRF ontologies. The idea is that if concepts in the two ontologies share a common UMLS CUI, they would be mapped together.

Regards,
Pradip

________________________________
From: Madani,Sina [mailto:AHMadani at mdanderson.org]
Sent: Thursday, December 09, 2010 1:20 PM
To: Kanjamala, Pradip P.
Subject: FW: SNOMED and ICD10
Hi Pradip,

in addition to that, can you also tell me what LexEVS_UMLS_Mapper does? Is it a module (in LexEVS? NCBO?) that automatically provides mapping based on CUI in terminologies extracted (subset) from UMLS?



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From: Paul R Alexander [mailto:palexander at stanford.edu]
Sent: Wednesday, December 08, 2010 5:05 PM
To: 'Kanjamala, Pradip P.'; Madani,Sina
Subject: Fwd: SNOMED and ICD10

Pradip,

Can you comment on Sina's issues with loading below? This is a group running our virtual appliance, not trying to get it to work at bioportal.bioontology.org.

Thanks!

Paul

-------- Original Message --------
Subject:

SNOMED and ICD10

Date:

Wed, 8 Dec 2010 09:32:25 -0600

From:

Madani,Sina <AHMadani at mdanderson.org><mailto:AHMadani at mdanderson.org>

To:

support at bioontology.org<mailto:support at bioontology.org> <support at bioontology.org><mailto:support at bioontology.org>

CC:

Paul R Alexander <palexander at stanford.edu><mailto:palexander at stanford.edu>


Good morning,

is there any specific instruction for uploading and parsing SNOMED OWL/ RRF and ICD10CM RRF formats?
I am getting:
parsing error on SNOMED OWL , and  ICD10CM RRF
uploading error on SNOMED RRF

I generated SNOWMED owl with the perl script that shipped with the July 2010 version. RRF ontologies are subsets from UMLS2010 AB. For ICD10CM apparently there is a problem with urn that I fixed in our LexEVS instance by manually inserting and OID inside mapping file within the runtime jar file but I don't know how to do/fix this in NCBO appliance.


Thanks
Sina
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