Re: SHRINE\SCILHS metadata enhancements and maintenance plan proposed by Nebraska

2018-02-19 Thread Klann, Jeffrey G. 
Sounds great! Quick note, our ontology is currently in release 3.1, not 2.2: 
https://github.com/ARCH-commons/arch-ontology/blob/master/README.md

I see that some of our READMEs on GitHub are outdated, but version #s in the 
ontology are correct.

Thanks,
Jeff

Jeffrey Klann, PhD
Instructor of Medicine, Harvard Medical School
Director, SCILHS Query Core

From: "Campbell, James R" 
Date: Monday, February 19, 2018 at 2:48 PM
To: Jeffrey KLANN 
Cc: "Narayana, Yeshwanth R" , "Pedersen, Jay G" 
, "Campbell, Walter S" , GPC 
STANDARDS 
Subject: SHRINESCILHS metadata enhancements and maintenance plan proposed by 
Nebraska

Jeff
From our call  10 days ago, we are proceeding with the plan below for support 
of i2b2 metadata for our SNOW SHRINE network.  Relative to the INITIAL release 
and to support SCILHS sites that want to use our metadata expansions, we 
propose to add the following metadata sets to SCILHS 2.20:
1) SNOMED CT diagnoses grafted onto the "\PCORI\DIAGNOSIS\SM\" root in 
DIAGNOSIS in DIAGNOSIS
2) New Lab/Path LOINC ontology grafted onto "\PCORI\LAB_RESULT_CM\LAB_CODES\" 
in LAB_RESULT_CM
3) New medications by ingredient  grafted onto "\PCORI\MEDICATION\INGREDIENT\" 
in MEDICATIONS
4) SNOMED CT Procedure history grafted onto "\PCORI\PROCEDURE\SM\" in PROCEDURES


OPERATIONAL PROPOSAL
NEBRASKA I2B2 SNOW SHRINE METADATA PUBLICATION AND SUPPORT
February 19, 2018


  1.  OBJECTIVES:

 *   Provide timely, comprehensive and historically complete i2b2 metadata 
for relevant subsets of all ONC terminology and HIPAA transaction standards 
specifically SNOMED CT(Clinical Findings, Events, Situations, Procedures, 
Organisms), LOINC(laboratory and clinical), RXNORM, NDC, ICD*, ICD-10-PCS and 
CPT4
 *   Provide resources for sites to easily and quickly process metadata 
updates in order to encourage prompt installation of terminology updates and 
synchronization for interoperation across SNOW SHRINE network.  The goal will 
be to support metadata version update via DELTA with < 4 hours of technical 
time per site.

  1.  RELEASE AND MAINTENANCE SCHEDULE:

 *   All publication files will be freely available through Nebraska 
Lexicon website repository.  Users will be required to have a valid UMLS 
account and license to negotiate security and download SNOMED CT (and probably 
CPT4)
 *   Support six monthly maintenance cycle (April-October to allow 
processing of SNOMED International and NLM|US extension)
 *   Strict version control will be maintained, supported by version 
specific release notes number 1.0, 1.1, etc.
 *   Release notes will accompany each version release and detail standards 
development  and metadata changes
 *   All i2b2 metadata will be distributed as:

*   a current FULL 
release of Nebraska Lexicon© metadata tables in CSV format with accompanying 
load scripts.  Historical FULL releases will be archived and deleted from the 
site.
*  a version 
specific DELTA metadata update consisting of SQL files to update metadata from 
the last release
* FULL and DELTA 
SHRINE adapter metadata sets

 *   All DELTA releases will be maintained historically in the repository 
and documented by version.
 *   An INITIAL release forking development from SCILHS 2.2 and ACT with 
DELTA to Nebraska Lexicon 1.0 will be published for those sites who are 
currently using those ontologies.
 *   A library of web references to the EPIC and CERNER userwebs supporting 
ETL sharing between sites using compatible software

  1.  Other NEBRASKA LEXICON© Publications Supported six monthly

 *   RF2 release of Nebraska Lexicon© SNOMED CT extension including 
laboratory, anatomic and molecular pathology and clinical modules.
 *   RF2 release of SNOMED CT LOINC mapsets
 *   Coded and structured CAP® Cancer Checksheets distributed as PDF and 
Excel spreadsheets
Nebraska Lexicon© SNOMED CT web browser inclusive of laboratory, anatomic and 
molecular pathology and clinical terminology enhancements.

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only for the use of the addressee(s) above. Any unauthorized use or disclosure 
of this information is prohibited. If you have received this e-mail by mistake, 
please delete it and immediately contact the sender.


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SHRINE\SCILHS metadata enhancements and maintenance plan proposed by Nebraska

2018-02-19 Thread Campbell, James R 
Jeff
>From our call  10 days ago, we are proceeding with the plan below for support 
>of i2b2 metadata for our SNOW SHRINE network.  Relative to the INITIAL release 
>and to support SCILHS sites that want to use our metadata expansions, we 
>propose to add the following metadata sets to SCILHS 2.20:
1) SNOMED CT diagnoses grafted onto the "\PCORI\DIAGNOSIS\SM\" root in 
DIAGNOSIS in DIAGNOSIS
2) New Lab/Path LOINC ontology grafted onto "\PCORI\LAB_RESULT_CM\LAB_CODES\" 
in LAB_RESULT_CM
3) New medications by ingredient  grafted onto "\PCORI\MEDICATION\INGREDIENT\" 
in MEDICATIONS
4) SNOMED CT Procedure history grafted onto "\PCORI\PROCEDURE\SM\" in PROCEDURES


OPERATIONAL PROPOSAL
NEBRASKA I2B2 SNOW SHRINE METADATA PUBLICATION AND SUPPORT
February 19, 2018


  1.  OBJECTIVES:
 *   Provide timely, comprehensive and historically complete i2b2 metadata 
for relevant subsets of all ONC terminology and HIPAA transaction standards 
specifically SNOMED CT(Clinical Findings, Events, Situations, Procedures, 
Organisms), LOINC(laboratory and clinical), RXNORM, NDC, ICD*, ICD-10-PCS and 
CPT4
 *   Provide resources for sites to easily and quickly process metadata 
updates in order to encourage prompt installation of terminology updates and 
synchronization for interoperation across SNOW SHRINE network.  The goal will 
be to support metadata version update via DELTA with < 4 hours of technical 
time per site.
  2.  RELEASE AND MAINTENANCE SCHEDULE:
 *   All publication files will be freely available through Nebraska 
Lexicon website repository.  Users will be required to have a valid UMLS 
account and license to negotiate security and download SNOMED CT (and probably 
CPT4)
 *   Support six monthly maintenance cycle (April-October to allow 
processing of SNOMED International and NLM|US extension)
 *   Strict version control will be maintained, supported by version 
specific release notes number 1.0, 1.1, etc.
 *   Release notes will accompany each version release and detail standards 
development  and metadata changes
 *   All i2b2 metadata will be distributed as:
*   a current FULL 
release of Nebraska Lexicon© metadata tables in CSV format with accompanying 
load scripts.  Historical FULL releases will be archived and deleted from the 
site.
*  a version 
specific DELTA metadata update consisting of SQL files to update metadata from 
the last release
* FULL and DELTA 
SHRINE adapter metadata sets
 *   All DELTA releases will be maintained historically in the repository 
and documented by version.
 *   An INITIAL release forking development from SCILHS 2.2 and ACT with 
DELTA to Nebraska Lexicon 1.0 will be published for those sites who are 
currently using those ontologies.
 *   A library of web references to the EPIC and CERNER userwebs supporting 
ETL sharing between sites using compatible software
  3.  Other NEBRASKA LEXICON© Publications Supported six monthly
 *   RF2 release of Nebraska Lexicon© SNOMED CT extension including 
laboratory, anatomic and molecular pathology and clinical modules.
 *   RF2 release of SNOMED CT LOINC mapsets
 *   Coded and structured CAP® Cancer Checksheets distributed as PDF and 
Excel spreadsheets

Nebraska Lexicon© SNOMED CT web browser inclusive of laboratory, anatomic and 
molecular pathology and clinical terminology enhancements.



The information in this e-mail may be privileged and confidential, intended 
only for the use of the addressee(s) above. Any unauthorized use or disclosure 
of this information is prohibited. If you have received this e-mail by mistake, 
please delete it and immediately contact the sender.
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