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Fw: FHIR genomic resources

From: mdmiller <mdmiller53@comcast.net>
Date: Fri, 12 Jul 2013 07:28:00 -0700
Message-ID: <26654FAB71EA4774A467B4E215EC9169@mmPC>
To: <public-semweb-lifesci@w3.org>, "Charlie Mead" <charlie.mead@yahoo.com>, "Josh Mandel" <jmandel@gmail.com>, "Hans Constandt" <hans@ontoforce.com>, "Christel Daniel" <christel.daniel@crc.jussieu.fr>, "'Sajjad Hussain'" <sajjad.hussain@crc.jussieu.fr>, "Mustafa Yuksel" <mustafa@srdc.com.tr>, "Gokce Banu Laleci Erturkmen" <gokce@srdc.com.tr>, "Erick Von Schweber" <erick@surveyorhealth.com>, "Solbrig, Harold R." <Solbrig.Harold@mayo.edu>, "Stan Huff" <Stan.Huff@imail.org>, "Jiang, Guoqian, M.D., Ph.D." <Jiang.Guoqian@mayo.edu>, "Emory Fry \(Google Drive\)" <eafry@gmx.com>, "Conor Dowling" <conor-dowling@caregraf.com>, "David Booth" <david@dbooth.org>
Cc: "Amnon Shabo" <SHABO@il.ibm.com>
hi all,

interesting presentation this last tuesday to the CG working group at HL7.  mentions XML and JSON but not RDF but the principles are around the subject of this call, http://smartgenomics.wikispaces.com/presentation

amnon also e-mailed out this.  the presentation is from 2011, and as far as i know GVF may be better but VCFs are still ubiquitous:

"Dear CGers. 
I came across this NHGRI presentation on GVF: http://www.genome.gov/Pages/Health/HealthCareProvidersInfo/Yandell_NHGRI_Data_Standards_April_27_2011.pdf 

Here are a few statements from this presentation, some of which are aligned with what we are trying to accomplish in this group: 
  a.. "structured genetic/genomic data must be available within the EHR in a computable and consistent format" 
  b.. "Variant files are [currently] not standardized" 
  c.. "Badly needed : a standard format" 
  d.. [needed an ontology for descriptive terms hence SO - the Sequence Ontology] 
  e.. "Data standards have great power to unify and enable the community" 
  f.. "Standardized file formats enable downstream software applications for analysis" 
  g.. "GVF: a standardized file format for variation files" 
  h.. "GVF is now the output of EBI variant annotation pipeline" 
  i.. "Standards enable comparative genomics of people, platforms and variant calling methods" 
  j.. "Standards enable tools for clinical decision support" 
  k.. "Develop HL7 compliant XML DTD for embedding GVF in EHRs"

Note the last bullet (appears on the next steps slide) - does anyone know if that step has been followed? 

Also, slide 15 compares GVF to VCF (see below) and according this comparison, it seems to me that GVF is more suitable for key data encapsulation within HL7 structures.


How is GVF different from VCF?

* Descriptive terms typed via the Sequence Ontology. 
* Library of existing software for analysis and visualization (GMOD tools) 
* Focus is on clinical annotation and functional consequence of variant"


Michael Miller
Software Engineer
Institute for Systems Biology

----- Original Message ----- 
From: Amnon Shabo 
To: clingenomics@lists.hl7.org 
Sent: Monday, July 08, 2013 8:12 AM
Subject: FHIR genomic resources

Dear CGers, 
In tomorrow's call we'll have a discussion on an effort led by Dr. Gil Alterovitz (Harvard) to develop FHIR genomic resources. 
For background information, please see slide 21 in Gil's presentation on SMART here: http://smartgenomics.wikispaces.com/presentation 

Since the usual WebEx will not be available tomorrow, let's use this one: http://www.ibm.com/collaboration/meeting/join?id=1136358 

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Received on Friday, 12 July 2013 14:28:31 UTC

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