Clinical Genomics

Conference Call

Meeting Minutes

July 9, 2003 11:00am to 12:30 pm EST

Attendance

First Name / Last Name / Organization / Email
Pravat / Das / Mayo Clinic /
Peter / Elkin / Mayo Clinic /
Scott / Getzin / Eli Lilly /
Rick / Haddorff / Mayo Clinic /
Jim / Holeman / HP Nonstop Enterprise Division /
Shosh / Israel / Hadassah University Hospital, Israel
Jill / Kaufman / IBM Life Sciences /
Amnon / Shabo / IBM Research, Haiffa, Israel /
Sue Jane / Wang / FDA /
Scott / Whyte / CGEY Health /
Katie / Wittrup / Mayo Clinic /
Chuang / Xu / Genaissance /

Welcome and UpdatesJill Kaufman

  • Introductions – Each attendee introduced themselves
  • Electronic Health Record – Team discussed Clinical Genomics attendance and input to the EHR initiative. Action Item – Peter to organize response to EHR team (Peter will be a speaker on August call addressing the topic: “Genomic Input to Electronic Health Record”)
  • Scott confirmed he would take minutes for today’s conference call

Tissue Typing Model ReviewAmnon Shabo with Shosh Israel

  • Amnon Referred to the Hand-outs he distributed via email:
  • Zip HL7-Clinical-Genomics-DIMs.zip
  • HL7-Genotype-DIM.jpg and *.vsd
  • genotype-data-model.doc (subsequent email updated this file to *1.doc)
  • HL7-TT-Observation-DIM.jpg and *.vsd
  • HL7-TT-DIM.jpg and *.vsd
  • Review of Word Doc
  • Note on CMET – can drag and drop Genomic CMET. In CDA committee, replaced CMETs with more committee-specific models. RCRIM also looking at alternative models.
  • Next steps – Amnon will convert the HL7 Visio model into a UML model. Also, he’ll convert HL7 Visio into XML schemas and then into XML instances (use case specific).
  • Peter – “What’s the shadow – is it related to differences in spin may affect phenotypic expression?” Shosh, no. Only dealing with DNA, not things that make it phenotypically different.
  • Observation DIM (file HL7-TT-Observation-DIM.vsd)
  • Shadow is potential match (for transplant, crime, paternity etc.)
  • Patient is original person
  • Note – no common vocabulary to describe level of matching. Bone marrow groups are working on common vocabulary. (note 3rd model – Genotype addresses some of the data/vocabulary issues per locus)
  • Genotype DIM (file HL7-Genotype-DIM.vsd)
  • Note on entry point at middle top of diagram - DIM doesn’t have a specific entry point yet (DIM doesn’t have a root like XML). Amnon will register an entry point with HL7.
  • Jill – How long is the sequence of the Allele? Answer – Shosh, can be hundreds or thousands of base pairs. Need to base in AGAVE or BSML (noted in ‘code’ attribute).
  • Chuanbo – SNP only covers one type of variation. Also, comment on methods. Amnon – Look at ‘method code’ (need a vocab for the method). For a given polymorphism, can use multiple methods.
  • Scott – Proposed adding a ‘Method’ as a new class. Chuanbo – Genaissance has separate tables for methods and source. They commonly compare and validate method. Amnon – Noted Stan Huff’s LOINC MOLGEN section. Shosh – Agreed that there is a need for attributes describing the method. Amnon - This may change standard HL7 RIM. There aren’t attributes for Method. May want a specialization of the Observation class instead of a brand new class. Amnon will follow-up.
  • Word Document – Review of model comments and action items.
  • See middle of pg. 3 – before open issues. Suggest adding specialized observation class instead of trying to add attributes to the existing class.

Closing Comments and Follow-upTeam

  • Jill – We’ll plan on reviewing Amnon’s updated Genotype models in Memphis on Tuesday morning.
  • Rick and Jim will try to normalize CF with the Tissue Typing models.
  • Amnon will share models with Charlie Mead.
  • Next CG SIG Con Call is August 20, 5pm EST. Jill will email dial-in prior to call.
  • Next HL7 meeting is September in Memphis. CG SIG will meet the 8th, 9th and 10th.
  • Scott to distribute minutes for today’s conference call.

10/21/2018 11:53 AM1Clinical Genomics SIG ConCall 07 09 03 v1.doc