1 / 14

HL7-CDISC-PGx Pharmacogenomics Vocabularies

HL7-CDISC-PGx Pharmacogenomics Vocabularies. Initial Scouting Report Mark Sharp sharp@merck.com May 2006. Methodology. Study Amnon’s “walk-through” Make a checklist of data elements ( PGx_elements.xls ) Pick out ones which seem to call for controlled vocabularies

meara
Download Presentation

HL7-CDISC-PGx Pharmacogenomics Vocabularies

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. HL7-CDISC-PGxPharmacogenomics Vocabularies Initial Scouting Report Mark Sharp sharp@merck.com May 2006

  2. Methodology • Study Amnon’s “walk-through” • Make a checklist of data elements (PGx_elements.xls) • Pick out ones which seem to call for controlled vocabularies • Scout out available vocab resources • Index analysis files to PGx_elements.xls

  3. Issues • Availability • Authority • Coverage (size, granularity) • Relationships (Medline, etc.) • “Quality” • Agreement with other vocabs • Agreement/coverage of • Amnon’s proposed codes • Peter Elkins’ mutation types, test types • Joyce’s example data • Other?

  4. www.scils.rutgers.edu/~msharp/HL7_PGx

  5. Chromosomal Loci

  6. Chromosomal Loci • “Position" has ambiguous semantics: sequence occupies part/most/all of position. • Chromosomal loci are known/encoded to variable degrees of precision (>100 cases of "1" in HUGO). • This leads to variable cardinality between sequences, chromosomal loci, and approved gene names (i.e., "1" doesn't tell you much). • Should the chromosomal loci values in HUGO, GenBank, etc., be used like the gene names for vocabulary control, given that a new specific locus may be more meaningful than "1"? • These thoughts suggest a function for automatic computation of gene-gene relationships based on a hierarchy of [known] chromosomal loci.

  7. Chromosomal Locus String Length is a Rough Measure of Precision

  8. ~24% GenBank ~11% HUGO

More Related