OHDSI MEETINGS THIS WEEK
No OHDSI community meeting this week - Tuesday’s OHDSI call has been cancelled for election day.
Hadoop Working Group Meeting - Friday, November 11th at 11am EThttp://cloudera.webex.com/meet/sdolley
NLP Work Group Meeting - Wednesday at 2pm EThttp://www.ohdsi.org/web/wiki/doku.php?id=projects:workgroups:nlp-wg
ANNOUNCEMENTS
Don’t forget to vote for the OHDSI symposium best poster - We’re asking all OHDSI community members to vote for their favorite posters from the 2016 OHDSI Symposium. Vote here: https://docs.google.com/a/ohdsi.org/forms/d/e/1FAIpQLSege_RoSOh-gdI87ac0rtp2SwEC0rDxyK_AyrcvNVFcZXi59Q/viewform
Symposium Recordings - Recordings from the main symposiums are now available online: http://www.ohdsi.org/2016-ohdsi-symposium-materials/2016-ohdsi-symposium-videos/
Tutorial Recordings - We’re currently reviewing tutorial recordings and will be posting them online shortly. Once they are available, all symposium attendees will be notified via email. A notification will also be posted in the forum.
COMMUNITY PUBLICATIONS
Identifying axial spondyloarthritis in electronic medical records of United States Veterans.
JA Walsh, Y Shao, J Leng, T He, CC Teng, D Redd, Q Treitler Zeng, Z Burningham, DO Clegg and BC Sauer,
Arthritis care & research , 2017 09
Large database research in axial spondyloarthritis (SpA) is limited by a lack of methods for identifying most types of axial SpA. Our objective was to develop methods for identifying axial SpA concepts in the free text of documents from electronic medical records.Veterans with documents in the national Veterans Health Administration Corporate Data Warehouse between January 1, 2005 and June 30, 2015 were included. Methods were developed for exploring, selecting, and extracting meaningful terms that were likely to represent axial SpA concepts. With annotation, clinical experts reviewed sections of text containing the meaningful terms (snippets) and classified the snippets according to whether or not they represented the intended axial SpA concept. With natural language processing (NLP) tools, computers were trained to replicate the clinical experts' snippet classifications.Three axial SpA concepts were selected by clinical experts, including sacroiliitis, terms including the prefix spond*, and HLA-B27 positivity (HLA-B27+). With supervised machine learning on annotated snippets, NLP models were developed with accuracies of 91.1% for sacroiliitis, 93.5% for spond*, and 97.2% for HLA-B27+. With independent validation, the accuracies were 92.0% for sacroiliitis, 91.0% for spond*, and 99.0% for HLA-B27+.We developed feasible and accurate methods for identifying axial SpA concepts in the free text of clinical notes. Additional research is required to determine combinations of concepts that will accurately identify axial SpA phenotypes. These novel methods will facilitate previously impractical observational research in axial SpA and may be applied to research with other diseases.
Incidence of Exposure of Patients in the United States to Multiple Drugs for Which Pharmacogenomic Guidelines Are Available.
M Samwald, H Xu, K Blagec, PE Empey, DC Malone, SM Ahmed, P Ryan, S Hofer and RD Boyce,
PloS one , 2016
Pre-emptive pharmacogenomic (PGx) testing of a panel of genes may be easier to implement and more cost-effective than reactive pharmacogenomic testing if a sufficient number of medications are covered by a single test and future medication exposure can be anticipated. We analysed the incidence of exposure of individual patients in the United States to multiple drugs for which pharmacogenomic guidelines are available (PGx drugs) within a selected four-year period (2009-2012) in order to identify and quantify the incidence of pharmacotherapy in a nation-wide patient population that could be impacted by pre-emptive PGx testing based on currently available clinical guidelines. In total, 73 024 095 patient records from private insurance, Medicare Supplemental and Medicaid were included. Patients enrolled in Medicare Supplemental age > = 65 or Medicaid age 40-64 had the highest incidence of PGx drug use, with approximately half of the patients receiving at least one PGx drug during the 4 year period and one fourth to one third of patients receiving two or more PGx drugs. These data suggest that exposure to multiple PGx drugs is common and that it may be beneficial to implement wide-scale pre-emptive genomic testing. Future work should therefore concentrate on investigating the cost-effectiveness of multiplexed pre-emptive testing strategies.
Ontology Mapping for Life Science Linked Datahttp://ceur-ws.org/Vol-1709/BMDID_2016_paper_11.pdf
Semantic Research Platform for Model Organism Datahttp://ceur-ws.org/Vol-1709/BMDID_2016_paper_1.pdf
