Weekly OHDSI Digest – December 4, 2023


Please join our Dec. 5 community call (11 am ET) for our latest session focused on recent publications from the OHDSI community. We are excited to welcome the lead authors to present their recently published studies that feature OHDSI tools/practices or the OMOP Common Data Model:

Multinational patterns of second line antihyperglycaemic drug initiation across cardiovascular risk groups: federated pharmacoepidemiological evaluation in LEGEND-T2DM – BMJ Medicine (Lovedeep Dhingra and Arya Aminorroaya • Postdoctoral Associates, Yale School of Medicine)

Scalable Infrastructure Supporting Reproducible Nationwide Healthcare Data Analysis toward FAIR Stewardship – Scientific Data (Chungsoo Kim • PhD Candidate, Ajou University)

Transforming the Information System for Research in Primary Care (SIDIAP) in Catalonia to the OMOP Common Data Model and Its Use for COVID-19 Research – Clinical Epidemiology (Berta Raventós • Predoctoral Researcher, Institut Universitari d’Investigació en Atenció Primària (IDIAP) Jordi Gol)

European Health Data & Evidence Network—learnings from building out a standardized international health data network – JAMIA (Erica Voss • Senior Director, Janssen Research & Development)

Scalable and interpretable alternative to chart review for phenotype evaluation using standardized structured data from electronic health records – JAMIA (Anna Ostropolets • Director, Head of Innovation Lab, Odysseus Data Services, Inc.)

Everybody is invited. Calendar invites went out last week. If you did not receive one, please use this link to join the meeting. All recordings from these weekly calls are available within our Teams environment and will be posted on both our YouTube page and our OHDSI.org Community Calls page.


Upcoming Workgroup Calls – OHDSI


• Congratulations to the team of Fan Bu, Martijn Schuemie, Akihiko Nishimura, Louisa Smith, Kristin Kostka, Thomas Falconer, Jody-Ann McLeggon, Patrick Ryan, George Hripcsak, and Marc Suchard on the publication of Bayesian safety surveillance with adaptive bias correction in Statistics in Medicine.

• Congratulations to the team of Rupa Makadia, Azza Shoaibi, Gowtham Rao, Anna Ostropolets, Peter Rijnbeek, Erica Voss, Talita Duarte-SallesJuan Manuel Ramírez-Anguita, Miguel Mayer, Filip Maljković, Spiros Denaxas, Fredrik Nyberg, Vaclav Papez, Anthony Sena, Thamir Alshammari, Lana Lai, Kevin Haynes, Marc Suchard, George Hripcsak, and Patrick Ryan on the publication of Evaluating the impact of alternative phenotype definitions on incidence rates across a global data network in JAMIA Open.

• Congratulations to the team of Lin Lawrence Guo, Maryann Calligan, Emily Vettese, Sadie Cook, George Gagnidze, Oscar Han, Jiro Inoue, Joshua Lemmon, Johnson Li, Medhat Roshdi, Bohdan Sadovy, Steven Wallace, and Lillian Sung on the publication of Development and validation of the SickKids Enterprise-wide Data in Azure Repository (SEDAR) in Heliyon.

• Congratulations to the team of Manuel Rueda, Ivo Leist, and Ivo Gut on the publication of Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data in the Journal of Biomedical Informatics.

• Congratulations to Craig Mayer on the publication of Conversion of CPRD AURUM Data into the OMOP Common Data Model in Informatics in Medicine Unlocked.


The first OHDSI UK Study-A-Thon was held last week, which focused on use of fluoroquinolones across geographies and over time; and on the epidemiology and characterization of rectal prolapse and rectopexy. At the end of an intense week, the team generated three draft manuscripts almost ready for submission, and at least four conference abstracts in the making. We will hear more about this effort during a January community call.

• Alison Callahan is an Instructor in the Center for Biomedical Informatics and Clinical Data Scientist in the Stanford Health Care Data Science Team. Her current research uses informatics to extract perinatal health data from electronic health records, and to study medication usage and effectiveness in pregnancy. She is also the co-leader of the OHDSI Perinatal & Reproductive Health (PRHeG) working group. Her work in the SHC Data Science team focuses on developing and implementing methods to assess and identify high value applications of machine learning in healthcare settings. Alison discusses her career journey, how OHDSI impacts her research at Stanford, critical knowledge gaps that can be addressed by the Perinatal and Reproductive Health workgroup, and more in the latest edition of the Collaborator Spotlight.

• The latest edition of the OHDSI newsletter is now available, and it includes a quick retrospective on 10 years of OHDSI, recent community updates, a spotlight of Alison Callahan of Stanford Medicine, the Global Symposium plenary on “Improving the reliability and scale of case validation,” as well as November publications and presentations from the OHDSI community. If you don’t receive the newsletter in your inbox, you can subscribe here.

• Andrew Williams posted a document that describes how OHDSI workgroups form, the kinds of things they do, and the categories of workgroups that the OHDSI community is organized into. It is meant to help community members understand and how to use OHDSI workgroups to get things done. It also provides some tips on running workgroups. There is a request for comments until Jan. 1, 2024. To read more and access the document, please visit the forum post.

• Davera Gabriel has requested community input on the OMOP + FHIR Implementation Guide prior to Dec. 6. You can access the guide here.

• The next edition of the Early-Stage Researchers Career Speaker Series will be held Monday, Dec. 11, at 11 am ET. Fan Bu, a postdoctoral researcher at UCLA, will be the featured speaker. You can join the call here.

• Research from the 2023 Global Symposium Collaborator Showcase can be viewed on the Global Symposium Showcase page. Research is also being shared daily on OHDSI’s LinkedInTwitter/X and Instagram feeds as part of the #OHDSISocialShowcase. Below are posters (with study leads) that are featured this week:

Monday — Make Your Tools Work for You: Customizing the Data Quality Dashboard to Identify Changes in Source Data (Melanie Philofsky)

Tuesday — Assessment of Pre-trained Observational Large Longitudinal models in OHDSI (APOLLO) (Martijn Schuemie)

Wednesday — A use case of OHDSI ATLAS in a high-throughput genome wide association study pipeline (Craig Teerlink)

Thursday — Data-driven assessment of mental health among children and adolescents with food allergy (Natalie Flaks-Manov)

Friday — Quantification of Symptom Documentation on Disease Diagnosis Date in Structured Claims Data: An Application of the OHDSI Phenotype Library (Gowtham Rao)

• The 2023 Global Symposium home page has posted the video presentations and slides for all of the Friday talks, as well as the “Introduction to OHDSI” tutorial from Saturday morning. All posters from the collaborator showcase are also available. Please check out this page for all material related to the event.

 The latest edition of the Our Journey annual report was shared at the Global Symposium, but there is a digital version that you can access on the OHDSI website.

HADES Development Updates

• Ger Inberg announced the release of FeatureExtraction 3.3.2. It is a bugfix release.

• Adam Black announced the release of Andromeda 0.6.4. This is a patch release.

Job Openings

• Aedin Culhane announced the opening of two positions for a Postdoctoral Researcher (Level 1 or 2) in Cancer Digital Health Real World Evidence at the University of Limerick. As a Postdoctoral Researcher in the eHealth-Hub for Cancer, you will have responsibility for leading programming and development of analytical pipelines for harmonising cancer clinical data at partner sites to the best practice international standards. You will work with experts in the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM), mCODE and the GA4GH standard Phenopackets. You will have the opportunity to contribute to development of the OMOP-CDM oncology extension, oncology genomics data standards, connecting Irish cancer data to All of US, the UK Biobank, PIONEER, OPTIMA, and a federated network of global cancer datasets. You will contribute to the coding and reviewing of R or python packages for the federated analysis of OMOP-mapped real-world cancer data. The application deadline is Dec. 15, 2023. Further description and an application link are available here.

• Cynthia Sung shared two openings at the Bill and Melinda Gates Foundation, one for a Distinguished Scientist, Artificial Intelligence & Large Language Models, and one for a Deputy Director, Quantitative Sciences. More details about both positions are available within the direct links.

• Stephanie Leonard shared an opening at Stanford University for a postdoctoral scholar in perinatal pharmacoepidemiology. The scholar will work closely with faculty members with expertise in epidemiology, medical informatics, and clinical medicine on NIH-funded research projects on the comparative safety and effectiveness of medications in pregnancy and related research topics. Our projects employ advanced analytical methods in large databases, including OHDSI network studies using claims data and electronic health record data in the OMOP CDM. Current topical focus areas include mental health, behavioral health and cardiovascular health of people who are pregnant or postpartum. Further details are available here: https://postdocs.stanford.edu/prospective/opportunities/open-postdoctoral-position-faculty-mentor-brian-bateman 1. Please send any questions to Dr. Leonard at stephanie.leonard@stanford.edu. Details on postdoc resources at Stanford: https://postdocs.stanford.edu/.

• Ajit Londhe recently posted that Boehringer Ingelheim is hiring for two positions: (1) Director, Real World Data & Analytics – Data Domain Owner (this position will lead acquisition strategy for real-world data sources for possible in-license/ purchase and additional analytical tools for in-house analytic needs across the organization … responsible for oversight of operational governance tasks & real-world data life cycle governance … US-based, remote location); and (2) Real World Evidence Data Engineer (IT position supporting RWE teams’ technology needs, including OHDSI stack support … based in Spain only).

• Yuan Lu, Assistant Professor at Yale University, announced an opening for a Postdoctoral Associate/Data Analyst at the Yale University School of Medicine. This person will work on the LEGEND Hypertension Project. More information, including job description, key responsibilities and qualifications, are available here. If interested, please reach out to Dr. Lu at y.lu@yale.edu.


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