Weekly OHDSI Digest – December 11, 2023


On Dec. 16, 2013, George Hripcsak led the official formation of the OHDSI community. Within a month, the first face-to-face meeting was held within the Department of Biomedical Informatics at Columbia University. How did we get from there to a global community of more than 3,800 collaborators? Please join us for our Dec. 12 community call (11 am ET) to celebrate 10 years of OHDSI, while also looking back at our progress in 2023!

If you are able to join us, please wear your favorite OHDSI swag (if you joined at previous symposia), bring a favorite OHDSI memory from the last 10 years, and even feel free to have your own OHDSI-themed cake for a ‘Happy Birthday’ celebration!

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 Marek Oja, Sirli Tamm, Kerli Mooses, Maarja Pajusalu, Harry-Anton Talvik, Anne Ott, Marianna Laht, Maria Malk, Marcus Lõo, Johannes Holm, Markus Haug, Hendrik Šuvalov, Dage Särg, Jaak Vilo, Sven Laur, Raivo Kolde, and Sulev Reisberg on the publication of Transforming Estonian health data to the Observational Medical Outcomes Partnership (OMOP) Common Data Model: lessons learned in JAMIA Open.

• Congratulations to the team of Varvara Kalokyri, Haridimos Kondylakis, Stelios Sfakianakis, Katerina Nikiforaki, Ioannis Karatzanis, Simone Mazzetti, Nikolaos Tachos, Daniele Regge, Dimitrios Fotiadis, Konstantinos Marias, and Manolis Tsiknakis on the publication of MI-Common Data Model: Extending Observational Medical Outcomes Partnership-Common Data Model (OMOP-CDM) for Registering Medical Imaging Metadata and Subsequent Curation Processes in JCO Clinical Cancer Informatics.

• Congratulations to the team of Kyungseon Choi, Sang Jun Park, Sola Han, Yongseok Mun, Da Yun Lee, Dong-Jin Chang, Seok Kim, Sooyoung Yoo, Se Joon Woo, Kyu Hyung Park, and Hae Sun Suh on the publication of Patient-Centered Economic Burden of Exudative Age-Related Macular Degeneration: Retrospective Cohort Study in JMIR Public Health and Surveillance.


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.

• 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 — From OMOP to CDISC SDTM: Successes, Challenges, and Future Opportunities of using EHR Data for Drug Repurposing in COVID-19 (Wesley Anderson)

Tuesday — Mapping gravity value sets to OMOP CDM: The case of the food insecurity screening (Adam Bouras)

Wednesday — Enhancing Precision and Validity: Leveraging Multiple Error-Prone Phenotypes in EHR-Based Association Studies (Yiwen Lu)

Thursday — Enabling Innovation at the Bedside using STARR-OMOP (Priya Desai)

Friday — Guidance for Communication of the OHDSI Network Study Approach with Institutional Review Boards (Ben Martin)

• 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.

HADES Development Updates

• Martijn Schuemie announced the release of both DatabaseConnector 6.3.2 and SelfControlledCaseSeries 5.1.0. The former is a bugfix release, while the latter includes various improvements when running large number analyses (e.g. when performing risk discovery).

• Egill Fridgeirsson announced the release of DeepPatientLevelPrediction 2.0.2. This is mostly a bugfix with some refactoring.

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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