projects:workgroups:clinicalstudy
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projects:workgroups:clinicalstudy [2020/10/12 19:34] saraujo |
projects:workgroups:clinicalstudy [2024/08/19 14:14] (current) mikehamidi |
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| **Objective**: To allow adequate representation of clinical trial data in OMOP. | **Objective**: To allow adequate representation of clinical trial data in OMOP. | ||
| - | **First use case**: To convert clinical trial data in CDISC SDTM format to OMOP, with a view to allowing trial planning optimization. | + | **First use case**: To convert clinical trial data in [[https://www.cdisc.org/standards/foundational/sdtm|CDISC SDTM]] format to [[https://www.ohdsi.org/data-standardization/the-common-data-model/|OMOP]], with a view to allowing trial planning optimization. |
| - | **Approach**: We advocate minimum changes to the OMOP CDM and Standardized Vocabularies because we want to ensure minimum impact on OHDSI tools like Atlas, whilst providing a value-add SDTM-to-OMOP conversion with minimum data loss. We have proposed conventions introducing new concepts and modifiers, but no new CDM tables; and providing guidance for ETL developers where appropriate. Our proposals are built on OMOP CDM v6 and the Oncology extension, with v5.3.1 backward compatibility. | + | **Approach**: We advocate minimum changes to the OMOP CDM and Standardized Vocabularies because we want to ensure minimum impact on OHDSI tools like Atlas, whilst providing a value-add SDTM-to-OMOP conversion with minimum data loss. We have proposed conventions introducing new concepts and modifiers, but no new CDM tables; and providing guidance for ETL developers where appropriate. Our proposals were originally built on OMOP CDM v6 and the Oncology extension, with v5.3 backward compatibility. In a new v5.4 the additions from the Oncology extension became standard, which made our changes minimal, thereby, making our proposals fully compatible with v5.4. |
| - | + | ||
| - | **Status**: | + | |
| - | - Proposals submitted to the OHDSI community in July 2020. | + | |
| - | - Currently applying our proposed conventions to the PHUSE database (a synthetic SDTM database). | + | |
| - | + | ||
| - | **WG Lead**: Sonia Araujo, IQVIA, London, UK (sonia.araujo@iqvia.com) | + | |
| - | + | ||
| - | **Current Members** | + | |
| - | ^ Name ^ Organization & Location ^ | + | |
| - | | Alexander Davydov | Odysseus Data Services Inc., Cambridge, MA, USA | | + | |
| - | | Alexandra Orlova | Odysseus Data Services Inc., Cambridge, MA, USA | | + | |
| - | | Andrew Williams | Tufts Institute for Clinical Research and Health Policy Studies, Boston, MA, USA | | + | |
| - | | Asiyah Yu Lin | Center for Devices and Radiological Health, FDA, Silver Spring, MD, USA; National Center for Ontological Research, Buffalo, New York, USA | | + | |
| - | | Bess LeRoy | CDISC, Tucson, AZ, USA | | + | |
| - | | Chris Roeder | School of Medicine, University of Colorado, CO, USA | | + | |
| - | | Cynthia Sung | Bill & Melinda Gates Medical Research Institute, Seattle, WA, USA | | + | |
| - | | {nowrap|Eldar Allakhverdiiev} | Odysseus Data Services Inc., Cambridge, MA, USA | | + | |
| - | | Emma Vos | The Hyve, Utrecht, The Netherlands | | + | |
| - | | Gregory Klebanov | Odysseus Data Services Inc., Cambridge, MA, USA | | + | |
| - | | James Liddil | M2Gen, Tampa, FL, USA | | + | |
| - | | Joshua F. Ransom | BEKHealth Inc, Wayland, MA, USA | | + | |
| - | | Katy Sadowski | TrialSpark, New York, New York, USA | | + | |
| - | | Lina Clover | SAS, Raleigh-Durham, NC, USA | | + | |
| - | | Maxim Moinat | The Hyve, Utrecht, The Netherlands | | + | |
| - | | Michael Kallfelz | Odysseus Data Services Inc., Cambridge, MA, USA | | + | |
| - | | Mike Hamidi | CDISC, Audubon, PA, USA | | + | |
| - | | Philip Solovyev | Odysseus Data Services Inc., Cambridge, MA, USA | | + | |
| - | | Rebecca Baker | CDISC, Austin, Texas, USA | | + | |
| - | | Rhonda Facile | Elligo, Austin, Texas, USA | | + | |
| - | | Sonia Araujo | IQVIA, London, UK | | + | |
| - | | Ted Bebi | Medidata, Boston, MA, USA | | + | |
| - | | Tom Walpole | Trials.ai, San Diego, CA, USA | | + | |
| - | | Vojtech Huser | National Library of Medicine, National Institutes of Health, Bethesda, MD, USA | | + | |
| + | **Status**:\\ | ||
| + | - 2024: The finalization of C-Path SDTM-to-OMOP mappings is underway, with an emphasis on matching concept codes using Usagi. The next step is to execute ETL queries to generate the OMOP CDM tables. Additionally, a secondary objective is to identify general conventions and best practices for clinical trials. These conventions will be applied to additional C-Path SDTM study data to uncover any further gaps or challenges. \\ | ||
| + | - 2023: The team has transitioned from using Vivli (due to access constraints) data to leveraging SDTM data provided by C-Path for tuberculosis. The development of mapping specifications for the subsequent ETL process will proceed from the initial stages.\\ | ||
| + | - 2022: CTWG has been granted access to 20 Vivli clinical study packages in SDTM format. The team is conducting an inventory of these study packages to prioritize SDTM-to-OMOP mappings. The current CTWG guidance topics will be further evaluated, with new topics identified as needed. \\ | ||
| + | - 2021: CTWG conducted an assessment of clinical trial data providers to identify sources of accessible SDTM data. This assessment led to discussions with Vivli, focusing on general data usage agreements and evaluating the feasibility of their platform. \\ | ||
| + | - 2020: Used a synthetic representation of the CDISC SDTM data via PHUSE Test Data. Initial guidance topics were codified but require further testing with diverse real world SDTM data. The CTWG proposals submitted to the OHDSI community in July 2020.\\ | ||
| </WRAP> | </WRAP> | ||
| + | |||
| Line 53: | Line 27: | ||
| https://github.com/OHDSI/ClinicalTrialsWGETL | https://github.com/OHDSI/ClinicalTrialsWGETL | ||
| + | Recent WG Updates: | ||
| + | [[https://www.ohdsi-europe.org/images/symposium-2024/Posters/CTWG%20OHDSI%20Europe%20poster_v3%20-%20Cynthia%20Sung.pdf|2024 EU OHDSI Symposium Poster]]; [[https://youtu.be/pWW72a9A5YE|Nov. 2022 Presentation]]; [[https://youtu.be/ctPADsAoYpM|Oct. 2021 Presentation]] and [[https://ohdsiorg.sharepoint.com/:b:/s/Workgroup-Clinicaltrials/EXbVRrl7hQNEiPhC48Zx0t4BfILfVjMiW85MtWBmGHRzFA?e=nThgMV|Slides]] | ||
| + | ---- | ||
| ==== Meetings ==== | ==== Meetings ==== | ||
| - | **Schedule**: Biweekly calls on Fridays, 3pm UK time (10am Eastern) | + | **Bi-weekly on Fridays from 11:30 AM to 12:00 PM EST (Eastern Standard Time) or 4:30 PM to 5:00 PM UTC (Universal Time Coordinated)** is accessible on the OHDSI Teams environment. \\ |
| + | |||
| + | *** Note on accessing Teams channel:**\\ | ||
| + | * If you use the Teams desktop app and have multiple accounts, ensure you are already in the OHDSI Teams account before clicking the link above\\ | ||
| + | * Alternatively, select the "web app" button in the link above for accessing meetings on your browser\\ | ||
| + | * Join our WG here if you haven't: https://ohdsi.org/join-the-journey/. | ||
| + | |||
| + | ---- | ||
| + | |||
| + | ==== Membership ==== | ||
| + | |||
| + | **WG co-leads**: | ||
| + | Mike Hamidi | ||
| + | and | ||
| + | Kenneth Wilkins | ||
| + | |||
| + | |||
| + | **Active members**\\ | ||
| + | |||
| + | ^ Name ^ Organization ^ Location ^ ^ | ||
| + | | Chidi Asuzu | | USA | | | ||
| + | | Rebecca Baker | CDISC | Austin, TX, USA | | | ||
| + | | Ian Braun | Critical Path Institute | Tucson, AZ, USA | | | ||
| + | | Melissa Cook | Essex Management | Boston, MA, USA | [[http://www.linkedin.com/in/mkcook|{{:wiki:linkedinicon.png?20}}]] | | ||
| + | | Diane Corey | Critical Path Institute | Tucson, AZ, USA | | | ||
| + | | Shital Desai | Independent | USA | | | ||
| + | | Kerry Goetz | National Institute of Health; \\ National Eye Institute | Bethesda, MD, USA | [[https://www.linkedin.com/in/kerrygoetz/|{{:wiki:linkedinicon.png?20}}]] | ||
| + | | Mike Hamidi | DataInterop LLC | New Jersey, USA | [[https://www.linkedin.com/in/kamiar-mike-hamidi-0a908164/|{{:wiki:linkedinicon.png?20}}]] | | ||
| + | | Dan Hartley | Critical Path Institute | USA | | | ||
| + | | Ying Huang |National Institute of Health | USA | | | ||
| + | | Asiyah Yu Lin | National Institute of Health | Bethesda, MD, USA | | ||
| + | | Zhen Lin * | Robot Bacon | Houston, TX, USA | [[https://www.linkedin.com/in/zhen-lin/|{{:wiki:linkedinicon.png?20}}]], [[https://twitter.com/zhenLinPhDRN|{{:wiki:twittericon.png?20}}]] | | ||
| + | | Zhixin Lun | University of Colorado Anschutz Medical Campus | Aurora, CO, USA | | | ||
| + | | Terrence McHugh | Critical Path Institute | Tucson, AZ, USA | | | ||
| + | | Priya Meghrajani | Talosix | Seattle, WA, USA | | | ||
| + | | Paul Orona | | USA | | | ||
| + | | Daniel Olson | Critical Path Institute | Tucson, AZ, USA | | | ||
| + | | Katy Sadowski | TrialSpark | New York, NY, USA | | | ||
| + | | Philip Solovyev | Odysseus Data Services Inc. | Vilnius, Lithuania | [[https://www.linkedin.com/in/filippsolovev|{{:wiki:linkedinicon.png?20}}]] | | ||
| + | | Cynthia Sung | OHDSI | Seattle, WA, USA | [[https://www.linkedin.com/in/cynthia-sung-phd-fcp-ba01703/|{{:wiki:linkedinicon.png?20}}]] | | ||
| + | | Ramona Walls | Critical Path Institute | Tucson, AZ, USA | [[https://www.linkedin.com/in/ramona-walls-41aa7599/|{{:wiki:linkedinicon.png?20}}]], [[https://twitter.com/Ramona_Walls|{{:wiki:twittericon.png?20}}]], [[https://github.com/ramonawalls|{{:wiki:githubicon.png?15}}]] | | ||
| + | | Tom Walpole * | ZS Associates | Princeton, NJ, USA | | | ||
| + | | Kenneth Wilkins | National Institute of Health | Bethesda, MD, USA | | | ||
| + | | Ying Xiao | Penn Medicine, University of Pennsylvania | Philadelphia, PA, USA | | | ||
| + | | Qi Yang | IQVIA | Plymouth Meeting, PA, USA | | | ||
| + | |||
| + | ---- | ||
| - | **Recordings** | + | **Other members**\\ |
| - | ^ Q4 2020 ^ Q3 2020 ^ Q2 2020 ^ Q1 2020 ^ | + | ^ Name ^ Organization ^ Location ^ |
| - | | [[https://us02web.zoom.us/rec/share/TmCU0nV_ByKiMBZHlqFGUQr85h7rwEia4egZFgiIBnL8QgXFFJdUfc4zKidX5uce.tYuPTCbITOfbtld3|02 Oct]] | [[https://us02web.zoom.us/rec/share/qIJb-2XQqoYikO8A1v9sgySXr0PRLSIGl-kjM_bUMd8nSqgIdLh_cXUt-mIwFj2m.i9Ik-IrMOkf79mpC|18 Sep]] | [[https://youtu.be/bBW8Znz2hQI|26 Jun]] | [[https://youtu.be/ISWQpqGH_Hg|20 Mar]] | | + | | Eldar Allakhverdiiev | Odysseus Data Services Inc. | Cambridge, MA, USA| ^ |
| - | | | [[https://us02web.zoom.us/rec/share/RO8Hv1l9LI3kHtEmoFKwEEz5kJHLK8zOHQIQ-qEKhK6Rk3SoEi7_xHwscbDZ2LSZ.u3bSdaUhhBu8r0fD|04 Sep]] | [[https://youtu.be/F7LLaGKwa-I|22 May]] | [[https://youtu.be/1UyrBVa28aU|06 Mar (partial)]] | | + | | Sonia Araujo * | IQVIA | London, UK | |
| - | | | [[https://us02web.zoom.us/rec/share/zPIlcpb_q1NLHrPAxXHnda4DHKbLX6a8gXBI_foEnh3KAq9t9Jn-HnZGOKa5xLwt|21 Aug]] | [[https://youtu.be/u_9_AHs6bdc|15 May]] | [[https://youtu.be/95vD4A12gWE|07 Feb]] | | + | | Junn Bautista | Genentech | South San Francisco, CA, USA | | |
| - | | | [[https://us02web.zoom.us/rec/share/zOhxAJXo_URLYLPnxRDOZ5x9Rbn3eaa80Xcaq6cEy0n08H9Y3PXgXXWc8MnRB86h|14 Aug]] | [[https://youtu.be/cRvHcwaO-yg|01 May]] | [[https://youtu.be/_7billAOg60|10 Jan]] | | + | | Elise Berliner | | | |
| - | | | | [[https://youtu.be/51nEFDCSH0g|03 Apr]] | | | + | | Ted Bebi | Medidata | Boston, MA, USA | |
| + | | Lina Clover | SAS | Raleigh-Durham, NC, USA | | ||
| + | | Alexander Davydov | Odysseus Data Services Inc. | Cambridge, MA, USA | | ||
| + | | Shawn Dolley | Open Global Health | Arlington, Virginia, USA | | ||
| + | | Rhonda Facile | CDISC | Austin, Texas, USA | | ||
| + | | Stephen Fortin | | | | ||
| + | | Vojtech Huser | National Library of Medicine,\\ National Institutes of Health | Bethesda, MD, USA | | ||
| + | | Michael Kallfelz | Odysseus Data Services Inc. | Berlin, Germany | [[https://www.linkedin.com/in/michael-kallfelz/|{{:wiki:linkedinicon.png?20}}]] | | ||
| + | | Gregory Klebanov | Odysseus Data Services Inc. | Cambridge, MA, USA | | ||
| + | | Bess LeRoy | CDISC | Tucson, AZ, USA | | ||
| + | | James Liddil | M2Gen | Tampa, FL, USA | | ||
| + | | Maxim Moinat | The Hyve | Utrecht, The Netherlands | | ||
| + | | Alexandra Orlova | Odysseus Data Services Inc. | Cambridge, MA, USA | | ||
| + | | Joshua F. Ransom | BEKHealth Inc | Wayland, MA, USA | | ||
| + | | Chris Roeder | School of Medicine, University of Colorado | CO, USA | | ||
| + | | Anthony Sunjaya | The George Institute for Global Health,\\ UNSW Sydney | Sydney, NSW, Australia | | | ||
| + | | Emma Vos | The Hyve | Utrecht, The Netherlands| | ||
| + | | Andrew Williams | Tufts Institute for Clinical Research \\ and Health Policy Studies | Boston, MA, USA | | ||
| + | | Ariana Winder | Javara Research | State College, Pennsylvania, USA | [[https://www.linkedin.com/in/amwinder/|{{:wiki:linkedinicon.png?20}}]] | | ||
| + | | Stella Zhu | Bill & Melinda Gates Medical Research Institute | Seattle, WA, USA| | ||
| - | **Q4 2019** [[https://youtu.be/Fc9OHg8qCq0|06 Dec]] - initial presentations from the Hyve, Medidata and Odysseus | + | * Past leads |
| + | ---- | ||
| - | **Want to contribute to the group?** Email sonia.araujo@iqvia.com | + | **Want to contribute to the group?** [[https://ohdsi.org/join-the-journey/|Opt-in here]]. \\ |
| + | [[https://ohdsi.org/this-week-in-ohdsi/|Click here to catch up recent calls and job openings]] | ||
| ~~NOTOC~~ | ~~NOTOC~~ | ||
projects/workgroups/clinicalstudy.1602531276.txt.gz · Last modified: 2020/10/12 19:34 by saraujo
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