OHDSI has a variety of ongoing projects lead by workgroup teams. We would be delighted to have your participation. Please contact the team lead to join.
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To build and evaluate a computational pipeline for electronic phenotyping – which defines criteria to algorithmically select sets of patients based on stored clinical data – in the OHDSI project. Our approach for learning statistical models of clinical phenotypes is called XPRESS, which stands for eXtraction of Phenotypes from clinical REcords using Silver Standards.
Project Leads: Nigam Shah, MBBS, PhD
The plan:
Jan 2015: final XPRESS pipeline ready
March 2015: 10 models built
May 2015: Test portability of 10 models
July 2015: Run the XPRESS vs. “queries” comparison at a non-stanford site.
Oct 2015: Decide the approach to use in OHDSI
The Participants:
Juan Banda
Vibhu Agarwal
George Hripsack (+ Barnett Chiu, Sunny Chang)
Nicholas Tatonetti (+ Alexandre Yahi)
Jon Duke (+ Saeed Malas)
Design framework for large-scale analysis in population-level estimation, including software infrastructure for methods and database repository for HOMER results
Establish scope for population-level estimation, ex: including risk identification (estimating risk of adverse effects of medical products), and comparative effectiveness (comparing risk of outcomes between alternative treatments for a given indication)
Implement open-source software that is capable of executing suite of methods against OMOP CDM v5 for any/all drugs and any/all outcomes
Use positive/negative controls to calibrate effect estimates and provide Bayesian interpretation of results
Incorporate existing estimation methods from OMOP methods library (including: cohort, case-control, and self-controlled designs) and allow for inclusion of new methods
Identify areas for estimation methods development and write proposals to fund this research
Document and disseminate estimation methods to OHDSI community
Objective: The objective of this workgroup (WG) is to establish an ETL Specification Document and an ETL implementation for each of the following data sets:
Medicare SynPUF Data
SEER Medicare
Medicare Limited Data Set
Additionally, we intend to provide a downloadable copy of the Medicare SynPUF files in OMOP CDMv5 format.
第四部分、Projects & Workgroups
Project Workgroups
WIKI-项目下属的工作组
1、知识库工作组(Knowledgebase (LAERTES) Workgroup)
目标在于建立一个用于研究药品效果的开源的标准化的知识库，以及与之配套的管理维护流程。 整体介绍请参考论文：Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest. 目前已有的成果是 LAERTES (Largescale Adverse Effects Related to Treatment Evidence Standardization) –该系统整合了大量的用于研究药物与疗效关联关系的不同来源的证据。 预计2015年4月会发布第一个版本.
项目经理: Richard D. Boyce, PhD
成员列表:
See Members List
启动日期: 6/10/2014
源码库: https://github.com/OHDSI/KnowledgeBase
WG Minutes: Knowledge Base WG Minutes
WG Agendas: Knowledge Base WG Agendas
2、队列定义工作组Cohort Definition Workgroup (Circe)
目标在于实现一个基于web的开源系统，能够让用户通过UI界面自定义准入条件，能够在一定范围共享。这个系统有三部分组成：条件的语法表达、UI界面和将条件语法转换成CDM查询的转换层。 后台数据库CDM的版本是 CDM5
项目经理: Christopher Knoll
启动日期: 6/10/2014
源码库: https://github.com/OHDSI/Circe Meetings
Schedule: Every other Thursday starting from December 11th, 2014
Call in Number: 1-877-565-9999 (US)
Attendee access code: 536 106 50
Show global numbers
WebEx: https://jjconferencing.webex.com/jjconferencing/j.php?J=740979963 Development Status (as of 12/11/2014)
3、Cohort Summarization Workgroup (Heracles)
目的在于实现一个web的开源系统，能够通过UI界面对事先定义好的存储在CDM数据库中的队列数据进行探索研究 CDM的版本CDM5, 项目经理: Jon Duke
启动日期: 9/1/2014
Repository: https://github.com/OHDSI/Heracles
4、词汇/术语工作组Vocabulary Improvement Working Group
目的在于提高标准化术语的质量，扩大国际化编码系统、术语的覆盖范围。用于辅助分析
项目经理: Christian Reich, Patrick Ryan
启动日期: 15-Jan-2015 源码库: https://github.com/OHDSI/vocabulary-v5.0 (very dirty, not ready for prime time).
5、CDM数据仓库工作组 Development Working Group
目标在于为系统化、大规模的医疗数据分析开发OMOP数据模型
项目经理: Christian Reich, Patrick Ryan
启动日期: 15-Jan-2015
相关文档: OMOP Common Data Model V5.0
源码库: https://github.com/OHDSI/CommonDataModel
表型工作组 Phenotyping workgroup
目标在于:
To build and evaluate a computational pipeline for electronic phenotyping – which defines criteria to algorithmically select sets of patients based on stored clinical data – in the OHDSI project. Our approach for learning statistical models of clinical phenotypes is called XPRESS, which stands for eXtraction of Phenotypes from clinical REcords using Silver Standards.
Project Leads: Nigam Shah, MBBS, PhD
The plan:
The Participants:
Start Date: January 2015.
Repository: TBD
WG Minutes: Need to find a good place
WG Agendas: Need to find a good place
评估方法工作组 Estimation methods workgroup
Objectives:
Project Leads: Martijn Schuemie, PhD,Marc Suchard, MD, PhD
CMS/Medicare ETL Workgroup
Objective: The objective of this workgroup (WG) is to establish an ETL Specification Document and an ETL implementation for each of the following data sets:
Additionally, we intend to provide a downloadable copy of the Medicare SynPUF files in OMOP CDMv5 format.
Project Lead: Mark Danese, PhD
Start Date: 02/04/2015
Repository: https://github.com/OHDSI/ETL-CMS
WG Minutes: CMS ETL WG Minutes
WG Agendas: CMS ETL Agendas