Software and Data

Completely or partially funded by grants R01LM009886 and 3OT3-TR002027-01S1.
Name Authors Status Link to demo or license Description
Chia Fabrício Kury, Alex Butler, Chi Yuan, Li-heng Fu, Yingcheng Sun, Hao Liu, Ida Sim, Simona Carini & Chunhua WengFabrício Kury, Alex Butler, Chi Yuan, Li-heng Fu, Yingcheng Sun, Hao Liu, Ida Sim, Simona Carini, Chunhua Weng Open-source Source code Chia, a novel, large annotated corpus of patient eligibility criteria extracted from 1,000 interventional, Phase IV clinical trials registered in ClinicalTrials.gov. This dataset includes 12,409 annotated eligibility criteria, represented by 41,487 distinctive entities of 15 entity types and 25,017 relationships of 12 relationship types.
PICO Parser Tian Kang, Chunhua Weng Open-source Source code A scalable deep learning method to extract PICO statements from RCT articles.
COVID-19 Trial Finder Alex Butler, Yingcheng Sun, Fengyang Lin, Hao Liu, Cong Liu, Chi Yuan, Chunhua Weng Open-source Demo Source code A simplified method for patients, clinicians and healthy volunteers to search for appropriate COVID-related clinical trials in their general location. This system also allows potential candidates to pre-screen their eligibility for such trials through a set of short medical questions.
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Criteria2Query Yilu Fang, Yingcheng Sun, Hao Liu, Chi Yuan, Patrick Ryan, Yixuan Guo, Chunhua Weng Open-source Demo
Source code
A system for transforming free-text eligibility criteria into structured database queries for identifying eligible patients from clinical databases.
Doc2HPO Cong Liu, Chunhua Weng Open-source Source code
COHD Casey Ta, Nick Tatonetti, George Hripcsak, Chunhua Weng Open-source URL
API
API source code
Columbia Open Health Data (COHD). COHD provides public access to observational prevalence rates and co-occurrence frequencies of conditions, drugs, procedures, and demographics measured from electronic health records from 5M+ patients in the CUMC’s OHDSI database.
SNOMEDTxT Olga Lyudovyk, Chunhua Weng Open-source Demo
Source code
It is built with SNOMED CT US Snapshot version. SNOMED CT files were downloaded and pre-processed before they could be used in this project.
EliXR-CDM Gal Fix, Anil Yaman, Chunhua Weng Prototype The winner of the 2015 AMIA Joint Summit for Clinical Research Informatics Design Challenge
EliIE Tian Kang, Chunhua Weng Prototype A machine learning based parser for clinical research eligibility criteria
Valx Tony Hao, Chunhua Weng Prototype Source code A parser for numeric expressions in clinical trial summaries.
VITTA Zhe He, Riccardo Miotto, Tony Hao, Ida Sim, Simona Carini, Chunhua Weng Prototype A visualization system of aggregated patterns of clinical trial eligibility criteria
eTACTS Riccardo Miotto, Chunhua Weng Prototype; Open-source Source code Search engine for clinical trials allowing users to refine the results of an initial search through cloud of tags automatically extracted from the eligibility criteria.
AQUA Stephen Johnson, David Campbell, Eneida Mendonca, Robert Duffy, Chunhua Weng License available #2943 (freely available) An dependency parser for biomedical text Patent Status: Software Copyright
BBW Prediction Handong Ma, Chunhua Weng Linked clinical trials and drug adverse events data Code Link public data resources for predicting post-marketing drug safety label changes by analyzing the Convergent Focus Shift patterns among drug testing trials.
Questionable Criteria Handong Ma, Chunhua Weng Questionable Criteria and Disease Facts Code A method for identifying questionable exclusion criteria for 38 mental disorders.
Completely or partially funded by grant UL1TR001873 and 1OT2TR003434-01.
Name Authors Status Link to demo or license Description
CTKB Hao Liu, Yuan Chi, Alex Butler, Yingcheng Sun , Chunhua Weng Open-source URL Clinical Trial Knowledge Base, a regularly updated knowledge base of discrete clinical trial eligibility criteria equipped with a web-based user interface for querying and aggregate analysis of common eligibility criteria.
Completely or partially funded by grant R01LM010815.
Name Authors Status Link to demo or license Description
IMPACT Yat So, J Thomas Bigger, Linda Busacca, Carlos Lopez, Richard Steinman, Chunhua Weng In use at CTSA of CUIMC CU license A research scheduling and resource allocation software.

Last Updated: 06/2022