Software & Data Sets

Completely or partially funded by grants R01LM009886 and 3OT3-TR002027-01S1.


Name
Authors
Status
Link to demo or license
Description and References
Criteria2Query
Chi Yuan, Patrick Ryan, Chunhua Weng
Open-sourced

A system for transforming free-text eligibility criteria into structured database queries for identifying eligible patients from clinical databases.
Live version: http://www.ohdsi.org/web/criteria2query/ .
Open source: https://github.com/OHDSI/Criteria2Query
COHD
Casey Ta, Nick Tatonetti, George Hripcsak, Chunhua Weng
Open-sourced

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.

Link to demo or license:
API: http://cohd.nsides.io
Analysis source code: https://github.com/CaseyTa/ehr_prevalence
API source code: https://github.com/CaseyTa/cohd

EliXR-CDM
Gal Fix, Anil Yaman, Chunhua Weng
Prototype
demo
The winner of the 2015 AMIA Joint Summit for Clinical Research Informatics Design Challenge
EliIE
Tian Kang, Chunhua Weng
Prototype
source code
A machine learning based parser for clinical research eligibility criteria
Valx
Tony Hao, Chunhua Weng
Prototype
demo
source code
A parser for numeric expressions in clinical trial summaries.

Publication: Hao T, Liu H, Weng C, Valx: A System for Extracting and Structuring Numeric Comparison Statements from Text, Methods of Information in Medicine, 2016.
VITTA
Zhe He, Riccardo Miotto, Tony Hao, Ida Sim, Simona Carini, Chunhua Weng
Prototype
demo
A visualization system of aggregated patterns of clinical trial eligibility criteria

Contributions of key developers:  Riccardo Miotto designed the concept extraction algorithm from clinical trial summaries, Tony Hao designed the numeric expression parser (Valx), Zhe He organized the output from the above parsers in a relational database and designed the graphic user interface.

Publications: He Z, Carini S, Sim I, Weng C, Visual Aggregate Analysis of Eligibility Features in Clinical Trials, J Biomed Inform, 2015 Jan 20. pii: S1532-0464(15)00007-6. PMID: 25615940
eTACTS
Riccardo Miotto,
Chunhua Weng
Prototype;
Open-source
demo
source code
Publications: Miotto, R., Jiang, S., Weng, C. (2013) eTACTS: A Method for Dynamically Filtering Clinical Trial Search Results. Journal of Biomedical Informatics, 2013 Dec;46(6):1060-7.
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
Licensing Status: Available for Licensing

Publications: David Campbell, Stephen Johnson. A transformational-based learner for dependency grammars in discharge summaries. Proceedings of the Association for Computational Linguistics Workshop on Natural Language Processing in the Biomedical Domain, 37-44. Philadelphia, July 2002.
Other EliXR tools
Weng Lab
Prototype
demo

BBW Prediction
Handong Ma,
Chunhua Weng
linked clinical trials and drug adverse events data
Link
Publications: Ma H, Weng C, Prediction of Black Box Warning by Mining Patterns of Convergent Focus Shift in Clinical Trial Study Populations Using Linked Public Data, J Biomed Inform, 2016.
Questionable Criteria
Handong Ma,
Chunhua Weng
Questionable Criteria and Disease Facts
Link
Publications: Ma H, Weng C, Identification of Questionable Exclusion Criteria in Mental Disorder Clinical Trials Using a Medical Encyclopedia, 2016 Pacific Symposium on Biocomputing.


Completely or partially funded by grant R01LM010815

Name
Authors
Status
Link to demo or license
References
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.

Publication: Weng C, Li Y, Berhe S, Boland MR, Gao J, Hruby GW, Steinman RC, Lopez-Jimenez C, Busacca L, Hripcsak G, Bakken S, Bigger JT,
An Integrated Model for Patient Care and Clinical Trials (IMPACT) to Support Clinical Research Visit Scheduling Workflow for Future Learning Health Systems, J Biomed Inform, 2013 Aug;46(4):642-52.  PMID: 23684593.