Repository for Informed Decision Making  

Table of Contents

Project Members:
Dina Demner-Fushman, George Thoma

Introduction

The long-term goal of the Repository for Informed Decision Making is to provide access to key facts needed to support clinical decision making. At present, the facts are extracted from biomedical literature sources. The development of the Repository is guided by the Evidence Based Medicine (EBM) principles for finding and appraising information.

The current prototype implementation extracts key clinical concepts from clinical text and MEDLINE® abstracts using MetaMap and UMLS. Key facts in the form of clinical outcomes and other descriptors of a clinical study (for example, number of participants) are extracted from MEDLINE abstracts found using Essie or PubMed and search parameters specified in the client request.

RIDeM Processes

2006 Overview of Processes: text

2006 Overview of Processes: slideshow

Publications

  1. Demner-Fushman D, Mork JG, Shooshan SE, Aronson AR. UMLS Content Views Appropriate for NLP Processing of the Biomedical Literature vs. Clinical Text. AMIA Annu Symp Proc. San Francisco, CA, November 2009.
  2. Overby CL, Tarczy-Hornoch P, Demner-Fushman D. The potential for automated question answering in the context of genomic medicine: an assessment of existing resources and properties of answers. BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S8.
  3. Overby CL, Tarczy-Hornoch P, Demner-Fushman D. The Potential for Automated Question Answering in the Context of Genomic Medicine: An Assessment of Existing Resources and Properties of Answers. In Proceedings of the 2009 AMIA Summit on Translational Bioinformatics. March 15-17, 2009 San Francisco, California
  4. Fiszman M, Demner-Fushman D, Kilicoglu H, Rindflesch TC. Automatic summarization of MEDLINE citations for evidence-based medical treatment: A topic-oriented evaluation. J Biomed Inform. 2009 Oct;42(5):801-13.
  5. Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB. Towards automatic recognition of scientifically rigorous clinical research evidence. J Am Med Inform Assoc. 2009 Jan-Feb;16(1):25-31.
  6. Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB. Toward Automatic Recognition of High Quality Clinical Evidence. AMIA Annu Symp Proc. 2008 Nov 6:368.
  7. Aronson AR, Mork JG, Neveol A, Shooshan SE, Demner-Fushman D. Methodology for creating UMLS content views appropriate for biomedical natural language processing. AMIA Annu Symp Proc. 2008 Nov 6:21-5.
  8. Sneiderman CA, Demner-Fushman D, Fiszman M, Ide NC, Rindflesch TC. Knowledge-Based Methods to Help Clinicians Find Answers in MEDLINE. J Am Med Inform Assoc. December 2007;14(6):772-780
  9. Ahlers CB, Fiszman M, Demner-Fushman D, Lang FM, Rindflesch TC. Extracting semantic predications from Medline citations for pharmacogenomics. Pac Symp Biocomput. 2007:209-20.
  10. Lin J, Demner-Fushman D. Semantic clustering of answers to clinical questions. AMIA Annu Symp Proc. 2007 Oct 11:458-62.
  11. Fiszman M, Demner-Fushman D, Lang FM, Goetz P, Rindflesch TC. Interpreting Comparative Constructions in Biomedical Text. Proc. 2007 Workshop on Biomedical Natural Language Processing (BioNLP'07). Prague, Czech Republic. June 2007:137-44
  12. Demner-Fushman D, Lin J. Answering Clinical Questions with Knowledge-Based and Statistical Techniques. Computational Linguistics. March 2007;33(1):63-103
  13. Huang X, Lin J, Demner-Fushman D. Evaluation of PICO as a knowledge representation for clinical questions. AMIA Annu Symp Proc. 2006:359-63.
  14. Demner-Fushman D, Hauser SE, Humphrey SM, Ford GM, Jacobs JL, Thoma GR. MEDLINE as a source of just-in-time answers to clinical questions. AMIA Annu Symp Proc. 2006:190-4.
  15. Demner-Fushman D, Lin J. Answer Extraction, Semantic Clustering, and Extractive Summarization for Clinical Question Answering. Proceedings of the 21st International Conference on Computational Linguistics. Sydney, Australia. July 2006:841-8
  16. Demner-Fushman D, Lin J. Situated Question Answering in the Clinical Domain: Selecting the Best Drug Treatment for Diseases. Proceedings of COLING/ACL 2006 Workshop on Task-Focused Summarization and Question Answering. Sydney, Australia. July 2006:24-31
  17. Demner-Fushman D, Hauser S, Thoma G. The role of title, metadata and abstract in identifying clinically relevant journal articles. AMIA Annu Symp Proc. 2005:191-5.
  18. Demner-Fushman D, Few B, Hauser SE, Thoma G. Automatically identifying health outcome information in MEDLINE records. J Am Med Inform Assoc. 2006 Jan-Feb;13(1):52-60.
  19. Demner-Fushman D, Hauser SE, Ford G, Thoma GR. Organizing literature information for clinical decision support. Stud Health Technol Inform. 2004;107(Pt 1):602-6.