Repository for Informed Decision Making (RIDeM)

Table of Contents

Project Members:
Dina Demner-Fushman, George Thoma

Introduction

RIDeM is one of the LHNCBC Clinical Decision Support projects. The long-term goal of the Repository for Informed Decision Making is to provide access to key facts needed to support clinical decision making. The facts are extracted from biomedical literature and clinical text 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, MEDLINE® abstracts and PubMed Central (PMC) Open Access Subset using MetaMap and UMLS. Key facts in the form of clinical outcomes (bottom-line advice) and other descriptors of a clinical study (for example, number of participants) are extracted from publications found using Essie or PubMed and search parameters specified in the clients' requests.

RIDeM Processes

2006 Overview of Processes: text

2006 Overview of Processes: slideshow

Publications

  1. Demner-Fushman D, Abhyankar S, Callaghan FM, McDonald CJ. Extracting sources of admission and discharge destinations from discharge summaries. AMIA 2011 Fall Symposium.
  2. Callaghan FM, Demner-Fushman D, Abhyankar S, McDonald CJ. Addressing errors in a retrospective observational ICU database AMIA 2011 Fall Symposium.
  3. Jimeno-Yepes A, Wilkowski B, Mork JG, Van Lenten E, Demner-Fushman D, Aronson AR. A bottom-up approach to MEDLINE indexing recommendations. AMIA 2011 Fall Symposium
  4. Apostolova E, Tomuro N, Demner-Fushman D. Automatic Extraction of Lexico-Syntactic Patterns for Detection of Negation and Speculation Scopes. ACL 2011:283-287.
  5. Rance B, Demner-Fushman D, Rindflesch TC, Bodenreider O. Exploring automatic approaches to extracting pharmacogenomic information from the biomedical literature. Proceedings of the 2011 PSB Workshop on Mining the Pharmacogenomics Literature 2011.
  6. Demner-Fushman D, Mork JG, Shooshan SE, Aronson AR. UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. J Biomed Inform. 2010 Aug,43(4):587–594
  7. Demner-Fushman D, Karpinski J, Thoma GR. Automatically building a repository to support evidence based practice. Proceedings of  the 2nd Workshop on Building and evaluating resources for biomedical text mining (BioTxtM 2010),  7th Language Resources and Evaluation Conference (LREC 2010). May 17-23, Valetta, Malta
  8. Bekhuis T, Demner-Fushman D.  Towards automating the initial screening phase of a systematic review. Proceedings of the 13th World Congress on Medical and Health Informatics (MEDINFO 2010). 2010 Sep 12-15; Cape Town, South Africa. IOS Press
  9. Apostolova E, Channin DS, Demner-Fushman D, Furst J, Lytinen S, Raicu D. Automatic segmentation of clinical texts. Conf Proc IEEE Eng Med Biol Soc. 2009;2009:5905-8.
  10. 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.
  11. 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.
  12. 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
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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
  18. 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.
  19. Lin J, Demner-Fushman D. Semantic clustering of answers to clinical questions. AMIA Annu Symp Proc. 2007 Oct 11:458-62.
  20. 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
  21. Demner-Fushman D, Lin J. Answering Clinical Questions with Knowledge-Based and Statistical Techniques. Computational Linguistics. March 2007;33(1):63-103
  22. Huang X, Lin J, Demner-Fushman D. Evaluation of PICO as a knowledge representation for clinical questions. AMIA Annu Symp Proc. 2006:359-63.
  23. 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.
  24. 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
  25. 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
  26. 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.
  27. 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.
  28. 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.