An overview of MetaMap: historical perspective and recent advances

2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text.

Clinical information extraction applications: A literature review.

MedEx: a medication information extraction system for clinical narratives.

Data from clinical notes: a perspective on the tension between structure and flexible documentation.

We developed the KnowledgeMap (KM) system as an online, concept-based database of medical school curriculum documents. It uses the KM concept indexer to map full-text documents and match search queries to concepts in the Unified Medical Language System (UMLS). In this paper, we describe the design of KM and report the first seven months of its implementation into a medical school. Despite being emphasized in only two first year courses and one fourth year course, students from all four classes used KM to search and browse documents. All faculty members involved with courses piloting KM used the system to upload and manage lecture documents. Currently, we are working with eight course directors to transition their courses to KM for next year.

The KnowledgeMap project: development of a concept-based medical school curriculum database.

Objective To determine the impact of adding audio-feed to an online lecture on screening given to medical students who were participating in an outpatient clerkship.



Design  Prospective, randomised, controlled study.



Setting  Vanderbilt University School of Medicine, Nashville and Wake Forest Medical School, Winston-Salem.



Participants  A total of 59 Years 3 and 4 medical students.



Main outcome measures  Students' use of time, satisfaction with the lecture experience, and knowledge.



Educational intervention  The online lecture was developed at Vanderbilt University. At Vanderbilt, 16 Year 4 medical students were randomised to the lecture on screening with audio and 17 Year 4 medical students were randomised to the same lecture without audio. At Wake Forest, 13 Year 3 medical students were randomised to the lecture on screening with audio and 13 Year 3 students were randomised to the same lecture without audio.



Results  The audio lecture required 20 more minutes to complete than the non-audio lecture. Students in the audio group were more satisfied with their experience than students in the non-audio group. Students in the audio-feed group achieved a trend for higher post-intervention knowledge scores, with the difference attributed to the students at Vanderbilt.



Conclusion  Audio narration is an important aspect of an online lecture. The distribution of online lectures to students at different sites and different training levels requires further study.

A randomised trial of an online lecture with and without audio.

BACKGROUND: Often, medical educators and students do not know where important concepts are taught and learned in medical shcool. Manual efforts to identify and track concepts covered across the curriculum are inaccurate and resource intensive. OBJECTIVE: To test the ability of a web-based application called KnowledgeMap (KM) to automatically locate where broad biomedical concepts are covered in lecture documents in the Vanderbilt School of Medicine. METHODS: In 2003, the authors derived a gold standard set of curriculum documents by ranking 383 lecture documents as high, medium, or low relevance in their coverage of 4 broad biomedical concepts: genetics, women’s health, dermatology, and radiology. We compared the gold standard rankings to KM, an automated tool that generates a variable number of subconcepts for each broad concept to calculate a relevance score for each document. Receiver operating characteristic (ROC) curves and area-under-the-curve were derived for each ranking using varying relevance score cutoffs. RESULTS: Receiver operating characteristic curve areas were acceptably high for each broad concept (range 0.74 to 0.98). At relevance scores that optimized sensitivity and specificity, 78% to 100% of highly relevant documents were identified. The best results were obtained with the application of 63 to 1437 subconcepts for a given broad concept. The search time was fast. CONCLUSIONS: The KM tool capably and automatically locates the detailed coverage of broad concepts across medical school documents in real time. Use of KM or similar tools may prove useful for other medical schools to identify broad concepts in their curricula.

"Where do we teach what?" Finding broad concepts in the medical school curriculum.

The Vanderbilt KnowledgeMap (KM) project created a series of tools for conceptual mapping and analysis of medical text documents, using a novel approach based on both the NLM UMLS Metathesaurus and heuristic, approximate NLP techniques. The authors compared the performance of the KM concept matcher with the National Library of Medicine's MetaMap (MM) using a selected subset of curriculum documents (for which domain experts had identified key concepts manually). The two systems identified key medical concepts with a recall of 86% (KM) and 81% (MM). The precision was 92% for KM and 89% for MM.

A New Tool to Identify Key Biomedical Concepts in Text Documents, with Special Application to Curriculum Content

In order to determine where genetics is taught in our medical school curriculum, we used the KnowledgeMap(KM) concept indexer to index twenty lecture document by UMLS concepts. Half of these lectures had been pre-categorized as having “high genetics” and half as “low genetics” content. UMLS concepts from two genetics term sources: NIH genetics glossary and MeSH “genetics tree” terms served as the sources of “genetics” markers. Percentage of concept matches from “NIH” markers was 14% in “high genetics” 2.7% in “low genetics” content lectures. For MeSH markers, there was a 6% concept match rate in “high” and 0.4% in “low genetics” lectures. Thus, these two sources, combined with the KM program, proved useful for identifying genetics content.

Using Concept Markers to Find Genetics Content in a Medical School Curriculum.

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