This Small Business Innovation Research (SBIR) Phase I project aims to provide novel web-based mechanisms to biomedical researchers for the integration and efficient analysis of the vast amount of biomedical literature. The analysis will include the detection of important connections between candidate active substances (drugs), clinical indications (diseases), and even connections to academic experts/specialists on such drugs and diseases. Delivering such novel web-based mechanisms requires research on entity resolution, flexible on-line analytical processing and controlled crowdsourcing. Entity resolution is needed because the pharmaceutical researcher draws his information from multiple sources, which often use different terminologies and identification schemes for the same entity (e.g., the same substance). Controlled crowdsourcing is needed because humans and automatic agents will cooperate in creating a quality information asset, where it is important that there is clear trace to who provided each piece of information and how credible it is. Finally, on-line analytical processing technologies, which have been very successful in corporate business intelligence (e.g., sales analysis) will need to be extended for the purpose of analyzing the biomedical literature.

The broader impact/commercial potential of this project is reduced costs in the drug discovery process and enablement of promising new drug discoveries. The project can impact the effectiveness of researchers and decision making executives working on drug discovery either in pharmaceutical companies or in academic organizations. Impact will come in the following ways: 1) Reduction of costs in the research department by reducing the time that the researchers spend in searching and browsing the vast amount of biomedical literature for interesting emerging ideas. The proposed novel ways of biomedical literature analysis will allow the researcher to obtain, summarize and observe trends in the latest scientific facts, without copiously browsing thousands of citations at a time. 2) Enabling of new drug discovery by revealing drug/disease/molecular target connections that can feed the drug discovery pipeline and would otherwise be overlooked. The impact of discovering novel drugs can be huge given the rising medical costs that the country faces.

Project Report

This Small Business Innovation Research Phase I project developed, a web application for researchers and decision making pharmaceutical executives, who work on the early stages of drug discovery. BioHeatMap addresses an acute problem: It has became next to impossible for the pharma researcher and the pharma executive to absorb the huge amount of information that becomes available to them. PubMed, the leading source of biomedical publications, currently has 20 million articles and more than a million are added every year. The 2012 version of <> enables its users to quickly discover, analyze and visualize connections between substances, diseases, molecular targets, authors and other entities of interest. For example, the user may formulate questions such as "report substances associate with diabetes diseases, showing how many articles discussed each substance/disease pair", "show how the publication activity on a particular drug/disease combination is trending", "show who are the lead researchers working on the latest generation of drugs for diabetes" and many more. The user can easily navigate into the data, drill-down for more details, ask for further analysis and eventually reach the most interesting articles. Results can be shared among researchers and within the pharmaceutical company, enabling the formulation of a knowledge asset. Furthermore, various elaborate searches can be preset and then reused or modified by anyone in a company. The business benefit comes in both 1. cost reduction in the research department by reducing the time spent in searching and browsing the vast amount of biomedical literature for interesting emerging ideas. 2. revenue generation opportunities by enabling the discovery of connections and findings that feed the drug discovery pipeline and would otherwise be overlooked. BioHeatMap is accessible online via the browser. You may request an account at

National Science Foundation (NSF)
Division of Industrial Innovation and Partnerships (IIP)
Standard Grant (Standard)
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Program Officer
Juan E. Figueroa
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Bioheatmap Inc
San Diego
United States
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