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Dr. Harsha Gurulingappa

Principal Scientist
Molecular connections Pvt. Ltd.

Brief Biography:

I am a Prinicipal Scientist in Text Mining and Knowledge Managament group at Molecular Connections Pvt. Ltd. (India).


Academic positions:

Work Experience

1. Jun. 2012 – Current: Principal Scientist; Molecular Connections Pvt. Ltd. Basavanagudi, Bangalore, India
2. Nov. 2008 – Apr. 2012: Research Fellow; Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Sankt Augustin, Germany
3. Nov. 2007 – Sep. 2008: Research Assistant; Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Sankt Augustin, Germany
4. Sept. 2007 – Sept. 2009: Marketing Partner; Hamburg Münchener Krankenkasse Köln, Germany

Organizational and Scientific Achievements/Commitments

1. Official Supervisor of Master Thesis entitled “Strategies for Retrieval and Analysis of Patents describing Neurodegenerative Disease Drugs and Human Brain Pharmacome Mapping” submitted to Bonn University in Nov 2012.
2. Ranked within best three in international text mining research competitions i.e. Text Retrieval Conference - Chemical Track (USA, 2010), i2b2/VA Shared-Task and Workshop Challenges in Natural Language Processing for Clinical Data (USA, 2010), and Text Retrieval Conference - Medical Records Track (USA, 2011).
3. Served as Joint Coordinator during the Text Retrieval Conference (TREC) Chemical Track 2011, Gaithersburg, Maryland, USA.
4. Scholarly Reviewer of WebMed Central, an open-access biomedical publisher.
5. Served as Joint Secretary of BIET student’s association during the academic year 2005-06.
6. Served as Student Coordinator during “Biochemexcel 05”, National level student symposium held at BIET on 24th & 25th Nov. 2005.
7. Served as Indian Society for Technical Education (ISTE) Student Representative during the academic year 2003-04.


Research interests:

My research interests are information extraction (concept identification, context disambiguation, relation identification, text classification) and information retrieval (VSMs, indexing, probabilistic models for document retrieval) in the biomedical domain.


Any other information:

Publication (14 published and 2 under review)

1. Harsha Gurulingappa, Corinna Kolarik, Martin Hofmann-Apitius, and Juliane Fluck. Concept-based Semi- Automatic Classification of Drugs, Journal of Chemical Information and Modeling, 2009, 49 (8), pp 1986–1992.
2. Harsha Gurulingappa, Abdul-Mateen Rajput, Angus Roberts, Juliane Fluck, Martin Hofmann-Apitius, and Luca Toldo. Development of a Benchmark Corpus to Support the Automatic Extraction of Drug-related Adverse Effects from Medical Case Reports, Journal of Biomedical Informatics, 2012, 45(5), pp 885-892.

Scientific Exhibits (selected)

1. An Empirical Evaluation of Resources for the Identification of Diseases and Adverse Effects in Biomedical Literature. In The Second Workshop on Building and Evaluating Resources for Biomedical Text Mining, Valletta, Malta, Mar. 18, 2010.
2. Concept Identification and Assertion Classification in Patient Health Records. In The Fourth i2b2/VA Shared-Task and Workshop Challenges in Natural Language Processing for Clinical Data, Washington DC, USA, Nov. 12-13, 2010.

Poster Presentations (selected)

1. Abstracts versus Full Texts and Patents: A Quantitative Analysis of Biomedical Entities. In The First Information Retrieval Facility Conference (IRFC 2010), Vienna, Austria, May 31, 2010.
2. Patent Retrieval in Chemistry based on Semantically Tagged Named Entities. In The Seventh Fraunhofer Symposium on Text Mining in Life Sciences, Bonn, Germany, Oct. 2009

Invited Talks

1. Methods for Automated Mining in Patents: Current State of the Art and Examples for their Successful Application. In General Meeting of Working Group for Patent Information in Dutch (WON), Utrecht, Netherlands, April 2011.
2. Methods for Automated Mining of Chemistry Patents. In The annual Conference of the Italian Association of Patent Documentalists (AIDB), Pula, Sardinia, May 2011.


What I think of the idea behind WebmedCentral:

Rapid publication and a new concept of "post publication review"! Also want to be a part of this growing community