United States National Library of Medicine National Institutes of Health

Licensee Research Use of MEDLINE^®/PubMed^® Data:
Summary Report Sorted by Country

This report is sorted alphabetically first by country and second by organization/institution. It lists NLM's MEDLINE/PubMed licensees who submitted information about their use of the data for research and permitted NLM to make their information available on the Web.

Click on the Project Summary for the corresponding complete report, or the Research Category title to view the summary report for that research category. General information about NLM's Web site for licensees' research projects is available.

Australia

1	ChemGenex Pharmaceuticals
	Jeremy Jowett jjowett@idi.org.au
	Research Category: Biological Knowledge Discovery
	Research Project: Data mining for functional information on positional candidate genes for diabetes and obesity
	Project Summary: To collate and present functional information about a list of candidate genes for a range of complex diseases including diabetes, obesity, depression and anxiety.

2	Monash University and The Beddoes Group
	Adam Tucker adam.tucker@med.monash.edu.au	mail@allori.org
	Research Category: Other
	Research Project: Anaesthesia and Medline
	Project Summary: A descriptive study describing the corpus of articles relating to anaesthesia and related fields

Canada

1	University Health Network Jurisica Lab
	David Otasek
	Research Category: Information Extraction or Retrieval Methods
	Research Project:
	Project Summary: Automated extraction of protein-protein interactions from Medline/PubMed abstracts.

2	University Health Network, Microarray Centre MaRS Centre, Toronto Medical Discovery Tower, 9-308G
	LU ZHIBIN zlu@uhnresearch.ca
	Research Category: Biological Knowledge Discovery
	Research Project:
	Project Summary: We are constantly looking for ways to enhance the annotation of our microarrays. This includes finding homologs, placement in gene network and general knowledge discovery of proteins.

Denmark

1	Novo Nordisk A/S DK-2880 Bagsvaerd
	Henning Nielsen hepn@novonordisk.com
	Research Category: Biological Knowledge Discovery
	Research Project:
	Project Summary: Teh Novo Group of Companies (Novo Nordisk, Novozymes, and Novo A/S)is a Danish Based Research, Pharmaceutical and Biotech Companies. Our main research focus is on the therapy areas Diabetes, Haemophilia, Growth Hormone, Hormone Replacement Therapy and Industrial Enzymes.

Italy

1	ATA SpA - Advanced Technology Assessment
	Massimo Riccaboni info@atalab.com
	Research Category: Information Extraction or Retrieval Methods
	Research Project:
	Project Summary: The main goals of this project are to set up automated or semi-automated procedures to translate affiliation information provided by PubMed into structured data, with a particular emphasis on separating and identifying geographical information, and to develop suitable approaches to analysis of un-structured texts in the bio-medical domain.

2	CINECA
	Andrew Emerson a.emerson@cineca.it
	Research Category: Biological Knowledge Discovery
	Research Project: MedMOLE - Mining On-Line Expert on MedLine
	Project Summary: MedMOLE is a tool that improves the comprehension of microarray experimental results by grouping co-regulated genes on the basis of the informational content of MEDLINE documents.

Japan

1	Canaledge Inc.
	Yoshiyuki Kobayashi yashi@canaledge.com	Takao Asanuma asanuma@canaledge.com
	Research Category: Information Extraction or Retrieval Methods
	Research Project: text-mining system development
	Project Summary: Development of a text-mining system for finding the data of protein/protein interactions or gene/disease or gene/chemical compound relationships, etc.

2	Fujitsu Limited Makuhari Systems Laboratory
	Shuhei Kinoshita kino@strad.ssg.fujitsu.com	Masato Mori masatom@strad.ssg.fujitsu.com
	Research Category: Information Extraction or Retrieval Methods
	Research Project: Bio Chemical Information Project
	Project Summary: Development of NLP programs which extracts Protein-Protein or Protein-Compound relationships.

3	NAIST
	Kouichi Doi doy@is.naist.jp
	Research Category: Information Extraction or Retrieval Methods
	Research Project:
	Project Summary: We research automatic extraction of protein protein interaction. Our sub goals are named entity of proteins, classification of verb or verb phrase and extraction of abbrevation.

4	Nara Institute of Science and Technology
	Yuji Matsumoto	Masashi Shimbo
	Research Category: Information Extraction or Retrieval Methods
	Research Project:
	Project Summary: We apply statistical natural language processing techniques to the information extraction and retrieval from Medline abstracts.

Netherlands

1	Erasmus MC Department of Urology
	Guido Jenster g.jenster@erasmusmc.nl
	Research Category: Biological Knowledge Discovery
	Research Project: Gene information extraction from MEDLINE
	Project Summary: We link genomic (microarray analyses) and proteomic data (protein expression analyses) to MEDLINE to be able to perform high-throughput and automated MEDLINE searches to extract relationships between genes and their gene products.

2	Wageningen University and Research Centre Laboratory of Bioinformatics
	Jack Leunissen jack.leunissen@wur.nl
	Research Category: Information Extraction or Retrieval Methods
	Research Project: BIOMETA
	Project Summary: Development of text mining techniques, including concept weighting and term disambiguation

Poland

1	Polish Academy of Sciences Institute of Biochemistry & Biophysics
	Pawel Siedlecki
	Research Category: Information Extraction or Retrieval Methods
	Research Project:
	Project Summary: Usage of medline database for searching information about aminoacid sequences

Singapore

1	National University of Singapore
	Ailing Zhu	Jian Li
	Research Category: Biological Knowledge Discovery
	Research Project:
	Project Summary: disease gene mining from MEDLINE

Spain

1	Spanish National Biotechnology Center (CNB-CSIC) Protein Design Group
	Martin Krallinger martink@cnb.uamm.es	martingenetech@yahoo.com
	Research Category: Information Extraction or Retrieval Methods
	Research Project: NATURAL LANGUAGE PROCESSING STRATEGIES
	Project Summary: This work explores basic aspects of text mining and NLP strategies for providing functional information for protein s and genes in the context of functional descriptions of genes such as using protein - GGene Ontology term associations

Taiwan, Province of China

1	Food Industry Research & Development Institute
	Wang Chun-lin clw@firdi.org.tw
	Research Category: Biological Knowledge Discovery
	Research Project:
	Project Summary: Establishment the knowledge of the bioresource usage in the MEDLINE/PubMed data

2	National Cheng-Kung University Department of Computer Science and Information Engineering
	Wen-Hsiang Lu whlu@mail.ncku.edu.tw
	Research Category: Information Extraction or Retrieval Methods
	Research Project: MMODE: Cross-Language Medical Information Retrieval for Consumers
	Project Summary: Many consumers in non-English-speaking countries are eager to access up-to-date health information from the U.S. authoritative medical websites, such as PubMed and MedlinePlus. However, currently, there is no any cross-language medical information retrieval (CLMIR) system that could provide Taiwanese consumers to overcome the language

United Kingdom

1	EMBL-European Bioinformatics Institute Rebholz Group
	Peter Stoehr
	Research Category: Information Extraction or Retrieval Methods
	Research Project: Whatizit
	Project Summary: We focus on extraction of facts from scientific literature in molecular biology. This is mainly based but not limited to Pattern Matching and other High-Throughput methods. The group has experience in chunk parsing, natural language processing (NLP), and has applied its methods to different tasks. This includes identification of terminology, of abbreviations, of mutations and of relations between named entities, e.g. protein-protein interactions.

2	Public Health Genetics Unit, Cambridge
	Julian Higgins julian.higgins@mrc-bsu.cam.ac.uk	Roger Hale roger.hale@linguamatics.com
	Research Category: Information Extraction or Retrieval Methods
	Research Project:
	Project Summary: Investigation of I2E text-mining system in human genome epidemiology

3	University of Sheffield Department of Computer Science
	Angus Roberts
	Research Category: Other
	Research Project: CLEF postgraduate studentship
	Project Summary: PhD studentship on the extraction of part whole relations from biomedical texts

United States

1	Advanced Health Media 2840 Morris Ave, Union, NJ 07083
	Eric Johnson
	Research Category: Information Extraction or Retrieval Methods
	Research Project: IM2 KOL Identification
	Project Summary: Currently, InsiteResearch uses the platform to retrieve data on therapeutic class experts to act as investigators or speakers for healthcare companies

2	Arity Corporation Research & Development
	Peter Gabel peter.gabel@arity.com	Pamela Schaepe pamela.schaepe@arity.com
	Research Category: Information Extraction or Retrieval Methods
	Research Project: NLP Information Extraction for Biomedical Research & Development
	Project Summary: Goal of the project is to utilize sophisticated Natural Lanugage Processing techniques to maximize accuracy in extractio of facts, associations, assertions and rules from biomedical literature.

3	Carnegie Mellon University
	Eric Nyberg
	Research Category: Information Extraction or Retrieval Methods
	Research Project:
	Project Summary: Research in the use of language processing technology to provide more intelligent access to information in MEDLINE abstracts

4	Children's Hospital of Philadelphia
	Peter White white@genome.chop.edu
	Research Category: Information Extraction or Retrieval Methods
	Research Project: Mining the bibliome: Information extraction of the biomedical literature
	Project Summary: Our goal is qualitatively better methods for automatically extracting information from the biomedical literature, relying on recent progress and new research in three areas: high-accuracy parsing, shallow semantic analysis, and integration of large volumes of diverse data.

5	Columbia University
	Stephen Johnson sbj2@columbia.ed
	Research Category: Information Extraction or Retrieval Methods
	Research Project: CIQR
	Project Summary: CQIR (seeker) explores Context-Initiated Question and Response: responding to physicians' questions when they are in the context of patient care.

6	David Calloway
	David Calloway calloway@novatechnologies.net
	Research Category: Information Extraction or Retrieval Methods
	Research Project: wikipdf
	Project Summary: The wikipdf tool (http://www.wikipdf.com) automatically generates glossaries of unusual terms for any article identified by a Medline citation.

7	Marquette University
	Craig Struble craig.struble@marquette.edu
	Research Category: Information Extraction or Retrieval Methods
	Research Project:
	Project Summary: We are using MEDLINE to develop information extraction tools for experimental techniques and protein kinase inhibitors.

8	OmniViz, Inc.
	Jeffrey Saffer
	Research Category: Information Extraction or Retrieval Methods
	Research Project: Development of Visualization Software
	Project Summary: Development of software capable of visualizing Medline data.

9	SUNY Stony Brook Dept. of Computer Science
	Steven Skiena skiena@cs.sunysb.edu
	Research Category: Information Extraction or Retrieval Methods
	Research Project:
	Project Summary: TextMed is a search engine for medical entities: diseases, drugs, chemicals, organs and organisms.TextMed aims to identify relationships between these medical entities. TextMed uses natural language processing techniques to track medical entity references from the scientific literature, and a variety of statistical techniques to analyze the relationships between them.

10	U TX-Houston School of Health Information Sciences
	Elmer Bernstam Elmer.V.Bernstam@uth.tmc.edu
	Research Category: Information Extraction or Retrieval Methods
	Research Project: MedlineQBE
	Project Summary: The goals of this project are to facilitate access to the biomedical literature by using techniques adapted from the World Wide Web. We are currently exploring citation analysis and collaborative filtering. In addition, we are exploring novel evaluation methods to compare alternative retrieval strategies.

11	UCLA
	Robert Bilder rbilder@mednet.ucla.edu
	Research Category: Ontologies or Classification Schema
	Research Project: Cognitive Phenotyping for Neuropsychiatric Therapeutics
	Project Summary: This project (part of NIH Roadmap Initiative) aims to develop strategies for interdisciplinary research on cognitive phenotypes. One goal is development of informatics approaches to cognitive phenotype definition.

12	University of Arizona The Artificial Intelligence Lab
	Hsinchun Chen hchen@eller.arizona.edu	Cathy Larson cal@eller.arizona.edu
	Research Category: Biological Knowledge Discovery
	Research Project: GeneScene (please note that the name of this project is undergoing revision and will soon change)
	Project Summary: GeneScene develops text mining and data mining techniques to support automated extraction and inference of biological regulatory pathways from biomedical literature and experimental data. We also provide visualization tools to facilitate related research.

13	University of Oklahoma 101 David L. Boren Blvd.
	Jonathan Wren Jonathan.Wren@OU.edu
	Research Category: Biological Knowledge Discovery
	Research Project:
	Project Summary: Knowledge discovery using entities found within MEDLINE-for both shared relationship analysis (e.g.to find commonalities for microarray responders) and implicit relationship analysis (e.g. to discover previously unknown/undocumented relationships)

14	University of Texas at Austin Center for Computational Biology and Bioinformatics
	Edward Marcotte
	Research Category: Information Extraction or Retrieval Methods
	Research Project:
	Project Summary: The focus of our lab is in the study of protein functions and protein-protein interactions by combining computational and bioinformatic approaches with experimental techniques

15	UT Southwestern Medical Center at Dallas NA2.226
	Harold Garner	Justin Hicks
	Research Category: Biological Knowledge Discovery
	Research Project: INNOVATION LABS DATA MINING
	Project Summary: We are interested in Biological Knowledge Discovery, pubmed-like searching and any useful literature-based tools development that can be useful for researchers.

Last updated: 22 August 2007
First published: 01 August 2005
Metadata| Permanence level: Permanence Not Guaranteed

Licensee Research Use of MEDLINE®/PubMed® Data: Summary Report Sorted by Country