Sat, 26 Jul 2008 17:00:18 BST CiteULike: Gaetan Rebholz-Schuhmann http://www.citeulike.org/user/Gaetan/author/Rebholz-Schuhmann CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/Gaetan/article/2653988 <i>Bioinformatics (Oxford, England) (9 April 2008)</i><br /><br />SUMMARY: Search engines running on MEDLINE abstracts have been widely used by biologists to find publications that are related to their research. The existing search engines such as PubMed, however, have limitations when applied for the task of seeking textual evidence of relations between given concepts. The limitations are mainly due to the problem that the search engines do not effectively deal with multi-term queries which may imply semantic relations between the terms. To address this problem, we present MedEvi, a novel search engine that imposes positional restriction on occurrences matching multi-term queries, based on the observation that terms with semantic relations which are explicitly stated in text are not found too far from each other. MedEvi further identifies additional keywords of biological and statistical significance from local context of matching occurrences in order to help users reformulate their queries for better results. AVAILABILITY: http://www.ebi.ac.uk/tc-test/textmining/medevi/ CONTACT: kim@ebi.ac.uk, pezik@ebi.ac.uk. MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline. Jung-Jae Kim Piotr Pezik Dietrich Rebholz-Schuhmann doi:10.1093/bioinformatics/btn117 Bioinformatics (Oxford, England) (9 April 2008) 2008-04-11T13:37:51-00:00 2008 Bioinformatics (Oxford, England) 1460-2059 ebm medline pubmed http://www.citeulike.org/user/Gaetan/article/1922911 <i>Bioinformatics (15 November 2007), btm557.</i><br /><br />Motivation: Text-mining (TM) solutions could turn are developing into efficient services to researchers in the biomedical research community. Such solutions have to scale with the growing number and size of resources (e.g., available controlled vocabularies), with the amount of literature to be processed (e.g., about 17 million documents in PubMed) and with the demands of the user community (e.g., different methods for fact extraction). These demands induce the development of server-based solutions that can be accessed programmatically. Whatizit is a suite of modules that analyse text for contained information, e.g. any own text documents, scientific publications or Medline abstracts. Each module identifies terms and then links them to the corresponding entries in bioinformatics databases such as UniProtKb/Swiss-Prot data entries and gene ontology concepts. Other modules identify a set of selected annotation types like the set produced by the EBIMed analysis pipeline for proteins. In the case of Medline abstracts, Whatizit offers access to EBI's inhouse installation via PMID or term query. For large quantities of own text, the server can be operated in a streaming mode. (http://www.ebi.ac.uk/webservices/whatizit) 10.1093/bioinformatics/btm557 Text processing through Web services: Calling Whatizit Dietrich Rebholz-Schuhmann Miguel Arregui Sylvain Gaudan Harald Kirsch Antonio Yepes doi:10.1093/bioinformatics/btm557 Bioinformatics (15 November 2007), btm557. 2007-11-15T15:47:04-00:00 2007 Bioinformatics btm557 medline http://www.citeulike.org/user/Gaetan/article/1640649 <i>IEEE Trans Inf Technol Biomed, Vol. 11, No. 3. (May 2007), pp. 237-243.</i><br /><br />This paper reports on an analysis of the bioinformatics and medical informatics literature with the objective to identify upcoming trends that are shared among both research fields to derive benefits from potential collaborative initiatives for their future. Our results present the main characteristics of the two fields and show that these domains are still relatively separated. Medical informatics and bioinformatics: a bibliometric study. JY Bansard D Rebholz-Schuhmann G Cameron D Clark E van Mulligen E Beltrame E Barbolla Fdel H Martin-Sanchez L Milanesi I Tollis J van der Lei JL Coatrieux IEEE Trans Inf Technol Biomed, Vol. 11, No. 3. (May 2007), pp. 237-243. 2007-09-10T08:42:12-00:00 2007 IEEE Trans Inf Technol Biomed 1089-7771 11 3 237 243 no-tag