Please use this identifier to cite or link to this item: http://hdl.handle.net/1822/41302

TitleBIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines
Author(s)Jácome, Alberto G.
Fdez-Riverola, Florentino
Lourenço, Anália
Keywordssearch engine framework
biomedical literature
vertical engine
text mining
web application
Issue dateJul-2016
PublisherElsevier
JournalComputer Methods and Programs in Biomedicine
CitationJácome, Alberto G.; Fdez-Riverola, Florentino; Lourenço, Anália, BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines. Computer Methods and Programs in Biomedicine, 131, 63-77, 2016
Abstract(s)Background and Objectives: Text mining and semantic analysis approaches can be applied to the construction of biomedical domain-specific search engines and provide an attractive alternative to create personalized and enhanced search experiences. Therefore, this work introduces the new open-source BIOMedical Search Engine Framework for the fast and lightweight development of domain-specific search engines. The rationale behind this framework is to incorporate core features typically available in search engine frameworks with flexible and extensible technologies to retrieve biomedical documents, annotate meaningful domain concepts, and develop highly customized Web search interfaces. Methods: The BIOMedical Search Engine Framework integrates taggers for major biomedical concepts, such as diseases, drugs, genes, proteins, compounds and organisms, and enables the use of domain-specific controlled vocabulary. Technologies from the Typesafe Reactive Platform, the AngularJS JavaScript framework and the Bootstrap HTML/CSS framework support the customization of the domain-oriented search application. Moreover, the RESTful API of the BIOMedical Search Engine Framework allows the integration of the search engine into existing systems or a complete web interface personalization. Results The construction of the Smart Drug Search is described as proof-of-concept of the BIOMedical Search Engine Framework. This public search engine catalogs scientific literature about antimicrobial resistance, microbial virulence and topics alike. The keyword-based queries of the users are transformed into concepts and search results are presented and ranked accordingly. The semantic graph view portraits all the concepts found in the results and the researcher may look into the relevance of different concepts, the strength of direct relations, and non-trivial, indirect relations. The number of occurrences of the concept shows its importance to the query, and the frequency of concept co-occurrence is indicative of biological relations meaningful to that particular scope of research. Conversely, indirect concept associations, i.e. concepts related by other intermediary concepts, can be useful to integrate information from different studies and look into non-trivial relations. Conclusions The BIOMedical Search Engine Framework supports the development of domain-specific search engines. The key strengths of the framework are modularity and extensibility in terms of software design, the use of open-source consolidated Web technologies, and the ability to integrate any number of biomedical text mining tools and information resources. Currently, the Smart Drug Search keeps over 1,186,000 documents, containing more than 11,854,000 annotations for 77,200 different concepts.
TypeArticle
DescriptionThe Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef
URIhttp://hdl.handle.net/1822/41302
DOI10.1016/j.cmpb.2016.03.030
ISSN0169-2607
Publisher versionhttp://www.cmpbjournal.com/
Peer-Reviewedyes
AccessOpen access
Appears in Collections:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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