BIOMedical Search Engine Framework: Lightweight and customized implementation of domain-specific biomedical search engines. Issue 131 (July 2016)

• Record Type: Journal Article
• Authors: Jácome, Alberto G.; Fdez-Riverola, Florentino; Lourenço, Anália
• Is Part Of: Computer methods and programs in biomedicine. Issue 131(2016)
• Page Start: 63
• Page End: 77
• Publication Date: 2016-07
• Subjects: Search engine framework -- Biomedical literature -- Vertical engine -- Text mining -- Web application; Medicine -- Computer programs -- Periodicals; Biology -- Computer programs -- Periodicals; Computers -- Periodicals; Medicine -- Periodicals; Médecine -- Logiciels -- Périodiques; Biologie -- Logiciels -- Périodiques; Biology -- Computer programs; Medicine -- Computer programs; Periodicals; Electronic journals; 610.28
• DOI: 10.1016/j.cmpb.2016.03.030
• Languages: English
• ISSNs: 0169-2607

Abstract

Highlights: The wealth of knowledge laying in biomedical publications is invaluable to make new scientific discoveries. Domain-specific search engines aim to improve retrieval performance and to enhance user search experience. The BIOMedical Search Engine Framework aims to speed up the construction of biomedical domain-specific search engines. The BIOMedical Search Engine Framework enables the retrieval and annotation of biomedical documents and the customised visualisation of indexed concepts and documents. The BIOMedical Search Engine Framework supported the construction of the Smart Drug Search (SDS) in assistance of antimicrobial research. Abstract: 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 extensibilityin 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. The Smart Drug Search is publicly accessible athttp://sing.ei.uvigo.es/sds/ . The BIOMedical Search Engine Framework is freely available for non-commercial use athttps://github.com/agjacome/biomsef .