Advances in Distributed Computing and Artificial Intelligence Journal
Crawling PubMed with web agents for literature search and alerting services
Authors:
Carlos CARVALHAL, Sérgio DEUSDADO, Leonel DEUSDADO
DOI:
10.14201/ADCAIJ2013241922
Volume:
Regular Issue 2 (1), 2013
In this paper we present ASAP - Automated Search with Agents in PubMed, a web-based service aiming to manage and automate scientific literature search in the PubMed database. The system allows the creation and management of web agents, parameterized thematically and functionally, that crawl the PubMed database autonomously and periodically, aiming to search and retrieve relevant results according the requirements provided by the user. The results, containing the publications list retrieved, are emailed to the agent owner on a weekly basis, during the activity period defined for the web agent. The ASAP service is devoted to help researchers, especially from the field of biomedicine and bioinformatics, in order to increase their productivity, and can be accessed at: http://esa.ipb.pt/~agentes.
BETHESDA, Entrez Programming Utilities Help. National Center for Biotechnology Information (US), 2010.
BRUSILOVSKY, P. et al. The adaptive web: methods and strategies of web personalization. Berlin?; New York: Springer, 2007.
HAKENBERG, J. NENADIC, G. REBHOLZ-SCHUHMANN, D. and KIM, J.-D. Literature Mining Solutions for Life Science Research, Advances in Bioinformatics, vol. 2013, pp. 1–2, 2013.
HOKAMP, K. and WOLFE, K. H. PubCrawler: keeping up comfortably with PubMed and GenBank, Nucleic Acids Res., vol. 32, no. Web Server issue, pp. W16–19, Jul. 2004.
M. KOBAYASHI, M. and TAKEDA, K. Information retrieval on the web, ACM Computing Surveys, vol. 32, no. 2, pp. 144–173, Jun. 2000.
LOURENÇO, A. CARREIRA, R. CARNEIRO, S. MAIA, P. GLEZ-PEÑA, D. FDEZ-RIVEROLA, FERREIRA, E. C. ROCHA I., and ROCHA, M. @Note: A workbench for Biomedical Text Mining, Journal of Biomedical Informatics, vol. 42, no. 4, pp. 710–720, Aug. 2009.
MANCONI, A. VARGIU, E. ARMANO, G. and L. MILANESI, Literature Retrieval and Mining in Bioinformatics: State of the Art and Challenges, Advances in Bioinformatics, vol. 2012, pp. 1–10, 2012.
E. W. SAYERS, E. W. et al., Database resources of the National Center for Biotechnology Information, Nucleic Acids Res., vol. 39, no. Database issue, pp. D38–51, Jan. 2011.