ELSNET-list archive

Category:   E-Material
Subject:   Presenting BeCAS
Email:   tiago.nunes_(on)_ua.pt
Date received:   05 Jun 2013

Dear ELSNET-List members, We are pleased to announce BeCAS, a web application, API and widget for biomedical concept identification. BeCAS identifies and annotates species, anatomical concepts, microRNAs, enzymes, genes, proteins, chemicals, drugs, diseases, metabolic pathways, cellular components, biological processes and molecular functions. BeCAS provides annotations for isolated, nested and intersected entities. It identifies concepts from multiple semantic groups, providing preferred names and enriching them with references to public knowledge resources. Users can choose the types of entities for identification and highlighting in real-time. To facilitate annotation of PubMed abstracts, BeCAS automatically fetches publications from NCBI servers and renders them with identified concepts highlighted. BeCAS was validated against CRAFT, AnEM and the NCBI Diseases corpora, achieving f-measure results for overlap matching of 76 0.000000or genes and proteins, 95 0.000000or species, 65 0.000000or chemicals, 83 0.000000or cellular components, 92 0.000000or cells, 63 0.000000or molecular functions and biological processes, 83 0.000000or anatomical entities, and 85 0.000000or diseases. In addition to the web frontend, BeCAS is also accessible through an HTTP API, producing results in multiple formats, such as JSON, XML, A1 (GENIA/Brat) and CoNLL. The API can also be easily used through a Python client and CLI tool. Concept identification and highlighting capabilities can be embedded in external webpages by using a customizable Javascript widget. You can read more about BeCAS in the following manuscript: * Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btt317?ijkey=LmfxRZmyeb4aPWj&keytype=ref * PDF: http://bioinformatics.oxfordjournals.org/content/early/2013/06/04/bioinformatics.btt317.full.pdf?keytype=ref&ijkey=LmfxRZmyeb4aPWj Resources: * Web Application: http://bioinformatics.ua.pt/becas/ * API Documentation: http://bioinformatics.ua.pt/becas/api * Widget Documentation: http://bioinformatics.ua.pt/becas/widget * Python client and CLI tool: http://bioinformatics.ua.pt/becas/#api__interface_clients We welcome all feedback and comments (contact at http://bioinformatics.ua.pt/becas/contact) on any aspect of the system. Thank you for your time. -- Tiago Nunes Bioinformatics Group IEETA, University of Aveiro http://bioinformatics.ua.pt __________________________________________ - ELSNET mailing list Elsnet-list_(at)_elsnet.org - To manage your subscription go to: http://mailman.elsnet.org/mailman/listinfo/elsnet-list

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