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
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
* 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.
IEETA, University of Aveiro
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