<div dir="ltr"><div style="font-family:arial,sans-serif;font-size:13px"><font face="arial, sans-serif">Dear Corpora-List</font><font face="arial, sans-serif"> members,</font></div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px"><font face="arial, sans-serif">We are pleased to announce </font>BeCAS<font face="arial, sans-serif">, a web application, API and widget</font></div><div style="font-family:arial,sans-serif;font-size:13px">
<font face="arial, sans-serif">for biomedical concept identification.</font> BeCAS id<font face="arial, sans-serif">entifies and</font></div><div style="font-family:arial,sans-serif;font-size:13px">annotates species, anatomical concepts, microRNAs, enzymes, genes,</div>
<div style="font-family:arial,sans-serif;font-size:13px">proteins, chemicals, drugs, diseases, metabolic pathways,</div><div style="font-family:arial,sans-serif;font-size:13px">cellular components, biological processes and molecular functions. </div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">BeCAS pr<font face="arial, sans-serif">ovides annotations for isolated, nested and intersected</font></div>
<div style="font-family:arial,sans-serif;font-size:13px">entities. It identifies concepts from multiple semantic groups,</div><div style="font-family:arial,sans-serif;font-size:13px">providing preferred names and enriching them with references to</div>
<div style="font-family:arial,sans-serif;font-size:13px">public knowledge resources. Users can choose the types of entities</div><div style="font-family:arial,sans-serif;font-size:13px">for identification and highlighting in real-time.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px"><font face="arial, sans-serif">To facilitate annotation of PubMed abstracts</font>, BeCAS au<font face="arial, sans-serif">tomatically</font></div>
<div style="font-family:arial,sans-serif;font-size:13px">fetches publications from NCBI servers and renders them with</div><div style="font-family:arial,sans-serif;font-size:13px">identified concepts highlighted.</div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px">BeCAS was v<font face="arial, sans-serif">alidated against CRAFT, AnEM and the NCBI Diseases corpora,</font></div><div style="font-family:arial,sans-serif;font-size:13px">
achieving f-measure results for overlap matching of 76% for genes</div><div style="font-family:arial,sans-serif;font-size:13px">and proteins, 95% for species, 65% for chemicals, 83% for cellular</div><div style="font-family:arial,sans-serif;font-size:13px">
components, 92% for cells, 63% for molecular functions and biological</div><div style="font-family:arial,sans-serif;font-size:13px">processes, 83% for anatomical entities, and 85% for diseases.</div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px"><font face="arial, sans-serif">In addition to the web fron</font>tend, BeCAS is<font face="arial, sans-serif"> also accessible</font></div><div style="font-family:arial,sans-serif;font-size:13px">
through an HTTP API, producing results in multiple formats, such as</div><div style="font-family:arial,sans-serif;font-size:13px">JSON, XML, A1 (GENIA/Brat) and CoNLL. The API can also be easily used</div><div style="font-family:arial,sans-serif;font-size:13px">
through a Python client and CLI tool.</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Concept identification and highlighting capabilities can be embedded</div>
<div style="font-family:arial,sans-serif;font-size:13px">in external webpages by using a customizable Javascript widget.</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">
<font face="arial, sans-serif">You can read more about </font>BeCAS i<font face="arial, sans-serif">n the following manuscript:</font></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">
* <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btt317?ijkey=kZExzXwEWUYQY0e&keytype=ref" target="_blank" style="background-color:rgb(242,239,232)">http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btt317?</a></div>
<a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btt317?ijkey=kZExzXwEWUYQY0e&keytype=ref" target="_blank" style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(242,239,232)">ijkey=kZExzXwEWUYQY0e&keytype=ref</a><span style="font-family:arial,sans-serif;font-size:13px"></span><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px">Resources:</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px"><font face="arial, sans-serif">* Web Application: </font><a href="http://bioinformatics.ua.pt/becas/" target="_blank"><font face="arial, sans-serif">http://</font><font face="arial, sans-serif">bioinformatics.ua.pt/</font>becas<font face="arial, sans-serif">/</font></a></div>
<div style="font-family:arial,sans-serif;font-size:13px"><font face="arial, sans-serif">* API Documentation: </font><a href="http://bioinformatics.ua.pt/becas/api" target="_blank"><font face="arial, sans-serif">http://</font><font face="arial, sans-serif">bioinformatics.ua.pt/</font>becas<font face="arial, sans-serif">/api</font></a></div>
<div style="font-family:arial,sans-serif;font-size:13px"><font face="arial, sans-serif">* Widget Documentation: </font><a href="http://bioinformatics.ua.pt/becas/widget" target="_blank"><font face="arial, sans-serif">http://</font><font face="arial, sans-serif">bioinformatics.ua.pt/</font>becas<font face="arial, sans-serif">/</font><font face="arial, sans-serif">widget</font></a></div>
<div style="font-family:arial,sans-serif;font-size:13px"><font face="arial, sans-serif">* Python client and CLI tool: </font><a href="http://bioinformatics.ua.pt/becas/#api__interface_clients" target="_blank"><font face="arial, sans-serif">http://bioinformatics.</font><font face="arial, sans-serif">ua.pt/</font>becas<font face="arial, sans-serif">/#api__interface_</font><font face="arial, sans-serif">clients</font></a></div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">We welcome all feedback and comments (contact at</div><div style="font-family:arial,sans-serif;font-size:13px">
<a href="http://bioinformatics.ua.pt/becas/contact" target="_blank"><font face="arial, sans-serif">http://bioinformatics.ua.pt/</font>becas<font face="arial, sans-serif">/contact</font></a><font face="arial, sans-serif">) from the</font></div>
<div style="font-family:arial,sans-serif;font-size:13px"><font face="arial, sans-serif">Corpora-List community on any aspect of the system.</font></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">
Thank you for your time.</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">--</div><div style="font-family:arial,sans-serif;font-size:13px">Tiago Nunes</div>
<div style="font-family:arial,sans-serif;font-size:13px">Bioinformatics Group</div><div style="font-family:arial,sans-serif;font-size:13px">IEETA, University of Aveiro</div><div style="font-family:arial,sans-serif;font-size:13px">
<a href="http://bioinformatics.ua.pt/" target="_blank">http://bioinformatics.ua.pt</a></div></div>