{"id":112362,"date":"2009-02-05T13:21:00","date_gmt":"2009-02-05T13:21:00","guid":{"rendered":"http:\/\/weblogs.madrimasd.org\/\/bioinformatica\/archive\/2009\/02\/05\/112362.aspx"},"modified":"2009-02-05T13:21:00","modified_gmt":"2009-02-05T13:21:00","slug":"biocreative-ii-5","status":"publish","type":"post","link":"https:\/\/www.madrimasd.org\/blogs\/bioinformatica\/2009\/02\/05\/112362","title":{"rendered":"BioCreative II.5"},"content":{"rendered":"<p>Siguiendo la nueva tendencia en las competiciones bianuales en \u00e1reas de la Bioinform\u00e1tica, <A href=\"http:\/\/weblogs.madrimasd.org\/bioinformatica\/archive\/2008\/01\/22\/82952.aspx\">comenzada por CASP6.5 y continuada en CASP7.5<\/a>, BioCreative, la competici\u00f3n relacionada con el \u00e1rea de <i>text-mining<\/i>, va a celebrar su propia edici\u00f3n fraccional (<a href=\"http:\/\/www.biocreative.org\/\">BioCreative II.5<\/a>). Esta edici\u00f3n est\u00e1 principalmente pensada para participantes, debido a que las fechas proporcionadas por el comunicado oficial de la organizaci\u00f3n apuntan a los distintos plazos que tienen para entrenar sus herramientas, probarlas y evaluarlas.<\/p>\n<p>Ya est\u00e1 abierto el plazo de inscripci\u00f3n, y se cerrar\u00e1 el pr\u00f3ximo 3 de Abril. Aunque todav\u00eda no hay datos sobre el lugar de celebraci\u00f3n ni las fechas de las reuniones que se suelen celebrar al final de estas competiciones, la <a href=\"http:\/\/www.biocreative.org\/\">p\u00e1gina web de BioCreative II.5<\/a> va a ir actualiz\u00e1ndose con informaci\u00f3n adicional. Adem\u00e1s, hay una lista de correo electr\u00f3nico dedicada a la competici\u00f3n: <a href=\"http:\/\/lists.sourceforge.net\/mailman\/listinfo\/biocreative-participant\">http:\/\/lists.sourceforge.net\/mailman\/listinfo\/biocreative-participant<\/a><\/p>\n<p>El anuncio completo original del evento viene a continuaci\u00f3n:<br \/><!--more--><\/p>\n<h2><a href=\"http:\/\/www.biocreative.org\/\">BioCreative II.5 Challenge (2009)<\/a><\/h2>\n<h3>Can Information Extraction contribute to the creation of StructuredDigital Abstracts (SDAs)?<br \/><\/h3>\n<ul>\n<li>BioCreative II.5 builds on the FEBS Letters experiment for the creation of SDAs.<\/li>\n<li>BC II.5 will systematically assess the potential use of automated IEin the curation of full-text articles.<\/li>\n<\/ul>\n<p>See previous controversial articles:<\/p>\n<ul>\n<li>Ceol et al., <a href=\"http:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0014-5793%2808%2900196-8\">Linking entries in protein interaction database to structured text<\/a>: The FEBS Letters experiment., FEBS Letters (2008) vol. 582 (8) pp. 1171-7<br \/><a href=\"http:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0014-5793%2808%2900196-8\">http:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0014-5793%2808%2900196-8<\/a><\/li>\n<li>Gerstein et al., <a href=\"http:\/\/www.nature.com\/nature\/journal\/v447\/n7141\/full\/447142a.html\">Structured digital abstract makes text mining easy<\/a>., Nature (2007) May 10;447(7141):142<br \/><a href=\"http:\/\/www.nature.com\/nature\/journal\/v447\/n7141\/full\/447142a.html\">http:\/\/www.nature.com\/nature\/journal\/v447\/n7141\/full\/447142a.html<\/a><\/li>\n<li>* Hahn et al., <a href=\"http:\/\/www.nature.com\/nature\/journal\/v448\/n7150\/full\/448130b.html\">Text mining: powering the database revolution<\/a>., Nature(2007) May 10;447(7141):142<br \/><a href=\"http:\/\/www.nature.com\/nature\/journal\/v448\/n7150\/full\/448130b.html\">http:\/\/www.nature.com\/nature\/journal\/v448\/n7150\/full\/448130b.html<\/a><\/li>\n<li>Leitner et al., <a href=\"http:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0014-5793%2808%2900195-6\">A text-mining perspective on the requirements forelectronically annotated abstracts<\/a>., FEBS Letters (2008) vol. 582 (8)pp. 1178-81<br \/><a href=\"http:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0014-5793%2808%2900195-6\">http:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0014-5793(08)00195-6<\/a><\/li>\n<\/ul>\n<p><\/p>\n<h3><u>CALL FOR PARTICIPATION<\/u><\/h3>\n<h4>OVERVIEW<\/h4>\n<div align=\"justify\">The BioCreative challenge evaluation consists of a community-wide effortfor promoting the development and evaluation of text mining andinformation extraction systems applied to the biological domain.Previous BioCreative challenges attracted considerable interest not onlyin the bio-text mining community but also in the bioinformatics andbiological database domain, resulting in two special journal issues anduseful data resources for the development of biomedical text miningsystems.<\/div>\n<p><\/p>\n<div align=\"justify\">BioCreative II.5 will evaluate real-time text mining capabilities onfull text articles and explore future possibilities for author-assistedannotations using information extraction tools.<\/div>\n<p>Interesting new aspects of BioCreative II.5 relate to:<\/p>\n<div align=\"justify\">\n<ol>\n<li>The use of an online MetaServer platform as basic evaluation infrastructure, allowing direct comparison of multiple participatingsystems.<\/li>\n<li>Collaboration of article authors, publishers and expert humanannotators (for the preparation of task resources).<\/li>\n<li>Use of full text articles in various formats including XML.<\/li>\n<li>Alignment of various tasks on a common data collection.<\/li>\n<\/ol>\n<\/div>\n<h4>TASKS<\/h4>\n<ol>\n<li><b>INT &#8211; Interaction normalization task<\/b><br \/>(Given an article extract a set of biological entities, namely mentionedinteractor proteins)<\/li>\n<li><b>IPT &#8211; Interaction pair task<\/b><br \/>(Extraction of biological relations, namely pairs of interacting proteins)<\/li>\n<li><b>ACT &#8211; Article categorization task<\/b><br \/>(Binary classification of articles as relevant for extractinginteraction annotations)<\/li>\n<\/ol>\n<p>For more information on the tasks, please visit the website at:<a href=\"http:\/\/www.biocreative.org\/events\/biocreative-ii5\/biocreative-ii5\/\">http:\/\/www.biocreative.org\/events\/biocreative-ii5\/biocreative-ii5\/<\/a><\/p>\n<h4>EVALUATION<\/h4>\n<div align=\"justify\">Evaluation will be based on direct comparison of automatically generated predictions by participating systems against a Gold Standard of manuallygenerated annotations, so-called Structured Digital Abstracts (SDAs)generated by the original article authors themselves as well we byexpert biological database annotators. In order to assure a more robustevaluation setting and to be able to directly compare and visualizedifferent online predictions the BioCreative MetaServer (BCMS) platformwill be used.<\/div>\n<h4>PUBLICATIONS<\/h4>\n<div align=\"justify\">The BioCreative II.5 challenge will result in high-impact publicationsfollowing the line of previous BioCreative publications, includingcollaborative papers, evaluation articles and technical descriptions.<\/div>\n<ul>\n<li>BioCreative I &#8211; BMC Bioinformatics<br \/><a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/6?issue=S1&amp;page=1\">http:\/\/www.biomedcentral.com\/1471-2105\/6?issue=S1&amp;page=1<\/a><\/li>\n<li>BioCreative II &#8211; Genome Biology<br \/><a href=\"http:\/\/genomebiology.com\/supplements\/9\/S2\">http:\/\/genomebiology.com\/supplements\/9\/S2<\/a><\/li>\n<\/ul>\n<h4>MAILING LIST \/ REGISTRATION<\/h4>\n<p>To join the BioCreative mailing list visit:<a href=\"http:\/\/lists.sourceforge.net\/mailman\/listinfo\/biocreative-participant\">http:\/\/lists.sourceforge.net\/mailman\/listinfo\/biocreative-participant<\/a><\/p>\n<p>To obtain data (BioCreative data and workshop proceedings):<a href=\"http:\/\/www.biocreative.org\/accounts\/register\/\">http:\/\/www.biocreative.org\/accounts\/register\/<\/a><\/p>\n<p>If you are interested in the BC II.5 challenge, register at:<a href=\"http:\/\/www.biocreative.org\/team\/create\/\">http:\/\/www.biocreative.org\/team\/create\/<\/a><\/p>\n<p><i>(Note: Servers will be down on Sat., 7th Feb., from 9:00-14:00 GMT formaintenance.)<\/i><\/p>\n<h4>DATES<\/h4>\n<div align=\"left\">\n<ul>\n<li><u>Registration Opening<\/u>: now<\/li>\n<li><u>Training Phase\/AS testing<\/u>: Feb. 16th, 2009<\/li>\n<li><u>Registration Closing<\/u>: Apr. 3rd, 2009<\/li>\n<li><u>Test Phase<\/u>: Apr. 8th, 2009<\/li>\n<li><u>Evaluation Phase<\/u>: Apr. 10th, 2009<\/li>\n<\/ul>\n<\/div>\n<p>We encourage you to visit the website and sign up for further information.<\/p>\n<h4>REFERENCES AND LINKS<\/h4>\n<ul>\n<li>BioCreative website (new!): <a class=\"moz-txt-link-freetext\" href=\"http:\/\/www.biocreative.org\/\">http:\/\/www.biocreative.org<\/a><\/li>\n<li>BioCreative MetaServer (BCMS): <a class=\"moz-txt-link-freetext\" href=\"http:\/\/bcms.bioinfo.cnio.es\/\">http:\/\/bcms.bioinfo.cnio.es<\/a><\/li>\n<li>Author-based annotations (FEBS Letters SDAs):<\/li>\n<ul>\n<li>summary [<a class=\"moz-txt-link-freetext\" href=\"http:\/\/www.febsletters.org\/content\/sda_summary\">http:\/\/www.febsletters.org\/content\/sda_summary<\/a>]<\/li>\n<li>special issue[<a class=\"moz-txt-link-freetext\" href=\"http:\/\/www.sciencedirect.com\/science\/issue\/4938-2008-994179991-684107\">http:\/\/www.sciencedirect.com\/science\/issue\/4938-2008-994179991-684107<\/a>]<\/li>\n<\/ul>\n<li>BioCreative I: special issue<br \/>[<a class=\"moz-txt-link-freetext\" href=\"http:\/\/www.biomedcentral.com\/1471-2105\/6?issue=S1&amp;page=1\">http:\/\/www.biomedcentral.com\/1471-2105\/6?issue=S1&amp;page=1<\/a>]<\/li>\n<li>BioCreative II: special issue<br \/>[<a class=\"moz-txt-link-freetext\" href=\"http:\/\/genomebiology.com\/supplements\/9\/S2\">http:\/\/genomebiology.com\/supplements\/9\/S2<\/a>]<\/li>\n<\/ul>\n<blockquote><p>Thank you,<\/p>\n<blockquote><p>the BioCreative Organizers<\/p><\/blockquote>\n<\/blockquote>\n<blockquote>\n<blockquote><p>Alfonso Valencia<br \/>Martin Krallinger<br \/>Florian Leitner<br \/>* CNIO &#8211; Spanish National Cancer Research Centre<\/p>\n<p>Lynette Hirschman<br \/>Scott Mardis<br \/>* The MITRE Corporation<\/p>\n<p>Gianni Cesareni<br \/>* MINT Database<\/p><\/blockquote>\n<\/blockquote>\n","protected":false},"excerpt":{"rendered":"<p>Siguiendo la nueva tendencia en las competiciones bianuales en \u00e1reas de la Bioinform\u00e1tica, comenzada por CASP6.5 y continuada en CASP7.5, BioCreative, la competici\u00f3n relacionada con el \u00e1rea de text-mining, va a celebrar su propia edici\u00f3n fraccional (BioCreative II.5). Esta edici\u00f3n est\u00e1 principalmente pensada para participantes, debido a que las fechas proporcionadas por el comunicado oficial de la organizaci\u00f3n apuntan a los distintos plazos que tienen para entrenar sus herramientas, probarlas y evaluarlas. Ya est\u00e1 abierto el plazo de inscripci\u00f3n, y se cerrar\u00e1 el pr\u00f3ximo 3 de Abril. Aunque todav\u00eda no hay datos sobre el lugar de celebraci\u00f3n ni las fechas\u2026<\/p>\n","protected":false},"author":25,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"ngg_post_thumbnail":0},"categories":[31],"tags":[],"blocksy_meta":{"styles_descriptor":{"styles":{"desktop":"","tablet":"","mobile":""},"google_fonts":[],"version":4}},"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/www.madrimasd.org\/blogs\/bioinformatica\/wp-json\/wp\/v2\/posts\/112362"}],"collection":[{"href":"https:\/\/www.madrimasd.org\/blogs\/bioinformatica\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.madrimasd.org\/blogs\/bioinformatica\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.madrimasd.org\/blogs\/bioinformatica\/wp-json\/wp\/v2\/users\/25"}],"replies":[{"embeddable":true,"href":"https:\/\/www.madrimasd.org\/blogs\/bioinformatica\/wp-json\/wp\/v2\/comments?post=112362"}],"version-history":[{"count":0,"href":"https:\/\/www.madrimasd.org\/blogs\/bioinformatica\/wp-json\/wp\/v2\/posts\/112362\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.madrimasd.org\/blogs\/bioinformatica\/wp-json\/wp\/v2\/media?parent=112362"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.madrimasd.org\/blogs\/bioinformatica\/wp-json\/wp\/v2\/categories?post=112362"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.madrimasd.org\/blogs\/bioinformatica\/wp-json\/wp\/v2\/tags?post=112362"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}