{"id":4396,"date":"2020-06-08T14:53:12","date_gmt":"2020-06-08T14:53:12","guid":{"rendered":"https:\/\/temu.bsc.es\/cantemist\/?p=4396"},"modified":"2022-09-06T15:36:45","modified_gmt":"2022-09-06T14:36:45","slug":"submission","status":"publish","type":"post","link":"https:\/\/temu.bsc.es\/distemist\/submission\/","title":{"rendered":"Submission"},"content":{"rendered":"\n<p>The evaluation of the competition will be done against a manually annotated data set purposely created for this task.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Submission format<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Sub-track 1 DisTEMIST-Entities<\/h3>\n\n\n\n<p>Participating teams will have to generate a tsv file with the annotations detected for each of the test documents according to the following column structure:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><em>filename<\/em>: Name of the file from which the disease mention has been extracted.<\/li><li><em>mention label<\/em>: In this case it will always be ENFERMEDAD<\/li><li><em>starting character offset<\/em>:  Character number where the detected mention starts. <\/li><li><em>ending character offset<\/em>: Character number where the detected mention ends. <\/li><li><em>mention span<\/em>: Mention extracted from text<\/li><\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code>filename\tlabel\toff0\toff1\tspan\nes-S0004-06142007000600016-2\tENFERMEDAD\t330\t374\tlesi\u00f3n nodular s\u00f3lida en cabeza de epid\u00eddimo\nes-S0004-06142007000600016-2\tENFERMEDAD\t436\t467\ttumor adenomatoide de epid\u00eddimo\nes-S0004-06142007000600016-5\tENFERMEDAD\t1136\t1167\ttumor adenomatoide de epid\u00eddimo\n<\/code><\/pre>\n\n\n\n<h3 class=\"wp-block-heading\">Sub-track 2 Distemist-Linking<\/h3>\n\n\n\n<p>Participating teams will have to generate a tsv file with the annotations detected for each of the test documents according to the following column structure:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><em>filename<\/em>: Name of the file from which the disease mention has been extracted.<\/li><li><em>mention label<\/em>: It will always be ENFERMEDAD<\/li><li><em>starting character offset<\/em>:  Character number where the detected mention starts. <\/li><li><em>ending character offset<\/em>: Character number where the detected mention ends. <\/li><li><em>mention span<\/em>: Mention extracted from text<\/li><li><em>code<\/em>: List of Snomed-CT concept codes linked to the mention. If there is more than one code associated with a mention, they will be concatenated by the symbol \u201c+\u201d<\/li><\/ul>\n\n\n\n<pre class=\"wp-block-code\"><code>filename\tlabel\toff0\toff1\tspan\tcode\nes-S0004-06142007000600016-2\tENFERMEDAD\t330\t374\tlagunaas coriorretinianas\t302893000\nes-S0004-06142007000600016-2\tENFERMEDAD\t436\t467\tanomal\u00edas de la migraci\u00f3n neuroral\t253146009\nes-S0004-06142007000600016-5\tENFERMEDAD\t1136\t1167\tafectaci\u00f3n macular\t312999006\n<\/code><\/pre>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>To evaluate your systems AFTER June 2022, do it in Codalab: <a rel=\"noreferrer noopener\" href=\"https:\/\/codalab.lisn.upsaclay.fr\/competitions\/7162\" target=\"_blank\">https:\/\/codalab.lisn.upsaclay.fr\/competitions\/7162<\/a><\/strong><\/h4>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>The following sections are kept here for historical reasons. They are not relevant AFTER June 2022<\/strong><\/h4>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<h2 class=\"wp-block-heading\">Evaluation dates (OLD: shared task)<\/h2>\n\n\n\n<ul class=\"wp-block-list\"><li><span style=\"color: initial;\">10 May 09:00 GMT &#8211; 15 May 09:00 GMT<\/span><\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Submission instructions (OLD: shared task)<\/h2>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"https:\/\/temu.bsc.es\/distemist\/wp-content\/uploads\/2022\/05\/DISTEMIST-submission-tutorial.pdf\" target=\"_blank\">Download here the submission tutorial<\/a><\/p>\n\n\n\n<p><a href=\"https:\/\/temu.bsc.es\/distemist\/wp-content\/uploads\/2022\/04\/distemist-test.zip\">Download here a submission ZIP example<\/a>.<\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n\n\n\n<p>To submit your results, (1)&nbsp;<a href=\"http:\/\/participants-area.bioasq.org\/accounts\/register\">register at BioASQ<\/a>&nbsp;website and (2), follow the following instructions:<\/p>\n\n\n\n<p><strong>A<\/strong>. 5 submissions per sub-track will be allowed.<\/p>\n\n\n\n<p><strong>B<\/strong>. You must submit&nbsp;<strong>ONE SINGLE&nbsp;<\/strong>ZIP file with the following structure:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li><strong>One subdirectory per subtask&nbsp;<\/strong>in which you are participating.&nbsp;<\/li><li>In addition, in the parent directory, you must add a&nbsp;<strong>README.txt<\/strong>&nbsp;file with your contact details and a really short explanation of your system.<\/li><li>If you have more than one system, you can include their predictions and we will evaluate them (<strong>up to 5 prediction runs<\/strong>).<\/li><li>For each prediction run:<ul><li>You must include the&nbsp;<strong>tab-separated file<\/strong>&nbsp;with your predictions.&nbsp;<\/li><li><strong>One single file with all the predictions.<\/strong><\/li><li>With a&nbsp;<strong>.tsv<\/strong>&nbsp;file extension.&nbsp;&nbsp;<\/li><li>If you have more than one system, include&nbsp;<strong>one tab-separated file for each system<\/strong>.<\/li><li>If you have more than one system, name the tab-separated files with&nbsp;<strong>numbers and<\/strong>&nbsp;a more or less recognizable&nbsp;<strong>name<\/strong>. For example, 1-systemDL.tsv and 2-systemlookup.tsv<\/li><\/ul><\/li><\/ul>\n\n\n\n<p><strong>C. <\/strong>With this ZIP file, go to the participants area of BioASQ (<a href=\"http:\/\/participants-area.bioasq.org\/Tasks\/distemist\/\">http:\/\/participants-area.bioasq.org\/Tasks\/distemist\/<\/a>) and submit there your file.<\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The evaluation of the competition will be done against a manually annotated data set purposely created for this task. Submission format Sub-track 1 DisTEMIST-Entities Participating teams will have to generate a tsv file with the annotations detected for each of the test documents according to the following column structure: filename: Name of the file from [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3],"tags":[],"class_list":["post-4396","post","type-post","status-publish","format-standard","hentry","category-evaluation"],"_links":{"self":[{"href":"https:\/\/temu.bsc.es\/distemist\/wp-json\/wp\/v2\/posts\/4396","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/temu.bsc.es\/distemist\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/temu.bsc.es\/distemist\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/temu.bsc.es\/distemist\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/temu.bsc.es\/distemist\/wp-json\/wp\/v2\/comments?post=4396"}],"version-history":[{"count":18,"href":"https:\/\/temu.bsc.es\/distemist\/wp-json\/wp\/v2\/posts\/4396\/revisions"}],"predecessor-version":[{"id":4964,"href":"https:\/\/temu.bsc.es\/distemist\/wp-json\/wp\/v2\/posts\/4396\/revisions\/4964"}],"wp:attachment":[{"href":"https:\/\/temu.bsc.es\/distemist\/wp-json\/wp\/v2\/media?parent=4396"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/temu.bsc.es\/distemist\/wp-json\/wp\/v2\/categories?post=4396"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/temu.bsc.es\/distemist\/wp-json\/wp\/v2\/tags?post=4396"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}