{"id":10,"date":"2022-01-28T16:09:59","date_gmt":"2022-01-28T15:09:59","guid":{"rendered":"https:\/\/temu.bsc.es\/livingner\/?p=10"},"modified":"2022-09-06T15:48:32","modified_gmt":"2022-09-06T14:48:32","slug":"submission","status":"publish","type":"post","link":"https:\/\/temu.bsc.es\/livingner\/2022\/01\/28\/submission\/","title":{"rendered":"Submission"},"content":{"rendered":"\n<p>Evaluation process: (1) you submit your results, (2) we perform the evaluation off-line and (3) return the final scores.<\/p>\n\n\n\n<p><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Submission format<\/h3>\n\n\n\n<p><strong>LivingNER &#8211; Species NER track<\/strong>. A TSV file with one row per mention, headers and the following columns: <\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>filename<\/li><li>mark<\/li><li>label (mention label)<\/li><li>off0 (starting character offset)<\/li><li>off1 (ending character offset)<\/li><li>span (mention span)<\/li><\/ul>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"597\" height=\"102\" src=\"https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/Screenshot-from-2022-04-06-16-37-48.png\" alt=\"\" class=\"wp-image-325\" srcset=\"https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/Screenshot-from-2022-04-06-16-37-48.png 597w, https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/Screenshot-from-2022-04-06-16-37-48-300x51.png 300w\" sizes=\"auto, (max-width: 597px) 100vw, 597px\" \/><figcaption>Figure 1. Example of submission file for LivingNER-Species NER track<br><\/figcaption><\/figure>\n<\/div>\n\n\n<p><strong>LivingNER &#8211; Species Norm track<\/strong>. A TSV file with one row per mention, headers and the following columns: <\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>filename<\/li><li>mark<\/li><li>label (mention label)<\/li><li>off0 (starting character offset)<\/li><li>off1 (ending character offset)<\/li><li>span (mention span)<\/li><li>NCBITax (mention code in NCBITaxonomy)<\/li><\/ul>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"691\" height=\"106\" src=\"https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/Screenshot-from-2022-04-06-16-37-55.png\" alt=\"\" class=\"wp-image-326\" srcset=\"https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/Screenshot-from-2022-04-06-16-37-55.png 691w, https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/Screenshot-from-2022-04-06-16-37-55-300x46.png 300w\" sizes=\"auto, (max-width: 691px) 100vw, 691px\" \/><figcaption>Figure 2. Example of submission file for LivingNER-Species Norm track<\/figcaption><\/figure>\n<\/div>\n\n\n<p><strong>LivingNER &#8211; Clinical IMPACT track<\/strong>. A TSV file with one row per document, headers and the following columns:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>filename<\/li><li>isPet (Yes\/No)<\/li><li>PetIDs (NCBITaxonomy codes of pet &amp; farm animals present in document)<\/li><li>isAnimalInjury (Yes\/No)<\/li><li>AnimalInjuryIDs (NCBITaxonomy codes of animals causing injuries present in document)<\/li><li>isFood (Yes\/No)<\/li><li>FoodIDs (NCBITaxonomy codes of food mentions present in document)<\/li><li>isNosocomial (Yes\/No)<\/li><li>NosocomialIDs (NCBITaxonomy codes of nosocomial species mentions present in document)<\/li><\/ul>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"976\" height=\"71\" src=\"https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/Screenshot-from-2022-04-06-16-41-53.png\" alt=\"\" class=\"wp-image-328\" srcset=\"https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/Screenshot-from-2022-04-06-16-41-53.png 976w, https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/Screenshot-from-2022-04-06-16-41-53-300x22.png 300w, https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/Screenshot-from-2022-04-06-16-41-53-768x56.png 768w\" sizes=\"auto, (max-width: 976px) 100vw, 976px\" \/><figcaption>Figure 2. Example of submission file for LivingNER-Clinical Impact track<\/figcaption><\/figure>\n<\/div>\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:\u00a0<\/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<h3 class=\"wp-block-heading\">Submission method<\/h3>\n\n\n\n<p>Submissions will be made via SFTP.<\/p>\n\n\n\n<p><a href=\"https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/05\/livingner-submission-tutorial.docx.pdf\">Submission tutorial<\/a><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Submission instructions<\/h3>\n\n\n\n<p>5 submissions per sub-track will be allowed.<\/p>\n\n\n\n<p>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 each subdirectory, you must include the results in a TSV file with the format defined in the &#8220;Submission format&#8221; section.<\/li><li>The TSV file must have the&nbsp;<strong>.tsv<\/strong>&nbsp;file extension and include ALL your predictions.<\/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>). Use separate files for each run, with n<strong><strong>umbers and<\/strong>&nbsp;a recognizable&nbsp;<strong>name<\/strong>. For example, 1-systemDL and 2-systemlookup<\/strong>.<\/li><li>In addition, in the parent directory, you must add a&nbsp;<strong>README.txt<\/strong>&nbsp;file with your contact details (team name, affiliation, and authors) and a really short explanation of your system.<\/li><\/ul>\n\n\n\n<p>E<a href=\"https:\/\/temu.bsc.es\/livingner\/wp-content\/uploads\/2022\/04\/livingner-test.zip\">xample submission ZIP file<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Evaluation process: (1) you submit your results, (2) we perform the evaluation off-line and (3) return the final scores. Submission format LivingNER &#8211; Species NER track. A TSV file with one row per mention, headers and the following columns: filename mark label (mention label) off0 (starting character offset) off1 (ending character offset) span (mention span) [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-10","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/temu.bsc.es\/livingner\/wp-json\/wp\/v2\/posts\/10","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/temu.bsc.es\/livingner\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/temu.bsc.es\/livingner\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/temu.bsc.es\/livingner\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/temu.bsc.es\/livingner\/wp-json\/wp\/v2\/comments?post=10"}],"version-history":[{"count":16,"href":"https:\/\/temu.bsc.es\/livingner\/wp-json\/wp\/v2\/posts\/10\/revisions"}],"predecessor-version":[{"id":473,"href":"https:\/\/temu.bsc.es\/livingner\/wp-json\/wp\/v2\/posts\/10\/revisions\/473"}],"wp:attachment":[{"href":"https:\/\/temu.bsc.es\/livingner\/wp-json\/wp\/v2\/media?parent=10"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/temu.bsc.es\/livingner\/wp-json\/wp\/v2\/categories?post=10"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/temu.bsc.es\/livingner\/wp-json\/wp\/v2\/tags?post=10"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}