{"id":5804,"date":"2025-07-01T10:37:05","date_gmt":"2025-07-01T08:37:05","guid":{"rendered":"https:\/\/cetaf.org\/dest\/?page_id=5804"},"modified":"2025-11-12T14:06:23","modified_gmt":"2025-11-12T13:06:23","slug":"liberation-of-data-how-to-liberate-data-from-publications-and-how-to-reuse-it","status":"publish","type":"page","link":"https:\/\/cetaf.org\/dest\/liberation-of-data-how-to-liberate-data-from-publications-and-how-to-reuse-it\/","title":{"rendered":"Liberation of data: how to liberate data from publications and how to reuse it"},"content":{"rendered":"<p style=\"text-align: center;\"><a href=\"https:\/\/cetaf.org\/dest\/wp-content\/uploads\/2025\/07\/DEST_training.tif\"><img class=\"alignnone size-full wp-image-5822\" src=\"https:\/\/cetaf.org\/dest\/wp-content\/uploads\/2025\/07\/DEST_training.tif\" alt=\"\" \/><\/a> <img loading=\"lazy\" class=\"alignnone size-medium wp-image-5823\" src=\"https:\/\/cetaf.org\/dest\/wp-content\/uploads\/2025\/07\/DEST_training-207x300.jpeg\" alt=\"\" width=\"207\" height=\"300\" \/><\/p>\n<h4><strong>Description<\/strong><\/h4>\n<p>This training session will offer participants a deep dive into the processes of annotating and sharing biodiversity data. The session will begin with an online theoretical introduction, providing an overview of the current state of biodiversity literature, the move towards the liberation of taxonomic data and the new opportunities this offers. This will be followed by two days of hands-on, in-person training focused on practical workflows for structuring, annotating, and circulating biodiversity data from scientific publications. Participants will explore how to annotate biodiversity datasets, ensuring they are properly formatted for reuse, and how to facilitate the sharing and circulation of these datasets within the scientific community. Trainees will also learn how to access and reuse data for their own research needs.<\/p>\n<p>By the end of the session, attendees will be equipped with the skills to enhance the accessibility and reusability of biodiversity data, contributing to more effective data exchange.<\/p>\n<p>&nbsp;<\/p>\n<h3><strong>Online session <\/strong><\/h3>\n<p><strong>15 October 2025<\/strong><\/p>\n<p><strong>14.00-16.00 Introduction: The state of biodiversity literature and the move towards data liberation\u00a0<\/strong><\/p>\n<ul>\n<li>Welcome: getting to know each other and trainees\u2019 expectations<\/li>\n<li>General introduction to the course<\/li>\n<li>Technical requirements<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<h3><strong>Face to face\u00a0<\/strong><\/h3>\n<p><strong>10 November 2025<\/strong><\/p>\n<p><strong>Day 1: Structuring and annotating biodiversity data<\/strong><\/p>\n<p><strong>09.00-10.00 Module 1: Concepts<\/strong><\/p>\n<ul>\n<li>Principles of semantics<\/li>\n<li>The elements structuring a biodiversity publication<\/li>\n<li>Annotations, attributes and linking: FAIR data<\/li>\n<li>Workflows: template, individual extraction, born digital <em>versus <\/em>scanned documents<\/li>\n<\/ul>\n<p><strong>10.00-10.30 &#8211; Coffee break<\/strong><\/p>\n<p><strong>10.30-13.00 Module 2: XML-first workflow<\/strong><\/p>\n<ul>\n<li>Introduction to the XML-first workflow<\/li>\n<li>Structuring a taxonomy\/biodiversity paper<\/li>\n<li>XML conversion and enrichment of the metadata<\/li>\n<li>Annotating the data in JATS-Taxpub<\/li>\n<\/ul>\n<p><strong>13.00-14.00 &#8211; Lunch<\/strong><\/p>\n<p><strong>14.00-15.30 Module 3: Golden Gate<\/strong><\/p>\n<ul>\n<li>The PDF workflow to enable re-use of data<\/li>\n<li>Conversion and annotation of legacy literature<\/li>\n<li>Learning and becoming a certified contributor<\/li>\n<\/ul>\n<p><strong>15.30-16.00 &#8211; Coffee break<\/strong><\/p>\n<p><strong>16.00-17.00 Module 3: Continuation<\/strong><\/p>\n<h4><\/h4>\n<p>&nbsp;<\/p>\n<p><strong>11 November 2025<\/strong><\/p>\n<p><strong>Day 2: <\/strong><strong>Accessing and re-using biodiversity data<\/strong><\/p>\n<p><strong>9.00-10.30 Module 4: Curation and re-use of data from publications<\/strong><\/p>\n<ul>\n<li>Curation and quality control of data already available in online repositories<\/li>\n<li>TreatmentBank<\/li>\n<li>Biodiversity Literature Repository<\/li>\n<li>Synospecies<\/li>\n<li>Ocellus<\/li>\n<\/ul>\n<p><strong>10.30-11.00 &#8211; Coffee break<\/strong><\/p>\n<p><strong>11.00-12.30 Module 4: Continuation<\/strong><\/p>\n<p>&nbsp;<\/p>\n<p><strong>12.30-13.30 &#8211; Lunch<\/strong><\/p>\n<p><strong>13.30-15.00 Module 5: Complementary re-use of data from publications<\/strong><\/p>\n<ul>\n<li>Biodiversity PMC: specific annotation to question and answering\n<ul>\n<li>Biodiversity front end user interfaces<\/li>\n<li>SIBiLS Collections<\/li>\n<li>SIBiLS back-end services<\/li>\n<li>SIBILS API &amp; Data access channels<\/li>\n<li>Curation-support tools<\/li>\n<li>Advanced triage systems<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><strong>15.00-15.30 &#8211; Coffee break<\/strong><\/p>\n<p><strong>15.30-17.00 Module 5: Continuation<\/strong><\/p>\n<ul>\n<li>GBIF: occurrences to taxonomic names\n<ul>\n<li>GBIF &#8211; hosted portals<\/li>\n<\/ul>\n<\/li>\n<li>ChecklistBank: integrating names in CoL<\/li>\n<\/ul>\n<h4><\/h4>\n<h4><strong>Trainers<\/strong><\/h4>\n<table width=\"590\">\n<tbody>\n<tr>\n<td width=\"169\">\u00a0\u00a0\u00a0<img loading=\"lazy\" class=\"size-medium wp-image-5831 aligncenter\" src=\"https:\/\/cetaf.org\/dest\/wp-content\/uploads\/2025\/07\/Laurence-Benichou.jpg\" alt=\"\" width=\"120\" height=\"126\" \/><\/td>\n<td width=\"421\"><strong>Laurence B\u00e9nichou<\/strong> (<a href=\"https:\/\/orcid.org\/0000-0002-0713-0751\">https:\/\/orcid.org\/0000-0002-0713-0751<\/a>) is a French publisher. She is the Head of the Paris Museum Science Press (MNHN), and \u00a0founded in 2011 the <em>European Journal of Taxonomy<\/em> with a board of European colleagues and serves now as the Liaison officer for the journal.<\/p>\n<p>Since 2018, she leads the E-Publishing working group of CETAF. An expert in the field of scientific publishing for the Ministry of French higher education and research, she specialized in Linnaean Taxonomy publishing, Communication Design and Media. Her research is focused on diamond open access, digital publishing and data mining.<\/td>\n<\/tr>\n<tr>\n<td width=\"169\"><\/td>\n<td width=\"421\"><strong>Chris Le Coquet<\/strong> (<a href=\"https:\/\/orcid.org\/0009-0006-7416-8983\">https:\/\/orcid.org\/0009-0006-7416-8983<\/a>) is a French publisher. He is a desk editor for the <em>European Journal of Taxonomy<\/em>, and is also in charge of digital projects focused on the FAIRisation of biodiversity data at the Paris Museum Science Press (MNHN).<\/td>\n<\/tr>\n<tr>\n<td width=\"169\"><img loading=\"lazy\" class=\"alignnone size-full wp-image-5828 aligncenter\" src=\"https:\/\/cetaf.org\/dest\/wp-content\/uploads\/2025\/07\/Donat-Agosti-.jpg\" alt=\"\" width=\"103\" height=\"130\" \/><\/td>\n<td width=\"421\"><strong>Donat Agosti<\/strong> (<a href=\"https:\/\/orcid.org\/0000-0001-9286-1200\">https:\/\/orcid.org\/0000-0001-9286-1200<\/a>) is a Swiss biologist with over 30 years of experience, focused on making biodiversity data openly accessible. He co-founded Plazi in 2008, a Swiss NGO that develops workflows to convert scientific literature into FAIR data. Through partnerships with institutions like GBIF, NIH, Zenodo, and Biodiversity PMC, Plazi\u2019s work enables the reuse of published data in global research infrastructures, with Plazi being the largest data contributor to Zenodo, GBIF and COL. He is also a widely published researcher in taxonomy and biodiversity informatics.<\/td>\n<\/tr>\n<tr>\n<td width=\"169\"><img loading=\"lazy\" class=\"size-medium wp-image-5830 aligncenter\" src=\"https:\/\/cetaf.org\/dest\/wp-content\/uploads\/2025\/07\/Julia-Giora.jpg\" alt=\"\" width=\"128\" height=\"131\" \/><\/td>\n<td width=\"421\"><strong>Julia Giora<\/strong> (<a href=\"https:\/\/orcid.org\/0009-0006-7416-8983\">https:\/\/orcid.org\/0009-0006-7416-8983<\/a>) is a Brazilian biologist with PhD and postdoctoral training in Animal Biology, with over 20 years of experience in research, higher education, and biodiversity data. Currently leading the Learning &amp; Engagement team at Plazi, working internationally with FAIR scientific data and training. Also active as a content developer for universities and Brazilian NGOs focused on biodiversity conservation. Author of more than 20 scientific publications, including peer-reviewed articles, books, and book chapters.<\/td>\n<\/tr>\n<tr>\n<td width=\"169\"><img loading=\"lazy\" class=\"size-medium wp-image-5829 aligncenter\" src=\"https:\/\/cetaf.org\/dest\/wp-content\/uploads\/2025\/07\/Emilie-Pasche.jpg\" alt=\"\" width=\"94\" height=\"123\" \/><\/td>\n<td width=\"421\"><strong>Emilie Pasche<\/strong> (<a href=\"https:\/\/orcid.org\/0000-0002-9118-5762\">https:\/\/orcid.org\/0000-0002-9118-5762<\/a>) is a research associate at HES-SO Geneva and SIB, and is involved in Biodiversity PMC.<\/td>\n<\/tr>\n<tr>\n<td width=\"169\"><img loading=\"lazy\" class=\"size-medium wp-image-5832 aligncenter\" src=\"https:\/\/cetaf.org\/dest\/wp-content\/uploads\/2025\/07\/Markus-Doring.jpg\" alt=\"\" width=\"132\" height=\"130\" \/><\/td>\n<td width=\"421\"><strong>Markus D\u00f6ring<\/strong> (<a href=\"https:\/\/orcid.org\/0000-0001-7757-1889\">https:\/\/orcid.org\/0000-0001-7757-1889<\/a>) is a German botanist and biodiversity informatician currently working for the Global Biodiversity Information Facility (GBIF) in Copenhagen, Denmark.<br \/>\nTrained originally as a botanist, Markus bridges the gap between taxonomy and data infrastructure. He has played a key role in developing the GBIF Backbone Taxonomy, ChecklistBank and the integrated publishing toolkit (IPT). He is the lead developer for the Catalogue of Life and has been engaged in Biodiversity Information Standards (TDWG) since 2001 with contributions to Darwin Core and TCS.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>&nbsp;<\/p>\n<p><strong>\u00a0<\/strong><\/p>\n<h4><strong>Dates of Training period<\/strong><\/h4>\n<p>One theoretical online session, plus two working days (October to November 2025) divided as follows:<\/p>\n<p><span style=\"text-decoration: underline;\">Online session<\/span><\/p>\n<p>Wednesday 15th of October 2025<\/p>\n<p><span style=\"text-decoration: underline;\">Face to face practical experience<\/span><\/p>\n<p>Monday 10th and Tuesday 11th of November 2025<\/p>\n<h4><\/h4>\n<h4><strong>Location<\/strong><\/h4>\n<p><a href=\"https:\/\/maps.app.goo.gl\/kU3Q7ri4gs6dmFGv9\" target=\"_blank\" rel=\"noopener\">Villa Engler \u2013 Freie Universit\u00e4t Berlin, Altensteinstr. 2, 14195 Berlin<\/a><\/p>\n<h4><\/h4>\n<h4><strong>Course\u2019s language<\/strong><\/h4>\n<p>English<\/p>\n<h4><\/h4>\n<h4><strong>Target audience<\/strong><\/h4>\n<p>Editors \/ Publishers \/ Librarians \/ Researchers \/ Students<\/p>\n<h4><\/h4>\n<h4><strong>Fee<\/strong><\/h4>\n<p>The school enrolment is free. All the other costs are at the expense of participants.<\/p>\n<h4><strong>Registration deadline<\/strong><\/h4>\n<p>Registration has closed on 30 September 2025<\/p>\n<h4><\/h4>\n<h4><strong>Mode of trainees\u2019 assessment <\/strong><\/h4>\n<ul>\n<li>A short quiz will be provided at the end of the theoretical introduction;<\/li>\n<li>Short exercises will be provided at the end of each practical module.<\/li>\n<\/ul>\n<h4><\/h4>\n<h4><strong>Participant quota (min and max number of trainees)<\/strong><\/h4>\n<p>10\u201320\u00a0 (1-2 groups)<\/p>\n<h4><\/h4>\n<h4><strong>Types of training\/ Implementation method<\/strong><\/h4>\n<ol>\n<li>Theoretical modules\/Online and in-person lectures<\/li>\n<li>Practical experience \/ face to face\n<ul>\n<li>Structuring and annotating biodiversity data. \/ Hands-on exercises using XML-first workflow and Golden Gate<\/li>\n<li>Exploring and reusing biodiversity data \/ Hands-on exercises using TreatmentBank, BLR, GBIF, BiodiversityPMC, etc.<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n<h4><\/h4>\n<h4><strong>Training Course<\/strong> <strong>learning outcomes<\/strong><\/h4>\n<p>The present course will cover a variety of topics from purely theoretical to the development of practical skills in the field of biodiversity data. The main expected outcomes are:<\/p>\n<ul>\n<li>Learn about the state of biodiversity literature and the move to liberate biodiversity data from publications<\/li>\n<li>Familiarise with the standards and workflows in biodiversity data<\/li>\n<li>Practice the structuration of biodiversity paper<\/li>\n<li>Practice the annotation of biodiversity data<\/li>\n<li>Learn how to efficiently access and reuse biodiversity data<\/li>\n<li>Practice data infrastructures such as TreatmentBank, GBIF and BiodiversityPMC<\/li>\n<li>First step to become a certified contributor to TreatmentBank<\/li>\n<\/ul>\n<h4><\/h4>\n<h4><strong>Certifications provided<\/strong><\/h4>\n<ol>\n<li>Certificate of Attendance by CETAF DEST with 5 ECVET Units (<em>European Credit system for Vocational Education and Training<\/em>)<\/li>\n<li>Certificate by CETAF DEST according to Europass Certificate Supplement (certifying analytically the knowledge, skills and competences gained)<\/li>\n<\/ol>\n<h4><\/h4>\n<h4><strong>What trainees need to bring<\/strong><\/h4>\n<ol>\n<li>Laptop (up-to-date OS)<\/li>\n<li>Microsoft Word<\/li>\n<li>Java ver. 23<\/li>\n<li>Libre Office ver. 7.6.5.2 (provided)<\/li>\n<li>XML Mind ver. 9.5.1 (provided)<\/li>\n<li>Golden Gate Imagine (provided)<\/li>\n<\/ol>\n<p>&nbsp;<\/p>\n<p><strong>Registration\u00a0<\/strong><\/p>\n<p>Registration has closed<\/p>\n<p><a href=\"https:\/\/www.cognitoforms.com\/CETAFDEST\/LiberationOfDataHowToLiberateDataFromPublicationsAndHowToReuseItEvaluationForm\" target=\"_blank\" rel=\"noopener\"><strong>Evaluation form<\/strong><\/a><\/p>\n<p><strong>More details: <\/strong><a href=\"mailto:dest@cetaf.org\">dest@cetaf.org<\/a><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Description This training session will offer participants a deep dive into the processes of annotating and sharing biodiversity data. 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