{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T11:12:19Z","timestamp":1774437139115,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,11,13]],"date-time":"2020-11-13T00:00:00Z","timestamp":1605225600000},"content-version":"vor","delay-in-days":317,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002749","name":"Belgian Federal Science Policy Office","doi-asserted-by":"publisher","award":["BR\/165\/A1\/TrIAS"],"award-info":[{"award-number":["BR\/165\/A1\/TrIAS"]}],"id":[{"id":"10.13039\/501100002749","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Species checklists are a crucial source of information for research and policy. Unfortunately, many traditional species checklists vary wildly in their content, format, availability and maintenance. The fact that these are not open, findable, accessible, interoperable and reusable (FAIR) severely hampers fast and efficient information flow to policy and decision-making that are required to tackle the current biodiversity crisis. Here, we propose a reproducible, semi-automated workflow to transform traditional checklist data into a FAIR and open species registry. We showcase our workflow by applying it to the publication of the Manual of Alien Plants, a species checklist specifically developed for the Tracking Invasive Alien Species (TrIAS) project. Our approach combines source data management, reproducible data transformation to Darwin Core using R, version control, data documentation and publication to the Global Biodiversity Information Facility (GBIF). This checklist publication workflow is openly available for data holders and applicable to species registries varying in thematic, taxonomic or geographical scope and could serve as an important tool to open up research and strengthen environmental decision-making.<\/jats:p>","DOI":"10.1093\/database\/baaa084","type":"journal-article","created":{"date-parts":[[2020,9,8]],"date-time":"2020-09-08T19:10:59Z","timestamp":1599592259000},"source":"Crossref","is-referenced-by-count":29,"title":["A checklist recipe: making species data open and FAIR"],"prefix":"10.1093","volume":"2020","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7484-9267","authenticated-orcid":false,"given":"Lien","family":"Reyserhove","sequence":"first","affiliation":[{"name":"Research Institute for Nature and Forest (INBO), Havenlaan, B-1000 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Desmet","sequence":"additional","affiliation":[{"name":"Research Institute for Nature and Forest (INBO), Havenlaan, B-1000 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damiano","family":"Oldoni","sequence":"additional","affiliation":[{"name":"Research Institute for Nature and Forest (INBO), Havenlaan, B-1000 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tim","family":"Adriaens","sequence":"additional","affiliation":[{"name":"Research Institute for Nature and Forest (INBO), Havenlaan, B-1000 Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Diederik","family":"Strubbe","sequence":"additional","affiliation":[{"name":"Terrestrial Ecology Unit, Ghent University, Karel Lodewijk Ledeganckstraat, 35, B-9000 Ghent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy J S","family":"Davis","sequence":"additional","affiliation":[{"name":"Terrestrial Ecology Unit, Ghent University, Karel Lodewijk Ledeganckstraat, 35, B-9000 Ghent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sonia","family":"Vanderhoeven","sequence":"additional","affiliation":[{"name":"Belgian Biodiversity Platform, WTC III, Boulevard Simon Bolivar 30, Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Filip","family":"Verloove","sequence":"additional","affiliation":[{"name":"Meise Botanic Garden, Nieuwelaan 38, B-1860 Meise, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0596-5376","authenticated-orcid":false,"given":"Quentin","family":"Groom","sequence":"additional","affiliation":[{"name":"Meise Botanic Garden, Nieuwelaan 38, B-1860 Meise, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,11,11]]},"reference":[{"key":"2020120621045777600_R1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1002295","article-title":"Public data archiving in ecology and evolution: how well are we doing?","volume":"13","author":"Roche","year":"2015","journal-title":"PLoS Biol."},{"key":"2020120621045777600_R2","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.ecoinf.2015.06.010","article-title":"Ecological data sharing","volume":"29","author":"Michener","year":"2015","journal-title":"Ecol. Inform."},{"key":"2020120621045777600_R3","article-title":"The methodological assessment report on scenarios and models of biodiversity and ecosystem services. Secretariat of the intergovernmental science-policy platform on biodiversity and ecosystem services","author":"Ferrier","year":"2016"},{"key":"2020120621045777600_R4","doi-asserted-by":"crossref","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"2020120621045777600_R5","doi-asserted-by":"crossref","first-page":"361","DOI":"10.3233\/ISU-170846","article-title":"Open science \u2013 towards reproducible research","volume":"37","author":"Jomier","year":"2017","journal-title":"Inf. Serv. Use"},{"key":"2020120621045777600_R6","doi-asserted-by":"crossref","first-page":"49","DOI":"10.3233\/ISU-170824","article-title":"Cloudy, increasingly FAIR; revisiting the FAIR data guiding principles for the European open science cloud","volume":"37","author":"Mons","year":"2017","journal-title":"Inf. Serv. Use"},{"key":"2020120621045777600_R7","volume-title":"A Guide to Reproducible Code in Ecology and Evolution","author":"BES","year":"2017"},{"key":"2020120621045777600_R8","volume-title":"Secretariat of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services","author":"IPBES","year":"2016","edition":"(eds)"},{"key":"2020120621045777600_R9","article-title":"The IUCN red list of threatened species","author":"IUCN","year":"2020"},{"key":"2020120621045777600_R10","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14435","article-title":"No saturation in the accumulation of alien species worldwide","volume":"8","author":"Seebens","year":"2017","journal-title":"Nat. Commun."},{"key":"2020120621045777600_R11","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0029715","article-title":"Darwin Core: an evolving community-developed biodiversity data standard","volume":"7","author":"Wieczorek","year":"2012","journal-title":"PLoS One"},{"key":"2020120621045777600_R12","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0102623","article-title":"The GBIF Integrated Publishing Toolkit: facilitating the efficient publishing of biodiversity data on the internet","volume":"9","author":"Robertson","year":"2014","journal-title":"PLoS One"},{"key":"2020120621045777600_R13","doi-asserted-by":"crossref","first-page":"119","DOI":"10.3391\/mbi.2015.6.2.02","article-title":"The importance of open data for invasive alien species research, policy and management","volume":"6","author":"Groom","year":"2015","journal-title":"Manag. Biol. Invasions"},{"key":"2020120621045777600_R14","doi-asserted-by":"crossref","DOI":"10.1038\/sdata.2017.202","article-title":"Introducing the global register of introduced and invasive species","volume":"5","author":"Pagad","year":"2018","journal-title":"Sci. Data"},{"key":"2020120621045777600_R15","volume-title":"Global Biodiversity Facility","author":"Remsen","year":"2010"},{"key":"2020120621045777600_R16","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1038\/nbt.3780","article-title":"Reproducibility of computational workflows is automated using continuous analysis","volume":"35","author":"Beaulieu-Jones","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"2020120621045777600_R17","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1093\/comjnl\/27.2.97","article-title":"Literate Programming","volume":"27","author":"Knuth","year":"1984","journal-title":"Comput. J."},{"key":"2020120621045777600_R18","volume-title":"Manual of the Alien Plants of Belgium","author":"Verloove","year":"2020"},{"key":"2020120621045777600_R19","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v059.i10","article-title":"Tidy data","volume":"14","author":"Wickham","year":"2014","journal-title":"Am. Stat."},{"key":"2020120621045777600_R20","volume-title":"R for Data Science: import, Tidy, Transform, Visualize, and Model Data","author":"Wickham","year":"2017"},{"key":"2020120621045777600_R21","article-title":"World Geographical Scheme for Recording Plant Distributions. Biodiversity Information Standards (TDWG) (eds.)","author":"Brummitt","year":"2001"},{"key":"2020120621045777600_R22","volume-title":"(2020) R Markdown: the Definitive Guide","author":"Xie","year":"2020"},{"key":"2020120621045777600_R23","article-title":"GBIF Metadata Profile: how-to guide. Global biodiversity information facility, Copenhagen","author":"GBIF","year":"2011"},{"key":"2020120621045777600_R24","doi-asserted-by":"publisher","DOI":"10.15468\/39omei","volume-title":"GBIF Backbone Taxonomy. Checklist dataset","author":"GBIF Secretariat","year":"2020"},{"key":"2020120621045777600_R25","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004668","article-title":"A quick introduction to version control with Git and GitHub","volume":"12","author":"Blischak","year":"2016","journal-title":"PLoS Comput. Biol."},{"key":"2020120621045777600_R26","doi-asserted-by":"crossref","DOI":"10.3897\/rio.3.e13414","article-title":"Tracking invasive alien species (TrIAS): building a data-driven framework to inform policy","volume":"3","author":"Vanderhoeven","year":"2017","journal-title":"Res. Ideas Outcomes"},{"key":"2020120621045777600_R27","article-title":"Pathways of introduction of invasive species, their prioritization and management. UNEP\/CBD\/SBSTTA\/18\/9\/Add.1","author":"CBD","year":"2014"},{"key":"2020120621045777600_R28","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/j.tree.2011.03.023","article-title":"A proposed unified framework for biological invasions","volume":"26","author":"Blackburn","year":"2011","journal-title":"Trends Ecol. Evol."},{"key":"2020120621045777600_R29","article-title":"Improving Darwin Core for research and management of alien species","volume":"3","author":"Groom","year":"2019","journal-title":"Biodivers. Inf. Sci. Stand."},{"key":"2020120621045777600_R30","article-title":"TDWG vocabulary maintenance specification. Biodiversity Information Standards (TDWG)","author":"Baskauf","year":"2017"},{"key":"2020120621045777600_R31","article-title":"Checklist recipe: a template for reproducible standardization of species checklist data","author":"Reyserhove","year":"2018"},{"key":"2020120621045777600_R32","volume-title":"Handbook of Alien Species in Europe. Handbook of Alien Species in Europe","author":"DAISIE","year":"2009"},{"key":"2020120621045777600_R33","doi-asserted-by":"crossref","first-page":"235","DOI":"10.3391\/bir.2012.1.4.01","article-title":"Building the European alien species information network (EASIN): a novel approach for the exploration of distributed alien species data","volume":"1","author":"Katsanevakis","year":"2012","journal-title":"BioInvasions Rec."},{"key":"2020120621045777600_R34","doi-asserted-by":"crossref","DOI":"10.3391\/mbi.2015.6.2.05","article-title":"European alien species information network (EASIN): supporting European policies and scientific research","volume":"6","author":"Katsanevakis","year":"2015","journal-title":"Manag. Biol. Invasions"},{"key":"2020120621045777600_R35","volume-title":"Invasive alien species. Pathway Analysis and horizon scanning for countries in Northern Europe","author":"NOBANIS","year":"2015"},{"key":"2020120621045777600_R36","doi-asserted-by":"crossref","first-page":"429","DOI":"10.32582\/aa.58.3.4","article-title":"Setting-up a billboard of marine invasive species in the ESENIAS area: current situation and future expectancies","volume":"58","author":"Karachle","year":"2017","journal-title":"Acta Adriat."},{"key":"2020120621045777600_R37","first-page":"261","article-title":"The Esenias countries\u2019 marine alien species experts: an updated inventory","author":"Karachle","year":"2017","journal-title":"Acta Zool. Bulg."},{"key":"2020120621045777600_R38","article-title":"DAISIE - Inventory of alien invasive species in Europe","volume-title":"Version 1.6. Checklist dataset. DAISIE - Inventory of alien invasive species in Europe. Version 1.6. Checklist dataset (2019)","author":"Roy","year":"2019"},{"key":"2020120621045777600_R39","article-title":"Global register of introduced and invasive species - Belgium","volume":"1","author":"Desmet","year":"2019","journal-title":"Checklist Dataset. Version"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaa084\/34283832\/baaa084.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaa084\/34283832\/baaa084.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,7]],"date-time":"2020-12-07T04:15:20Z","timestamp":1607314520000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaa084\/5979745"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,1]]},"references-count":39,"URL":"https:\/\/doi.org\/10.1093\/database\/baaa084","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020]]},"published":{"date-parts":[[2020,1,1]]},"article-number":"baaa084"}}