{"refrec":{"BRefID":359571,"RR":"<b>Agosti, D.; Bénichou, L.; Addink, W.; Arvanitidis, C.; Catapano, T.; Cochrane, G.; Dillen, M.; Döring, M.; Georgiev, T.; Gérard, I.; Groom, Q.; Kishor, P.; Kroh, A.; Kvacek, J.; Mergen, P.; Mietchen, D.; Pauperio, J.; Sautter, G.; Penev, L.</b> (2022). Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing. <i>Research Ideas and Outcomes 8</i>: e97374. <a href=\"https://dx.doi.org/10.3897/rio.8.e97374\" target=\"_blank\">https://dx.doi.org/10.3897/rio.8.e97374</a>","BEntID":357286,"PublicFlag":1,"CheckedFlag":0,"wosflag":0,"vabbflag":0,"RefStringPartII":". <i>Research Ideas and Outcomes 8</i>: e97374. <a href=\"https://dx.doi.org/10.3897/rio.8.e97374\" target=\"_blank\">https://dx.doi.org/10.3897/rio.8.e97374</a>","DocTypID":8,"DocType":"Journal article","MarineFlag":0,"FreshFlag":0,"BrackishFlag":0,"TerrestrialFlag":0,"Authorstring":"Agosti, D.; Bénichou, L.; Addink, W.; Arvanitidis, C.; Catapano, T.; Cochrane, G.; Dillen, M.; Döring, M.; Georgiev, T.; Gérard, I.; Groom, Q.; Kishor, P.; Kroh, A.; Kvacek, J.; Mergen, P.; Mietchen, D.; Pauperio, J.; Sautter, G.; Penev, L.","OrigTitleTranslFlag":0,"Authorstringtrunc":"Agosti, D. <i>et al.</i>","Englishabstract":"The paper summarises many years of discussions and experience of biodiversity publishers, organisations, research projects and individual researchers, and proposes recommendations for implementation of persistent identifiers for article metadata, structural elements (sections, subsections, figures, tables, references, supplementary materials and others) and data specific to biodiversity (taxonomic treatments, treatment citations, taxon names, material citations, gene sequences, specimens, scientific collections) in taxonomy and biodiversity publishing. The paper proposes best practices on how identifiers should be used in the different cases and on how they can be minted, cited, and expressed in the backend article XML to facilitate conversion to and further re-use of the article content as FAIR data. The paper also discusses several specific routes for post-publication re-use of semantically enhanced content through large biodiversity data aggregators such as the Global Biodiversity Information Facility (GBIF), the International Nucleotide Sequence Database Collaboration (INSDC) and others, and proposes specifications of both identifiers and XML tags to be used for that purpose. A summary table provides an account and overview of the recommendations. The guidelines are supported with examples from the existing publishing practices.","AbstractOtherLang":null,"BibLvlCode":"AS","StandardTitle":"Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing","OrigTitleLangCode":"en","OrigTitleLangCodeExtended":"eng","OrigTitleLangID":15,"DateLastModified":{"date":"2025-11-29 01:32:34.280960","timezone_type":1,"timezone":"+01:00"},"UserAccessRight":null,"UserAccID":null,"AuthorKeywords":"semantic publishing, taxonomy publishing, semantic annotation, persistent identifiers, treatments, XML, JATS, TaxPub","OtherDescriptors":null,"Notes":null,"AnaPub":2022,"MonPub":null,"DateUpdate":"2022-12-05","DateCreate":"2022-12-01","SecASFANote":null,"ConfID":null,"PeerRev":1,"VlizCoreFlag":1,"WoScode":null,"VABBcode":null,"OpenAcc":1,"DOI":"10.3897/rio.8.e97374"},"refs":null,"anarec":{"AnaID":359571,"PubliDate":2022,"Pagination":"e97374","XtraPublOfAnaID":null,"ISBN":null,"Volume":"8","Issue":null,"BRefMon":null,"BRefMonRR":null,"BRefXtra":null,"BRefXtraRR":null,"SerBRefID":259920,"SerRR":"Research Ideas and Outcomes. Pensoft Publishers: Sofia.  e-ISSN 2367-7163","StandardTitleSer":"Research Ideas and Outcomes","ISSN":null,"AbbrevSer":null,"StandardTitleMon":null,"StartPage":null,"Pages":null,"ToPubliDate":null,"BRefBibLvlCode":"S","SerNotes":null},"monrec":null,"serrec":null,"relations":null,"relationsRev":null,"addrec":null,"othpubs":null,"ownerships":null,"authors":[{"AutName":"Agosti","Firstname":"Donat","Initials":"D.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":234155,"OrderNr":1,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Bénichou","Firstname":"Laurence","Initials":"L.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":147593,"OrderNr":2,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Addink","Firstname":"Wouter","Initials":"W.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":289767,"OrderNr":3,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Arvanitidis","Firstname":"Christos","Initials":"C.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":21729,"OrderNr":4,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":4765,"InsID":null},{"AutName":"Catapano","Firstname":"Terence","Initials":"T.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":510340,"OrderNr":5,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Cochrane","Firstname":"Guy","Initials":"G.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":84064,"OrderNr":6,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Dillen","Firstname":"Mathias","Initials":"M.","Affiliation":"Meise Botanic Garden","Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":510342,"OrderNr":7,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":"Vlaamse overheid; Beleidsdomein Economie, Wetenschap en Innovatie; Plantentuin Meise","ORCID":"0000-0002-3973-1252","PersID":37962,"InsID":146},{"AutName":"Döring","Firstname":"Markus","Initials":"M.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":209559,"OrderNr":8,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Georgiev","Firstname":"Teodor","Initials":"T.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":124958,"OrderNr":9,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Gérard","Firstname":"Isabelle","Initials":"I.","Affiliation":"Royal Museum for Central Africa, Tervuren","Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":147595,"OrderNr":10,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"KMMA","InsFSN":"Koninklijk Museum voor Midden Afrika","ORCID":null,"PersID":27676,"InsID":1489},{"AutName":"Groom","Firstname":"Quentin","Initials":"Q.","Affiliation":"Meise Botanic Garden","Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":400682,"OrderNr":11,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":"Vlaamse overheid; Beleidsdomein Economie, Wetenschap en Innovatie; Plantentuin Meise","ORCID":"0000-0002-0596-5376","PersID":34113,"InsID":146},{"AutName":"Kishor","Firstname":"Puneet","Initials":"P.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":510347,"OrderNr":12,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Kroh","Firstname":"Andreas","Initials":"A.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":154228,"OrderNr":13,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":"0000-0002-8566-8848","PersID":19332,"InsID":null},{"AutName":"Kvacek","Firstname":"Jiri","Initials":"J.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":280168,"OrderNr":14,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Mergen","Firstname":"Patricia","Initials":"P.","Affiliation":"Royal Museum for Central Africa","Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":210959,"OrderNr":15,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":"KMMA","InsFSN":"Koninklijk Museum voor Midden Afrika","ORCID":"0000-0003-2848-8231","PersID":8764,"InsID":1489},{"AutName":"Mietchen","Firstname":"Daniel","Initials":"D.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":510351,"OrderNr":16,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Pauperio","Firstname":"Joana","Initials":"J.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":510352,"OrderNr":17,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Sautter","Firstname":"Guido","Initials":"G.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":234164,"OrderNr":18,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null},{"AutName":"Penev","Firstname":"Lyubomir","Initials":"L.","Affiliation":null,"Discriminator":null,"CorporateFlag":0,"BEntID":357286,"AutID":124956,"OrderNr":19,"DegrID":null,"EditorFlag":0,"CorrespFlag":0,"IllustratorFlag":0,"ReviserFlag":0,"TranslatorFlag":0,"InsAcronym":null,"InsFSN":null,"ORCID":null,"PersID":null,"InsID":null}],"mapdetails":null,"datasets":null,"monographs":null,"monparts":null,"serparts":null,"BEntOpen":null,"BEntPrivate":null,"availability":[{"BInstID":385235,"LibID":36,"BRefID":359571,"EmbargoDate":null,"FullEmbargoDate":null,"PhysMedID":16,"hasOCRd":1,"ShelfLocCode":"385235","RFID":null,"PaidValue":null,"Medium":"Server","Description":"VLIZ Open Access","Acronym":"VLIZ","Library":"Vlaams Instituut voor de Zee","DutchTerm":"Open access","URL":null,"ClassifID":53,"Classification":"Open access","ReqLink":null,"ClassifTypID":1,"URLLocation":"https://www.vliz.be/imisdocs/publications/","SubDir":null,"InternalReq":0,"LoggedInReq":0,"Disclaimer":null,"DutchDisclaimer":null,"FileFormat":".pdf","FileDescr":"pdf","InsPub":1,"InsID":36,"FileFormID":6,"LendableFlag":1,"PublicFlag":1,"orderLib":"A","Notes":null,"AccConID":null,"AccessConstraint":null,"LicURL":null}],"litstyles":null,"thespers":null,"arch2discl":null,"SERpubls":[{"PublName":"Pensoft Publishers","City":"Sofia"}],"MONpubls":null,"pictures":[],"thestermsPath":[{"ThesaurusTerm":"Biodiversity","ThestID":9471,"Acronym":"ASFA","ThesTermPath":"Biodiversity"},{"ThesaurusTerm":"Sequences","ThestID":84934,"Acronym":"CSA","ThesTermPath":"Sequences"},{"ThesaurusTerm":"Specimens","ThestID":77998,"Acronym":"CSA","ThesTermPath":"Specimens"},{"ThesaurusTerm":"Tagging","ThestID":8341,"Acronym":"ASFA","ThesTermPath":"Tagging"},{"ThesaurusTerm":"Taxa","ThestID":8371,"Acronym":"ASFA","ThesTermPath":"Taxa"}],"thestermsASFA":[{"ThesaurusTerm":"Biodiversity"},{"ThesaurusTerm":"Sequences"},{"ThesaurusTerm":"Specimens"},{"ThesaurusTerm":"Tagging"},{"ThesaurusTerm":"Taxa"}],"taxtermsASFA":null,"geotermsASFA":null,"collections":[{"Collection":"VLIZ Acknowledged Publications","ShortName":"VLIZ ackn"}],"conf":null,"proj":null,"Physdatasets":null,"spcols":{"923":{"SpName":"Lifewatch acknowledged","SpColID":923,"ParSpColID":null,"TopParID":null,"ShortName":"Lifewatch ackn","URLLocation":null,"LibID":36,"OpenRepoFlag":null,"SpTypID":null,"TopParIDNotWebsite":null,"SpColPath":"Lifewatch ackn"},"941":{"SpName":"LifeWatch Species Information Backbone","SpColID":941,"ParSpColID":39,"TopParID":39,"ShortName":"LifeWatch Species Information Backbone","URLLocation":null,"LibID":36,"OpenRepoFlag":null,"SpTypID":null,"TopParIDNotWebsite":39,"SpColPath":"VLIZ ackn/LifeWatch Species Information Backbone"},"39":{"SpName":"VLIZ Acknowledged Publications","SpColID":39,"ParSpColID":null,"TopParID":null,"ShortName":"VLIZ ackn","URLLocation":null,"LibID":36,"OpenRepoFlag":null,"SpTypID":null,"TopParIDNotWebsite":null,"SpColPath":"VLIZ ackn"},"507":{"SpName":"World Register of Marine Species","SpColID":507,"ParSpColID":null,"TopParID":null,"ShortName":"WoRMS website","URLLocation":null,"LibID":null,"OpenRepoFlag":null,"SpTypID":null,"TopParIDNotWebsite":null,"SpColPath":"WoRMS website"},"915":{"SpName":"World Register of Marine Species (WoRMS) acknowledged","SpColID":915,"ParSpColID":941,"TopParID":39,"ShortName":"WoRMS ackn","URLLocation":null,"LibID":36,"OpenRepoFlag":null,"SpTypID":null,"TopParIDNotWebsite":39,"SpColPath":"VLIZ ackn/LifeWatch Species Information Backbone/WoRMS ackn"},"947":{"SpName":"WoRMS ackn - direct reference","SpColID":947,"ParSpColID":915,"TopParID":39,"ShortName":"WoRMS ackn - direct","URLLocation":null,"LibID":36,"OpenRepoFlag":null,"SpTypID":null,"TopParIDNotWebsite":39,"SpColPath":"VLIZ ackn/LifeWatch Species Information Backbone/WoRMS ackn/WoRMS ackn - direct"}},"doi":null,"publs":null,"serparttypes":null,"monauthors":null,"MParts":null,"SParts":null,"hLibs":null,"langs":[{"BEntID":357286,"AbstractFlag":0,"LangID":15,"LangCode":"en","Lang":"English","DutchTerm":"Engels","LangCodeExtended":"eng"},{"BEntID":357286,"AbstractFlag":1,"LangID":15,"LangCode":"en","Lang":"English","DutchTerm":"Engels","LangCodeExtended":"eng"}],"urls":[{"URL":"https://dx.doi.org/10.3897/rio.8.e97374","externalID":"10.3897/rio.8.e97374","URLTypeCode":"DOI","URLID":108344,"URLTypID":13,"URLType":"DOI","URLPrefix":"http://dx.doi.org/"}],"thesterms":[{"ThesaurusTerm":"Biodiversity","ThestID":9471,"Acronym":"ASFA","ThesTypID":1,"ThesType":"ASFA Thesaurus List"},{"ThesaurusTerm":"Sequences","ThestID":84934,"Acronym":"CSA","ThesTypID":2,"ThesType":"CSA Technology Research Database Master Thesaurus"},{"ThesaurusTerm":"Specimens","ThestID":77998,"Acronym":"CSA","ThesTypID":2,"ThesType":"CSA Technology Research Database Master Thesaurus"},{"ThesaurusTerm":"Tagging","ThestID":8341,"Acronym":"ASFA","ThesTypID":1,"ThesType":"ASFA Thesaurus List"},{"ThesaurusTerm":"Taxa","ThestID":8371,"Acronym":"ASFA","ThesTypID":1,"ThesType":"ASFA Thesaurus List"}],"taxterms":null,"geoterms":null,"othterms":null,"asfacodes":null,"asfa2codes":null,"thestermsFRIS":[{"ThesaurusTerm":"Biodiversity","DutchTerm":"Biodiversiteit","ThestID":9471,"Acronym":"ASFA","ThesTypID":1,"ThesType":"ASFA Thesaurus List"},{"ThesaurusTerm":"Sequences","DutchTerm":null,"ThestID":84934,"Acronym":"CSA","ThesTypID":2,"ThesType":"CSA Technology Research Database Master Thesaurus"},{"ThesaurusTerm":"Specimens","DutchTerm":null,"ThestID":77998,"Acronym":"CSA","ThesTypID":2,"ThesType":"CSA Technology Research Database Master Thesaurus"},{"ThesaurusTerm":"Tagging","DutchTerm":"Labellen","ThestID":8341,"Acronym":"ASFA","ThesTypID":1,"ThesType":"ASFA Thesaurus List"},{"ThesaurusTerm":"Taxa","DutchTerm":null,"ThestID":8371,"Acronym":"ASFA","ThesTypID":1,"ThesType":"ASFA Thesaurus List"}],"taxtermsFRIS":null,"geotermsFRIS":null,"othtermsFRIS":null,"resmessage":"","complete":1,"sessions":{"newSesName":"Chisala, Chilekwa, C.","newSesDate":{"date":"2022-12-01 10:59:16.800000","timezone_type":3,"timezone":"Europe/Brussels"},"updSesName":"Chisala, Chilekwa, C.","updSesDate":{"date":"2022-12-05 10:38:26.790000","timezone_type":3,"timezone":"Europe/Brussels"}}}
