From taxonomic literature to cybertaxonomic content

Miller, Jeremy A.; Dikow, Torsten; Agosti, Donat; Sautter, Guido; Catapano, Terry; Penev, Lyubomir; Zhang, Zhi‐Qiang; Pentcheff, N. Dean; Pyle, Richard L.; Blum, Stan; Parr, Cynthia; Freeland, Chris; Garnett, Tom; Ford, Linda; Muller, Burgert S.; Smith, Leo F.; Strader, Ginger; Georgiev, Teodor; Bénichou, Laurence

doi:10.1186/1741-7007-10-87

Cited by 30 publications

(23 citation statements)

References 13 publications

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“…Aggregated global biodiversity data is an increasingly powerful resource supporting research, conservation, policy, and public bioliteracy ( Hardisty et al 2013 , Arzberger et al 2004 ). Along with databases devoted to specimen collections and observation records, literature is an integral part of the biodiversity informatics ecosystem ( Miller et al 2012 , Penev et al 2012 , Penev et al 2011a , Penev et al 2011b ). Pensoft journals pioneered the routine distribution of primary specimen data from publications to a collection of online resources, including the Global Biodiversity Information Facility (GBIF) and the Encyclopedia of Life (EOL) ( Penev et al 2009 , Penev et al 2008 , Penev et al 2010 , Smith et al 2013 , Chavan and Penev 2011 , Penev et al 2012 , Faulwetter et al 2014 ).…”

Section: Main Textmentioning

confidence: 99%

Corrected data re-harvested: curating literature in the era of networked biodiversity informatics

Miller¹,

Georgiev²,

Stoev³

et al. 2015

BDJ

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Section: Main Textmentioning

confidence: 99%

Corrected data re-harvested: curating literature in the era of networked biodiversity informatics

Miller¹,

Georgiev²,

Stoev³

et al. 2015

BDJ

Self Cite

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“…Open access publishing models promoted by publishers like Pensoft will revolutionize publishing (Miller et al 2012), but there remains a large amount of literature still in copyright and mostly available online as PDFs behind subscription services or individually available by download from the publisher for a set price per article.…”

Section: Hard Copy To Digital: Flora Neotropica Monographsmentioning

confidence: 99%

Hard Copy to Digital: Flora Neotropica and the World Flora Online

Thomas

Tulig

2015

Rodriguésia

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One of the greatest challenges in achieving the goals of the World Flora Online (WFO) will be to make available the huge amount of botanical information that is not yet available digitally. The New York Botanical Garden is using the Flora Neotropica monograph series as a model for digitization. We describe our efforts at digitizing Flora Neotropica monographs and why digitization of hardcopy descriptions must be a priority for the WFO project. Key words: Electronic monographs, open access, Flora Neotropica, monographs. ResumoUm dos maiores desafios para alcançar as metas do projeto World Flora Online (WFO), será a disponibilizar a enorme quantidade de informações botânicas que ainda não estão disponíveis digitalmente. O New York Botanical Garden está utilizando a série de monografias da Flora Neotropica como um modelo para a digitalização. Nós aqui descrevemos nossos esforços na digitalização das monografias da Flora Neotropica e porque a digitalização das descrições impressas deve ser uma prioridade para o projeto WFO. Palavras-chave:Monografias eletrônicas, open access, Flora Neotropica, monografias.Rodriguésia 66(4): 983-987. 2015

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“…Because of their contribution to revisions, monographs, descriptions, and other primary taxonomic literature, these specimen records are among the highest quality biodiversity data available ( Meier and Dikow 2004 , Dikow et al 2009 ). In an age when we have the tools to effectively manage and analyze large quantities of data, and also when environmental changes call for data-driven decision-making, digitization, structuring and extraction of content from taxonomic literature is needed to provide a more comprehensive supply of information and an historical perspective to current societal issues involving the biosphere ( Miller et al 2012 , Penev et al 2011 , Penev et al 2010 ). For these data to be effective, they must be in a structured digital form that can be aggregated and universally queried.…”

Section: Introductionmentioning

confidence: 99%

Integrating and visualizing primary data from prospective and legacy taxonomic literature

Miller¹,

Agosti²,

Penev³

et al. 2015

BDJ

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Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions.

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From taxonomic literature to cybertaxonomic content

Cited by 30 publications

References 13 publications

Corrected data re-harvested: curating literature in the era of networked biodiversity informatics

Corrected data re-harvested: curating literature in the era of networked biodiversity informatics

Hard Copy to Digital: Flora Neotropica and the World Flora Online

Integrating and visualizing primary data from prospective and legacy taxonomic literature

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