Digital accessible knowledge: Mobilizing legacy data and the future of taxonomic publishing

Fawcett, Susan; Agosti, Donat; Cole, Selina R.; Wright, David F.

doi:10.18061/bssb.v1i1.8296

Cited by 7 publications

(4 citation statements)

References 24 publications

(30 reference statements)

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“…construction of citation networks or/and the development of relevant citation metrics (Nielsen et al 2017). These practices often require substantial effort to not only discover the bibliographic reference implicit in authorship of a taxon (Fawcett et al 2022), but also to get a copy of the cited publication (Page 2016).…”

Section: What Is the Problem?mentioning

confidence: 99%

Joint statement on best practices for the citation of authorities of scientific names in taxonomy by CETAF, SPNHC and BHL

Bénichou¹,

Buschbom²,

Campbell³

et al. 2022

RIO

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This joint statement aims at encouraging all authors, publishers and editors involved in scientific publishing to give the bibliographic source of the authorities of taxonomic names. This initiative, written by members of the three communities, has been approved by the executive boards of the SPNHC (Society for the Preservation of Natural History Collections), CETAF (Consortium of European Taxonomic Facilities) and BHL (Biodiversity Heritage Library).

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Section: What Is the Problem?mentioning

confidence: 99%

Joint statement on best practices for the citation of authorities of scientific names in taxonomy by CETAF, SPNHC and BHL

Bénichou¹,

Buschbom²,

Campbell³

et al. 2022

RIO

Self Cite

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“…The rise of deep neural networks is promising as well in all different tasks of Information Extraction, as seen in TaxoNERD (Le Guillarme and Thuiller, 2022). Lastly, the community is pushing to Semantic Publishing, FAIR completeness of new data and new taxonomic publishing guidelines to eliminate the need of text mining and curation in current publications (Penev et al, 2019;Fawcett et al, 2022).…”

Section: Future Outlookmentioning

confidence: 99%

Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow

et al. 2022

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Historical biodiversity documents comprise an important link to the long-term data life cycle and provide useful insights on several aspects of biodiversity research and management. However, because of their historical context, they present specific challenges, primarily time- and effort-consuming in data curation. The data rescue process requires a multidisciplinary effort involving four tasks: (a) Document digitisation (b) Transcription, which involves text recognition and correction, and (c) Information Extraction, which is performed using text mining tools and involves the entity identification, their normalisation and their co-mentions in text. Finally, the extracted data go through (d) Publication to a data repository in a standardised format. Each of these tasks requires a dedicated multistep methodology with standards and procedures. During the past 8 years, Information Extraction (IE) tools have undergone remarkable advances, which created a landscape of various tools with distinct capabilities specific to biodiversity data. These tools recognise entities in text such as taxon names, localities, phenotypic traits and thus automate, accelerate and facilitate the curation process. Furthermore, they assist the normalisation and mapping of entities to specific identifiers. This work focuses on the IE step (c) from the marine historical biodiversity data perspective. It orchestrates IE tools and provides the curators with a unified view of the methodology; as a result the documentation of the strengths, limitations and dependencies of several tools was drafted. Additionally, the classification of tools into Graphical User Interface (web and standalone) applications and Command Line Interface ones enables the data curators to select the most suitable tool for their needs, according to their specific features. In addition, the high volume of already digitised marine documents that await curation is amassed and a demonstration of the methodology, with a new scalable, extendable and containerised tool, “DECO” (bioDivErsity data Curation programming wOrkflow) is presented. DECO’s usage will provide a solid basis for future curation initiatives and an augmented degree of reliability towards high value data products that allow for the connection between the past and the present, in marine biodiversity research.

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“…At the same time, the taxonomic work that underpins specimen identification remains chronically undervalued ( Zeppelini et al 2021 ; Gorneau et al 2022 ; although see Costello et al 2013 ). To preserve taxonomic knowledge, efforts could be made to invest in taxonomy courses (e.g., Smithsonian Training in Tropical Taxonomy), grants that fund curation and systematics (e.g., Paleontological Society Arthur James Boucot Research Grants), and taxonomy databases ( Costello et al 2013 ; Fawcett et al 2022 ; Grenié et al 2023 ). Investments in systematics might, in turn, encourage stronger connections between genus- and species-level analyses when studying biodiversity through time.…”

Section: Introductionmentioning

confidence: 99%

Challenges and directions in analytical paleobiology

Dillon

Dunne

Womack³

et al. 2023

Paleobiology

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Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite—or even spurred by—this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.

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Digital accessible knowledge: Mobilizing legacy data and the future of taxonomic publishing

Abstract: No abstract available.

Cited by 7 publications

References 24 publications

Joint statement on best practices for the citation of authorities of scientific names in taxonomy by CETAF, SPNHC and BHL

Joint statement on best practices for the citation of authorities of scientific names in taxonomy by CETAF, SPNHC and BHL

Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow

Challenges and directions in analytical paleobiology

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