Improving Taxonomic Name Finding in the Biodiversity Heritage Library

Richard, Joel M.

doi:10.3897/biss.4.58482

Cited by 2 publications

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“…It offers an API and can be installed locally. GNA is also used by the BHL platform to locate taxonomic names within the pages of its collections (Richard, 2020).…”

Section: Named Entity Recognitionmentioning

confidence: 99%

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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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“…It offers an API and can be installed locally. GNA is also used by the BHL platform to locate taxonomic names within the pages of its collections (Richard, 2020).…”

Section: Named Entity Recognitionmentioning

confidence: 99%

“…Taxonfinder 32 is a web application for the extraction of scientific names mentioned in web pages. It features an API that was used in BHL for large scale annotations of taxonomic names until 2019, when it was replaced by GNfinder (Richard, 2020).…”

Section: Named Entity Recognitionmentioning

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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#RetroPIDs: The missing link to the foundation of biodiversity knowledge

Kearney¹,

Funkhouser²,

Lichtenberg³

et al. 2021

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The Biodiversity Heritage Library (BHL) will soon upload its 60 millionth page of open access biodiversity literature onto the BHL website and the BHL's Internet Archive Collection. The BHL’s massive repository of free knowledge includes content that is available nowhere else online, as well as accessible versions of content that are locked behind paywalls elsewhere. If we are to continue to expand our understanding of life on Earth, we must ensure that the foundation of biodiversity knowledge provided by BHL is discoverable by the tools we rely on to navigate the ever-expanding internet. These tools – search engines and their algorithms – preferentially deliver (and rank) content with good metadata and persistent identifiers (PIDs). In modern online publishing, PID assignment and linking happens at the point of publication: DOIs (Digital Object Identifiers) for publications, ORCIDs (Open Researcher and Contributor IDs) for people, and RORs (Research Organization Registry IDs) for organisations. The DOI system provided by Crossref (the DOI registration agency for scholarly content) delivers reciprocal citations, enabling convenient clicking from article to article, and citation tracking, enabling authors and institutions to track the impact and reach of their research output. Publications that lack PIDs, which include the vast majority of legacy literature, are hard to find and sit outside the linked network of scholarly research. This makes it nearly impossible to determine whether they are being cited, let alone viewed, mentioned, shared or liked. At TDWG 2020, Page 2020, Kearney 2020, Richard 2020 (and 2019, Page 2019b, Page 2019a, Kearney 2019b, Kearney 2019a and 2018, Kearney 2018), we emphasised the need to bring the historic biodiversity literature into the modern linked network of scholarly research. In October 2020, BHL launched a new working group to do exactly this. The BHL Persistent Identifier Working Group (Team #RetroPID) brings together expertise from across BHL’s global community. Over the past year, we have worked tirelessly to make it easier to find, cite, link, share and track the content on BHL, adding article-level metadata to journals and retrospectively assigning DOIs (#RetroPIDs). Most importantly, we have developed the tools and documentation that will enable the entire BHL community to take contributed content from “just” accessible to persistently discoverable. This paper will detail our efforts to retrofit the historic literature (a square peg) into the modern PID system (a round hole) and will present both the achievements and the challenges of this important work.

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Improving Taxonomic Name Finding in the Biodiversity Heritage Library

Cited by 2 publications

References 0 publications

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

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

#RetroPIDs: The missing link to the foundation of biodiversity knowledge

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