Workflow and Current Achievements of BIOfid, an Information Service Mobilizing Biodiversity Data from Literature Sources

Driller, Christine; Koch, Markus; Schmidt, Marco; Weiland, Claus; Hörnschemeyer, Thomas; Hickler, Thomas; Abrami, Giuseppe; Ahmed, Sajawel; Gleim, Rüdiger; Hemati, Wahed; Uslu, Tolga; Mehler, Alexander; Pachzelt, Adrian; Rexhepi, Jashar; Risse, Thomas; Schuster, Janina; Kasperek, Gerwin; Hausinger, Angela

doi:10.3897/biss.2.25876

Cited by 2 publications

(2 citation statements)

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“…Data mobilization is the focus of several efforts in biodiversity informatics, since it became evident that data stored in the form of journal articles need to be extracted, organized in line with appropriate standards, and aggregated into online databases. Some recent examples in this direction are the BIOfid information service ( Driller et al 2018 ), the PLAZI workflow ( Agosti et al 2019 ), and the Open Biodiversity Knowledge Management System ( OBKMS ) initiative ( Penev et al 2018 ). For the creation of “FlorItaly”, a collaborative effort was initiated between Project “Dryades” of the University of Trieste ( Nimis et al 2003 ), and the leading authors of the two checklists, in order to make their data accessible online as an actual information system capable of complex queries, and as a “core” for aggregating, and linking further data and resources.…”

Section: Discussionmentioning

confidence: 99%

FlorItaly – the portal to the Flora of Italy

Martellos¹,

Bartolucci²,

Conti³

et al. 2020

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Digital data concerning the flora of Italy are largely fragmented among different resources hosted on different platforms, and often with different data standards, which are neither connected by a common access point, nor by web services, thus constituting a relevant obstacle to data access and usage. Taxonomic incongruences add a further complication. This paper describes “FlorItaly”, an online information system which allows to access and query updated information on the checklist of the flora of Italy, aiming at becoming an aggregator for Italian botanical resources. “FlorItaly” was developed in a collaborative effort by more than 50 taxonomists, with the support of the Italian Botanical Society, and of Project “Dryades” (University of Trieste), to provide a better and reliable organization of botanical knowledge in Italy, as well as a relevant simplification for data retrieval, and a further stimulus towards a more collaborative approach in botanical research.

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Section: Discussionmentioning

confidence: 99%

FlorItaly – the portal to the Flora of Italy

Martellos¹,

Bartolucci²,

Conti³

et al. 2020

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“…TextAnnotator 27 , provided by the specialised information service BIOfid 28 , is focused on information extraction about taxon names of vascular plants, birds, moths and butterflies, location and time mentioned in German texts (Driller et al, 2018;Driller et al, 2020). This could be extended to other environments, languages and taxonomic groups with the BIOfid Github page 29 serving as the starting point.…”

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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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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Workflow and Current Achievements of BIOfid, an Information Service Mobilizing Biodiversity Data from Literature Sources

Cited by 2 publications

References 0 publications

FlorItaly – the portal to the Flora of Italy

FlorItaly – the portal to the Flora of Italy

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

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