EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases

Faulwetter, Sarah; Pafilis, Evangelos; Fanini, Lucia; Bailly, Nicolas; Agosti, Donat; Arvanitidis, Christos; Boicenco, Laura; Capatano, Terry; Claus, S.; Dekeyzer, Stefanie; Georgiev, Teodor; Legaki, Aglaia; Mavraki, Dimitra; Oulas, Anastasis; Papastefanou, Gabriella; Penev, Lyubomir; Sautter, Guido; Schigel, Dmitry; Senderov, Viktor; Teacă, Adrian; Tsompanou, Marilena

doi:10.3897/rio.2.e9774

Cited by 4 publications

(5 citation statements)

References 18 publications

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“…This is particularly the case for occurrence data, as globally researchers have yet to adopt the routine deposition of species occurrences in OBIS as a cultural norm, in the way that genetic sequence data is deposited in GenBank. To this end, improving incentives for researchers to add their data to global repositories in an important goal [25], while data archaeology and rescue initiatives can help to ensure that historical data are captured [68]. Equally, it remains vital that ongoing survey schemes are properly valued [69], even as novel exploration is planned.…”

Section: Discussionmentioning

confidence: 99%

Linking dimensions of data on global marine animal diversity

Webb

Vanhoorne

2020

Phil. Trans. R. Soc. B

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Recent decades have seen an explosion in the amount of data available on all aspects of biodiversity, which has led to data-driven approaches to understand how and why diversity varies in time and space. Global repositories facilitate access to various classes of species-level data including biogeography, genetics and conservation status, which are in turn required to study different dimensions of diversity. Ensuring that these different data sources are interoperable is a challenge as we aim to create synthetic data products to monitor the state of the world's biodiversity. One way to approach this is to link data of different classes, and to inventory the availability of data across multiple sources. Here, we use a comprehensive list of more than 200 000 marine animal species, and quantify the availability of data on geographical occurrences, genetic sequences, conservation assessments and DNA barcodes across all phyla and broad functional groups. This reveals a very uneven picture: 44% of species are represented by no record other than their taxonomy, but some species are rich in data. Although these data-rich species are concentrated into a few taxonomic and functional groups, especially vertebrates, data are spread widely across marine animals, with members of all 32 phyla represented in at least one database. By highlighting gaps in current knowledge, our census of marine diversity data helps to prioritize future data collection activities, as well as emphasizing the importance of ongoing sustained observations and archiving of existing data into global repositories. This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.

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Section: Discussionmentioning

confidence: 99%

Linking dimensions of data on global marine animal diversity

Webb

Vanhoorne

2020

Phil. Trans. R. Soc. B

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“…Historical biodiversity documents (also known as legacy, ancient or simply old documents) comprise literature from 1000 AD until 1960 and therefore are stored in an analogue and/ or obsolete format (Lotze and Worm, 2009;Beja et al, 2022). These old documents can be found in institutional libraries, publications, books, expedition logbooks, project reports, newspapers (Faulwetter et al, 2016;Mavraki et al, 2016;Kwok, 2017) or other types of legacy formats (e.g. stored in floppy disks, microfilms or CDs).…”

Section: Introductionmentioning

confidence: 99%

“…The third task is named Information Extraction (IE) as it involves the steps of named entity recognition, mapping and normalisation of biodiversity information (Thessen et al, 2012). Here, the curators may compile a species' occurrence census enriched with metadata of the study, geolocation, environment, sampling methods and traits among others (Faulwetter et al, 2016). Lastly, the fourth task, is the data publishing to online biodiversity databases/repositories (Costello et al, 2013;Penev et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…Several factors may turn the curation of historical documents into a serious challenge (Faulwetter et al, 2016;Beja et al, 2022). Errors from the first and second tasks, as presented in Figure 1 (i.e.…”

Section: Introductionmentioning

confidence: 99%

“…Some of the aforementioned issues are presented in Figure 2. Because of these limitations, the manual curation of data and metadata is mandatory when it comes to historical data (Faulwetter et al, 2016).7…”

Section: Introductionmentioning

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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A 21st Century Vision for Neotropical Snake Systematics

Pyron¹

2018

Rev Latin Herp

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We live in an unprecedented age for systematics and biodiversity studies. Ongoing global change is leading to a future with reduced species richness and ecosystem function (Pereira, Navarro, & Martins, 2012). Yet, we know more about biodiversity now than at any time in the past. For squamates in particular, we have range maps for all species (Roll et al., 2017), phylogenies containing estimates for all species (Tonini, Beard, Ferreira, Jetz, & Pyron, 2016), and myriad ecological and natural-history datasets for a large percentage of species (Meiri et al., 2013; Mesquita et al., 2016). For neotropical snakes, a recent synthesis of museum specimens and verified localities offers a fine-grained perspective on their ecogeographic distribution in Central and South America, and the Caribbean (Guedes et al., 2018).

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EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases

Cited by 4 publications

References 18 publications

Linking dimensions of data on global marine animal diversity

Linking dimensions of data on global marine animal diversity

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

A 21st Century Vision for Neotropical Snake Systematics

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