Abstract
The fields of taxonomy and biodiversity research have witnessed an exponential growth in published literature. This vast corpus of articles holds information on the diverse biological traits of organisms and their ecologies. However, access to and extraction of relevant data from this extensive resource remain challenging. Advances in text and data mining (TDM) and Natural Language Processing (NLP) techniques offer new opportunities for liberating such information from the literature. Testing and using such approaches to annotate articles in machine actionable formats is therefore necessary to enable the exploitation of existing knowledge in new biology, ecology, and evolution research. Here we explore the potential of these methods to annotate and extract organismal and ecological trait data for the most diverse animal group on Earth, the arthropods. The article processing workflow uses manually curated trait dictionaries with trained NLP models to perform labelling of entities and relationships of thousands of articles. A subset of manually annotated documents facilitated the formal evaluation of the performance of the workflow in terms of entity recognition and normalisation, and relationship extraction, highlighting several important technical challenges. The results are made available to the scientific community through an interactive web tool and queryable resource, the ArTraDB Arthropod Trait Database. These methodological explorations provide a framework that could be extended beyond the arthropods, where TDM and NLP approaches applied to the taxonomy and biodiversity literature will greatly facilitate data synthesis studies and literature reviews, the identification of knowledge gaps and biases, as well as the data-informed investigation of ecological and evolutionary trends and patterns.
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ARPHA Preprints
https://doi.org/10.3897/arphapreprints.e153174 (18 Mar 2025)
https://doi.org/10.3897/arphapreprints.e153174 (18 Mar 2025)
Published in: Biodiversity Data Journal https://doi.org/10.3897/BDJ.13.e153070
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ARPHA Preprints
doi:
10.3897/arphapreprints.e153174
First posted
18 Mar 2025
Authors
Dalle Molle Institute for Artificial Intelligence Research (IDSIA USI-SUPSI), Lugano, Switzerland
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
Dalle Molle Institute for Artificial Intelligence Research (IDSIA USI-SUPSI), Lugano, Switzerland
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
Plazi, Bern, Switzerland
Digital Society Initiative, University of Zurich, Zurich, Switzerland
Dalle Molle Institute for Artificial Intelligence Research (IDSIA USI-SUPSI), Lugano, Switzerland
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
Robert M Waterhouse
- Corresponding author
Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
Conflict of interest
The authors have declared that no competing interests exist.
Disclaimer: This article is (co-)authored by any of the Editors-in-Chief, Managing Editors or their deputies in this journal.
Supporting agencies
SNF - Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
This is an open access preprint distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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