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Biodiversity Information Science and Standards :
Conference Abstract
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Emilie Pasche‡, Julien Gobeill‡, Donat Agosti§, Lyubomir Penev|,¶, Quentin Groom#, Teodor Georgiev¤, Esteban Gaillac‡, Alexandre Flament‡, Déborah Caucheteur‡, Pierre-André Michel‡, Patrick Ruch«|
Corresponding author: Patrick Ruch (patrick.ruch@sib.swiss)
Received: 25 Aug 2023 | Published: 28 Aug 2023
© 2023 Emilie Pasche, Julien Gobeill, Donat Agosti, Lyubomir Penev, Quentin Groom, Teodor Georgiev, Esteban Gaillac, Alexandre Flament, Déborah Caucheteur, Pierre-André Michel, Patrick Ruch
This is an open access article 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.
Citation:
Pasche E, Gobeill J, Agosti D, Penev L, Groom Q, Georgiev T, Gaillac E, Flament A, Caucheteur D, Michel P-A, Ruch P (2023) From SIBiLS to Biodiversity PMC: Foundations for the One Health Library. Biodiversity Information Science and Standards 7: e111660. https://doi.org/10.3897/biss.7.111660
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Abstract
One Health is an integrated, unifying approach that aims to sustainably balance and optimize the health of people, animals and ecosystems in compliance with the United Nations development goals (
Leveraging the Swiss Institute of Bioinformatics Literature Services (SIBiLS), which are already mirroring MEDLINE (30+ million abstracts) and PubMed Central contents (5+ million full-text articles) from the the United States National institutes of Health's National Library of Medicine, as well as biodiversity-specific contents (e.g., Plazi's treatments and non-PMC articles from Pensoft), we will deliver a unique entry point to broadly search biodiversity publications, the so-called "Biodiversity PMC".
We will demonstrate how the new resource can help answer a wide range of biodiversity questions. The demo will provides examples of users' information requests and how the new resource can help support biodiversity sciences. We will review the different search modalities of the new service: language-model powered Question-Answering; SPARQL endpoint; search in supplementary data files; exploration of biotic interactions (biotXplorer); and how these different modalities are connected to navigate accross the different services. The demo will follow a "Bring Your Own Questions" style and we encourage participants to identify a research question, as well as the corresponding factoid answers, and a traceable author statement as found in the literature (e.g., Where is Potamopyrgus antipodarum an invasive species? Answer: [Europe, North America]. Traceable author statement (source: Plazi TreatmentBank): "Native to New Zealand and its adjacent islands and invasive in North America and Europe (Winterbourn 1970; Kerans et al. 2005)."*
Keywords
information retrieval, literature services, text mining, life sciences, health sciences
Presenting author
Patrick Ruch
Presented at
TDWG 2023
Acknowledgements
This project receives funding from the European Union's Horizon 2020 Research and Innovation Action under grant agreement No 101007492 (BICIKL). We also would like to thank the ELIXIR Data Platform for the discussions about JATS.
Funding program
Swissuniversities Open science program
Hosting institution
SIB Swiss Institute of Bioinformatics
Author contributions
Patrick Ruch: project leader, technical and software support of "Biodiversity PMC"
Donat Agosti, Lyubomir Penev, Teodor Georgiev: designed the services and co-developed the harvesting channels.
Quentin Groom: design of services
Emilie Pasche, Julien Gobeill, Esteban Gaillac, Déborag Caucheteur, Alexandre Flament: co-designed and developed the services.
Conflicts of interest
References
- One Health as a catalyst for sustainable development.Nature Microbiology7:467‑468. https://doi.org/10.1038/s41564-022-01076-1