BiodiversityPMC: The One Health Library (Poster)

Conference: 2024 Conference Health, a common good
Location: Geneva, Switzerland
Date and Time:
Session: Health and Environment

Time: all day Presenters: Emilie Pasche, Julien Gobeill, Donat Agosti, Lyubomir Penev, Quentin Groom, Teodor Georgiev, Esteban Gaillac, Alexandre Flament, Déborah Caucheteur, Pierre-André Michel, Marie Kolsch, Anaïs Mottaz, Patrick Ruch

One Health is a comprehensive and unified approach that recognises the close connection between the health of people, animals and whole ecosystems. While life and health sciences are widely represented in digital libraries such as PubMed Central, articles focussing on biodiversity, ecology or environmental sciences are relatively marginal. Addressing this critical gap, we introduce a novel Research Infrastructure named “BiodiversityPMC”, leveraging the Swiss Institute of Bioinformatics Literature Services (SIBiLS), which are already mirroring MEDLINE (over 36 million abstracts), PubMed Central contents (over 6 million full-text articles) and supplementary data files associated to scientific publications (over 6 million supplementary files including OCRized images and tables). The coverage of SIBiLS is expanded to encompass a broader range of biodiversity-related content, including environmental sciences and ecology. This involves indexing half a million taxonomic treatments and articles harvested from Plazi, and a growing set of full-text articles from journals in the field (e.g., Pensoft, European Journal of Taxonomy), which are not included into the original PubMed Central. To ensure comprehensive and standardized access, the contents are normalized using a large collection of life sciences terminologies and ontologies. Each instance of a term (or its synonym) is assigned a unique accession number, to support a semantically richer search experience. Of particular interest for the biodiversity communities, SIBiLS contents are normalized using ENVO (Environmental Ontology), ROBI (Relation Ontology Biotic Interactions), an enriched subset of RO (Relation Ontology), and LOTUS, a natural products database. Further, taxonomic names are normalized using both the NCBI Taxonomy and the Open Tree of Life, which include names from the Catalogue of Life. The resulting data graph contains more than 10 billion normalized descriptors. Access to BiodiversityPMC is facilitated through a new graphic user interface, an OpenAPI and a SPARQL endpoint. BiodiversityPMC not only offers traditional search methods (access via keyword search), but also introduces innovative approaches for navigating the complex landscape of health and environmental sciences. An original question-answering interface can help provide new perspectives over the literature. BidoversityPMC stands out as a valuable resource proficient in addressing a wide spectrum of questions related to biodiversity in the broad sense.