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Biodiversity PMC

SPARQL Endpoint

The SIBiLS SPARQL endpoint allows to run SPARQL queries on a subset of annotated PMC publications. The textual content and structure (title, sections, paragraphs, etc.) is described as well as a list of named entities (multidimensional concepts) found and located in the full text of the publications. The ontology used to describe the publications can be found here. The triple store contains a sample of 3000 publications at the moment. The content of the triple store will be extended in the future and include alternate publication sources as well.


The biotic interactions browser searches the literature to identify pairs of species that could have a biotic relationship. Each identified interaction is accompanied by one or several relevant passages extracted from the scientific literature. With this tool, users can discover new biotic interactions and understand how they are established.


Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive task, which includes searching the literature for a large set of variants. The lack of universally adopted standard nomenclature for variants requires the development of variant-specific literature search engines. We develop a system to perform triage of publications relevant to support an evidence-based decision. Together with providing a ranked list of articles for a given variant, the system is also able to prioritize variants, as found in a Variant Calling Format, assuming that the clinical actionability of a genetic variant is correlated with the volume of literature published about the variant. Our system searches within four pre-annotated document collections: MEDLINE abstracts, PubMed Central full-text articles, supplementary materials associated with publications, and clinical trials. A variant synonym generator is used to increase the comprehensiveness of the set of retrieved documents. We then apply different strategies to rank the publications.