Pierre-Marie Allard, University of Fribourg, Switzerland
Patrick Ruch, SIB
SIBiLS, Plazi, EBI (ChEBI), CERN (BLR, Zenodo), OpenBioDiv
NCBI (PubChem), Wikimedia foundation (Wikidata), Nanodash (Nanopublications)
Fig.1. Improving the exploitation of publicly available past knowledge and building news forms of knowledge dissemination for natural products research.
We are currently launching the Digital Botanical Gardens Initiative (DBGI) with the ambition to explore innovative solutions for the acquisition, management and sharing of digital information acquired on living botanical collections. A particular focus is placed on the large-scale characterization of the chemodiversity of living plant collections through mass spectrometry. The acquired data will be structured, organised and connected with relevant metadata through semantic web technology. After validation and application in wild ecosystems, the gathered knowledge will inform ecosystem functioning research and orient biodiversity conservation projects.
One central aspect of the DBGI thus resides in the acquisition of high quality information on the digitised chemodiversity which in turns rely essentially in efficient metabolite annotation. For this we employ a taxonomically informed metabolite annotation process (https://doi.org/10.3389/fpls.2019.01329), which we have shown to systematically improve the performance of state-of-the computational metabolite annotation solutions. A requirement for this process is to access comprehensive ressources documenting the biological occurrence of small molecules. For this we recently opened the LOTUS ressource (https://elifesciences.org/articles/70780) to the community. However, numerous biological occurrences of natural products are still lacking.
We would like to evaluate the BiCICKL Research Infrastructures to:
Through the combined expertise of SIBILS, ARPHA, Plazi, BLR, GBIF and OpenBioDiv we expect to achieve the following outcomes.
For the “Improve past knowledge exploitation” part:
For the “Enhance future knowledge dissemination” part: