We submitted last year a proposal for the

This proposal was entitled "Exploiting and sharing existing and new knowledge in the frame of the Digital Botanical Gardens Initiative."

It aims to explore several aspects related to knowledge exploitation and sharing of small molecules and their occurrences.

The abstract was :

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, organized 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 (, 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 ( to the community. However, numerous biological occurrences of natural products are still lacking.

We would like to evaluate the BiCICKL Research Infrastructures to:

  • Improve past knowledge exploitation: extract pairs of chemical compound and taxon from literature not present in LOTUS and relevant to the DBGI (papers describing phytochemical investigation of plants of the Swiss Botanical Gardens, e.g.

  • Enhance future knowledge dissemination: explore publication solutions to efficiently disseminate knowledge acquired from metabolomics, that is, putative occurrences of chemical structures in biological matrices (simple RDF triples, Nanopublications ( or similar).


On the 20th February we received the good news that our proposal was accepted ! Which means we will get support (in the form of time, expertise and implementations from the BiCICKL team, no money) to advance this project.

First meeting

Today (Thursday 02 March 2023) we had a first meeting to launch this small project and discuss initial ideas.

The notes have been taken here

Also backed up there first-meeting


Started a discussion category at

  1. first-meeting
  2. nanopublication
  3. report