Pierre-Marie Allard, Patrick Ruch, Donat Agosti, Alexandre Flament, Adriano Rutz


NB: The project is using an OpenNotebook Science (

Project description


  • project presentation,
  • Todo
  • [...]
  • The Digital Botanical Gardens Initiative
  • From earth metabolome to botanic species
  • Mass spec is used to characterize fingerprints with localization
  • All exposed with a RDF endpoints
  • LOTUS provides the link between (natural) small molecules and their occurrence
  • All data in LOTUS is also in Wikidata
  • Global Metabolome Initiative

Challenge: Create a link between the treatments in TB, the material citation and the small molecules

Gap: some knowledge is still found only in PDF, here comes the TNA project !

Possible extension of the first tasks: A possible extension would be to move towards nano-publications

Key: the level of evidence (silver level of evidence → Evidence and Code Ontology ECO) for the inferred statements is relatively weak as it uses mass spectrometry

annotate articles in SIBiLS using an extended SIBiLS ontology

how to share the extracted knowledge: -talking nonopubs

get a list of journals (the most important ones) -Phytochemistry -Journal of Natural Products

small molecule names Who is providing the the list? Are there tools to recognize molecule names are tools available to discover names based on figure in the article?

1st step. Get the articles to find out what molecule classes are present in an article 2nd step.

get a get a vocabulary that includes all the methods, such as also HMBC


PDF contents Annotation types New relationships Extend the SiBiLS ontology with small molecules possible? how to type the relation ship molecule - organism; eaten by, tested on, living in, from where do we get the dictionnary of small molecules: source could be pubchem can the provenance of users be monitored to give him project related access

Ex: of wd LOTUS entry ​​

Links: SIBiLS ontology: SPARQL endpoint: Example of SPARQL queries:

Example journals:

PubChem RDF for compounds dictionary:

To Do:

  • PM & Adriano provide a list of the articles
  • PM & Adriano provide ca 20 articles where the elements are highlighted that need to be extracted
  • DA get Journal of Natural Products and Phytochemistry articles
  • DA talk to GS/CN to scrape
  • PM & Adriano defines the annotation schema: molecules, taxon, predicate, methods, specimen, organs (PO), habitats/location
  • PM & Adriano provides a list of vocabularies/ontologies for each entities
  • PM & Adriano provide annotated articles
  • PR/AF check how to hide access to closed access into SIBiLS

Next meeting / recurring meeting March 16, 2023, 2 - 3 pm