Program

Agenda Wednesday 12 July 2023

Starting at 9:30

• Physical at Pavillon Vert. See here for location details https://www.unifr.ch/scimed/fr/pavillonvert
• Remote at https://meet.jit.si/DBGI_talks

Welcome and workshop members’ introduction (15 min)

EMI and DBGI presentation + overview of current chemodiversity description approaches (45 min)

The objective here will be to understand what are the main ways to characterize chemodiversity from complex biological matrices (at least the ones used in EMI). This overview will recap which objects are handled in natural products research and computational mass spec and how they are generated. This recap should allow us to start on the same page when working on the semantic model.

Coffee break

Define the main purposes of the Earth Metabolome semantic model (15 min)

- What do we have in hands ? Review of the current ENPKG model https://enpkg.commons-lab.org/doc/index.html and Fig S1 in https://doi.org/10.26434/chemrxiv-2023-sljbt

Eg.: structure existing data, Swiss Botanical Garden use case

Review: ontology engineering activities (rest of the morning)

• Organism taxonomy
• Natural Product Taxonomy (with SKOS - NPClassifier)
• MS2 spectrum and LCMS analysis

Lunch (12:30?)

Review: ontology engineering activities (afternoon)

• Spectrum annotation
• Chemical structure representation
• Coffee break (10 min)
• Laboratory object description
• Metadata for provenance (e.g, Prov-O)
• Links / cross-references ? To which resources?

See Supporting Sustainability of Chemistry by Linking Research Data with Physically Preserved Research Materials Maybe would it also worth having a look at metadata ressources such as the CEDAR workbench.

Final remarks and next steps

Notes over there Notes