Giving metabolites (and lipids) a chemical and biological context with open science

Talk given at the fourth Nordic Metabolomics Conference in Turku in August 2024.

Abstract: 

A metabolite or lipid in vacuum is nice to look at, but when it comes into contact with other chemicals, things become interesting. However, finding and accessing knowledge about single chemicals is already not trivial, let alone that of multiple interacting chemicals. Maybe it was possible 100 years ago to know everything in your field, we now need to bridge many domains and many resources. This talk will sketch the roles open science is playing in giving metabolites and lipids their needed chemical and biological context. It will cover open source cheminformatics for linking metabolite and lipid databases (SMILES, InChI, CXSMILES), open standards for interoperability of knowledge (semantic web), open data to support metabolite and lipid identification (Wikidata and linked data), and linking knowledge via publications to their original research. Furthermore, it will explore mechanisms to describe the interactions these chemicals have in open biological pathway databases (WikiPathways).