add proper relation names (choose specific labels, not just "relationto...". In what concrete relationship stands a Sample to a Study ? e.g. prefer meaningful intrinsic labels, e.g. use "takesPartIn" rather than "relates_to_study". The latter is just too general, almost tautologic and is infested with meta-terminology ('relates' is implicit in the fact that its an object property)
rectify namespace prefixes
What are the Squared boxes ?
Align Naming Conventions to a project-wide coherent set (Classes and relations all lowercase, underscore)
Considering the triple: SampleName relate_to_metabolite-ident Metabolite_identification
Is Metabolite_identification of datatype String or a class? Maybe reformulate: MoleculeSample proxy_for identified_molecule ?
Adjust the metabolights graph and upload the .ttl ontology to github.