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Elementary Multiperspective Material Ontology (EMMO)
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V1.0.0-beta5: Chemistry - Improved Modelling of Molecules and Chemical Reactions ? #248

Open markdoerr opened 1 year ago

markdoerr commented 1 year ago

Dear EMMO developers,

a while ago there existed a "Chemistry" branch (which I do not find anymore). Since v1.0.0.-beta5 made some good progress in consistency of the overall modelling I am wondering, what your plans are regarding chemical entities, like molecules, polymers, mixtures and reactions ?

To my impression, the modelling of Molecules could be improved: if one tries to build a SPARQL query, that asks (with 1.0.0-beta5), if a Molecule consists of Atoms, one might not get a simple answer, the same seems true for Hetero- / Homonuclear Molecules. Bulk properties, like Molecular Mass (in its various definitions, also capturing isotopic compositions) and Density as well as chemical composition are also not easy derivable with SPARQL queries of the current version.

Is it planned to add at least some very basic terms describing chemical reactions ? You could consider adding some "glue terms" in the main EMMO ontolgoy and build a EMMO-chemistry sub-ontology (module).

Thanks :)

jesper-friis commented 1 year ago

The chemistry module should still be included in 1.0.0-beta5. You can find in in disciplines/chemistry.ttl.

It is one of the modules that we want to update. It needs more discussions, but I think that a basic description of chemical reactions would be a natural thing to cover in this module. For now I will suggest that you take a look at the electrochemistry domain ontology (https://github.com/emmo-repo/domain-electrochemistry).

markdoerr commented 1 year ago

Thanks, Jesper, I am glad, that it still exists (I think, it was not loaded in protegee by default). I will have a look.

markdoerr commented 8 months ago

Hi @jesper-friis and @emanueleghedini , I am currently inspecting the latest branch: 1.0.0-final-dev-branch, but I do not see an import of the above mentioned chemistry ontology module to the main EMMO. Will the chemistry part kept separately ? If yes, shouldn't there be at least a well defined "anchor" in EMMO ?

In the main EMMO there is currently no notion of a chemical reaction / process. How should it be possible to describe the (chemical) origin of a material with the "EM Material Ontology" ? ;)

jesper-friis commented 8 months ago

Hi @jesper-friis , I am currently inspecting the latest branch: 1.0.0-final-dev-branch, but I do not see an import of the above mentioned chemistry ontology module to the main EMMO. Will the chemistry part kept separately ? If yes, shouldn't there be at least a well defined "anchor" in EMMO ?

The emmo.ttl file in the root directory imports disciplines, which in turn should import the chemistry module. Are you sure you don't get it?

In the main EMMO there is currently no notion of a chemical reaction / process. How should it be possible to describe the (chemical) origin of a material with the "EM Material Ontology" ? ;)

Chemical reactions are currently described in the electrochemistry domain ontology: https://github.com/emmo-repo/domain-electrochemistry

In the future, some key concepts, like chemical reactions, may be moved into EMMO core.