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Re: What is the difference between a ChemicalSubstance and a MolecularEntity?

From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Tue, 18 Jun 2019 15:51:36 +0200
Message-ID: <CAMPqvY_Xsdi0AR4bK=mBYQkV5V-ZG6cQZTJ0WUYZMU-3ZvQHwQ@mail.gmail.com>
To: Jerven Bolleman <jerven.bolleman@sib.swiss>
Cc: public-bioschemas@w3.org
Hi Jerven,

On Mon, Jun 17, 2019 at 10:19 AM Jerven Bolleman <jerven.bolleman@sib.swiss>
wrote:

> Could the ChemicalSubstance then have a definition which is not  a
> repeat of it's name.


The current description is "a portion of matter of constant composition,
composed of molecular entities of the same type or of different types" [0].
What do you see and where?

0. https://bioschemas.org/specifications/drafts/ChemicalSubstance/


> Also its unique properties refer in it's text to molecular entity not to
> the ChemicalSubstance.
>

Good call!

bioChemInteraction should indeed read: "Interaction of the biochemical
entity with other BioChemical entities".

And others similar. I will discuss fixing that with Alasdair.


> chemicalRole
> A role played by the *molecular* entity within a chemical context.
>
> molecularFormula
> The empirical formula is the simplest whole number ratio of all the
> atoms in a *molecule*.
>

Yes, that is wrong. I've proposed chemicalComposition, with the description
"The chemical composition describes the identity and relative ratio of the
chemical elements that make up the substance."


> potentialUse
> Intended use of the *molecular* entity by humans.

(Whom else could use it ?)
>

Animals? More seriously, I think the point


> Perhaps, because during development they have been moved from one to the
> other (These properties also exist in MolecularEntity). In any case not
> quite consistent.
>

Yes, and agreed. Thanks for catching it.


> Regarding the naming of the MolecularEntity is there a specific reason
> why it is called Molecular and not Chemical? Is this because the root
> class is BioChemEntity and BioChemEntity -> ChemicalEntity would be weird?
>

Because the idea was to use that type really for connected, fairly
well-defined entities, "molecules". ChemicalEntity would be a lot more
things, like you or me.

Egon

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-----
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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Received on Tuesday, 18 June 2019 13:52:10 UTC

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