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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>

> 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.


Hi, do you like citation networks? Already 51% of all citations are
available <https://i4oc.org/> available for innovative new uses
<https://twitter.com/hashtag/acs2ioc>. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
the RSC and many others already did <https://i4oc.org/#publishers>.

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/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
ImpactStory: https://impactstory.org/u/egonwillighagen
Received on Tuesday, 18 June 2019 13:52:10 UTC

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