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

From: Jerven Bolleman <jerven.bolleman@sib.swiss>
Date: Mon, 17 Jun 2019 10:18:34 +0200
To: public-bioschemas@w3.org
Message-ID: <76efc1be-3458-16a8-90f6-abcd6701cbc5@sib.swiss>
Hi Egon, All,

Could the ChemicalSubstance then have a definition which is not  a 
repeat of it's name. Also its unique properties refer in it's text
to molecular entity not to the ChemicalSubstance.

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*.

potentialUse
Intended use of the *molecular* entity by humans.
(Whom else could use it ?)

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.

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?

Regards,
Jerven

On 6/16/19 8:02 AM, Egon Willighagen wrote:
> 
> On 2019-06-14 12:36, Jerven Tjalling Bolleman wrote:
>  > Regarding the request for comments. I would like to see a bit of
>  > an  explanation what the difference is between a MolecularEntity
>  > and a ChemicalSubstance.
> 
> This distinction loosely follows the ChEBI ontology:
> 
> MolecularEntity: Any constitutionally or isotopically distinct atom, 
> molecule, ion, ion pair, radical, radical ion, complex, conformer etc., 
> identifiable as a separately distinguishable entity.
> 
> ChemicalSubstance: A chemical substance is a portion of matter of 
> constant composition, composed of molecular entities of the same type or 
> of different types.
> 
> The need to distinguish this surfaces in various situations. Crystal 
> structures, for example, are not molecular entities, and protein crystal 
> structures normally indeed composed of different types of molecular 
> entities.
> 
>  > Specifically for ChemicalSubstance I would like to see a description
>  > on how it relates to the existing schema.org <http://schema.org> 
> Substance.
> 
> The schema.org <http://schema.org> Substance is a good example of a 
> chemical substance: it is a medical entity that contains an active 
> ingredient and additional stuff that makes up a pill, like filling 
> materials, etc.
> 
> I'm tempted to say that the schema.org <http://schema.org> Substance is 
> a subclass of the ChemicalSubstance.
> 
> Another example of chemical substances are nanomaterials, which contains 
> of a mixture of related molecular entities (but more or less different 
> size, composition, etc) and sometimes with impurities.
> 
> Egon
> 
> -- 
> Hi, do you like citation networks? Already 51% of all citations are 
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> <https://twitter.com/hashtag/acs2ioc>. Join me in asking the American 
> Chemical Society to join the Initiative for Open Citations too 
> <https://www.change.org/p/asking-the-american-chemical-society-to-join-the-initiative-for-open-citations>. SpringerNature, 
> 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 Monday, 17 June 2019 08:19:08 UTC

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