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

Just because I'm lazy, what are the matching git repo folders/files? So
that I can send you the correct patches / pull request?

Egon


On Tue, Jun 18, 2019 at 5:24 PM Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
wrote:

> Hi
>
> I think some of the confusion here is coming from differences between the
> proposed type
> https://bioschemas.org/types/ChemicalSubstance/
> And the profile
> https://bioschemas.org/specifications/drafts/ChemicalSubstance/
>
> Alasdair
>
> On 18 Jun 2019, at 14:51, Egon Willighagen <egon.willighagen@gmail.com>
> wrote:
>
>
> 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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> ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286>
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>
>
> --
> Alasdair J G Gray
> Associate Professor in Computer Science,
> School of Mathematical and Computer Sciences
> Heriot-Watt University, Edinburgh, UK.
>
> Email: A.J.G.Gray@hw.ac.uk <A.J.G.Gray@hw.ac.uk>
> Web: http://www.macs.hw.ac.uk/~ajg33
> ORCID: http://orcid.org/0000-0002-5711-4872
> Office: Earl Mountbatten Building 1.39
> Twitter: @gray_alasdair
>
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>
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-- 
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
<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