Re: What is the difference between a ChemicalSubstance and a MolecularEntity? from Gray, Alasdair J G on 2019-06-18 (public-bioschemas@w3.org from June 2019)

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Tue, 18 Jun 2019 17:05:35 +0000
To: Egon Willighagen <egon.willighagen@gmail.com>
CC: Jerven Bolleman <jerven.bolleman@sib.swiss>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <FAADFB4C-F7ED-4A47-841F-50D53E10901E@hw.ac.uk>

Hi Egon

The development is complex.

The types are developed in the schemaorg repository. The release version are on the Bioschemas-release-1 branch. We then have to manually copy and paste the changes from there to the _types directory in the bioschemas.github.io<http://bioschemas.github.io> repository.

Profiles are developed in the respective gSheet and then the GOWeb tool is used to generate the YAML that is then embedded in the corresponding page in the _devSpecs directory.

Alasdair

On 18 Jun 2019, at 16:31, Egon Willighagen <egon.willighagen@gmail.com<mailto:egon.willighagen@gmail.com>> wrote:

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<mailto: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<mailto:egon.willighagen@gmail.com>> wrote:

Hi Jerven,

On Mon, Jun 17, 2019 at 10:19 AM Jerven Bolleman <jerven.bolleman@sib.swiss<mailto: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/)
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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<mailto:A.J.G.Gray@hw.ac.uk>
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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<mailto:A.J.G.Gray@hw.ac.uk>
Web: http://www.macs.hw.ac.uk/~ajg33
ORCID: http://orcid.org/0000-0002-5711-4872
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Received on Tuesday, 18 June 2019 17:06:03 UTC