ontology around 'solubility' related terms (chemistry)?

[Erick Antezana]

Dear all,

I am looking for pointers to "solubility" related ontologies -- where the granularity level of related terms is relatively deep...

I found a few ontologies (e.g. CHMO) which cover certain areas but seem to miss others...  Any pointer is welcome!

(BTW, I "heard" that the IUPAC has datasets in RDF, but was not able to find any, has anybody worked with/found them?)

cheers,

Erick

[Egon Willighagen]

CHEMINF also only has one term for solubility.

What kind of granularity are you looking for? "solubility in water", "solubility in acetone", etc?

On Wed, Oct 14, 2020 at 4:37 PM Erick Antezana <erick.a...@gmail.com> wrote:

(BTW, I "heard" that the IUPAC has datasets in RDF, but was not able to find any, has anybody worked with/found them?)

Check out: https://www.nature.com/articles/npre.2010.4918.1

Egon

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Have you heard about Wikidata already? "Use Scholia and Wikidata to find scientific literature" is a new tutorial from my colleague Lauren Dupuis. https://laurendupuis.github.io/Scholia_tutorial/

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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/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen

[Alexander Garcia Castro]

Hi all, I see the need for ontologies in chemistry (spreaded throughout several existing ontologies, lack coverage, poor in synonyms, the whole domain is poorly represented, e.g. polymers, etc). I would like to know who would be interested in kick starting a community effort addressing this gap. here I am wearing my hat as BASF. I want to know who would be interested, we organize a call, and I present my plan, we discuss it (change it) and see how to move forward. 

Best. 

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Alexander Garcia
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[Ali Haider Bangash]

I'm all in for this. 🖒👌

Regards,

Ali Haider Bangash

On 15 Oct 2020 2:37 p.m., "Alexander Garcia Castro" <alexg...@gmail.com> wrote:

Hi all, I see the need for ontologies in chemistry (spreaded throughout several existing ontologies, lack coverage, poor in synonyms, the whole domain is poorly represented, e.g. polymers, etc). I would like to know who would be interested in kick starting a community effort addressing this gap. here I am wearing my hat as BASF. I want to know who would be interested, we organize a call, and I present my plan, we discuss it (change it) and see how to move forward. 

Best. 

On Wed, Oct 14, 2020 at 4:43 PM Egon Willighagen <egon.wil...@gmail.com> wrote:

CHEMINF also only has one term for solubility.

What kind of granularity are you looking for? "solubility in water", "solubility in acetone", etc?

On Wed, Oct 14, 2020 at 4:37 PM Erick Antezana <erick.a...@gmail.com> wrote:

(BTW, I "heard" that the IUPAC has datasets in RDF, but was not able to find any, has anybody worked with/found them?)

Check out: https://www.nature.com/articles/npre.2010.4918.1

Egon

--

Have you heard about Wikidata already? "Use Scholia and Wikidata to find scientific literature" is a new tutorial from my colleague Lauren Dupuis. https://laurendupuis.github.io/Scholia_tutorial/

-----

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
ImpactStory: https://impactstory.org/u/egonwillighagen

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Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
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http://www.linkedin.com/in/alexgarciac

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[Erick Antezana]

Egon, Pascale, Alex and Ali,

Many thanks for the replies and pointers.

@Egon: my colleagues want to characterise (to the most detail possible) aspects related to solubility such as for instance what solubility a substance/material has dependent on its form (crystallized, amorph) and polymorphism situation. Such detailed terminology should enable ML about solubility based on material characteristics (after building a knowledge base of course)...

@Alex: count me in for your idea -- perhaps something we could start discussing during the upcoming BH?

best regards,

Erick

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Alexander Garcia
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[Alexander Garcia Castro]

when is the upcoming BH? 

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[Erick Antezana]

9-13 Nov

https://www.biohackathon-europe.org/ 

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[Chris Mungall]

Hi Alex

Can you say a bit more about why CHEBI doesn't meet your needs?

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[Alexander Garcia Castro]

hi chris, 

lack of precise synonyms 

lack of coverage, e.g. polymers are vastly underrepresented, materials, relation to properties, etc. 

CAS and other identifiers 

etc etc etc... 

Chemistry is a huge domain, chebi is ok but hardly a comprehensive representation of the domain and subdomains . 

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[Chris Mungall]

Yes, it is challenging to cover all aspects of all chemicals

It does help if some of this can be captured on their tracker (all OBO trackers can be found via their page on the OBO site, e.g. http://obofoundry.org/ontology/chebi)

I agree about the precise synonyms - most other OBOs categorize synonyms into exact, broad, narrow, related, but CHEBI's database structure doesn't allow this.

It would be great to come up with a plan for some unifying ontology of chemistry rather than lots of databases with varying amounts of overlap and unclear mapping between them

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