re-using ChEBI

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re-using ChEBI

Citlalli Mejía Almonte
I've been building an ontology using chemical compounds as individuals and now I would like to extract their definitions from ChEBI, but in CheBI these chemical compounds are represented as classes, is there a way to extract the definitions from a class in ChEBI and used them to define the individuals of my ontology? Or should it be better to model my ontology using classes instead?

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Re: re-using ChEBI

Chris Mungall-2
Hi Citlalli,

Technically this is possible, you might have to write a short piece of
code using the OWLAPI or write a SPARQL query to do the transform.

However, if you do this your ontology will have difficulty
interoperating with ontologies in the OBO Library, where we treat
chemical entities as classes. Unless you have a particular need to model
these as individuals (e.g. explicit representation of cyclic structures)
then why not just treat them as classes?

On 23 Jun 2016, at 16:16, Citlalli Mejía Almonte wrote:

> I've been building an ontology using chemical compounds as individuals
> and
> now I would like to extract their definitions from ChEBI, but in CheBI
> these chemical compounds are represented as classes, is there a way to
> extract the definitions from a class in ChEBI and used them to define
> the
> individuals of my ontology? Or should it be better to model my
> ontology
> using classes instead?
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: re-using ChEBI

Alan Ruttenberg-2
Even if there is a need for something like cyclic structure's there are probably better solutions than duplicating ChEBI classes as instances. Happy to discuss your use case. 
Alan

On Thursday, June 23, 2016, Chris Mungall <[hidden email]> wrote:
Hi Citlalli,

Technically this is possible, you might have to write a short piece of code using the OWLAPI or write a SPARQL query to do the transform.

However, if you do this your ontology will have difficulty interoperating with ontologies in the OBO Library, where we treat chemical entities as classes. Unless you have a particular need to model these as individuals (e.g. explicit representation of cyclic structures) then why not just treat them as classes?

On 23 Jun 2016, at 16:16, Citlalli Mejía Almonte wrote:

I've been building an ontology using chemical compounds as individuals and
now I would like to extract their definitions from ChEBI, but in CheBI
these chemical compounds are represented as classes, is there a way to
extract the definitions from a class in ChEBI and used them to define the
individuals of my ontology? Or should it be better to model my ontology
using classes instead?
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protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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