Re: Property or class? cheminfo ontology.

[Michel Dumontier]

Hi Stian,
I'm reposting your email to the cheminf ontology mailing list
(please join if you haven't already). It looks to me that RCS is using
the term incorrectly.

m.

Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com


On Wed, Jan 7, 2015 at 3:14 AM, Stian Soiland-Reyes <st...@mygrid.org.uk> wrote:
> Hi,
>
> In
>
> http://semanticscience.org/resource/CHEMINF_000465
>
> I see:
>
> <rdf:Description
> rdf:about="http://semanticscience.org/resource/CHEMINF_000465">
> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
> <rdfs:label>ChemSpider validated synonym</rdfs:label>
> <rdfs:isDefinedBy
> rdf:resource="http://semanticscience.org/ontology/cheminf.owl"/>
> <rdfs:subClassOf
> rdf:resource="http://semanticscience.org/resource/CHEMINF_000044"/>
> <dc:identifier>CHEMINF:000465</dc:identifier>
> <ns0:IAO_0000115>A preferred name in ChemSpider by virtue of having been
> validated by a curator.</ns0:IAO_0000115>
> <ns0:IAO_0000117>Person: Colin Batchelor</ns0:IAO_0000117>
> </rdf:Description>
>
>
> This is also reflected in http://semanticscience.org/ontology/cheminf.owl
>
> How is this owl:Class meant to be used?
>
>
> In Open PHACTS we see this kind of data from RCS:
>
> from
> http://data.openphacts.org/1.4/rdf/OCRS/20131111/CHEMBL/SYNONYMS_CHEMBL20131111.ttl.gz
> (~300 MB)
>
> @prefix cheminf: <http://semanticscience.org/resource/> .
> @prefix ops: <http://ops.rsc.org/> .
> @prefix owl: <http://www.w3.org/2002/07/owl#> .
>
> cheminf:CHEMINF_000465 a owl:AnnotationProperty . # Validated Synonym
> <http://ops.rsc.org/OPS1769270> cheminf:CHEMINF_000465
> "2-naphthalenecarboxamide,
> 4-chlorodecahydro-4a-hydroxy-N-(4-methoxyphenyl)-8a-methyl-3-oxo-,
> (4R,4aS,8aS)-"@en .
>
>
> I know reusing a term both as an owl:Class and an owl:AnnotationProperty
> this is possible with OWL 2 Punning - but it sounds like something is not
> quite right in this case. Did RCS get it wrong? I would expect a 'preferred
> name' to be a property, not a class - why is it defined as a class in the
> ontology if it is really meant to be used as a property? Is there a
> rdf:value or similar property that should be used to provide the actual
> literal synonym? If so, with which property should we relate ops:OPS1769270
> to the synonym instance?
>
> I tried to visualize the cheminf ontology at
> http://www.essepuntato.it/lode/http://semanticscience.org/ontology/cheminf.owl
> but I must admit I get a bit confused by semi-numeric term names like
> "iao0000027" and "CHEMINF_000466".
>
>
>
> --
> Stian Soiland-Reyes, myGrid team
> School of Computer Science
> The University of Manchester
> http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718
>
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[Egon Willighagen]

Hi Stian,

We recently had this discussion too, and then it was said to be
intended use from a CHEMINF perspective...

On Wed, Jan 7, 2015 at 12:14 PM, Stian Soiland-Reyes
<st...@mygrid.org.uk> wrote:
> I would expect a 'preferred
> name' to be a property, not a class - why is it defined as a class in the
> ontology if it is really meant to be used as a property?

I guess this is the design decision of CHEMINF: it captures
"descriptors" of things (chemicals) and models these as OWL
ontologies. I do not see why "preferred name"s should be any different
from other things describing that chemical.

That is besides the question about whether this can be used as a
property, which was new to me last summer too.

> Is there a rdf:value or similar property that should be used to provide the actual
> literal synonym? If so, with which property should we relate ops:OPS1769270
> to the synonym instance?

Do any of these examples come close to what you mean?

https://code.google.com/p/semanticchemistry/wiki/Examples

> I tried to visualize the cheminf ontology at
> http://www.essepuntato.it/lode/http://semanticscience.org/ontology/cheminf.owl
> but I must admit I get a bit confused by semi-numeric term names like
> "iao0000027" and "CHEMINF_000466".

Yeah, that is a decision design in line with many other ontologies.
The downside is clear, but it has the advantage that you can fix the
title/label without getting conflicts with the URI... there may be
other advantages I forgot...

But they are hard to remember and the reason why I added a few tables
to the above Examples page...

Egon


--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
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ORCID: 0000-0001-7542-0286
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