I have been exploring the R ontoCAT package from Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/ontoCAT.html), but I noticed that there is no method for getting all of the instances of an ontology class.
Is there an R package that does this?
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written
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Alison Callahan •
I'm not sure what you mean with instance.
As far as I understand, this package 'only' handles an ontology ( a graph of classes) but it is not designed to create some instances (e.g: http://en.wikipedia.org/wiki/Charles_Darwin is an instanceOf the class 'MY_ONTOLOGY:Human' )
If you only want to find all the terms in the ontology, the documentation says:
To find all ontology terms two functions can be used: getAllTerms
- returns a list of OntologyTerm objects.
In turn, getAllTermIds
- returns a list of term accessions.
> getAllTerms(biotop)
> getAllTermIds(efo)
Yes, this is what I have come to realize. Just surprised that there isn't a function for handling instances...
So far there hasn't been much demand for this functionality, please feel free to request it via https://lists.sourceforge.net/lists/listinfo/ontocat-users if still interested.
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