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cran / ontologyIndex

:exclamation: This is a read-only mirror of the CRAN R package repository. ontologyIndex — Reading Ontologies into R
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No terms detected in ontology source for both Experimental Factor Ontology (EFO) and The Mammalian Phenotype Ontology (MP) .owl files #2

Open moldach opened 2 years ago

moldach commented 2 years ago

rBiopaxParser is not reading in multiple Web Ontology Language (OWL) files

This is my first time working with .owl files; I need to work with both Experimental Factor Ontology (EFO) and The Mammalian Phenotype Ontology (MP) but this package fails to read both: I've gotten from

Downloading resources

# EFO
wget -S https://github.com/EBISPOT/efo/releases/download/current/efo.owl

# MP
wget --no-check-certificate --no-proxy -O mp.owl https://www.ebi.ac.uk/ols/ontologies/mp/download

Try to load .owl files with {ontologyIndex}:

> library('ontologyIndex')
> ontology <- get_ontology('mp.owl')
Error in get_ontology("mp.owl") : No terms detected in ontology source
> ontology <- get_ontology('efo.owl')
Error in get_ontology("efo.owl") : No terms detected in ontology source
oganm commented 1 year ago

A bit late here, but ontologyIndex is written for obo files. You can use ROBOT to convert owl files to obo ones with some success. More info here

gaborcsardi commented 1 year ago

Hi, this is a read only mirror of CRAN, please see the package authors in the DESCRIPTION file. Look for Maintainer, BugReports and URL. Thanks!