Hi guys,
I’m trying to use the package ontoCAT but I keep having issues just starting up.
I followed the vignettes and wasn’t able to load the EFO ontologies

efo <- getEFO()
Sorry, can't create Ontology object for EFO by using URL "http://www.ebi.ac.uk/efo/efo.owl”.

I checked on the website, and there seem to be an owl file in there, so I tried the other function using the explicit URL

efo <- getOntology("http://www.ebi.ac.uk/efo/efo.owl")

WARN  [FileOntologyService] Multple labels found on <http://purl.obolibrary.org/obo/RO_0002215>
Sorry, can't create Ontology object for EFO by using URL "http://www.ebi.ac.uk/efo/efo.owl" or local file.
Sorry, can't create Ontology object. Please, check ontology's URI: http://www.ebi.ac.uk/efo/efo.owl.

I tried to look for a traceback but none is available:

> efo <- getEFO()
Sorry, can't create Ontology object for EFO by using URL "http://www.ebi.ac.uk/efo/efo.owl".
> traceback()
No traceback available 
> efo <- getOntology("http://www.ebi.ac.uk/efo/efo.owl")
Sorry, can't create Ontology object. Please, check ontology's URI: http://www.ebi.ac.uk/efo/efo.owl.
> traceback()
No traceback available 

Not sure if I’m doing something wrong, some help would be highly appreciated.

here’s my sessionInfo()
 

sessionInfo()

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ontoCAT_1.18.0       rJava_0.9-6          BiocInstaller_1.16.4

loaded via a namespace (and not attached):
[1] tools_3.1.2


cheers,
Francesco

Hi Francesco,

Would you please try to update ontoCAT from 1.18.0 to 1.20.0 (in current version of Bioconductor)?

It works for me:
> efo <- getEFO()
...
> getTermById(efo,"EFO_0000827")
EFO_0000827: obsolete_eye structure

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] ontoCAT_1.20.0       rJava_0.9-6          BiocInstaller_1.18.1

If the problem is still there then I would suggest to download owl file first and try getOntology from the local file (EFO is quite large ontology now):

file <- ".../efo.owl"
ontologyFromFile <- getOntology(file)

Hope it will help. Please let me know if the provided solutions do not work for you.

Regards,
Natalja

Hi Natalja,

thanks for your quick reply.
I've updated it from source (the version I get from biocLite is the one related to my R version 3.1 and not 3.2)
but it still doesn't work

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ontoCAT_1.20.0       rJava_0.9-6          BiocInstaller_1.16.4

loaded via a namespace (and not attached):
[1] tools_3.1.2
> efo <- getEFO()
Sorry, can't create Ontology object for EFO by using URL "http://www.ebi.ac.uk/efo/efo.owl".

I will upgrade R in my Mac, but the problem is that I can't keep R always to the latest version on the cluster where I am using it.
In short, version 1.20 still doesn't work if I'm using R 3.1

cheers, F

yep, and I can confirm is the combination of ontoCAT 20 + R 3.2

with this, it works.
thanks

> library(ontoCAT)
Loading required package: rJava
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.2 (Yosemite)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ontoCAT_1.20.0       rJava_0.9-6          BiocInstaller_1.18.1

loaded via a namespace (and not attached):
[1] tools_3.2.0
> efo <- getEFO()
WARN  [FileOntologyService] Multple labels found on <http://purl.obolibrary.org/obo/RO_0002215>
WARN  [FileOntologyService] Multple labels found on <http://purl.obolibrary.org/obo/RO_0002160>
WARN  [ReasonedFileOntologyService] The inverse object property has_part for part_of was not found in the ontology
INFO  [ReasonedFileOntologyService] Classified the ontology http://www.ebi.ac.uk/efo/efo.owl
WARN  [FileOntologyService] Multple labels found on <http://purl.obolibrary.org/obo/RO_0002215>
WARN  [FileOntologyService] Multple labels found on <http://purl.obolibrary.org/obo/RO_0002215>
WARN  [FileOntologyService] Multple labels found on <http://purl.obolibrary.org/obo/RO_0002160>
WARN  [FileOntologyService] Multple labels found on <http://purl.obolibrary.org/obo/RO_0002160>
> efo
An object of class "Ontology"
Slot "ontology":
[1] "Java-Object{uk.ac.ebi.ontocat.utils.OntologyParser@212ca458}"