ontoCAT getEFO error
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@lescai-francesco-5078
Last seen 3.1 years ago
Denmark

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

ontoCAT ontologies EFO • 973 views
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@natalja-kurbatova-7703
Last seen 2.2 years ago
United Kingdom

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

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@lescai-francesco-5078
Last seen 3.1 years ago
Denmark

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

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Entering edit mode
@lescai-francesco-5078
Last seen 3.1 years ago
Denmark

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}"

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