Using Neurolex through R

[Sine Zambach]

Dear Neurolex group,

I am working with ontologies in R and use the R-module "ontoCAT" to load ontologies into R. But apparently, I get the errors as pasted in the end of the mail.

Have any of you experienced similar? (Have any of you loaded the NIF-ontology into R with succes?)

Best regards,

Sine

> nif <- getOntology("http://purl.org/nif/ontology/nif.owl")
WARN  [OntologyLoader] Ontology could not be created. Waiting 30s and retrying once. http://purl.org/nif/ontology/nif.owlCould not load imported ontology: <http://ontology.neuinfo.org/NIF/Backend/NIF-Quality.owl> Cause: Could not load imported ontology: <http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl> Cause: Could not load imported ontology: <http://ontology.neuinfo.org/NIF/DigitalEntities/NEMO_vv2.98.owl> Cause: Could not load imported ontology: <http://purl.bioontology.org/NEMO/ontology/NEMO_annotation_properties.owl> Cause: connect timed out
Sorry, can't create Ontology object. Please, check ontology's URI: http://purl.org/nif/ontology/nif.owl.

--
Sine Zambach
Tlf: 21235533

[Stephen Larson]

I don't know of anyone who has done this before and wasn't aware of the ontoCAT module.  That is interesting though!

The ontologies should be able to be loaded with Protege.

I'm not sure what the errors could come from, but I have had experience with challenges in other software importing ontologies together.  Since those ontologies that are in the error message do appear to be on the web, there may be a problem in ontoCAT that doesn't deal with HTTP Redirects.  That would mean ontoCAT will need to be patched to accomplish this task.

The software headaches associated with exactly that problem is one of the reasons that the RDF / SPARQL query model via a web service has been so appealing.  It looks like there is a SPARQL R module here that could be used instead: http://www.r-bloggers.com/sparql-with-r-in-less-than-5-minutes/

Then you could use our SPARQL endpoint: http://neurolex.org/wiki/NeuroLex_SPARQL_endpoint

Thanks,

  Stephen

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[Chris Mungall]

Hi Sine,

The issue have been a temporary network outage. Or it may be an https issue as Stephen suggests (older versions of the OWLAPI had issues with this, but this has been fixed - you could ask the OntoCat developers to bundle the latest owlapi jar to see if that helps).

The nif.owl import chain is impressively large, but there are ways of handling this if you want to remain in OWL (which has a lot of advantages over working at the triple level).

(1) You can make a local cache of nif.owl and use a catalog file to direct everything to this local cache. See:
http://code.google.com/p/owltools/wiki/ImportChainMirroring

For example:

owltools http://ontology.neuinfo.org/NIF/Backend/NIF-Quality.owl --slurp-import-closure -d ~/mirror -c ./catalog-v001.xml

Will store everything in a directory called mirror, with the xml file acting as the lookup table

I'm not sure if OntoCat can work with catalogs but it should be an easy extension for the developers

(2) You can make modules corresponding to your areas of interest. See for example:

http://code.google.com/p/owltools/wiki/OortExtractingModules

[Helen Parkinson]

Hi

ontocat's from my group, I have passed this thread onto the personnel
involved, also copied here

Helen

On 23/01/2014 07:59, Chris Mungall wrote:
> Hi Sine,
>
> The issue have been a temporary network outage. Or it may be an https
> issue as Stephen suggests (older versions of the OWLAPI had issues
> with this, but this has been fixed - you could ask the OntoCat
> developers to bundle the latest owlapi jar to see if that helps).
>
> The nif.owl import chain is impressively large, but there are ways of
> handling this if you want to remain in OWL (which has a lot of
> advantages over working at the triple level).
>
> (1) You can make a local cache of nif.owl and use a catalog file to
> direct everything to this local cache. See:
> http://code.google.com/p/owltools/wiki/ImportChainMirroring
>
> For example:

> owltoolshttp://ontology.neuinfo.org/NIF/Backend/NIF-Quality.owl --slurp-import-closure -d ~/mirror -c ./catalog-v001.xml

> WARN [OntologyLoader] Ontology could not be created. Waiting 30s and retrying once.http://purl.org/nif/ontology/nif.owlCould not load imported ontology: <http://ontology.neuinfo.org/NIF/Backend/NIF-Quality.owl> Cause: Could not load imported ontology: <http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl> Cause: Could not load imported ontology: <http://ontology.neuinfo.org/NIF/DigitalEntities/NEMO_vv2.98.owl> Cause: Could not load imported ontology: <http://purl.bioontology.org/NEMO/ontology/NEMO_annotation_properties.owl> Cause: connect timed out

> Sorry, can't create Ontology object. Please, check ontology's URI:http://purl.org/nif/ontology/nif.owl.
>
>
>
> --
> Sine Zambach
> Tlf: 21235533
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Helen Parkinson
skype: helen.parkinson.ebi