Trying to load go-plus (gene ontology)

[jotomicron]

Hi.

I'm trying to load the GO (gene ontology).
The links for the OWL files are in here http://www.geneontology.org/page/download-ontology
In particular, I want to load go-plus (http://purl.obolibrary.org/obo/go/extensions/go-plus.owl)

However, I get an error, because two of the dependencies of this ontology are not in a owlready2 recognized format (AFAICT they use functional syntax).

With this, I'd like to submit two requests:

1. The error that is raised reads
"NTriples parsing error in file ???, line 1."
This does not allow me to understand what is actually happening (I spent more minutes than I would care to admit on finding exactly what was wrong here). Can this error message be changes to something more useful? For example saying that the file is not in a recognized format instead of mentioning NTriples, and also showing the actual ontology that is being loaded, possibly by leveraging the IRI?

2. Would there be any interest in me contributing with a loading driver for the functional syntax?
If so, where should I start?

Thank you.

[Jiba]

Hi,

For 1), I agree that the error message is not exactly appropriate... Owlready uses NTriples as default file format, so it is difficult to distinguish between a non-NTripes file and a errored NTriples file...

I'm going to change it to "NTriples parsing error (or unrecognized file format)" (a bit better).


For 2), any help is welcome!

For loading new file format, you shoul dlook at the rdfxml_2_ntriples.py and owlxml_2_ntriples.py files. These files are actually independent Python scripts that transform RDF/XML and OWL/XML in NTriples. They can be used either as in command line, printing NTriple to output, or in Python with Owlready : in this case, they produce triple in the form of Python tuples (to avoid parsing NTriple after parsing RDF/XML or OWL/XML).

Best regards,
Jiba

[jotomicron]

Thanks for the quick answer.

1) Could you also add the IRI of the file being parsed into the error message?

2) As soon as I find some time, I will try to see if this feature is something I am able to tackle.

On Wed, 23 Jan 2019 at 14:25, Jiba [via Owlready] <[hidden email]> wrote:

Hi,

For 1), I agree that the error message is not exactly appropriate... Owlready uses NTriples as default file format, so it is difficult to distinguish between a non-NTripes file and a errored NTriples file...

I'm going to change it to "NTriples parsing error (or unrecognized file format)" (a bit better).


For 2), any help is welcome!

For loading new file format, you shoul dlook at the rdfxml_2_ntriples.py and owlxml_2_ntriples.py files. These files are actually independent Python scripts that transform RDF/XML and OWL/XML in NTriples. They can be used either as in command line, printing NTriple to output, or in Python with Owlready : in this case, they produce triple in the form of Python tuples (to avoid parsing NTriple after parsing RDF/XML or OWL/XML).

Best regards,
Jiba

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[Jiba]

Hi,

For 1), I added URL in error messages.

Ok for 2).

Best regards,
Jiba