psidev-pi-dev

[Psidev-pi-dev] [HUPO-PSI/psi-ms-CV] Fix imports in psi-ms (#4)

[Chris M. <not...@gi...>]

Moving from here: https://github.com/MICommunity/psimi/issues/17

See https://github.com/owlcs/owlapi/issues/523

You should always use purls for imports, e.g

import: http://purl.obolibrary.org/obo/pato.obo
import: http://purl.obolibrary.org/obo/uo.obo

In fact we recommend that these are OWL. 

import: http://purl.obolibrary.org/obo/pato.owl
import: http://purl.obolibrary.org/obo/uo.owl

You can use an OboEdit catalog to have OE resolve these to a local obo cache. But really you should stop using OE, we do not support it any more. Contact me if you have problems


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Re: [Psidev-pi-dev] [HUPO-PSI/psi-ms-CV] Fix imports in psi-ms (#4)

[Chris M. <not...@gi...>]

Note this is causing the owl conversion to build:

```
>> Parser: OBOFormatOWLAPIParser
>> org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://pato.googlecode.com/svn/trunk/quality.obo
>>
>>
>> org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/Users/cjm/tmp/obobuild/src/ms.obo
>> Could not parse ontology.  Either a suitable parser could not be found, or parsing failed.  See parser logs below for explanation.
>> The following parsers were tried:
>> 1) RDFXMLParser
>> 2) OWLXMLParser
>> 3) OWLFunctionalSyntaxOWLParser
>> 4) TurtleOntologyParser
>> 5) KRSS2OWLParser
>> 6) ManchesterOWLSyntaxOntologyParser
>> 7) OBOFormatOWLAPIParser
```

You can always manually check this yourself with every release, either by:

 * opening the ms.obo file in Protege5 (__not__ 4)
 * running `owltools ms.obo`
 * running `robot convert -i ms.obo -o ms.owl` - see https://github.com/ontodev/robot/

I recommend going one step further and creating a travis job that will automatically check every commit or pull request made on this repo. You might find this useful https://douroucouli.wordpress.com/2015/12/16/creating-an-ontology-project-an-update/



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Re: [Psidev-pi-dev] [HUPO-PSI/psi-ms-CV] Fix imports in psi-ms (#4)

[Gerhard M. <not...@gi...>]

Hello Chris,

thanks for these hints. I updated the imports to use the PURL's for pato and uo.

But what I don't understand is that the nightly Jenkins build still picks up the old psi-ms.obo file (version 3.77.0) from
'https://raw.githubusercontent.com/MICommunity/psidev/master/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo'

instead the actual version 3.88.0 from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo


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