handling of imported ontology

classic Classic list List threaded Threaded
12 messages Options
gp
Reply | Threaded
Open this post in threaded view
|

handling of imported ontology

gp
Hello,

I am having difficulties working with imported ontologies. Specifically I used Protege to define some ontology which imports other ontologies.

I was expecting to be able to access these ontologies using the
onto.imported_ontologies  attribute but this one only returns an empty list.

I can otherwise access the classes, attributes etc without a problem.

Is there something I missed, especially with respect to namespace handling in this case ?

Cheers,
Guillaume

owl file beginning:
<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.definiens.com/ontologies/TissuePhenomicsOntology#"
     xml:base="http://www.definiens.com/ontologies/TissuePhenomicsOntology"
     xmlns:uberon="http://purl.obolibrary.org/obo/uberon#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
     xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:x_1.1="http://purl.org/dc/elements/1.1/"
     xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:doap="http://usefulinc.com/ns/doap#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:pato="http://purl.obolibrary.org/obo/pato#"
     xmlns:uo="http://purl.obolibrary.org/obo/uo#"
     xmlns:obo="http://purl.obolibrary.org/obo/"
     xmlns:foaf="http://xmlns.com/foaf/0.1/">
    <owl:Ontology rdf:about="http://www.definiens.com/ontologies/TissuePhenomicsOntology">
        <owl:versionIRI rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/0.1"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/uo/releases/2018-03-24/uo.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/obi/2018-02-12/obi.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/pato/releases/2018-03-28/pato.owl"/>
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2017-12-11/cl.owl"/>
        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">0.1</owl:versionInfo>
        <rdfs:isDefinedBy>gpotdevin@definiens.com</rdfs:isDefinedBy>
    </owl:Ontology>

[...]

Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

Jiba
Administrator
Hello,

There was a bug on imported ontologies, in particular when the ontology is loaded from its filename (instead of its IRI), or when it internal name changed during load (which is the case if the IRI is not of the basic form xxx.owl, such as in your example).

I've fixed the bug in the development version of OwlReady2 on BitBucket.

Best regards,
Jean-Baptiste Lamy
MCF, LIMICS, Université Paris 13

> Hello,
>
> I am having difficulties working with imported ontologies. Specifically I
> used Protege to define some ontology which imports other ontologies.
>
> I was expecting to be able to access these ontologies using the
> /onto.imported_ontologies / attribute but this one only returns an empty
> list.
>
> I can otherwise access the classes, attributes etc without a problem.
>
> Is there something I missed, especially with respect to namespace handling
> in this case ?
>
> Cheers,
> Guillaume
>
> owl file beginning:
> <?xml version="1.0"?>
> <rdf:RDF
> xmlns="http://www.definiens.com/ontologies/TissuePhenomicsOntology#"
>      xml:base="http://www.definiens.com/ontologies/TissuePhenomicsOntology"
>      xmlns:uberon="http://purl.obolibrary.org/obo/uberon#"
>      xmlns:owl="http://www.w3.org/2002/07/owl#"
>      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
>      xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
>      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>      xmlns:x_1.1="http://purl.org/dc/elements/1.1/"
>      xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#"
>      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>      xmlns:doap="http://usefulinc.com/ns/doap#"
>      xmlns:xml="http://www.w3.org/XML/1998/namespace"
>      xmlns:pato="http://purl.obolibrary.org/obo/pato#"
>      xmlns:uo="http://purl.obolibrary.org/obo/uo#"
>      xmlns:obo="http://purl.obolibrary.org/obo/"
>      xmlns:foaf="http://xmlns.com/foaf/0.1/">  
>     <owl:Ontology
> rdf:about="http://www.definiens.com/ontologies/TissuePhenomicsOntology">  
>         <owl:versionIRI
> rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/0.1"/>  
>         <owl:imports
> rdf:resource="http://purl.obolibrary.org/obo/uo/releases/2018-03-24/uo.owl"/>
>         <owl:imports
> rdf:resource="http://purl.obolibrary.org/obo/obi/2018-02-12/obi.owl"/>
>         <owl:imports
> rdf:resource="http://purl.obolibrary.org/obo/pato/releases/2018-03-28/pato.owl"/>
>         <owl:imports
> rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2017-12-11/cl.owl"/>
>         <owl:versionInfo
> rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">0.1</owl:versionInfo>  
>         <rdfs:isDefinedBy>[hidden email]</rdfs:isDefinedBy>
>     </owl:Ontology>
>
> [...]
>
>
>
>
>
> _______________________________________________
> If you reply to this email, your message will be added to the discussion below:
> http://owlready.8326.n8.nabble.com/handling-of-imported-ontology-tp273.html
> To start a new topic under Owlready, email [hidden email]
> To unsubscribe from Owlready, visit
gp
Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

gp
Bonjour Jean-Baptiste,

Somehow I could not get it to work. After removing the existing installed version and installing the one I cloned from BitBucket I run into the following error:

Traceback (most recent call last):
  File "C:\Program Files\JetBrains\PyCharm 181.4203.13\helpers\pydev\pydev_run_in_console.py", line 53, in run_file
    pydev_imports.execfile(file, globals, locals)  # execute the script
  File "C:\Program Files\JetBrains\PyCharm 181.4203.13\helpers\pydev\_pydev_imps\_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "C:/workspace/TissuePhenomicsOntologyDemonstrator/visualisationPrototype/ontoSerializer.py", line 9, in <module>
    tpo = god.TPOnto()
  File "C:\workspace\TissuePhenomicsOntologyDemonstrator\ontologyHelpers\getOntologyData.py", line 60, in TPOnto
    tpo.load(only_local=True)
  File "C:\winPython_365_onlyHoloViews\python-3.6.5\lib\site-packages\owlready2-0.8-py3.6.egg\owlready2\namespace.py", line 502, in load
    self._load_properties()
  File "C:\winPython_365_onlyHoloViews\python-3.6.5\lib\site-packages\owlready2-0.8-py3.6.egg\owlready2\namespace.py", line 527, in _load_properties
    props.append(Prop.python_name)
  File "C:\winPython_365_onlyHoloViews\python-3.6.5\lib\site-packages\owlready2-0.8-py3.6.egg\owlready2\entity.py", line 355, in __getattr__
    if Prop is None: raise AttributeError("'%s' property is not defined." % attr)
AttributeError: 'python_name' property is not defined.


Indeed my ontology imports some external file (several now actually, in order to keep things clean) which I created using ontofox.

Would you need the ontology file for reference?
I am sorry I am not yet able to debug these stuff by myself, somehow still on the learning curve when it comes to handling rdf and specifically owl data.

Cheers,
Guillaume




Hello,

There was a bug on imported ontologies, in particular when the ontology is loaded from its filename (instead of its IRI), or when it internal name changed during load (which is the case if the IRI is not of the basic form xxx.owl, such as in your example).

I've fixed the bug in the development version of OwlReady2 on BitBucket.

Best regards,
Jean-Baptiste Lamy
MCF, LIMICS, Université Paris 13

> Hello,
>
> I am having difficulties working with imported ontologies. Specifically I
> used Protege to define some ontology which imports other ontologies.
>
> I was expecting to be able to access these ontologies using the
> /onto.imported_ontologies / attribute but this one only returns an empty
> list.
>
> I can otherwise access the classes, attributes etc without a problem.
>
> Is there something I missed, especially with respect to namespace handling
> in this case ?
>
> Cheers,
> Guillaume
>
> owl file beginning:
> <?xml version="1.0"?>
> <rdf:RDF
> xmlns="http://www.definiens.com/ontologies/TissuePhenomicsOntology#"
>      xml:base="http://www.definiens.com/ontologies/TissuePhenomicsOntology"
>      xmlns:uberon="http://purl.obolibrary.org/obo/uberon#"
>      xmlns:owl="http://www.w3.org/2002/07/owl#"
>      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
>      xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
>      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>      xmlns:x_1.1="http://purl.org/dc/elements/1.1/"
>      xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#"
>      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>      xmlns:doap="http://usefulinc.com/ns/doap#"
>      xmlns:xml="http://www.w3.org/XML/1998/namespace"
>      xmlns:pato="http://purl.obolibrary.org/obo/pato#"
>      xmlns:uo="http://purl.obolibrary.org/obo/uo#"
>      xmlns:obo="http://purl.obolibrary.org/obo/"
>      xmlns:foaf="http://xmlns.com/foaf/0.1/">  
>     <owl:Ontology
> rdf:about="http://www.definiens.com/ontologies/TissuePhenomicsOntology">  
>         <owl:versionIRI
> rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/0.1"/>  
>         <owl:imports
> rdf:resource="http://purl.obolibrary.org/obo/uo/releases/2018-03-24/uo.owl"/>
>         <owl:imports
> rdf:resource="http://purl.obolibrary.org/obo/obi/2018-02-12/obi.owl"/>
>         <owl:imports
> rdf:resource="http://purl.obolibrary.org/obo/pato/releases/2018-03-28/pato.owl"/>
>         <owl:imports
> rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2017-12-11/cl.owl"/>
>         <owl:versionInfo
> rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">0.1</owl:versionInfo> 
>         <rdfs:isDefinedBy>[hidden email]</rdfs:isDefinedBy>
>     </owl:Ontology>
>
> [...]
>
>
>
>
>
> _______________________________________________
> If you reply to this email, your message will be added to the discussion below:
> http://owlready.8326.n8.nabble.com/handling-of-imported-ontology-tp273.html
> To start a new topic under Owlready, email [hidden email]
> To unsubscribe from Owlready, visit http://owlready.8326.n8.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=1&code=amliYWxhbXlAZnJlZS5mcnwxfDE1MTUzNDAxNDM=

gp
Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

gp
Ok I figured that, fairly weirdly, the first call to . load() results in the above mentioned error, but a successive call to the same method works without a problem.

ie.
tpo = owl.get_ontology(myfile_tissuePhenomics)
try:
    tpo.load(only_local=True)
except:
    tpo.load(only_local=True)

will work for instance (however a poor syntax that is).

Hope this helps,
Guillaume
Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

Jiba
Administrator
In reply to this post by gp
Bonjour,

> Would you need the ontology file for reference?

Yes please. I would like to remove all bugs from Owlready!

Your workaround suggests me that something gets wrong in ontology loading. Then "reloading" it does not reload but just returns a reference to the partially loaded ontology.

Best regards,
Jean-Baptiste Lamy
MCF, LIMICS, Université Paris 13
gp
Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

gp
Hello,
I had tried to contact you via email (using the Nabble forum interface) but I guess this did not work out.

Anyway, using the development version (0.9) from gitbucket the error is gone.
It does not seem like the imported ontologies get loaded though.

Here is my code:

import owlready2 as owl
myonto = r'C:\workspace\TissuePhenomicsOntologyDefinition\TissuePhenomics.owl'
owl.onto_path.append(r'C:\workspace\TissuePhenomicsOntologyDefinition')
owl.onto_path.append(r'C:\workspace\TissuePhenomicsOntologyDefinition\imports')
tpo = owl.get_ontology(myonto)
tpo.load(only_local=True)

tpo.imported_ontologies
> []

obo = tpo.get_namespace("http://purl.obolibrary.org/obo/")
print(obo.CHEBI_39077)
> None

obo.search(label='eosin b')
>---------------------------------------------------------------------------
>TypeError                                 Traceback (most recent call last)
><ipython-input-8-e2f5db6e2e85> in <module>()
>----> 1 obo.search(label='eosin b')
>
>TypeError: 'NoneType' object is not callable

My owl file starts like this
    <owl:Ontology rdf:about="http://www.definiens.com/ontologies/TissuePhenomicsOntology">
        <owl:versionIRI rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/0.1"/>
        <owl:imports rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/imports/pr_import.owl"/>
        <owl:imports rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/imports/pato_import.owl"/>
        <owl:imports rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/imports/chebi_import.owl"/>
        <owl:imports rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/imports/stato_import.owl"/>
        <owl:imports rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/imports/uo_import.owl"/>
        <owl:imports rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/imports/obi_import.owl"/>
        <owl:imports rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/imports/uberon_import.owl"/>
        <owl:imports rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/imports/go_import.owl"/>
        <owl:imports rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/imports/cl_import.owl"/>
        <rdfs:isDefinedBy>gpotdevin@definiens.com</rdfs:isDefinedBy>
        <obo:IAO_0000117>Guillaume Potdevin</obo:IAO_0000117>
        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">0.9</owl:versionInfo>
    </owl:Ontology>

Changing it to explicit file pathes like the following does not change things.
<owl:Ontology rdf:about="http://www.definiens.com/ontologies/TissuePhenomicsOntology">
        <owl:versionIRI rdf:resource="http://www.definiens.com/ontologies/TissuePhenomicsOntology/0.1"/>
        <owl:imports rdf:resource="http://git.definiens.local/gpotdevin/TissuePhenomicsOntologyDefinition/raw/master/imports/pr_import.owl"/>
        <owl:imports rdf:resource="http://git.definiens.local/gpotdevin/TissuePhenomicsOntologyDefinition/raw/master/imports/pato_import.owl"/>
        <owl:imports rdf:resource="http://git.definiens.local/gpotdevin/TissuePhenomicsOntologyDefinition/raw/master/imports/chebi_import.owl"/>
        <owl:imports rdf:resource="http://git.definiens.local/gpotdevin/TissuePhenomicsOntologyDefinition/raw/master/imports/stato_import.owl"/>
        <owl:imports rdf:resource="http://git.definiens.local/gpotdevin/TissuePhenomicsOntologyDefinition/raw/master/imports/uo_import.owl"/>
        <owl:imports rdf:resource="http://git.definiens.local/gpotdevin/TissuePhenomicsOntologyDefinition/raw/master/imports/obi_import.owl"/>
        <owl:imports rdf:resource="http://git.definiens.local/gpotdevin/TissuePhenomicsOntologyDefinition/raw/master/imports/uberon_import.owl"/>
        <owl:imports rdf:resource="http://git.definiens.local/gpotdevin/TissuePhenomicsOntologyDefinition/raw/master/imports/go_import.owl"/>
        <owl:imports rdf:resource="http://git.definiens.local/gpotdevin/TissuePhenomicsOntologyDefinition/raw/master/imports/cl_import.owl"/>
        <rdfs:isDefinedBy>gpotdevin@definiens.com</rdfs:isDefinedBy>
        <obo:IAO_0000117>Guillaume Potdevin</obo:IAO_0000117>
        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">0.9</owl:versionInfo>
    </owl:Ontology>

When using protege I make use of a catalog file.
 
I can also pass you the files themselves by email (I cannot publish them right now, though this will come).

Cheers,
Guillaume
gp
Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

gp
Ok my bad, I was experiencing a version conflict: somehow pip uninstall owlready2 did not do the work completely and the egg coming from the setuptool installation (dev version) was living next to the older official pip installation.

Cleaning manually the packages made the trick and now things are working like expected.

Sorry for the noise and congratulation again for the net package!
Guillaume
gp
Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

gp
Hello,

Time for me to revive this thread as I seem to experience the very same problem with the last version of owlready2 (0.12).
After importing some ontology which itselfs has several imports the .imported_ontologies is an empty list.

The same is true with owlready2==0.11 but things work as expected with owlready2==0.10 (.imported_ontologies is populated with the expected imports and I can access the corresponding entities).

Could it be the bug was re-introduced in 0.11 ?

Cheers,
Guillaume
Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

Jiba
Administrator
Hello,

Many things have changed in 0.12 with the new quadstore; so it is possible that some old bugs are back.

I tested importation on a single example and it worked. Could you send me a small example that reproduces your problem?

Best regards,
Jiba
gp
Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

gp
Hi,

You might give a try with the ontology placed in the following repo:
https://github.com/Definiens/TissuePhenomicsOntology


I could reproduce the issue using the following code:
import owlready2 as owl

owl.onto_path.append('.')
owl.onto_path.append('./imports')

tpo = owl.get_ontology('TissuePhenomics.owl').load(only_local=True)

assuming the script is placed in the cloned directory.

This worked on my machine after installing owlready2==0.10 but not with owlready2>=0.11

Cheers,
GP
Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

Jiba
Administrator
Hi,

I investigated the problem. It was caused by the fact that your ontologies use "TissuePhenomicsOntology" both as a path element (e.g. http://www.definiens.com/ontologies/TissuePhenomicsOntology/imports/uo_import.owl) and as a document (e.g. http://www.definiens.com/ontologies/TissuePhenomicsOntology#TPO0000044). Owlready was messing up and expected the ontology IRI to ends with a /.

It should be fixed in the development version now. Could you try it ?

Cheers,
Jiba
gp
Reply | Threaded
Open this post in threaded view
|

Re: handling of imported ontology

gp
Hello,

I tried the dev version in different scenarios and so far I did not have any glitch w.r.t the imported ontologies.

Thanks for the very quick fix!
GP