annotation properties with different namespaces

[Citlalli]

Salut Jean-Baptiste:
Hi,

I'm developing an ontology and I want to know what are the classes that are missing a definition. However, since I have merged many different subontologies, I have two "definition" annotation properties with two different namespaces. Specifically, if I do:

for ann_prop in ecco.annotation_properties():

    print (ann_prop)



I get

npo.definition
efo.definition.


When I try to print the definition with Class.npo.definition I get this error:


AttributeError: 'npo' property is not defined

If I try to print definition with clas.definition, I get only two definitions that are only efo.definition, but not all
definitions that are efo.definition.

Maybe I'm not getting well namespaces. How can I query annotation properties in different namespaces?


Merci beaucoup!

[Jiba]

Hi,

If two annotations have the same name, you cannot use the "class.annotation" syntax (it will defaults to one of the two annotaions, without being able to choose between them). You need to use the more complex "annotation[class]" syntax. This syntax requires to obtain the annotation as an object, this can be done using the ontology it belongs to, a namespace or its IRI:

# Choose one
annotation = IRIS["http://full/iri/to/definition"]
annotation = onto_npo.definition
annotation = onto.get_namespace("http://full/iri/to/").definition

print(annotation[your_class])

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

> Salut Jean-Baptiste:
> Hi,
>
> I'm developing an ontology and I want to know what are the classes that are
> missing a definition. However, since I have merged many different
> subontologies, I have two "definition" annotation properties with two
> different namespaces. Specifically, if I do:
>
> for ann_prop in ecco.annotation_properties():
>
>     print (ann_prop)
>
>
>
> I get
>
> npo.definition
> efo.definition.
>
>
> When I try to print the definition with Class.npo.definition I get this
> error:
>
>
> AttributeError: 'npo' property is not defined
>
> If I try to print definition with clas.definition, I get only two
> definitions that are only efo.definition, but not all
> definitions that are efo.definition.
>
> Maybe I'm not getting well namespaces. How can I query annotation properties
> in different namespaces?
>
>
> Merci beaucoup!
>
>
>
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[jkchang]

Hi, I've tried your suggestion. It works!

But using annotation[your_class] only can return the first annotation. If I have several definitions in the same namespace, how can I do to return list of definitions [definition 1, definition 2, definition 3]?

e.g.:

   

    <owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/>


   

    <owl:Class rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#CheeseyPizza">
        <rdfs:label xml:lang="en">CheesyPizza</rdfs:label>
        <rdfs:label xml:lang="pt">PizzaComQueijo</rdfs:label>
        <skos:definition xml:lang="en">definition 1.</skos:definition>
        <skos:definition xml:lang="en">definition 2.</skos:definition>
        <skos:definition xml:lang="en">definition 3.</skos:definition>
        <skos:prefLabel xml:lang="en">Cheesy Pizza</skos:prefLabel>
    </owl:Class>
   

Thank you very much.

[jkchang]

Solved~

I got list of annotation properties as follows:

cls = = onto.search_one(label = 'CheesyPizza' )
anno = onto.search_one(iri ='http://www.w3.org/2004/02/skos/core#definition')

print(anno[cls])

[Jiba]

Hello,

You should use IRIS (with an S for plural).

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