Uploading own custom Knowledge Base

[Anne Dirkson]

Dear other Inception users, 

I am trying to upload my own custom (local) Knowledge Base (KB) into the Inception tool to use for entity linking. 

The import is succesful but it does not recognize anything in my ontology as a concept (i.e. unless I press 'show all' it gives me an empty block under Concepts in the Knowledge Base tab). If I do press show all, I can scroll through my ontology just fine. I can also search in the search bar.  

This also means that for entity linking (in Annotation) none of the concepts in my ontology show up as options.

I have created my ontology using owlready2 in python. I have tried RDF, OWL and ntriple formats and it does not matter.

Does anyone recognize this issue or have experience with resolving it?

I attach my KB for replication. 

Kind regards

Anne Dirkson

[Richard Eckart de Castilho]

Hi,

> On 3. May 2021, at 12:03, Anne Dirkson <anne.d...@gmail.com> wrote:
>
> I am trying to upload my own custom (local) Knowledge Base (KB) into the Inception tool to use for entity linking.
>
> The import is succesful but it does not recognize anything in my ontology as a concept (i.e. unless I press 'show all' it gives me an empty block under Concepts in the Knowledge Base tab). If I do press show all, I can scroll through my ontology just fine. I can also search in the search bar.

Having had a look at the ontology, the reason that it does not load up in the knowledge base page is that the ontology root is `http://www.w3.org/2002/07/owl#Thing`. If "show all" is turned off, then any concepts from namespaces such as RDF, OWL, etc. are
filtered out because normally you'd not want to see e.g. OWL Class or RDF Label or similar things. Unfortunately, in your case
that also filters out the root of the ontology which causes nothing to appear at all. We should probably make an exception for
OWL Thing to the filtering.

Anyway, the way to fix this is to configure the knowledge base to use a different root concept. I can see that you have
a concept called `c:/Users/dirksonar/Documents/Data/Project13_LinkCoping/Ontology_Sub/coping_strategy.owl#CopingStrategy`.
You could also explicitly add `http://www.w3.org/2002/07/owl#Thing` as a root - that also works.
If you go to the KB settings, scroll down to the bottom and add that concept as a root, then you'll get results.

Best,

-- Richard

[Anne Dirkson]

Hi, 

Thank you for taking a look at this Richard. This worked like a charm. I can now indeed see my ontology automatically in the KB tab. 

However, the concepts in my ontology still do not show up as options when annotating. Might this be because they are classes? Do classes not show up as options while annotating? 

If so, is there an option to override this? The owlready package only has the option between instances and classes but not loose concepts as I see in the demo KB of inception. 

If not, do you have an idea what could be causing this?

Best regards, 

Anne 

Op di 4 mei 2021 om 14:29 schreef Richard Eckart de Castilho <richard...@gmail.com>:

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[Jan-Christoph Klie]

Hi Anne,

can you check the setting of the Concept feature in the layer configuration that you created? You can choose there between annotating concepts or instances or both. For named entities, the default is instances only which would maybe explain things [1].

[1]: https://inception-project.github.io/releases/0.19.3/docs/user-guide.html#_concept_features_270

Best,

Jan

[Anne Dirkson]

Thank you very much Jan! This is now fixed. You have both been most helpful. 

Best, 

Anne Dirkson

Op do 6 mei 2021 om 09:58 schreef Jan-Christoph Klie <rent...@gmail.com>:

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