Knowledge Base from scratch?

[Robert]

Hello and congratulations to the INCEpTION development team,

though I'm absolutely new to INCEpTION I think it's great software.

The import of the Test-Wine Knowledge Base works perfect.

Is there any (very basic) tutorial to see how a small local Knowledge Base can be established from scratch or could you give me a short example?

How does the json/XML (or whatever)-file of the Knowledge Base has to look like? How can it be accessed (schema/class/property-mapping/settings) by INCEpTION?

Kind regards,

Robert

[Jan-Christoph Klie]

Hi,

you can either create a blank KB in INCEpTION and use the buitl-in INCEpTION KB editor to create it. You can also create it externally and import it. We support the typical RDF formats, The types are not shown when you create an empty, local KB but afterwards in the Project settings under "Knowledge Base". I would suggest using an external tool to create these and then import it. I find writing Turtle the easiest, you could do it by hand with a text editor, some have RDF support like VScode [1]. A famous RDF editor e.g. is Protege  [2] . 

When creating your KB, you need to make sure it is compatible with INCEpTION. This mostly means that you need to have triples that indicate what concepts and instances are and what labels. These important properties can be configured in INCEpTION. OWL and SKONS are the most common schemas to model your KB after that we support. 

You can also programmatically create your KB e.g. by using RDFlib [3]. 

I hope that answers your question. I can give you some Python code for creating if that helps you, we do not have tutorials yet that show you how to externally create KBs and then import it. If you use Protege and then export it as OWL, and then create a KB as OWL and import it to INCEpTION, then it should work

Best,

Jan

[1]: https://marketplace.visualstudio.com/items?itemName=stardog-union.stardog-rdf-grammars

[2]: https://protege.stanford.edu/

[3]: https://rdflib.readthedocs.io/en/stable/

[Robert]

Dear Jan

Thanks for your quick and extensive reply. I understand there are 2 ways with inception to use Knowledge Bases. Import (of externally created KBs) or creating a KB with the inception-built-in-KB-editor.

Unfortunately I do not understand how to start the built-in-KB-editor. I guess a new KB must be created at the Project -> Knowledge Bases menu-item. How do I have to continue? Attached I send you my guesses.

Do I have to delete that? With only filling in the red text-fields I cannot "Finish". To have or not the Base Prefix doesn't make any difference.

I guess nothing has to be changed here...

What do I have to do here? IRI-Schema 'custom'?

Kind regards,

Robert

[Jan-Christoph Klie]

Hi Robert,

once you click finish and go to the project dashboard, a new tab "Knowledge base" appears.  You then need to understand the difference between concepts (classes) and instances, e.g. Obama is an instance of the class Person. As an example, you would create a uber concept like "Entity" and then subclass it to types of your choosing like "Person", "Location" or so. Then you can add a property "name", create an instance of a Person "Obama" and add a new relation that "Obama" has the name "Barack Obama". You can explain the wine ontolgy in the KB editor also to get a better grasp.

The mappings you configured tell INCEpTION what in your KB are classes, labels and so on so that we can properly work with it. There are different schemas defined that are typically used, RDFS, OWL, SKOS which use different relations to mark classes, instances, what property a label defines, ... If you start out from scratch, any schema is fine, it is more relevant if you then import an existing KB into INCEpTION.

If you create a KB in INCEpTION from scracth. then we recomend to do regular backups of the resulting RDF file. If you intend to create large KB from scratch, I would use an external editor . You could create a basic KB to understand the format and then write it yourself, I find turtle the most readable. What kind of KB do you intend to create if I might ask?

Best,

Jan

[Robert]

Dear Jan

I am mortally embarrassed about it but I think my problem is more basic as you may think ;-)

As you write 'once you click finish and go to the project dashboard...' I fail to click the finish button (at least nothing happens :-(  and no KB is started/instantiated as I have to press the decline-button to be able to leave the create-box).

I tried this at the level of menu-items 'Administration', 'Project' and 'Project dashboard'.

Inception works in the way you described and sent screenshots of when I open the imported Wine-KB, but still I cannot start a new KB.

I would like to create a KB with medical expressions and put them in a hierarchy of symptoms, lab results other medical findings of diagnostic tools and diagnoses.

I am sure something like this exists already. Maybe you know about that.

Kind regards,

Robert

[Richard Eckart de Castilho]

Hi,

> On 8. Dec 2021, at 11:37, Robert <rweite...@gmail.com> wrote:
>
> I would like to create a KB with medical expressions and put them in a hierarchy of symptoms, lab results other medical findings of diagnostic tools and diagnoses.

You can

* Go to the KB page in the project settings
* Press "Create"
* Enter a KB name
* Change the type to "local"
* Press next without changing any further setting until the finish button becomes active and then you press that
* Go to the KB page - there you should now see an empty KB
* Start by adding a root class

> I am sure something like this exists already. Maybe you know about that.

There are likely many ontologies in the bioinformatics domain, but if you are new to the general idea,
it probably doesn't hurt if you try playing around with your own first for a start. E.g. UMLS is a pretty
scarily large resource - also, it's not free and I'm also not aware of a RDF representation that could
easily be hooked up with INCEpTION - there could well be one, but I don't know it.

Cheers,

-- Richard

[Robert]

Dear Richard

Now I am really ashamed. Of course it worked now! (I was sure I tried it in your way for 100 times before...)

As a first instance I will create "schwere Geburt" (German expression for 'That took some doing') ;-)

Thanks for your time and help.

As you recommend in a next step I will play around and finally come back to existing resources...

Kind regards,

Robert