Issue with Wikidata Knowledge Base in INCEpTION

[Milica Ikonić Nešić]

Dear Community, 

Thank you for existing above all! 

I have been using the INCEpTION tool for a very long time and it has been extremely useful! At the moment, I am facing a problem: since noon, text connected to the Wikidata knowledge base shows an Error and returns the following message:

Unable to list root concepts: Please set a user-agent and respect our robot policy https://w.wiki/4wJS. See also T400119.

while running the query:

SELECT DISTINCT ?m ?dc ?dp ?subj WHERE { { { { VALUES ( ?subj ) { (<http://www.wikidata.org/entity/Q35120>) } } FILTER EXISTS { { ?subj <http://www.wikidata.org/prop/direct/P31> <http://www.wikidata.org/entity/Q35120> . } UNION { [] <http://www.wikidata.org/prop/direct/P279> ?subj . } UNION { ?subj <http://www.wikidata.org/prop/direct/P279> [] . } } } } OPTIONAL { ?pMatch <http://www.w3.org/2000/01/rdf-schema#subPropertyOf>* <http://www.w3.org/2000/01/rdf-schema#label> . } OPTIONAL { { ?subj ?pMatch ?m . FILTER ( ( LANGMATCHES( LANG( ?m ), "en" ) || LANG( ?m ) = "" ) ) } } OPTIONAL { { ?subj <http://www.w3.org/2000/01/rdf-schema#comment> ?dc . FILTER ( ( LANGMATCHES( LANG( ?dc ), "en" ) || LANG( ?dc ) = "" ) ) } } OPTIONAL { { ?subj <http://www.w3.org/2002/07/owl#deprecated> ?dp . FILTER ( ( LANGMATCHES( LANG( ?dp ), "en" ) || LANG( ?dp ) = "" ) ) } } } LIMIT 2000

Could anyone please help me resolve this problem?

Best regards,

Milica

[Richard Eckart de Castilho]

Hi,

I saw some post related to a change on the Wikidata mailing list, but
I didn't fully check it yet... I'll have a closer look at what new
requirements they have now and get back to you.

That said: the obvious way around those query limitations is that you
download the Wikidata dumps and set up your own SPARQL endpoint with
those and use that one instead of using the official Wikidata SPARQL
endpoint.

Cheers,

-- Richard

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[Richard Eckart de Castilho]

Hi,

> On 25. Aug 2025, at 19:06, Richard Eckart de Castilho <richard...@gmail.com> wrote:
>
> I saw some post related to a change on the Wikidata mailing list, but
> I didn't fully check it yet... I'll have a closer look at what new
> requirements they have now and get back to you.

I have just released INCEpTION 37.5 which should restore the ability to talk to
the WikiData SPARQL endpoint.

https://github.com/inception-project/inception/releases/tag/inception-37.5

Cheers,

-- Richard

[Milica Ikonić Nešić]

Hi Richard,

Thank you very much for your quick response and assistance! Everything is working perfectly now!

Best regards,

Milica  

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[Milica Ikonić Nešić]

Hi Richard, 

I used to see the description from Wikidata when I hovered over the linked entity, but now I don’t see it. How can I enable this again? 

Thanks in advance!  

Best regards,

Milica

[Richard Eckart de Castilho]

Hi,

> On 30. Aug 2025, at 00:21, Milica Ikonić Nešić <milica.ikon...@gmail.com> wrote:
>
> I used to see the description from Wikidata when I hovered over the linked entity, but now I don’t see it. How can I enable this again?

Check if a description is shown under the concept input field in the right sidebar.

When a description is shown there, I also get it in the hover popup when using WikiData.

-- Richard

[Milica Ikonić Nešić]

 

Hi, 

> I used to see the description from Wikidata when I hovered over the linked entity, but now I don’t see it. How can I enable this again?

Check if a description is shown under the concept input field in the right sidebar.

No, It’s not showing for me, although it used to.

When a description is shown there, I also get it in the hover popup when using WikiData.

-- Richard

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[Richard Eckart de Castilho]

Hi,

> On 30. Aug 2025, at 00:54, Milica Ikonić Nešić <milica.ikon...@gmail.com> wrote:
>
> > I used to see the description from Wikidata when I hovered over the linked entity, but now I don’t see it. How can I enable this again?
>
> Check if a description is shown under the concept input field in the right sidebar.
>
> No, It’s not showing for me, although it used to.

Try annotating something with "Obama" (http://www.wikidata.org/entity/Q11462618) - that shows a description for me.

If that description does not show, try creating a new entity linking project and check if it works for you there.
If it does, check if you changed anything in the knowledge base sesttings in your old project, in particular
in the mapping part where all the IRIs are set.

-- Richard

[Milica Ikonić Nešić]

Dear Richard,

I am using version 37.5 of INCEpTION, and everything has been working fine until now. Now it is showing this kind of message for linked entities with Wikidata.   

Could you please help me? The same issue is happening in every project, and it is no longer connecting to Wikidata.

Kind regards,

Milica Ikonić Nešić

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[Richard Eckart de Castilho]

Hi,

[Milica Ikonić Nešić]

Dear Richard,

This is the error I receive when I start annotating.

I understand that it is possible to copy the Wikidata SPARQL server and use it as a local knowledge base, but I am not sure how to do this properly. Could you please guide me through the process?

Thank you in advance for your help.

Kind regards,

Milica Ikonić Nešić

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>
>
> Could you please help me? The same issue is happening in every project, and it is no longer connecting to Wikidata.

I just tried it locally (with the latest version), creating a project from the entity linking template,
imported a document and tired linking a concept to wikidata - worked.

So maybe either...

... you hit a transient problem and it will start working again ...

... or if you use INCEpTION heavily against the official wikidata SPARQL endpoint, you might have been rate-limited or banned.

I *believe* Wikidata has an idea that their services should be used fairly and if they determine that usage might go beyond fair,
they *might* reserve the option to limit/ban users. No proof of this theory though.

Here is some more info on their limits: https://www.mediawiki.org/wiki/Wikidata_Query_Service/User_Manual

Mind that INCEpTION (or rather RDF4J) probably doesn't really respect the HTTP code 429 and the Retry-After header...

Maybe you see a more informative error message in the logs? (E.g. as admin, go to Administration in the menu bar and then to logs)

I always suggest to people asking me that for heavy usage, people should set up their own copy of a Wikidata SPARQL server and connect to that instead of using the public one.

Cheers,

-- Richard

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[Richard Eckart de Castilho]

Hi,

[Richard Eckart de Castilho]

> On 27. Feb 2026, at 21:37, Richard Eckart de Castilho <richard...@gmail.com> wrote:
>
>> On 27. Feb 2026, at 09:28, Milica Ikonić Nešić <milica.ikon...@gmail.com> wrote:
>>
>> This is the error I receive when I start annotating.
>

> Does the error persist after you restart INCEpTION / your computer?

So this error here

java.lang.IllegalStateException: Connection pool shut down

does not seem to come from Wikidata itself. It seems like INCEpTION might have gotten
into a weird state. Without further investigation, we cannot tell what caused it.
If oyu have administrator permissions, you can click on "Administration" in the
menu bar and then on "logs" to maybe see more relevant error messages. Mind that
the "logs" page auto-refreshes by default - turn off the refresh at the top to
facilitate scrolling and reading.

As I hinted at above, I would advise restarting INCEpTION and then looking if the
problem persists. With a little luck, it might be gone. And if it comes back,
looking into the logs would again be advised.

At TU Darmstadt, we had at a time a Virtuoso Server with a copy of Wikidata running,
but tbh, I was not involved in setting it up, so I can't give advice on it.
I googled that briefly, but assuming that you are an individual annotator,
you probably won't have the necessary server sources required to host your own
copy. And as an individual user I would hope you also wouldn't issue so many calls
to Wikidata that it would get you blocked... but we'd have to find out to be sure.

-- Richard

[Milica Ikonić Nešić]

Dear Richard,

Thank you very much.

I restarted Inception and now everything works, even faster. I could use your help,  is there an example project for relation annotation? 

I already have named entities annotated and I would like to annotate relations between them as well.  

Kind regards,

Milica

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[Richard Eckart de Castilho]

Hi,

> On 15. Mar 2026, at 19:56, Milica Ikonić Nešić <milica.ikon...@gmail.com> wrote:
>
> I restarted Inception and now everything works, even faster. I could use your help, is there an example project for relation annotation?
> I already have named entities annotated and I would like to annotate relations between them as well.

Go to the "Layers" section in the project settings, create a new relation layer and select the named entity layer in the "attach to layer" dropdown.
Once you have done that, you should be able to create relations between your entities by clicking/dragging one one and moving the mouse until an arrow appears
and releasing the mouse over the target entity.

-- Richard

[Milica Ikonić Nešić]

Dear Richard,

I am currently working on a WSD task and I would like to label two tokens that form a MWE and assign them a meaning, without having to include the tokens in between or annotate each token separately, while assigning them some shared ID that links them together. Is there any other way to do this?

Kind regards, Milica

[Richard Eckart de Castilho]

Hi,

> On 17. Mar 2026, at 19:57, Milica Ikonić Nešić <milica.ikon...@gmail.com> wrote:
>
> I am currently working on a WSD task and I would like to label two tokens that form a MWE and assign them a meaning, without having to include the tokens in between or annotate each token separately, while assigning them some shared ID that links them together. Is there any other way to do this?

INCEpTION does currently not support non-continuous annotations.
You could simulate them be introducing e.g. a "MWE fragement" span layer and a "fragments" slot feature linked to that layer in your MWE layer and then by convention annotate the first part of the MWE or its semantic head with the MWE layer and attache the other parts to the head using the fragments slots.

-- Richard

[Milica Ikonić Nešić]

Dear Richard,

 I’m having problems importing a file. When I split it into smaller files, it imports successfully, but when it contains more than 300 sentences it fails. I get the following error while uploading the document [sr-elexsis_WSD_KBid_final.tsv]: IllegalArgumentException: CAS type [de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity] does not have a feature called [KBid]. Do you maybe have any advice on what could be the issue? Every row has the same number of columns. I can also send the file if that would help.  

Kind regards,

Milica

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[Richard Eckart de Castilho]

Hi Milica,

> On 26. Mar 2026, at 21:53, Milica Ikonić Nešić <milica.ikon...@gmail.com> wrote:
>
> I’m having problems importing a file. When I split it into smaller files, it imports successfully, but when it contains more than 300 sentences it fails.
> I get the following error while uploading the document [sr-elexsis_WSD_KBid_final.tsv]: IllegalArgumentException: CAS type [de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity] does not have a feature called [KBid]. Do you maybe have any advice on what could be the issue? Every row has the same number of columns. I can also send the file if that would help.

Is it possible that this is a very old file, possibly from the WebAnno 1.x era around 2014 (personal note: around commit 423ca71f8de40d)?

It seems that in this file, somebody has added a custom feature to the built-in Named Entity layer.
As far as I can tell, this has not been possible for a very very long time.

If you can privately (!) send me the file, I can try to adjust it into a configuration compatible with INCEpTION.

Cheers,

-- Richard