Create Relation between different layers

[mohammadreza karmidehkordi]

Hi all,

I am currently using INCEpTION to annotate incident reports for a project. My setup includes an Entity layer and a separate Event layer.

I have successfully created a relation layer attached to the Entity layer, and I am able to annotate relations between spans within the same layer. However, I am unable to create a relation arc from a span in the Entity layer to a span in the Event layer. I’ve ensured that:

• Both layers are Span type with Tokens anchoring and Any overlap mode.
• The relation layer is attached to the Entity layer and has Cross-sentence enabled.
• I click the source (Entity) first, then the target (Event), while using the relation tool.

Despite this, the arc does not appear, and the relation is not created. I suspect this may be due to INCEpTION’s implicit restrictions on cross-layer relations.

Could you please advise whether cross-layer relations between different span layers (e.g., Entity → Event) are supported in this context, and if so, how to enable or work around this behavior?

Thank you for your time and assistance.

[Richard Eckart de Castilho]

Hi there,

> On 11. Jun 2025, at 23:51, mohammadreza karmidehkordi <mohammadreza.k...@gmail.com> wrote:
>
> Could you please advise whether cross-layer relations between different span layers (e.g., Entity → Event) are supported in this context, and if so, how to enable or work around this behavior?

Cross-layer relations are an experimental feature.

You can activate it by adding the following line to your `settings.properties` file.

```
ui.cross-layer-relations-enabled=true
```

Cf. https://inception-project.github.io/releases/36.5/docs/admin-guide.html#sect_settings_cross-layer-relations

Once this feature is enabled, you can create a new relation layer that connects to "Any" span layer.
Relations of this layer can then be created between span annotations on different layers.

Note that the feature has not seen extensive use yet. If (when) you run into problems, let me know.

Cheers,

-- Richard

[mohammadreza karmidehkordi]

Hello Richard,

Thank you for your response.

I’m reaching out regarding a different issue I’ve encountered. When I export my annotations in the BIO format using the CoNLL 2002 standard, all tokens are labeled as "O", even though I have entity tags in place.

Could you please assist me with resolving this issue?

Thank you very much for your help.

Best regards,

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[Richard Eckart de Castilho]

Hi,

> On 16. Jun 2025, at 20:16, mohammadreza karmidehkordi <mohammadreza.k...@gmail.com> wrote:
>
> I’m reaching out regarding a different issue I’ve encountered. When I export my annotations in the BIO format using the CoNLL 2002 standard, all tokens are labeled as "O", even though I have entity tags in place.

The CoNLL 2002 format will only export the "value" feature of the built-in Named Entity layer.
If you see "O" everywhere, maybe you are using a custom layer.

Cheers,

-- Richard

[mohammadreza karmidehkordi]

Dear Richard,

Thank you very much for your response.

You're exactly right — I had created a custom layer, which explains why I was seeing only "O" labels in the CoNLL 2002 export. I now understand that the CoNLL 2002 format only exports the "value" feature of the built-in Named Entity layer.

However, I’m still unsure how to structure my annotations using the built-in Named Entity layer to suit the needs of my task, and I would greatly appreciate your guidance.

My task involves three entity types with a hierarchical labeling structure:

• Entity 1 has four subclasses, and one of those subclasses includes 18 sub-subclasses.
• Entity 2 follows a similar structure, with four subclasses and 18 sub-subclasses under one of them.
• Entity 3 has 10 subclasses but no further subcategories.

The hierarchy is outlined below:

Entity 1	Sub_class 1 Sub_class 2 Sub_class 3 Sub_class 4	Sub_subclass 1 Sub_subclass 2 … Sub_subclass 18
Entity 2	Sub_class 1 Sub_class 2 Sub_class 3 Sub_class 4	Sub_subclass 1 Sub_subclass 2 … Sub_subclass 18
Entity 3	Sub_class 1 Sub_class 2 Sub_class 3 … Sub_class 10

Could you please advise if such a hierarchical structure can be supported using the built-in Named Entity layer in INCEpTION? I would also be grateful for any guidance on how to configure this setup so I can annotate the data and export it properly in BIO format.

Thank you again for your time and support.

Best regards,

Reza

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[Richard Eckart de Castilho]

Hi,

If you are going for a simple format like CoNLL 2002 BIO, then you would probably
conflate your labels all into a single string, e.g.

Entity1_SubClass_1_SubSubClass1
Entity2_SubClass_1_SubSubClass3
...

That is not as comfortable during annotation, but maps to the desired format.

Alternatively, you can export your data as CAS XMI or CAS JSON, read it in with
DKPro Cassis in Python and write your own serializer.

-- Richard