.owl file formats for ontologies?

[Steph Nowotarski]

Hello,

We're looking to incorporate an ontology we developed into our CATMAID annotation using a .owl file format. Can CATMAID do this, or must the ontology be in YAML like it is in the project file?  

Thanks! 

Steph Nowotarski

[Tom Kazimiers]

Hi Steph,

On Tue, Oct 08, 2019 at 06:27:26AM -0700, Steph Nowotarski wrote:
>We're looking to incorporate an ontology we developed into our CATMAID
>annotation using a .owl file format. Can CATMAID do this, or must the
>ontology be in YAML like it is in the project file?

This is unfortunately not possible at the moment and it turns out this
is our oldest open ticket on GitHub:

https://github.com/catmaid/CATMAID/issues/4

IIRC there is nothing that would prevent this from being implemented and
the CATMAID database schema should be able to represent OWL ontology
data. It's unlikely that I will have capacity to work on this anytime
soon though, but would be happy to assist if you or someone else would
want to pick this up.

The only way to import ontologies into CATMAID is currently the YAML
format that you refer to, explained here:

https://catmaid.readthedocs.io/en/stable/importing_data.html#ontology-and-classification-import

Best,
Tom

[Steph Nowotarski]

Thanks Tom!

For now, we'll probably just convert to YAML for what we need. 

Steph

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