Association file

[edusalcas]

Hey,

First of all, I love your work! I am working with a single cell ontology and I want to build an embedding of it. I have the ontology in owl format but I cant find a way to get the association file with the correct format. Is there any way to automatically generate this file once I have the ontology with all the entities?

Another question that I have is in what format the owl file should be.

Thanks in advance!

[azzatha]

Hi @edusalcas

Thanks for your comment. Yes, you can use the single-cell ontology in the same way that we use to generate other annotations.

• For the association file, it depends on the task that you are working on, so e.g., if your entities are genes, then you simply need to find the single-cell annotations for your genes, you can use ontoProc, you will find a function to collect the properties from a given Cell Ontology class. Then you need to process the result to get the associations:

351 <http://purl.obolibrary.org/obo/CL:0000127>
351  <http://purl.obolibrary.org/obo/CL:0000129>
2896 <http://purl.obolibrary.org/obo/CL:0000127>
2896 <http://purl.obolibrary.org/obo/CL:0000115>
4920 <http://purl.obolibrary.org/obo/CL:0000084>

Then follow the instructions to generate the embeddings for your entities.

• Regarding the owl file format, we use phenomenet.owl in this work, and you can have a look to the format here .

Let me know if you have any other questions. Good luck! Azza.

[edusalcas]

Thanks for the answer @azzatha.

Is it possible to create an embedding where the entities are single-cell projects? If it is possible, I have to create an association file with all the projects ids and their relations in my ontology?

I leave you an example file with three projects and their relationships to see if they are in a correct format.

Thanks again for your attention.

assotiation_example.txt