Would it be possible in the future to use other ontologies in addition to EDAM

[bayjan]

Would it be possible in the future to use other ontologies in addition to EDAM in annotating tools at bio.tools? This is necessary if a given term is not present in EDAM. Thank you.

[hansioan]

Hi @bayjan

I would be very interested to know what ontology / ontologies do you have in mind?

Also, if you think some concept is missing from the EDAM ontology you can always request to have it added at:
https://github.com/edamontology/edamontology/issues/new/choose

Thank you,
Hans

[bayjan]

Hi @hansioan

Thank you for your quick response. Actually I wanted to add some machine learning related concepts to some multiomics-related tools at bio.tools; however, such concepts needs to be present in EDAM or as you suggested it needs to be added. Someone had already opened an issue regarding some of these concepts and I asked about the status of that issue and @matuskalas from EDAM ontology re-opened that issue edamontology/edamontology#360, which is also related to this issue: edamontology/edam-bioimaging#17. So, I think some concepts will already be there and hopefully others can be added soon to EDAM, because direct transfer from other ontologies can be somewhat complicated.

Here are a few concepts out of many I am planning to add:

Concept	ontology_id
Machine learning	EDAM:topic_3474
Unsupervised learning	ENM:8000003
Supervised learning	ENM:8000002
Neural network	NCIT:C17429
Deep learning	MESH:D000077321
Dimensionality reduction	EDAM:operation_3935
Clustering	EDAM:operation_3432

Actually concepts like Unsupervised learning and Supervised learning are already present as narrow synonyms of machine learning, which I think bit misleading. So, probably more effort is needed to add such terms correctly, while not duplicating available concepts.

[hansioan]

Hi @bayjan

So adding some of the concepts in EDAM would be enough in your case? So no need for another ontology?

[matuskalas]

All what you mentioned is modelled as separate concepts in EDAM Bioimaging, and as such will be merged into the main EDAM in due course.

[bayjan]

Thanks, that is a very good news. So, I need to wait for the next EDAM release. Meanwhile I will check for the presence of all my concepts at WebProtégé for EDAM Bioimaging live version. I hope it is fine if I close this issue if all the concepts I want are already there at the EDAM Bioimaging live version.