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bio-tools / biotoolsSchema

biotoolsSchema : Tool description data model for computational tools in life sciences
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Would it be possible in the future to use other ontologies in addition to EDAM #216

Open bayjan opened 2 years ago

bayjan commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 https://github.com/edamontology/edamontology/issues/360, which is also related to this issue: https://github.com/edamontology/edam-bioimaging/issues/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 commented 2 years ago

Hi @bayjan

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

matuskalas commented 2 years ago

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 commented 2 years ago

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.