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I really like Charlie& #39;s take here, even though some of it will annoy many ontologists and my @OBOFoundry colleagues! Lots of sensible advice, would make a good PLOS 10 rules article. I do have a few suggestions and comments... 1/ https://twitter.com/cthoyt/status/1260307752796200961">https://twitter.com/cthoyt/st...
Great advice to use GitHub/GitLab, Travis-CI, etc. I have this as well as the general advice to use software development tools and principles in my top tip here: https://douroucouli.wordpress.com/2019/03/09/ontotip-lift-borrow-steal-software-engineering-principles/">https://douroucouli.wordpress.com/2019/03/0... 2/
We& #39;ve actually developed scripts that make it easy to get set up with everything you need for developing a new ontology with GitHub with the Ontology Development Kit https://github.com/INCATools/ontology-development-kit/">https://github.com/INCATools... 3/
The advice to generate the ontology from easy to manage TSVs is good - for certain kinds of ontologies or as part of a hybrid strategy. ROBOT provides a template command for doing this: http://robot.obolibrary.org/template ">https://robot.obolibrary.org/template&... 4/
As for throwing out @protegeproject and OWL... I can see where you are coming from. This can sometimes seem overkill, and many people use OWL badly, creating over-engineered baroque monstrosities... (not naming any names!) 5/
I& #39;d certainly recommend sticking to the EL subset of OWL used in @news4go, CL, @uberanat. This is usually sufficient for typical bio-ontologies. People often use the other constructs incorrectly making "impressive" looking but hard to understand and debug monsters... 6/
But in throwing this framework all out altogether you may be opening yourself for maintenance nightmares further down the line - but it depends a lot on properties of your ontology and your use case. No one-size-fits-all solution. Sometimes quick hacks are OK! 7/
It& #39;s a bit like seeing some over-engineered java code (we& #39;ve all been there) and then deciding to throw out structured programming altogether, writing everything in perl4 with no subroutines. IMHO we need to strive for the & #39;Python& #39; equivalent in building ontologies. 8/
Here& #39;s an older article on how we use OWL successfully in the GO: https://www.biorxiv.org/content/10.1101/010090v1.article-info">https://www.biorxiv.org/content/1... 9/9
