Ontology meeting 2015-01-06

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Follow-up: Protege 4 vs 5

Where are we with this? Background: (from call on Dec 9th)

Chris writes: "Protege 4 is stuck on an old version of the OWLAPI. This is not ideal - we have to do conversion separately and not natively. It's a bigger issue for ontologies like CL that are edited in OWL - lagging behind with the owlapi will cause even bigger diffs as TG edits alternate with Protege edits. From the perspective of software development, it would be hugely advantageous to switch to P5. We can build this from maven easily, and make versions that are in sync with TG. Also, P4 will presumably eventually rot. However, P5 is apparently currently unusable. Can we collect some of the requirements in a doc, place a request on the protege feedback list, and then evaluate our strategy based on the response? Has anyone else rather than DavidOS tried it out? "

Jane replies: "I was using P5 for a while, it was fine for me. It didn't cause any problems with the round-trip. The 'improved' search isn't perfect, but Matt gave us some tips on using it when he was here. I'd be happy to switch over."

Anyone else? Let's collect requirements.

Midori has been using P5 with the phenotype ontology a bit. Search function is lacking. Ideally searches could be performed in a similar way to OE, but are currently very limited. David OS suggests trying out the annotation plugin that’s been around for some time.

AI: David OS will look further into this to determine if we can realistically use P5 short-term and what we’d need.

 Notes from DOS. Search is slow
 Here's the ticket detailing how it could be improved.  https://github.com/protegeproject/protege/issues/87
 Also potential problems with explanation plugin?  https://github.com/protegeproject/protege/issues/100

AI: David to try full editing session and report. AI: Chris and Heiko to follow up on getting ELK working and test explanations.

Reactivation Ontology Release

Safe to restart the nightly release?


Remaining axioms in CHEBI that overclassify amino acids

Details here: https://docs.google.com/document/d/15diOvRWOMGNVbqQadf23EJej6PXMyPTMt7dgxW8nAWk/edit

Key questions:

1. Should creatine be classified as an alpha amino acid? No 2. Should glyco and lipid modified alpha-amino acids be classified as alpha-amino acids? No