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phyloref / phylo2owl

Tool to convert phylogenies to OWL ontologies
MIT License
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Added Pylint and code cleanup #24

Closed gaurav closed 6 years ago

gaurav commented 7 years ago

Added Pylint to standardize code style and changed the code to fix all Pylint errors. Also added Pylint to Travis so that code style will continue to be tested in the future.

I also tried to improve the phyloreference documentation. This work will be continued in phyloref/curation-tool#64.

gaurav commented 7 years ago

@hlapp Done! Check it out at https://github.com/gaurav/phylo2owl/blob/79466a9edfce2642feeef3afa389326d0b031470/examples/trees/journal.pone.0094199.md (take 2)

I think the OWL keywords look pretty good now, but I'd like the names to be more immediately recognizable as names-in-OWL, rather than just words. I tried putting ':' in front of them, but I think that just looks annoying: https://github.com/gaurav/phylo2owl/blob/c22fbb1bf47acc3eb5e45551be23c9ecb186cf36/examples/trees/journal.pone.0094199.md (take 3). So if I had to choose, take 2 is probably the best representation for right now.

We could potentially turn those names into URLs, which on browsers would make them visually distinct and would allow someone to immediately look up "excludes_lineage_to" and other terms. Do you think that'd be useful?

hlapp commented 7 years ago

We could potentially turn those names into URLs, which on browsers would make them visually distinct and would allow someone to immediately look up "excludes_lineage_to" and other terms. Do you think that'd be useful?

Yes, but that shouldn't be manual should it? Or what way to do this did you have in mind?

hlapp commented 6 years ago

@gaurav where are we at with this?

gaurav commented 6 years ago

This pull request covers two things:

  1. How to display phyloreferences in OWL Manchester syntax. This is largely deprecated by PHYX now: it's better to describe phyloreferences in terms of specifiers rather than as the OWL property restriction representing them. However, I've opened an issue so that users can view the OWL property restriction in the Curation Tool if they want to (phyloref/curation-tool#64).
  2. A minor code cleanup. Based on our experience with the Curation Tool, I've added pylint to our test suite and fixed all major Pylint errors. This is what this pull request primarily covers now, so I'll change its description to match that.

I forgot about this pull request because we've put phylo2owl on hold until we can replace it with the Python library being developed as part of the Clade Ontology. But thanks for flagging this pull request up -- once it's been reviewed and merged, phylo2owl can go properly on ice until it's time to work on it again.

Finally, this was from the bad old days when I would develop in my own fork before pushing to phyloref. I've moved all the other branches into the phyloref repository now. I'll keep this branch on my own fork until it's reviewed and merged, and then I'll delete my fork.