search

phyloref / clade-ontology

Ontology of Phylogenetic Clade Definitions
MIT License
1 stars 0 forks source link

Adds a phyx2ontology.js script for building a synthesized Clade Ontology #58

Closed gaurav closed 5 years ago

gaurav commented 5 years ago

This PR adds a script that can be used to create a synthesized Clade Ontology from the Phyx files in this repository. It currently generates an OWL 2 DL JSON-LD representation using phyx.js, and then converts it into a OWL 2 EL JSON-LD representation on the fly. I will eventually move this code into phyx.js, but only after JPhyloRef has been updated to be able to test OWL files using OWL 2 EL reasoners.

WIP -- this code is still very quick-and-dirty and will need a bunch of cleanup before it's ready for review. Also, there are still some bugs in the output -- for example, "Tomistominae (alt)" resolves to two nodes on the same phylogeny, which should be impossible -- so these should be fixed before this PR is reviewed.

Should be merged after PR #60 has been merged.

hlapp commented 5 years ago

"Tomistominae (alt)" resolves to two nodes on the same phylogeny, which should be impossible -- so these should be fixed before this PR is reviewed.

Ignore this. It's a logic consequence of the model in this concrete case.

gaurav commented 5 years ago

Just to be clear, this PR is not urgent, and will probably need a detailed review. Feel free to review it whenever you have the time!

gaurav commented 5 years ago

Good point! I've added a very basic test that just runs phyx2ontology.js and makes sure that it produces valid JSON output. I think that's good enough for this PR, and then #65 covers adding shape-based testing of the produced JSON-LD output. What do you think?