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phyloref / phylo2owl

Tool to convert phylogenies to OWL ontologies
MIT License
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Add support for duplicate taxon labels #18

Open gaurav opened 7 years ago

gaurav commented 7 years ago

DendroPy cannot load a phylogeny with duplicate taxon labels, which means that phylo2owl.py can't, either. Fixing this will mean moving away from our previous model of naming leaf nodes from the taxon name (e.g. "pg_2357:Alobevania_gattiae") to using the same Node-number scheme we use for internal nodes (e.g. "pg_2357:Node_134"), and then providing them with either an rdfs:label or making them explicit instances of cdao:TU and figuring out the best name of assigning taxonomic names to those.

hlapp commented 7 years ago

I think that's a good thing to do anyway. Abusing labels for identifiers is fine for getting a proof of concept started, but is still an abuse. So I agree let's start to think more thoroughly about what the model for describing OTUs should look like.

There's some work I've done previously that's somewhat related, in that it proposes a model for annotating OTUs (in this case with TNRS matches): https://github.com/phylotastic-legacy/ontologies/tree/master/tnrs