search

OpenTreeOfLife / hackathon

A repo for the 2014 OpenTree / Arbor / HIP hackathon
8 stars 1 forks source link

Taxonomic names from CSV/TSV -> OpenTree OTUs -> Tree -> NeXML #18

Closed gaurav closed 10 years ago

gaurav commented 10 years ago

This is a subproject of #16. I'm currently close to finishing a Python script designed to match names against multiple taxonomic sources, using other information contained in the file to pick sources to match against -- for example, a name in class Mammalia could be matched against the Mammal Species of the World, ITIS, and the Catalogue of Life, while a name in class Aves would be matched against global bird checklists, ITIS and the Catalogue of Life.

It'd be pretty easy to add support for the OpenTree taxonomy as a taxonomic source, but it'd be MUCH cooler to take the output of my script, get a pruned subtree from the OpenTree synthesized tree, and then add the metadata already contained into the input CSV file back into the final NeXML file.

This would also fit neatly with #17, as PhyloStyloTastic would then be able to render the NeXML along with its included metadata.

rvosa commented 10 years ago

For the BioVeL project we have developed a web service that folds CSV/TSV and/or JSON into NeXML. There are some conventions for specifying what objects to annotate, but it might be useful: https://www.biodiversitycatalogue.org/services/70

arlin commented 10 years ago

Can we combine this with issue #2 ? And possibly also with #1?

gaurav commented 10 years ago

Definitely similar to #2! Closing.