# Notes

## RNeXML

EML provides a nice illustration of the kind of metadata we would want to typically accompany character trait data; at minimum, at the attribute level.

Some of this is already there – we know if states are continuous or discrete, what possible states they can take on, and can add labels to state nodes to define what the symbols mean (however, perhaps an additional meta annotation node would be preferred). We don’t have a way to specify the units of a continuous trait, or longer definitions of the traits themselves, etc.

Obviously this is a hard problem, particularly in building any semantic reasoning around these traits. I gather that the phenoscape project is tackling this, but I’m not really up to speed on that. Long-term it would be nice to allow users to read and write trait metadata from R even without a working knowledge of the ontologies.

One idea I’m pondering is if we might be able to generate an EML metadata file the NeXML. The most trivial and straight forward approach is simply to use EML vocabularly itself in the metadata.

### Software to integrate into NeXML (long-term)

• Visualization: automatically generate the appropriate HTML+javascript page to render tree with jsPhyloSVG/phylotouch (example)
• Support for phenoscape onotlogy tools, e.g. see data as generated by phenex
• PhyloWS Generate a REST web service based on NeXML library(?)

### Issues

• Trying to understand if using nexml for comparative trait data will generate any confusion. (#44)