An Idea for the EOL Phylogenetic Tree Challenge

Earlier this year, the Encyclopedia of Life announced the EOL Phylogenetic Tree Challenge. The goal: to produce "a very large, phylogenetically-organized set of scientific names suitable for ingestion into the Encyclopedia of Life as an alternate browsing hierarchy". The prize: an all-expenses-paid trip to iEvoBio 2012 in Ottawa!

This interested me greatly, because:

1. It's exactly the sort of thing I'm working on for PhyloPic.
2. I can't really justify paying for a trip to iEvoBio this year. (Phyloinformatics is my hobby, not my profession!)

After reading Rod Page's thoughts on the challenge, I came up with a basic idea, and started to implement it. Unfortunately, now that we're two weeks from the deadline, I'm realizing that:

1. I do not have the time to complete it.
2. Even if it were paid for, I can't justify a trip on my own out of town right now.

Why not? Simply put, this.

So, instead, I'm going to outline the general approach I was going to take, and if someone else wants to run with it, knock yourself out. (Just give me partial credit.)

Wrapping Up In Portland

Yesterday was the last day of the iEvoBio Conference, and tonight is my last night in Portland. The conference was quite illuminating and I would definitely like to return for another one.

I've had some time tonight to address a few issues I would like to have tended to before the conference. For one, I hadn't updated the Names on Nodes website to link to the application! This has been remedied. In the process, I removed links to the NEXUS demo application, since it's a bit old and out of sync with the rest by now. I'll probably add it back after adding support for the NEXUS format to Names on Nodes.

I also made a few simple additions to Names on Nodes, including:

• Fullscreen mode
• Ability to specify which characters in a matrix you wish to import

The latter in particular should prove useful—some people were finding it impossible to open NexML files with character matrices. Since Names on Nodes only uses characters as part of apomorphy-based definitions, it's usually a big waste of time and memory to import entire matrices when only a few nomenclaturally-relevant characters (if any) are needed.

Once again I'd like to encourage people to check out the application and make feature requests and report issues on the BitBucket page.

Names on Nodes is finally online.

A month ago I got notice that my abstract had been accepted, and that I would be demoing Names on Nodes at the iEvoBio conference's Software Bazaar on June 29. This is the first time Names on Nodes has ever truly had a hard deadline. Since it's a personal project, until now I have had the luxury of languidly rebuilding and polishing and rebuilding and polishing. But now I have to get something up. So it's up.

Names on Nodes

There's still a lot left to do, but this will have to do for now. You can load NexML and Newick files (not NEXUS for now, sorry—although, really, you should be sorry for still using it when NexML is available). You can save as MathML and export PNG image files. You can create phylogenies and phylogenetic definitions on the fly using a visual interface that emphasizes drag-and-drop. Or you can type them in (as Newick and MathML, respectively), should you prefer that.


There are still a lot of bugs, and a lot of unimplemented features. If you come across issues or if you have feature requests, please feel free to submit an issue. And if you want to look at the code, it's open source (MIT license) and available on BitBucket.

Upcoming Names on Nodes Presentation

I'll also be presenting Names on Nodes at iEvoBio, at the Software Bazaar on June 29. Here's the abstract:

Names on Nodes: Automating the Application of Taxonomic Names within a Phylogenetic Context

Names on Nodes¹ is an open-source² Flex application which utilizes a mathematical approach to automate the application of phylogenetically-defined names to phylogenetic hypotheses. Phylogenetic hypotheses are modeled as directed, acyclic graphs, and may be read from bioinformatics or graph files (Nexus, NexML, Newick, and GraphML) or created de novo. Hypotheses may also be merged from multiple sources. Names on Nodes stores hypotheses as MathML, an XML-based language for representing mathematical content and presentation. Phylogenetic definitions may be constructed using a visual editor and exported in MathML. Thus, it is possible to create a dictionary of defined names and automatically apply them to phylogenetic hypotheses. In the current version of the application, such dictionaries exist only as MathML files, but in future versions definitions may also be loaded from databases (e.g., RegNum).

Additional functionality in Names on Nodes includes the ability to coarsen a phylogenetic graph (thereby simplifying it while still reflecting the overall structure) or to export it as an image file (raster or vector, potentially with semantic annotations).

1. Source code available at: http://bitbucket.org/keesey/namesonnodes-sa/
2. MIT license

I have my work cut out for me....

Upcoming Talk: Toward a Complete Phyloreferencing Language

I'll be giving a “Lightning Talk” (five minutes) at the iEvoBio Conference in Portland, Oregon. Here's the abstract:

Toward a Complete Phyloreferencing Language

A phyloreference is a statement indicating a taxon within a phylogenetic context. A common use for phyloreferences is in phylogenetic definitions, which tie taxonomic names to taxa via such statements. Several conventions for writing phyloreferences have been proposed, but most only cover a few “standard” forms (node-, branch-, and perhaps apomorphy-based clades) without the capacity to represent more “exotic” forms (e.g., ancestor-based clades and qualified/modified references). In order to build a complete phyloreferencing language, the mathematical underpinnings of phylogenetic contexts must be clarified. A phylogenetic context may be modeled as a directed, acyclic graph, wherein nodes model taxonomic units and directed edges model immediate descent. Higher taxa are modeled as unions of nodes. A phyloreferencing language must minimally allow for certain classes of entity: Boolean values, sets (including taxa, relations, and the empty set), and lists (including graphs and functions). It must also minimally allow for basic operations related to logic, set theory, and graph theory. Higher structures such as declarations and piecewise constructs must also be possible. With these as a basis, functions related to phylogeny can be defined: maximal, minimal, predecessor union/intersection, successor union/intersection, exclusive predecessors, synapomorphic predecessors, clade, crown clade, and total clade. I show how such a language may be used to represent various types of phyloreference, both “standard” and “exotic”.

Now to figure out how to condense that into a five-minute talk....