The Open Tree of Life has produced several fantastic resources for the phylogenetics community including a comprehensive taxonomy that is immediately useful for phylogenetic purposes (i.e., doesn’t have incertae sedis), a comprehensive and perpetually-updating phylogeny that includes all named species (present in the aforementioned taxonomy), a tree store that contains thousands of phylogenetic trees that have been mapped to the common taxonomy and therefore can be used for any number of comparative purposes, and a number of computational tools to interact with all these resources or construct your own comprehensive tree of life.
Several publications associated with the Open Tree of Life have discuss these resources and tools (e.g., Drew et al. 2013, Smith et al. 2013, Hinchliff et al 2015, McTavish et al. 2015, Redelings and Holder 2017, Rees and Cranston submitted). And recently, we in the Smith lab, submitted a paper using the tree store to better understand how scientific consensus is formulated using birds as a test case and the Open Tree tree store (Brown et al. submitted). We also constructed a new comprehensive synthesis tree for birds.
The utility of the products developed by Open Tree of Life project will surely continue to grow as folks come up with new uses and learn how to interact with the tools. Below is one of those practical (but mostly fun) uses I played with yesterday.
Here, I wanted to discuss a fun and practical use of Open Tree resources that demonstrate the flexibility and modularity of the tools. Since the development of the Open Tree of Life, I have been curious about what phylogenetic trees look like for menu items, or, more generally, ingredients in particular food items. So, I put up a bunch of resources to do this in opentree_pytoys repo that demonstrate some of the uses of the different tools from Open Tree. First thing I decided to try (and honestly, no idea why) was Taco Bell Fire Border Hot Sauce:
with the ingredients “Tomato puree (tomato paste, water), jalapeno peppers, vinegar, modified food starch, chili powder, minced onion, onion juice, spices, natural flavors (contains wheat and soy), xanthan gum, salt, potassium sorbate and sodium benzoate (P), garlic powder, paprika (VC). Contains: Wheat, Soy” from Taco Bell. I figured the species involved in the ingredients listed above include:
- Solanum lycopersicum
- Capsicum annuum
- Allium cepa
- Triticum aestivum
- Glycine max
- Xanthomonas campestris
I got taxonomy ids from Open Tree, pruned the draft 9.1 tree of life, and produced the pruned tree. The full instructions are here and result in this tree:
Pretty fun! Going to try out a bunch more and post them.
I would love to gather a bunch of these together in one place. So I am putting the list of things in the name_science_food repo on GitHub. However, for now, it is a bit ad hoc. If anyone has any ideas, I am all ears. Otherwise, we will see how this goes and keep adding.
One thing I am, as of yet, unsatisfied with is how these are visualized. So I am thinking of connecting to PhyloPic so that these can automatically be added to the trees. But, right now, that is just added to the long to-do-list. Anyone want to help?
In order to more efficiently do this, I have started a GitHub repo that is just a list with
common ingredient name, Scientific name, ottid and can be found here. If you want to contribute, all are welcome!
I am going to continue to play with these “phylogenetic ingredient trees” (can I coin the acronym “PITs”) but hopefully this also demonstrates some of the modularity of the tools from Open Tree.