THE TREE OF LIFE AS CENTRAL UNIFYING CONCEPT FOR THE INTEGRATION OF PHYLOGENETIC KNOWLEDGE

Rutger Vos

University of Reading

A simple example

At the Computational Phyloinformatics course two weeks ago, we worked through an example that explains the title of my talk

The Tree of Life Web Service

Using PhyloWS we traversed the Tree of Life and built a local, semantically annotated copy of a clade of interest

Adding taxonomic metadata

Using the uBio PhyloWS service we enhanced our tree with further taxonomic annotations and links, and expanded some genera

Fetching additional tree data

Using the TreeBASE PhyloWS service we fetched additional data to resolve the tree further using a “supertree” approach

Computing node ages

The TimeTree PhyloWS service allowed us to anchor molecular (i.e. relative) node ages on absolute date estimates

Adding occurrence data

Using the GBIF XML API, we then fetched occurrence records for the species in our tree

Visualizing the result

Conclusions

The tree of life can be covered with all sorts of metadata (taxonomic, molecular, biogeographic, paleontological), viewable in different ways

Standards still incompletely defined and adhered to, though