Tree of Life

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Full title: "The tree of life as central unifying artefact for the integration of phylogenetic knowledge." This is a brief intro presentation for the 2011 BioHackathon in Kyoto, Japan. I describe a simple workflow built around semantic web services that add metadata to a backbone of the Tree of Life. The take home message is that such a structure can be a useful anchor to which knowledge can be attached, but that there are still issues with standards definition and adoption.

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Tree of Life

  1. 1. The Tree of Life as central unifying concept for the integration of phylogenetic knowledge<br />Rutger Vos<br />University of Reading<br />
  2. 2. A simple example<br />At the Computational Phyloinformatics course two weeks ago, we worked through an example that explains the title of my talk<br />
  3. 3. The Tree of Life Web Service<br />Using PhyloWS we traversed the Tree of Life and built a local, semantically annotated copy of a clade of interest<br />
  4. 4. Adding taxonomic metadata<br />Using the uBio PhyloWS service we enhanced our tree with further taxonomic annotations and links, and expanded some genera<br />
  5. 5. Fetching additional tree data<br />Using the TreeBASE PhyloWS service we fetched additional data to resolve the tree further using a “supertree” approach <br />
  6. 6. Computing node ages<br />The TimeTree PhyloWS service allowed us to anchor molecular (i.e. relative) node ages on absolute date estimates<br />
  7. 7. Adding occurrence data<br />Using the GBIF XML API, we then fetched occurrence records for the species in our tree<br />
  8. 8. Visualizing the result<br />
  9. 9. Conclusions<br />The tree of life can be covered with all sorts of metadata (taxonomic, molecular, biogeographic, paleontological), viewable in different ways<br />Standards still incompletely defined and adhered to, though<br />

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