Synthesising disparate data resources to obtain composite estimates of geophylogeny

SYNTHESISING DISPARATE DATARESOURCES TO OBTAIN COMPOSITEESTIMATES OF GEOPHYLOGENYRutger Vos

A simple assignment? Refine a tree for the Primates with taxonomic and systematic data Add divergence dates Add occurrence data Visualize the result Use public web services

Actually not so easy…

The Tree of Life Web Service  Using PhyloWS we traversed the Tree of Life and built a local, semantically annotated copy of the Primate clade

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 TimeTreePhyloWS service allowed us to anchor molecular (i.e. relative) node ages on absolute dates

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

Visualizing the result

Implementation Except for GBIF, all services:  returnNeXML  implement PhyloWS Semantic annotations using RDFa Glued together with Perl

Challenges  Although some services have the same API, no GUI exists to chain them together  No web services for computationally intensive steps  Data and metadata are messy and sparse

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

Shameless plug: PhyloTastic  A web service to extract subsets of taxa from megatrees and annotate them  Deliverable of the first HIP hackathon, at NESCent, in June 2012

Acknowledgements

Synthesising disparate data resources to obtain composite estimates of geophylogeny

by Rutger Vos on May 10, 2012

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