What is the tree of lifeI present a simple idea, illustrated with a workflowWorkflow is based on PhyloWS, a URL API started at BH08Workflow uses semantic annotation using RDFa
*workflow developed at thecomphy course here in Kyoto*students learned how to operate on phylogenetic data using Bio* toolkits*one of the problem sets was on how to build a large phylogenetic tree and annotate it using web services.
*first we used ToL PhyloWS service*what is tolweb?*what does the service return?*students learned recursion by grafting children on their parent*service also returned metadata
*then we used uBio PhyloWS service*what is uBio?*what does the service return?*we expanded unresolved genera into their species*we also fetched linkout metadata
*one of the links out point to TreeBASE*what is TreeBASE?*fetched source trees to further resolve skeleton using supertree approach
*another uBio annotation is NCBI taxon IDs*we used this to access TimeTree PhyloWS service*what is TimeTree?*used node ages to anchor molecular branch lengths
*also accessed GBIF, which is not PhyloWS, but an XML REST API*what is GBIF?*what does it return?*we attached lat/lon coordinates to nodes in our tree
*now we have a topology…*and taxonomic statements*and age estimates*and paleontological data*and biogeographic data*we can view all these data in different ways, e.g. in google earth*we can see strepsirrhines, lemurs, lorises, old world monkeys and new world monkeys
*the tree of life can be overgrown with metadata*like epiphytes on a tree in a rainforest*we can view these metadata in different ways*unfortunately, services still need a lot of work: standards adoption, choosing the best predicates and values, identifiers!
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
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