TreeBASE is a public repository of peer-reviewed phylogenetic knowledge . Researchers submit their results to TreeBASE when they are writing a manuscript based on them for publication in a suitable journal. The submitted data are assigned permanent, unique identifiers and web addresses that authors can refer to in their article. Anyone can locate and access the data once the study has been published by TreeBASE and by the targeted journal. A prototype of this system has served the phylogenetics community well for a number of years, accumulating the results of thousands of studies. The usage model was that of a silo where data could only be accessed through a web browser, and only be downloaded in representations that omitted important associated metadata. A human with considerable expertise needed to read and interpret the web pages through which everything was served up to make sense out of what was available. This model is not always practical. For example, phyloinformatic research often uses so much data that automation is becoming necessary. Where human intervention is no longer feasible, machines – which are stupid – must be able to do the job instead; and they need to be told what is what. This has spurred more explicit standardization of the syntax and semantics of phylogenetic knowledge. The latest version of TreeBASE facilitates this by adopting a collection of community standards: • PhyloWS for automated searching using a contextual query language and retrieval using a clearly defined URL API. • NeXML for robust data syntax and flexible metadata annotation. • CDAO (and other ontologies) for defining the semantics of the metadata. We will present an overview of how these components work together to make phylogenetic knowledge accessible to machines on the semantic web. Using this new architecture, client side software (including off-the-shelve tools such as RSS readers) can query, transform and download TreeBASE data autonomously.

1. Rise of the machines Rutger A. Vos, Hilmar Lapp, William H. Piel, Val Tannen

7. PhyloWS Resource URI PURL domain Phylogenetics TreeBASE PhyloWS Object ID http://purl.org/phylo/treebase/phylows/study/TB2:S1787

10. External links Taxon Taxon variant Study

11. Example: Journal feeds prism.publicationName==Evolution

12. Example: UniProt sequences TreeBASE stores NCBI taxonomy identifiers Standard tools can rewrite these linkout URLs Result is a corresponding list of UniProt records

13. Example: ToLWeb pages TreeBASE maps to uBio using skos:closeMatch ... … and uBio to ToL using gla:mapping

14. Example: geocoding TreeBASE uses DarwinCore for lat/lon annotations

16. Acknowledgements