TreeBASE CIPRES

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  • Phylogenetic web resources are often closed data silos, i.e.applications that do not interact with other applications or information systems. Until recently this has also been the case forTreeBASE2's development: it has been constructed such that data can only be accessed through the browser interface, and only be downloaded in NEXUS format. To make TreeBASE2 a resource that is visited more often in the research cycle then just when research results need to be deposited prior to publication, this situation has had to change. To this end, the development team has started to incorporate the tools and practices created by the EvoInfo working group( http: //evoinfo . nescent .org ) in TreeBASE2's architecture. Among these are: "cool URIs" to identify and de-reference phylogenetic data objects; a PhyloWS-compliant web service interface allowing programmatic access to TreeBASE2 data; database searching using Common Query Language constructs; data export in NeXML and RDF. I will describe what the implications of each of these are, and what additional functionality we expect to add in the near future.
  • TreeBASE CIPRES

    1. 1. Interoperability among phylogenetic data resources Rutger Vos University of British Columbia Recent additions to the TreeBASE2 architecture
    2. 2. Introducing TreeBASE3.0 <ul><li>… OMG already? Yes: </li></ul><ul><li>A Web3.0, triples-aware community resource </li></ul>
    3. 3. Triples? <ul><li>A triple is a statement </li></ul>subject predicate object Using triples to describe data frees us from the constraints of a relational schema
    4. 4. Community standards <ul><li>Technologies for bootstrapping TreeBASE to 3.0: </li></ul>Image: EvoInfo
    5. 5. PhyloWS data access <ul><li>Permanent , simple, predictable URLs </li></ul><ul><li>Every object a resolvable resource </li></ul><ul><li>Objects can be found using CQL </li></ul><ul><li>Resources can be serialized in various formats </li></ul>
    6. 6. PhyloWS URL API http://purl.org phylo treebase phylows study/TB2:S1787 / / / / Permanent URL resolver domain Subdomain for any phylogenetic resource Subdomain for TreeBASE Subdomain for PhyloWS API Object ID
    7. 7. External links Taxon Taxon variant Study
    8. 8. NeXML data syntax <ul><li>Predictable, concise syntax for core objects </li></ul><ul><li>I/O in various libraries, applications and web services </li></ul><ul><li>Transforms to &quot;fat-free&quot; JSON </li></ul><ul><li>Extensible with annotations using RDFa </li></ul><ul><li>Transforms to semantically explicit CDAO </li></ul>
    9. 9. CDAO data semantics <ul><li>Well-defined semantics of core objects and concepts </li></ul><ul><li>Extensible using predicates and objects from other ontologies </li></ul><ul><li>Can be queried using SPARQL </li></ul>
    10. 10. What's next? <ul><li>Add CREATE/UPDATE programmatic access </li></ul><ul><li>Make TreeBASE extensible with additional annotations using external triple store </li></ul><ul><li>Make TreeBASE LinkedData compliant </li></ul>
    11. 11. Acknowledgements <ul><li>pPOD </li></ul><ul><li>NESCent </li></ul><ul><li>GSoC </li></ul><ul><li>VDC </li></ul><ul><li>DBCLS </li></ul><ul><li>Hackathon attendants </li></ul><ul><li>CIPRES </li></ul>

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