Version 4 (modified by hlapp, 16 years ago)


At present there is no standard web-service API for phylogenetic data that would allow integration of phylogenetic data and service providers into the programmable web. Hence, current approaches to integrate data and services into workflows are highly specific to the integration platform (CIPRES, Bioperl, Bio::Phylo, Kepler), and nearly unusable in other environments.

Here are several ideas for tasks we can work on at the hackathon:

  • Defining scope
    • Issue of identifiers and OTUs
  • Accumulating use-cases
    • OTU-oriented queries:
      • Need ability to obtain sequence(s) and taxon (taxa) for a leaf (or generally, a node)
      • Finding trees by sequence (rather than the OTU name)
  • Formulating a task-oriented API requirements description
  • Proposing a concrete REST or SOAP-based API
  • Propose input/output formats
  • Start a reference implementation, for example based on data in BioSQL

Gathering of use-cases and task-oriented requirements has started at