SWUG:Topics for future meetings

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This page should be treated like a whiteboard - feel free to note down any ideas


We have many excellent visualisation tools in the consortium - Mary's orthology graphs (add link), John's new graph explore (link to demo). There are also tools outside the consortium (eg QuickGO, CytoScape) that have popular visualisation paradigms. We should discuss the technical implementations of all these, and how better to share and reuse software and libraries

(schedule: dependent on WebEx)


  • Source
  • ID mapping
  • serial homology
  • Display
  • Database and API changes


  • New requirements
  • Faster loading
  • MySQL vs PostGreSQL
  • GODB Schema vs Chado vs OBD vs Others
  • Future of the API
  • Better integration with oboedit

ID Mapping

See ID Mapping Requirements

Fast google-like text searches in obo-edit and amigo

  • Lucene

The evolution of GO and the OBO model

  • new relations (regulates)
  • links between 3 GO ontologies
  • intra-ontology cross products (regulation graph and SO)
  • inter-ontology cross products
  • post-compositing terms at annotation time
  • obo-format 1.3

GO, The Semantic Web, RDF and OWL

  • introduction to OWL
  • other bio-ontologies groups using OWL (BioPAX, OBI, HCLS, ...)
  • what can this community offer us?
  • what can and should we offer them?

Community Annotation

Do we need to pay attention to the wiki meme?


How do the various software components developed by the SWUG fit together? Can we make things more seamless?


Timeline for the next few years