= Overview = Most of the discussions at this hackathon deal with technology issues relating to interoperability. A few of the discussions are discuss OpenBio* "platform specific implementations" - language APIs (BioRuby, BioJava, BioPerl, etc.), web service protocols (BioMoby ''et. al.'') and database implementations (i.e. BioSQL). A general issue relating to harmonization of community semantics or, at least, establishing a community process for semantics management, is recognized. This OpenSpace discussion is targeting this issue for further progress. The broader scope of this discussion is titled '''OpenBioSemantics''' rather than simply '''Ontology'''. = Convenor/faciltator: Richard Bruskiewich = = Proceedings = = Summary of Day 1 Discussions (11th Feb. Afternoon !AcademyHills) = == Preliminary Observations: Framing the Problem == Cathedral versus the Bazaar: the global community of bioinformatics are struggling with the issue of semantics, and various formalisms are currently being used to capture such semantics, i.e. * '''Formal Code Implementations:''' expressed as a body of computer code (e.g. [http://www.open-bio.org/wiki/Main_Page OpenBio*] initiatives) * '''Object models:''' expressed in UML (e.g. OMG style "Model Driven Architecture" using Unified Modeling Language (UML)) * '''Ontology initiatives:''' * '''OBO format driven:''' e.g. Gene Ontology (GO), Sequence Ontology (SO), etc. * '''OWL format initiatives:''' OBI * '''XML Schema driven languages:''' EMBRACE WS-I, !BioCase, Tapir, etc. * '''Common Database Schemata and Queries:''' BioSQL, [http://www.gmod.org Generic Model Organism (GMOD) Chado], [http://www.icis.cgiar.org International Crop Information System], etc. At this meeting, a general desire is being expressed to achieve interoperability, at least, between OpenBio* initiatives generally, and more specifically, between OpenBio* and web services protocols like BioMoby and EMBRACE. An addition targeted need is simply to harmonize specific ontology pertinent to key interoperability technology. A specific example of such a need (from M. Wilkinson) is the harmonization of [http://www.biomoby.org BioMoby] and [http://www.mygrid.ac.uk myGrid] service ontology. It is generally agreed that semantics is a hard community problem ("herding the cats") but can be made tractable by "divide and conquer" (witness the relative success of GO and other similar ontology development communities).