Version 1 (modified by r.bruskiewich, 10 years ago)



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.


=Summary of Day 1 Discussions (11th Feb. Afternoon AcademyHills?)=

==Preliminary Observations==

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.

* 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, BioCase/Tapir?, etc. * Common Database Schemata and Queries: BioSQL, Generic Model Organism (GMOD) Chado, International Crop Information System?, etc.