| | 1 | =Overview= |
| | 2 | |
| | 3 | 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. |
| | 4 | |
| | 5 | The broader scope of this discussion is titled '''OpenBioSemantics''' rather than simply '''Ontology'''. |
| | 6 | |
| | 7 | =Proceedings= |
| | 8 | |
| | 9 | =Summary of Day 1 Discussions (11th Feb. Afternoon AcademyHills)= |
| | 10 | |
| | 11 | ==Preliminary Observations== |
| | 12 | |
| | 13 | 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. |
| | 14 | |
| | 15 | * Object models: expressed in UML (e.g. OMG style "Model Driven Architecture" using Unified Modeling Language (UML)) |
| | 16 | * Ontology initiatives |
| | 17 | ** OBO format driven: e.g. Gene Ontology (GO), Sequence Ontology (SO), etc. |
| | 18 | ** OWL format initiatives: OBI |
| | 19 | * XML Schema driven languages: EMBRACE, BioCase/Tapir, etc. |
| | 20 | * Common Database Schemata and Queries: BioSQL, Generic Model Organism (GMOD) Chado, [wiki:http://www.icis.cgiar.org International Crop Information System], etc. |
