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.  OpenBio* initiatives)
• Data Formats: expressed as standard, human readable semi-structured text (e.g. sequence formats: FASTA, Genbank, EMBL)
• 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,  Generic Model Organism (GMOD) Chado,  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  BioMoby and  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).