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: implied semantics expressed as an API and 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 Unified Modeling Language (UML) (e.g.  Functional Genomics Experiment model and  Generation Challenge Programme domain model)
• Ontology initiatives:
  • OBO format driven: e.g.  Gene Ontology (GO),  Sequence Ontology (SO), etc.
  • OWL format initiatives:  Ontology for Biomedical Investigations
• XML Schema driven languages:  EMBRACE WS-I,  TDWG ABCD schema in !BioCase+Tapir, etc.
• Common Database Schemata and Queries: BioSQL,  Generic Model Organism (GMOD) Chado,  International Crop Information System, etc.
• Web Service Protocol Data Types: e.g.  BioMoby data type object hierarchy

At this meeting, a general desire is being expressed to achieve some level of 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). Efforts should and generally are, driven by a specific set of practical tasks in the community, on an "as needed" basis. The expectation to create a consensual "mother-of-all-biological-data-models" is most likely unrealistic, but can some agreement on the general principles, process and tools of semantic collaboration be achieved?