Herbert Sauro/Michael Galdzicki (Washington): Building Ontologies and Standards in Systems Biology (CBO 2009)
Herbert Sauro and others in the systems biology communities started with the modelling language and then went into ontologies. SBML is used to represent homogeneous multi-compartmental biochemical systems. You can have discrete events that either come from the outside or are generated internally. SBML started in ’99/’00, and now over 160 tools support SBML, and SBML files are accepted at a number of journals including Nature, Science and PLoS. CellML is philosophically different from SBML, as the former is math-centric and the latter is biology-centric.
In systems biology, SBML and related tools have allowed useful collaborations that were not available before. However, SBML is a common syntax, and what was also needed was a common semantics. The SemGen Annotator software is used to attach meaning to mathematical models, which can be loaded into a database such as BioModels.
Galdzicki had a reference to SED-ML, which would allow semantically-enriched publications to aid the interpretation of results. For instance, you could click on a figure of a model and be taken to a web application that can run the simulation for you. (Personal Note: there is an interesting paper about semantically marking-up publications: .)
In conclusion, remember that the use of an ontology must be an important criterion in its design.
Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!