Current Research into Reasoning over BioPAX and SBML

What’s going on these days in the world of reasoning and systems biology modelling? What were people’s experiences when trying to reason over systems biology data in BioPAX and/or SBML format? These were the questions that Andrea Splendiani wanted to answer, and so he collected three of us with some experience in the field to give 10-minute presentations to interested parties at a BioPAX telecon. About 15 people turned up for the call, and there were some very interesting talks. I’ll leave you to decide for yourselves if you’d class my presentation as interesting: it was my first talk since getting back from leave, and so I may have been a little rusty!

The first talk was given by Michel Dumontier, and covered some recent work that he and colleagues performed on converting SBML to OWL and reasoning over the resulting entities.

Essentially, with the SBMLHarvester project, the entities in the resulting OWL file can be divided into two broad categories: in silico entites covering the model elements themselves, and in vivo entities covering the (generally biological) subjects the model elements represent. They copied all of BioModels into the OWL format and performed reasoning and analysis over the resulting information. Inconsistencies were found in the annotation of some of the models, and additionally queries can be performed over the resulting data set.

I gave the second talk about my experiences a few years ago converting SBML to OWL using Model Format OWL (MFO) (paper) and then, more recently, using MFO as part of a larger semantic data integration project whose ultimate aim is to annotate systems biology models as well as create skeleton (sub)models.

I first started working on MFO in 2007, and started applying that work to the wider data integration methodology called rule-based mediation (RBM) (paper) in 2009. As with SBMLHarvester, libSBML and the OWLAPI are used in the creation of the OWL files based on BioModels entries. All MFO entries can be reasoned over and constraints present within MFO from the SBML XSD, the SBML Manual, and from SBO do provide some useful checks on converted SBML entries. The semantics of SBMLHarvester are more advanced than that of MFO, however MFO is intended to be a conversion of a format only, so that SWRL mappings can be used to input/output data from MFO to/from the core of the rule-based mediation. Slide 8 of the above presentation provides a graphic of how rule-based mediation works. In summary, you start with a core ontology which should be small and tightly-scoped to your biological domain of interest. Data is fed to the core from multiple syntactic ontologies using SWRL mappings. These syntactic ontologies can be either direct format conversions from other, non-OWL, formats or pre-existing ontologies in their own right. I use BioPAX in this integration work, and while I have mainly reasoned over MFO (and therefore SBML), I do also work with BioPAX and plan to work more with it in the near future.

The final presenter was Ismael Navas Delgado, whose presentation is available from Dropbox. His talk covered two topics: reasoning over BioPAX data taken from Reactome, and the use of a database back-end called DBOWL for the OWL data. By simply performing reasoning over a large number of BioPAX entries, Ismael and colleagues were able to discover not just inconsistencies in the data entries themselves, but also in the structure of BioPAX. It was a very interesting summary of their work, and I highly recommend looking over the slides.

And what is the result of this TC? Andrea has suggested that, after discussion on the mailing list (contact Andrea Splendiani if you are not on it and want to be added) and then have another TC in a couple of weeks. Andrea has also suggested that it would be nice to “setup a task force within this group to prepare a proof of concept of reasoning on BioPAX, across BioPAX/SBML, or across information resources (BioPAX/OMIM…)”. I think that would be a lot of fun. Join us if you do too!

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