The Physiome: Standardizing the Physiome

A closer look at the curation of models discussed in The Physiome: A Mission Imperative

Multi-scale quantitative models need to be validated and reproducible if they are to be useful for clinical workflows, says Hunter. The Physiome infrastructure developed by Hunter, Dr Poul Nielsen and their colleagues (and provided at makes that process more robust and transparent, he says. Researchers can confidently download an annotated model from knowing that it’s reproducible. The model can then be incorporated into larger scale workflows for use in a clinical setting.


“Having the means to incorporate the outputs of different groups through standards and interoperability is quite a worthwhile goal,” Hunter says. “And an essential one if we’re to get the modeling of biology into clinical processes.”  
Models held by the model repository use CellML, a markup language for biophysical models of cells. A repository at the European Bioinformatics Institute (EBI) contains models marked up with SBML, a language for systems biology models.  Hunter’s group is also creating a new standard called FieldML for integrating spatial information. In recent years, Hunter says, the CellML and SBML communities have become more integrated. “SBML and CellML are now working together jointly to curate models and develop standards around metadata.”


From funding agencies’ point of view, “We don’t want people to have to reinvent models,” Peng says. But at this point, “The different formats are all co-existing.  No one wants to stand up and say one is better than another.”


It’s also true that some multi-scale models require information that goes beyond what CellML or SBML can provide, McCulloch says. “It’s not possible to describe everything in our cardiovascular model using that system.” So McCulloch is building a database that includes metadata about his models that will be consistent with CellML and other model description formats but goes beyond them to include additional information.


Nic Smith agrees that standards are useful for sharing between different academic centers, but he says, an important step to embedding multi-scale models in clinical workflows is a demonstration that they add extra information that can be made available to physicians in a familiar format. “We are working on developing interfaces and putting them in a context where physicians are used to seeing them—in connection with imaging and clinical data accessed directly from the hospital’s computer system."

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