Pathways and Models Workgroup

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The Pathways and Models Workgroup is the BioPAX workgroup that deals with the intersection of pathways and models. By pathway, we mean any set of linked interactions or processes that can be expressed by BioPAX. By model, we mean any data structure used to compute predictions. This includes relationships between BioPAX and quantitative data, simulations, SBO, SBML, CellML and simulators like the Virtual Cell.

Chair: Oliver Ruebenacker

Forum

The Pathways and Models Workgroup has a forum on Google Groups which is here. Feel free to join either by going there or by sending an empty e-mail message to this address.

Topics

  • Provide Tools to use pathway data to:
    • Create models: Generate a new model or adding elements to an existing model.
    • Annotate models: Add information to a model that helps identify things corresponding to elements of the model.
  • Provide tools to use model data to:
    • Extract pathways: Generate a BioPAX dataset that represents the interactions or processes corresponding to a model.
    • Reference models and model elements: Create a cross-reference from a BioPAX dataset to an element in a model.
  • Extend BioPAX to support:
    • Kinetic data: add data related to measuring interactions and processes
    • Rule-based pathways (like rule-based models): formulate rules that determine what interactions are possible, from which specific interactions can be derived.
    • Systems and views of systems: express facts related to specific systems, or to specific views or reference frames.

Proposals

SBPAX3 - Adding Kinetic Data and other Systems Biology Information

SBPAX3 is a proposal for a BioPAX extension to include kinetic data and other systems biology information in BioPAX, using systems biology vocabulary such as the Systems Biology Ontology (SBO).

UOME - Units of Measurement Expressions

Need some units of measurements? Here is a way to define them. But most likely, we already defined it for you.

Units of Measurement Expressions (UOME - pronounced "You Ohm") is a proposal for a BioPAX extension to express units of measurements. It consists of two parts: UOME core provides the means define almost any conceivable unit both by controlled vocabulary (such as the OBO Unit Ontology) and by constructing expressions to derive new units from others by multiplication, division, exponentiation, offsetting and rescaling. UOME list features a long list of thusly predefined units, intended to include any unit in common use.