Difference between revisions of "L4Workgroups"

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(BioPAX Level 4 Workgroups: added the link to ValidationWorkgroup page (new))
(New name and description for Pathways and Models Workgroup)
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*'''[http://sourceforge.net/apps/mediawiki/biopax/index.php?title=ValidationWorkgroup Validation and best practices]''' Status: Initiated - Point of Contact [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=Igor_Rodchenkov Igor Rodchenkov]
 
*'''[http://sourceforge.net/apps/mediawiki/biopax/index.php?title=ValidationWorkgroup Validation and best practices]''' Status: Initiated - Point of Contact [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=Igor_Rodchenkov Igor Rodchenkov]
 
Develop rules and best practices for data and documenting and deliver these into the [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAXValidator BioPAX validator].
 
Develop rules and best practices for data and documenting and deliver these into the [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAXValidator BioPAX validator].
*'''Quantitative modeling vs. static relationship/SBML/CellML/VirtualCell'''  Status: Started - Point of Contact [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=OliverRuebenacker  Oliver Ruebenacker]
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*'''[http://sourceforge.net/apps/mediawiki/biopax/index.php?title=PathwaysAndModels Pathways and Models]'''  Status: Active - Point of Contact [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=OliverRuebenacker  Oliver Ruebenacker]
With respect to reaction rates and rate laws, some BioPAX users would like to have a stronger link between BioPAX and SBML.
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This workgroup deals with the intersection of pathways and model. By model, we mean any data structure used to compute predictions. This includes relationships between BioPAX and quantitative data,
In order to provide a technical link between BioPAX and SBML, this group will create a proposal and help to define a better bridge between the two languages and ultimately delegate to SBML.
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simulations, SBML and CellML.

Revision as of 19:37, 18 May 2011

BioPAX Level 4 Workgroups

Five Level 4 Workgroups were suggested at the November 2009 meeting in NYC.

The option of an extension to BioPAX to deliver layout (x,y coordinates only). A complete visualization extension for BioPAX would be a duplication of work and eventually SBGN will provide visualization exchange. In the interim, a workgroup could formulate a simple format for pathway visualization. This group would coordinate with SBGN.

  • Semantics: Generics/polymers/logic/ Status: Initiated - Emek Demir

Works toward extending BioPAX e.g. to enable the capture and exchange of generic reactions and generic pathways and extensions to the entityreference class.

Semantic web community wish list including Linked Data Project, Linking to other ontologies and ontology mapping, additional controlled vocabularies and architecture of controlled vocabularies are all areas where BioPAX needed improvement.

Develop rules and best practices for data and documenting and deliver these into the BioPAX validator.

This workgroup deals with the intersection of pathways and model. By model, we mean any data structure used to compute predictions. This includes relationships between BioPAX and quantitative data, simulations, SBML and CellML.