Difference between revisions of "L4Workgroups"

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BioPAX Level 4 Workgroups
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=BioPAX Level 4 Workgroups=
  
An outline of the Level4 Workgroups suggested at the November 2009 meeting in NYC are listed below.
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Five Level 4 Workgroups were suggested at the November 2009 meeting in NYC.
  
*'''Visualization and exchange'''
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*'''[http://sourceforge.net/apps/mediawiki/biopax/index.php?title=VisualisationExchange  Visualization and exchange]''' Status: Started - Point of Contact [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=MartijnVanIersel  Martijn Van Iersel]
The option of an extension to BioPAX to deliver layout (basic coordinates).
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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.
After a long discussion in Novemeber, it was agreed that this would be a duplication of work and that 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.
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*'''Semantics: Generics/polymers/logic/''' Status: Initiated - Emek Demir
*'''Semantics: Generics/polymers/logic/'''
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Works toward extending BioPAX e.g. to enable the capture and exchange of generic reactions and generic pathways and extensions to the entityreference class.
This would encompass extending BioPAX to enable the capture and exchange of generic reactions and generic pathways and extensions tot he entityreference class.
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*'''[http://sourceforge.net/apps/mediawiki/biopax/index.php?title=Semantic_web/linking/CVs Semantic web/linking/CVs] ''' Status: Started  - Point of Contact [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=AndreaSplendiani  Andrea Splendiani]
*'''Semantic web/linking/CVs '''
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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.
Semantic web community wish list including Linked Data Project, Linking to other ontologies and ontology mapping, additional controlled vocabularies and architecture of controlled vocabularies were all areas where BioPAX needed improvement.
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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]
*'''Validation/best practices'''
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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].
Form rules and best practices for data and documenting and delivering these into the BioPAX validator.
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*'''[http://sourceforge.net/apps/mediawiki/biopax/index.php?title=Pathways_and_Models_Workgroup Pathways and Models]''' Status: Active - Point of Contact [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=Oliver_Ruebenacker Oliver Ruebenacker]
*'''Quantitative modeling vs. static relationship/SBML/CellML/VirtualCell'''  
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The [http://sourceforge.net/apps/mediawiki/biopax/index.php?title=Pathways_and_Models_Workgroup Pathways and Models Workgroup] deals with the intersection of pathways and models. By pathway, we mean any connected system of 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,
With respect to reaction rates and rate laws, some people using BioPAX would like to have a stronger link between BioPAX and SBML.
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simulations, [http://www.ebi.ac.uk/sbo/main/ SBO], [http://www.sbml.org SBML], [http://www.cellml.org CellML] and simulators like the [http://vcell.org Virtual Cell].
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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Latest revision as of 21:33, 15 July 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.

The Pathways and Models Workgroup deals with the intersection of pathways and models. By pathway, we mean any connected system of 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.