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SBGN-PD Specification Updates: Enhancing Clarity and Semantics for Computational Validation

Explore the evolution of the SBGN-PD specification from Version 1.1 to the upcoming Level 1 Version 2.0, focusing on glyph ontology, semantic enhancements, and organizational improvements. Learn about new glyphs, rules enumeration, and roadmap for computational validation. Stay informed on unresolved issues and future changes.

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SBGN-PD Specification Updates: Enhancing Clarity and Semantics for Computational Validation

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  1. SBGN PD Current status, future changes and unresolved issues Harmony 2011 NYC

  2. PD Specification • Level 1 Version 1: Sep 2008 • Original specification • Level 1 Version 1.1: Sep 2009 • Fixed inconsistencies • Typos • Clarified “ontology” of glyphs • Nomenclature changes for consistency with other languages • Level 1 Version 1.2: Oct 2010 • Level 1 Version 1.3: Feb 2011 • Minor changes of clarity • Document errors • Level 1 Version 2.0 Apr/May 2011

  3. What’s in Version 2.0 • New/Modified Glyphs • Resolving semantic “issues” • Enumerated rules • Improve organisation/clarity of the spec

  4. Level 1 Version 2.0: Glyphs New Annotation Glyph State Glyph Change Empty Set Reversible Arc

  5. Synthetic Unique Names Confusing but correct? Level 1 Version 2.0: Semantics Subunits are not EPNS

  6. Level 1 Version 2.0: Semantics Process Duplication A A ZZZ ZZZ B B YYY YYY C C XXX XXX LABEL

  7. Level 1 Version 2.0: Semantics Source and Sink => Empty Set A Source Empty Set P A Sink

  8. Level 1 Version 2.0: Spec • Focus more on EPN types rather than glyphs • Integrate clone marker section • Integrate multimer section • Integrate semantic rules into glyphs • Enumerate rules – facilitate computational validation

  9. Road Map for PD • Level 1 Version 2.0 • Draft for Review: May 2011 • RFC: 2-3 Weeks • Release June 2011 • Tool support! • Level 2 Version 1.0 • Theme: RISC notation? • Start work in Harmony 2012? • Release First Draft COMBINE 2012?

  10. ER Issues • Delay • Can arrow come from entity • Can’t define initial state • Outcome not an Entity

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