What is SBGN? Limited amount of symbols (~30) Smooth learning curve
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1 SBGN Update
2 What is SBGN? A way to unambiguously describe biochemical and cellular events in graphs Graphical representation of quantitative models, biochemical pathways, at different levels of granularity Limited amount of symbols (~30) Smooth learning curve Can be translated into executable models, can graphically represent models (e.g. SBML, BioPAX), but can also exists independently Three languages Process Descriptions one state = one glyph Entity Relationships one entity = one glyph Activity Flow conceptual level
3 Three Languages in One Process Description maps Entity Relationships maps Activity Flow maps Unambiguous Mechanistic Sequential Combinatorial explosion Unambiguous Mechanistic Non-Sequential Ambiguous Conceptual Sequential
4 Three Languages in One Process Description Entity Relationships Activity Flow
5 Connection to other Standards From Demir et. al. (2010) Nat. Biotechn. 28:
6 Application Examples Maps from SBGN best map contests
7 Web Page
8 Software From Junker et. al. (2012) Nat. Protocols. 7(3):
9 Governance Editors Scientific committee
10 Last meeting
11 Documentation Split There was a technical specification only Too technical Focused on tool developers It was decided to split documentation into two parts Technical Specification: normative official description of the language User Manual: description of the use of language to teach end users User Manual is available for SBGN PD
12 Specification Status Update Fist draft of a user manual is available for SBGN PD Level 1 Version Manual/sbgn_PD-level1-user.pdf A first draft of SBGN PD Level 1 Version 2 (including user manual) is ready for review fication/sbgn_pd-level1.pdf A draft of SBGN ER Level 1 Version 2 is available for review n_er-level1.pdf A draft of SBGN AF Level Version 1.1 is available for review
13 Update SBGN PD Specification
14 Update SBGN 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: Q1 2014
15 What s in Version 2.0 New/modified Glyphs Resolving semantic issues Enumerated rules Improve organisation/clarity of the spec
16 Resolved Issues State glyph change New annotation glyph Callout Complex subunits are decorators EPN?????????????????? Empty set?????????????
17 Level 1 Version 2.0: Semantics Process Duplication A ZZZ A ZZZ B YYY B YYY C XXX C XXX
18 Level 1 Version 2.0: Semantics Source and Sink Empty Set A Source Sink B P
19 Level 1 Version 2.0: Semantics Source and Sink Empty Set A Empty Set B P
20 Cardinality Glyph
21 Road Map for PD Level 1 Version 2.0 Draft for Review: Q RFC: 2-3 Weeks Release Q2 2014
22 Update SBGN ER Specification
23 Entity Nesting
24 Road Map for AF Level 1 Version 2.0 Draft for Review: Q RFC: 2-3 Weeks Release Q2 2014
25 Update SBGN AF Specification
26 AF Phenotype HARMONY decision about how to deal with phenotype, no objections on mailing list The Activity Flow glyph for biological activity - phenotype
27 Road Map for AF Level 1 Version 1.1 (or 2.0) Draft for Review: Q RFC: 2-3 Weeks Release Q2 2014
28 Topics This Session SBGN survey The LEGO project from Gene Ontology - How SBGN can support it What is the optimal representation of a generalized metabolic model using SBML and SBGN? Identity gates
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