Suggestions for formal definition of graphical notation

Transcription

1 Suggestions for formal definition of graphical notation Fedor Kolpakov Institute of Systems Biology Laboratory of Bioinformatics, Design Technological Institute of Digital Techniques Novosibirsk, Russia

2 Motivation We need different diagram types to describe biological systems and pathways taking into account: different levels of abstraction and details peculiarities of existing databases (KEGG, TRANSPATH, BioCyc, GeneNet, etc.) formats for biological pathways and models (SBML, BioPAX, CellML, etc.) We need formal definition of graphic notation suitable both for human and computer. We need basic software architecture for rendering of biological models according to specified graphic notation and layout information.

3 SBML layout extension Why it is not enough? SBML layout extension allows only to visualize only diagrams that are already created and layoutted by some SBML-enabled tool The behavior is undefined for following situations: Adding new element to the diagram How new element will look like? Remove element from diagram May be some related elements should be removed too. For example if we will remove some specie then all related chemical reactions should be removed too. Move element on the diagram An element can be a part of complex and you can move only corresponding complex. Change element properties Possibly element image should be updated to visualize element properties.

4 Process diagram example (fragment)

5 Process diagram example (fragment) Need to formalize: - Object properties - Their mapping into SBML - Rules for objects and their properties visualization

6 BioUML experience A number of diagram types was developed for: Description of biological pathways on different levels of abstraction and details; for visualization of information from several databases, taking ito account their peculiarities (KEGG, TRANSPATH, GeneNet, BMOND/Biopath) visualization of biological pathways and models described for following formats: SBML, CellML, GinSim, GML, BioNetGen, BioPAX (under development). Graphic notation was defined formally as a set of Java interfaces. Software architecture for rendering of biological models according to specified graphic notation and layout information was developed.

7 Reconstruction and formal description of biological systems using different diagram types Formality, details 1. Semantic network Semi structured data 2. Pathway diagram (semantic network + gene network or metabolic pathway) 3. Metabolic pathway 3. Gene network Structured data (reactions and its components) 4. Pathway simulation (mathematical model) Kinetic data (kinetic laws, constants, initial values

8 Graphic notation

9 Stimulus activating NF-kappaB (semantic network, ontology)

10 The biosynthesis of catecholamines (metabolic pathway)

11 Cell cycle model of mammalian G1/S transition control with E2F feedback loops (pathway simulation diagram)

12

13 GeneNet diagram

14 KEGG pathway

15 CellML model

16 BioUML diagram type concept Diagram type defines: types of biological components and their interactions that can be shown on the diagram; diagram view builder - it is used to generate view for each diagram element taking into account problem domain peculiarities; semantic controller - provides semantic integrity of the diagram during its editing; filters hide or highlight diagram elements according to some selection criteria.

17 Suggestions for formal definition of graphical notation Formal definition of graphic notation as XML document. Integration between SBML format and graphic notation definition. General architecture of software for rendering (visualization) of models and database diagrams using specified graphic notation. SBGN or Process Diagrams as a test case.

18 Refined definition of graphic notation Object types (for example, protein, gene, reaction) Object properties (for example, complex, phosphorilated) User defined object properties - layout information (for example, size, color, location) Rules for objects and their properties visualization Rules for semantic control of diagram integrity Selection, highlighting, filtering

19 Formal definition of graphic notation as XML document and integration with SBML format Graphic notation components Defined as SBML element Object types XML <annotation> Object properties XML <annotation> User defined properties XML <layout> Rules for visualization JavaScript Rules for semantic control JavaScript Selection, highlighting Java Script

20 Why JavaScript It allows to implement complex logic for generation images for complex SBML elements It allows to invoke host environment (SBML-enabled tool) native functions. For this purpose hosting software tool can put into JavaScript context corresponding host objects and functions for access to model elements, graphical notation definition and image rendering. JavaScript interpreters/compilers available for major programming languages Java Rhino (Mozilla project), included into JDK 6 C, C++ Spider Monkey (Mozilla project, It is tested approach We have used XML documents that define mapping of text based formats into object model JavaScript functions were part of XML document for validating and processing text expressions XML documents were processed by Java and C++ programs.

21 JavaScript context SBML-enabled tool Native drawing and visualization functions JavaScript context JavaScript functions (interfaces defined by specification) Host object and functions (defined by API)

22 Basic software architecture for rendering of biological models according to specified graphic notation and layout information Diagram Rendering API JavaScript API for creating primitives similar with SBML layout extension Rendering engine JavaScript context JavaScript functions JavaScript API for data access Model API Notation API Layout API Initial data SBML BioPAX Graphic notation Layout information

23 SBGN or Process Diagrams as a test case (spike solution) We suggest to test our approach on SBGN or/and Process Diagrams. This work will include: Formal definition of graphic notation as XML document Integration with SBML format. Definition of API: Model API, Graphic notation API, Layout API Rendering API; Interfaces (JavaScript functions) for objects and their properties visualization semantic control of diagram integrity Developing of plug-in for BioUML workbench that will implement suggested architecture BioUML meta-model will be used as Model API and Layout API; BioUML DiagramType will be used as Graphic notation API; BioUML graphics library will be used as Rendering API; BioUML DiagramViewBuilder will be used as prototype for Rendering Engine.

24 Possible timetable October November initial implementation (spike solution according to XP exreme Programming - methodology) December draft of proposal

25 Why implementation is first, not proposal (specification) It is quite new BioUML team need more experience with SBGN or Process Diagrams Too many details We are following XP methodology

26 Acknowledgements Part of this work was partially supported by following grants: Volkswagen-Stiftung (I/75941), INTAS Nr RFBR Nr а Siberian Branch of Russian Academy of Sciences (interdisciplinary projects 46). Author is grateful to for useful comments, discussions and technical support Alexander Kel Sergey Zhatchenko Software developers Annotators Mikhail Puzanov Alexandr Koshukov Ruslan Sharipov Vasiliy Hudyakov Vlad Zhvaleev Elena Cheremushkina Oleg Onegov Igor Tyazhev Ekaterina Kalashnikova Artem Shaidukov