BioPAX (an introduction)

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BioPAX (an introduction)
Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012

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BioPAX (an introduction)

  1. 1. BioPAX (an introduction) Andrea Splendiani (BioPAX editor) Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  2. 2. BioPAX (an introduction) •What •How •Why Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  3. 3. BioPAX: Biological Pathway Exchange (language) •What is BioPAX ? Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  4. 4. BioPAX: Biological Pathway Exchange (language) •What is BioPAX ? Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  5. 5. BioPAX: Biological Pathway Exchange (language) •What is a pathway ? Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  6. 6. Examples: biochemical pathway • Regular structure • Enzymatic activity Source: http://www.genome.jp Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  7. 7. Examples: signaling pathway • Semi-regular structure • Activation/ inhibition • Compartments • “Antigen” Source: http://www.genome.jp Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  8. 8. Example: wikipathways • Well defined set of relations and symbols Source: http://www.wikipathways.org/index.php/Pathway:WP49 Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  9. 9. Example: “informal” descriptions Sources: http://www.biocarta.com http://www.singulex.com/images/cytokine_pathway_Th1.png Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  10. 10. Example: SBML • Pathway a set of reactions • Dynamic aspects/ modeling Source: http://www.biomodels.net Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  11. 11. Example: SBML • Pathway a set of reactions • Dynamic aspects/ modeling Source: http://www.biomodels.net Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  12. 12. Example: SBML • Pathway a set of reactions • Dynamic aspects/ modeling Source: http://www.biomodels.net Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  13. 13. Example: SBGN • Systems Biology Graphic Notation: • Process Description • Entity Relationship • Activity Flow Source: http://www.sbgn.org Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  14. 14. Example: “Reactome” • One big reaction network instead of pathways Source: http://web.expasy.org/cgi-bin/pathways/show_thumbnails.pl Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  15. 15. Example: network biology • Interactome • p-p interactions • genetic interactions Source: http://nd.edu/~networks/Image%20Gallery/gallery.htm#Biological Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  16. 16. Example: Gene Ontology • GO: Biological Process Source: http://www.sciencedirect.com/science/article/pii/S0012160611001758 Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  17. 17. What is a pathway ? • Pathways can be different kind of systems: biochemical reaction networks, signaling networks, “abstract” interaction networks • Detailed description vs coarse descriptions (kegg vs GO) • Static maps vs dynamic systems (Kegg vs SBML) • Pathways vs holistic view of of interactions Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  18. 18. What is BioPAX ? • Biological Pathway Exchange Language: • A language to represent different types of pathways • A language to enable interoperability of different pathway representations • = Integration Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  19. 19. What is BioPAX ? • Biological Pathway Exchange Language: • A language to represent different types of pathways • A language to enable interoperability of different pathway representations • = Integration Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  20. 20. What is BioPAX ? •Pathways and computation Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  21. 21. Example: over-representation analysis • Correlation between processes (annotation) and experimental evidence Andrea Splendiani Source: BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 http://www.springerimages.com/Images/LifeSciences/5-10.1186_1471-2229-10-85-7 martedì 22 ottobre 13
  22. 22. Example: network analysis • Clustering • Centrality measures (betweeness) • Systems properties (scale free networks) Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  23. 23. Example: dynamic simulations Source: http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=ModelMonth%2F2007-02 Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  24. 24. Pathway languages and computation A slide to note Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  25. 25. Pathway languages and computation A slide to note Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  26. 26. Pathway languages and computation • Are same nodes distinct across paths ? • All paths, or at least one path ? A slide to note Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  27. 27. What is BioPAX ? • A language that can represent different representation of pathways in an integrated way • A language that allows computability of pathway representations • Pathway Exchange -> Integration + Computability Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  28. 28. What is BioPAX ? • A language that can represent different representation of pathways in an integrated way • A language that allows computability of pathway representations • Pathway Exchange -> Integration + Computability Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  29. 29. Pathway representation trade-offs • BioPAX focus on integration, not simulation • Qualitative models • Captures evidence, provenance • Easy to be lost in translation! Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  30. 30. Pathway representation trade-offs • BioPAX focus on integration, not simulation • Qualitative models • Captures evidence, provenance • Easy to be lost in translation! Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  31. 31. BioPAX: community • BioPAX is a community project (www.biopax.org) - database providers • Release of BioPAX has been articulated in levels: • Level 1: Metabolic networks, 2004 • Level 2: Interaction (evidence, DNA), 2005 • Level 3: Signaling (states, generic entities, gene regulation, genetic interactions), 2010 Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  32. 32. BioPAX: Biological Pathway Exchange (language) •How ? Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  33. 33. Describing pathways in BioPAX: a bottom up example Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  34. 34. Describing pathways in BioPAX: a bottom up example Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  35. 35. Describing pathways in BioPAX: a bottom up example • Using RDF • Vocabularies (rdf, biopax,...) • Equivalent to triples re:res1 rdf:type bp:BiochemicalReaction re:res1 bp:displayName “Digestion...”^^xsd:String Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  36. 36. Describing pathways in BioPAX: a bottom up example • Biochemical reaction and reactants • Annotations Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  37. 37. Describing pathways in BioPAX: a bottom up example • Entity in context and entity reference Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  38. 38. Describing pathways in BioPAX: a bottom up example • Entity in context and entity reference Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  39. 39. Describing pathways in BioPAX: a bottom up example • Entity in context and entity reference Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  40. 40. Describing pathways in BioPAX: a bottom up example • Representation of catalysis • Entity references • Types Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  41. 41. Describing pathways in BioPAX: a bottom up example • Representation of catalysis • Entity references • Types Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  42. 42. Describing pathways in BioPAX: a bottom up example • Representation of catalysis • Entity references • Types Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  43. 43. Describing pathways in BioPAX: a bottom up example • Representation of catalysis • Entity references • Types Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  44. 44. Describing pathways in BioPAX: a bottom up example • Representation of catalysis • Entity references • Types Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  45. 45. Describing pathways in BioPAX: a bottom up example • Representation of catalysis • Entity references • Types Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  46. 46. Describing pathways in BioPAX: a bottom up example • Representation of catalysis • Entity references • Types Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  47. 47. Describing pathways in BioPAX: a bottom up example Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  48. 48. Describing pathways in BioPAX: a bottom up example • Abstraction • Integrated view of different representations Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  49. 49. Describing pathways in BioPAX: a bottom up example • Abstraction • Integrated view of different representations Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  50. 50. Describing pathways in BioPAX: a bottom up example • Meta description (computability) Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  51. 51. Describing pathways in BioPAX: a bottom up example • Meta description (computability) Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  52. 52. • Biological facts • Structure of the pathway • Getting it into triples... • Structure of the language Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  53. 53. What is BioPAX ? • BioPAX is a language, expressed in OWL, to represent pathways • BioPAX expresses pathways in RDF Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  54. 54. A Top Down view of BioPAX: classes • Entities: • Physical entities • Pathways • Interactions Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  55. 55. A Top Down view of BioPAX: classes • Utility classes: • Xrefs • Vocabularies • Entity References Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  56. 56. A Top Down view of BioPAX: properties • Object properties Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque-Tecnológico de Bizkaia - Nov. 7th 2012 Bilbao Nov. 7th 2012 martedì 22 ottobre 13
  57. 57. A Top Down view of BioPAX: properties • Object properties Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque-Tecnológico de Bizkaia - Nov. 7th 2012 Bilbao Nov. 7th 2012 martedì 22 ottobre 13
  58. 58. A Top Down view of BioPAX: properties • Datatype properties Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque-Tecnológico de Bizkaia - Nov. 7th 2012 Bilbao Nov. 7th 2012 martedì 22 ottobre 13
  59. 59. BioPAX representation details: entities Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  60. 60. BioPAX representation details: pathways Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  61. 61. BioPAX representation details: interactions Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  62. 62. BioPAX representation details: genetic interactions Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  63. 63. BioPAX representation details: control Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  64. 64. BioPAX representation details: template reactions Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  65. 65. BioPAX: Biological Pathway Exchange (language) •Why ? Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  66. 66. Why ? Data availability Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  67. 67. Why ? Data availability Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  68. 68. Why ? Simplified Access to Data • Pathway represented with a common Syntax and “Semantics” • Tools: SPARQL (RDF) or PaxTools (Object Model) • Derivate information (e.g.: SIF files) • Still not for end-users... Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  69. 69. Why ? Simplified Access to Data (SIF detail) • When possible! Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  70. 70. Why ? BioPAX and the Systems Biology Information ecosystem Database Exchange Formats Simulation Model Exchange Formats BioPAX Genetic Interactions PSI Interaction Networks Molecular Pro:Pro Non-molecular TF:Gene SBML, CellML High Detail Genetic Rate Formulas Molecular Interactions Pro:Pro All:All Small Molecules Low Detail High Detail • Harmony • Combine Regulatory Pathways Low Detail • Co-operation: Biochemical Reactions Metabolic Pathways Low Detail High Detail Gene ontology ? Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  71. 71. Why ? Integration and computability, the meaning of the BioPAX ontology • The BioPAX ontology describes the structure of pathways. • While the object of the ontology are “pathways” the way the ontology is designed is heavily influenced by the conceptualization of pathways as “information artifacts”. • While making use of OWL constructs, BioPAX offers little scope to classification (and consistency). • The design of BioPAX reflects an hybrid approach between ontologies and Object Oriented modeling. Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  72. 72. Why ? BioPAX and Bio-Ontologies A comparison with BFO Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  73. 73. Why ? BioPAX and Bio-Ontologies A comparison with BFO • Which is the conceptualization behind the top level of BioPAX ? Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  74. 74. Why ? BioPAX and Bio-Ontologies Not a pure ontology • Property definition in OBO Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  75. 75. Why ? BioPAX and Bio-Ontologies Not a pure ontology • Property description in BioPAX Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  76. 76. Why ? BioPAX and Bio-Ontologies Not a pure ontology • BioPAX Overloading Knowledge base: efficiency OWL Data Model PaxTools RDF Ontology XML Syntax, validation rules Exchange language Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  77. 77. Why ? BioPAX limitations • Different representations: • Generalization ? • Water ? • Pathway reconciliation is still in research Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  78. 78. Why ? • BioPAX provides a large amount of data represented in a coherent syntax • The semantics of the BioPAX ontology, while imperfect, represents a consensus among pathway providers • BioPAX provides a knowledge bases to which different conceptualizations can be applied • BioPAX is a bridge between standards (language + community) Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  79. 79. BioPAX: next • http://biopax.org • biopax-discuss@googlegroups.com • http://www.biopax.org/release/biopax-level3.owl • http://www.biopax.org/release/biopax-level3-documentation.pdf • The BioPAX community standard for pathway data sharing Emek Demir, Michael P Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D'Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenjun Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran Kandasamy, Alejandra C Lopez-Fuentes, Huaiyu Mi, Elgar Pichler, Igor Rodchenkov, Andrea Splendiani, Sasha Tkachev, Jeremy Zucker, Gopal Gopinath, Harsha Rajasimha et al. Nature Biotechnology 28, 935–942 (2010) Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13

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