biopax (an introduction)
DESCRIPTION
BioPAX (an introduction) Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012TRANSCRIPT
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX (an introduction)
Andrea Splendiani(BioPAX editor)
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX (an introduction)
•What•How•Why
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX: Biological Pathway Exchange (language)
•What is BioPAX ?
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX: Biological Pathway Exchange (language)
•What is BioPAX ?
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX: Biological Pathway Exchange (language)
•What is a pathway ?
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Examples: biochemical pathway• Regular
structure
• Enzymatic activity
Source: http://www.genome.jp
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Examples: signaling pathway• Semi-regular
structure
• Activation/inhibition
• Compartments
• “Antigen”
Source: http://www.genome.jp
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: wikipathways• Well defined
set of relations and symbols
Source: http://www.wikipathways.org/index.php/Pathway:WP49
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: “informal” descriptions
Sources: http://www.biocarta.comhttp://www.singulex.com/images/cytokine_pathway_Th1.png
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: SBML
• Pathway a set of reactions
• Dynamic aspects/modeling
Source: http://www.biomodels.net
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: SBML
• Pathway a set of reactions
• Dynamic aspects/modeling
Source: http://www.biomodels.net
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: SBML
• Pathway a set of reactions
• Dynamic aspects/modeling
Source: http://www.biomodels.net
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: SBGN
• Systems Biology Graphic Notation:
• Process Description
• Entity Relationship
• Activity Flow
Source: http://www.sbgn.org
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: “Reactome”
• One big reaction network instead of pathways
Source: http://web.expasy.org/cgi-bin/pathways/show_thumbnails.pl
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: network biology
• Interactome
• p-p interactions
• genetic interactions
Source: http://nd.edu/~networks/Image%20Gallery/gallery.htm#Biological
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: Gene Ontology
• GO: Biological Process
Source: http://www.sciencedirect.com/science/article/pii/S0012160611001758
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
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
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
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
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
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
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
What is BioPAX ?
•Pathways and computation
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: over-representation analysis
Source:http://www.springerimages.com/Images/LifeSciences/5-10.1186_1471-2229-10-85-7
• Correlation between processes (annotation) and experimental evidence
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: network analysis
• Clustering
• Centrality measures (betweeness)
• Systems properties (scale free networks)
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Example: dynamic simulations
Source:http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=ModelMonth%2F2007-02
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Pathway languages and computation
A slide to note
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Pathway languages and computation
A slide to note
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Pathway languages and computation
A slide to note
• Are same nodes distinct across paths ?
• All paths, or at least one path ?
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
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
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
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
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Pathway representation trade-offs
• BioPAX focus on integration, not simulation
• Qualitative models
• Captures evidence, provenance
• Easy to be lost in translation!
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Pathway representation trade-offs
• BioPAX focus on integration, not simulation
• Qualitative models
• Captures evidence, provenance
• Easy to be lost in translation!
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
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
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX: Biological Pathway Exchange (language)
•How ?
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Using RDF
• Vocabularies (rdf, biopax,...)
• Equivalent to triples
re:res1 rdf:type bp:BiochemicalReactionre:res1 bp:displayName “Digestion...”^^xsd:String
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Describing pathways in BioPAX: a bottom up example
• Biochemical reaction and reactants
• Annotations
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Entity in context and entity reference
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Entity in context and entity reference
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Entity in context and entity reference
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Representation of catalysis
• Entity references
• Types
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Representation of catalysis
• Entity references
• Types
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Representation of catalysis
• Entity references
• Types
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Representation of catalysis
• Entity references
• Types
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Representation of catalysis
• Entity references
• Types
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Representation of catalysis
• Entity references
• Types
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Representation of catalysis
• Entity references
• Types
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Describing pathways in BioPAX: a bottom up example
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Describing pathways in BioPAX: a bottom up example
• Abstraction
• Integrated view of different representations
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Describing pathways in BioPAX: a bottom up example
• Abstraction
• Integrated view of different representations
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Describing pathways in BioPAX: a bottom up example
• Meta description (computability)
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Describing pathways in BioPAX: a bottom up example
• Meta description (computability)
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Getting it into triples...
• Biological facts
• Structure of the pathway
• Structure of the language
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
What is BioPAX ?
• BioPAX is a language, expressed in OWL, to represent pathways
• BioPAX expresses pathways in RDF
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
A Top Down view of BioPAX: classes• Entities:
• Physical entities
• Pathways
• Interactions
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
A Top Down view of BioPAX: classes• Utility classes:
• Xrefs
• Vocabularies
• Entity References
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
A Top Down view of BioPAX: properties
• Object properties
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Bilbao - Nov. 7th 2012
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
A Top Down view of BioPAX: properties
• Object properties
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Bilbao - Nov. 7th 2012
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
A Top Down view of BioPAX: properties
• Datatype properties
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Bilbao - Nov. 7th 2012
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX representation details: entities
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX representation details: pathways
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX representation details: interactions
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX representation details: genetic interactions
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX representation details: control
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX representation details: template reactions
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
BioPAX: Biological Pathway Exchange (language)
•Why ?
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Why ? Data availability
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Why ? Data availability
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• 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...
Why ? Simplified Access to Data
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Why ? Simplified Access to Data (SIF detail)
• When possible!
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Why ? BioPAX and the Systems Biology Information ecosystem
BioPAX
PSISBML,CellML
GeneticInteractions
Molecular InteractionsPro:Pro All:All
Interaction NetworksMolecular Non-molecularPro:Pro TF:Gene Genetic
Regulatory PathwaysLow Detail High Detail
Database ExchangeFormats
Simulation ModelExchange Formats
RateFormulas
Metabolic PathwaysLow Detail High Detail
Biochemical Reactions
Small MoleculesLow Detail High Detail
• Co-operation:
• Harmony
• Combine
Gene ontology ?
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
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.
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
Why ? BioPAX and Bio-OntologiesA comparison with BFO
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Which is the conceptualization behind the top level of BioPAX ?
Why ? BioPAX and Bio-OntologiesA comparison with BFO
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Property definition in OBO
Why ? BioPAX and Bio-OntologiesNot a pure ontology
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Property description in BioPAX
Why ? BioPAX and Bio-OntologiesNot a pure ontology
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• BioPAX Overloading
Why ? BioPAX and Bio-OntologiesNot a pure ontology
Knowledge base:efficiency
RDF
OWL
PaxTools
XMLSyntax, validation rules
Ontology
Exchange language
Data Model
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• Different representations:
• Generalization ?
• Water ?
• Pathway reconciliation is still in research
Why ? BioPAX limitations
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• 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)
Why ?
martedì 22 ottobre 13
Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
• http://biopax.org
• http://www.biopax.org/release/biopax-level3.owl
• http://www.biopax.org/release/biopax-level3-documentation.pdf
• The BioPAX community standard for pathway data sharingEmek 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)
BioPAX: next
martedì 22 ottobre 13