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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
BioPAX (an introduction)

•What
•How
•Why
Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
What is BioPAX ?

•Pathways and
computation
Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
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
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
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
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
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
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
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
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
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
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
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
BioPAX: Biological Pathway Exchange (language)

•How ?

Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
• 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
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
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
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
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
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
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
BioPAX representation details: entities

Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
BioPAX representation details: pathways

Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
BioPAX representation details: interactions

Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
BioPAX representation details: genetic interactions

Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
BioPAX representation details: control

Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
BioPAX representation details: template reactions

Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
BioPAX: Biological Pathway Exchange (language)

•Why ?

Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
Why ? Data availability

Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
Why ? Data availability

Andrea Splendiani
BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012
martedì 22 ottobre 13
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
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
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
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
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
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
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
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
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
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
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
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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BioPAX (an introduction)

  • 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. • 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. 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. 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. 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. 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. 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. 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. BioPAX representation details: entities Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  • 60. BioPAX representation details: pathways Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  • 61. BioPAX representation details: interactions Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  • 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. BioPAX representation details: control Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  • 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. 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. Why ? Data availability Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  • 67. Why ? Data availability Andrea Splendiani BioPAX (an introduction) - Bioledge Workshop - Parque Tecnológico de Bizkaia - Nov. 7th 2012 martedì 22 ottobre 13
  • 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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