BioPAX (an introduction)

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

BioPAX (an introduction)

Andrea Splendiani(BioPAX editor)

martedì 22 ottobre 13


BioPAX (an introduction)

•What•How•Why



BioPAX: Biological Pathway Exchange (language)

•What is BioPAX ?




•What is BioPAX ?




•What is a pathway ?



Examples: biochemical pathway• Regular

structure

• Enzymatic activity

Source: http://www.genome.jp


http://www.wikipathways.org/index.php/Pathway:WP49



Examples: signaling pathway• Semi-regular

structure

• Activation/inhibition

• Compartments

• “Antigen”

Source: http://www.genome.jp





Example: wikipathways• Well defined

set of relations and symbols

Source: http://www.wikipathways.org/index.php/Pathway:WP49







Example: “informal” descriptions

Sources: http://www.biocarta.comhttp://www.singulex.com/images/cytokine_pathway_Th1.png


http://www.singulex.com/images/cytokine_pathway_Th1.png







Example: SBML

• Pathway a set of reactions

• Dynamic aspects/modeling

Source: http://www.biomodels.net





Example: SBML








Example: SBML








Example: SBGN

• Systems Biology Graphic Notation:

• Process Description

• Entity Relationship

• Activity Flow

Source: http://www.sbgn.org





Example: “Reactome”

• One big reaction network instead of pathways

Source: http://web.expasy.org/cgi-bin/pathways/show_thumbnails.pl







Example: network biology

• Interactome

• p-p interactions

• genetic interactions

Source: http://nd.edu/~networks/Image%20Gallery/gallery.htm#Biological







Example: Gene Ontology

• GO: Biological Process

Source: http://www.sciencedirect.com/science/article/pii/S0012160611001758







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



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



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



What is BioPAX ?

•Pathways and computation



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


http://www.springerimages.com/Images/LifeSciences/5-10.1186_1471-2229-10-85-7

http://www.springerimages.com/Images/LifeSciences/5-10.1186_1471-2229-10-85-7


Example: network analysis

• Clustering

• Centrality measures (betweeness)

• Systems properties (scale free networks)



Example: dynamic simulations

Source:http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=ModelMonth%2F2007-02


http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=ModelMonth%2F2007-02

http://www.ebi.ac.uk/biomodels-main/static-pages.do?page=ModelMonth%2F2007-02


Pathway languages and computation

A slide to note




A slide to note




A slide to note

• Are same nodes distinct across paths ?

• All paths, or at least one path ?



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



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



Pathway representation trade-offs

• BioPAX focus on integration, not simulation

• Qualitative models

• Captures evidence, provenance

• Easy to be lost in translation!



Pathway representation trade-offs

• BioPAX focus on integration, not simulation

• Qualitative models

• Captures evidence, provenance

• Easy to be lost in translation!



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


http://www.biopax.org

http://www.biopax.org



•How ?



Describing pathways in BioPAX: a bottom up example






• Using RDF

• Vocabularies (rdf, biopax,...)

• Equivalent to triples

re:res1 rdf:type bp:BiochemicalReactionre:res1 bp:displayName “Digestion...”^^xsd:String





• Biochemical reaction and reactants

• Annotations



• Entity in context and entity reference












• Representation of catalysis

• Entity references

• Types






• Types






• Types






• Types






• Types






• Types






• Types








• Abstraction

• Integrated view of different representations




• Abstraction

• Integrated view of different representations




• Meta description (computability)




• Meta description (computability)



• Getting it into triples...

• Biological facts

• Structure of the pathway

• Structure of the language



What is BioPAX ?

• BioPAX is a language, expressed in OWL, to represent pathways

• BioPAX expresses pathways in RDF



A Top Down view of BioPAX: classes• Entities:

• Physical entities

• Pathways

• Interactions



A Top Down view of BioPAX: classes• Utility classes:

• Xrefs

• Vocabularies

• Entity References



A Top Down view of BioPAX: properties

• Object properties

Andrea SplendianiBioPAX (an introduction) - Bioledge Workshop - Bilbao - Nov. 7th 2012




• Object properties





• Datatype properties




BioPAX representation details: entities



BioPAX representation details: pathways



BioPAX representation details: interactions



BioPAX representation details: genetic interactions



BioPAX representation details: control



BioPAX representation details: template reactions




•Why ?



Why ? Data availability



Why ? Data availability



• 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



Why ? Simplified Access to Data (SIF detail)

• When possible!



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 ?



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.



Why ? BioPAX and Bio-OntologiesA comparison with BFO



• Which is the conceptualization behind the top level of BioPAX ?

Why ? BioPAX and Bio-OntologiesA comparison with BFO



• Property definition in OBO

Why ? BioPAX and Bio-OntologiesNot a pure ontology



• Property description in BioPAX




• BioPAX Overloading


Knowledge base:efficiency

RDF

OWL

PaxTools

XMLSyntax, validation rules

Ontology

Exchange language

Data Model



• Different representations:

• Generalization ?

• Water ?

• Pathway reconciliation is still in research

Why ? BioPAX limitations



• 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 ?



• http://biopax.org

• [email protected]

• 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


http://biopax.org

http://biopax.org

mailto:[email protected]

mailto:[email protected]

http://www.biopax.org/release/biopax-level3.owl

http://www.biopax.org/release/biopax-level3.owl

http://www.biopax.org/release/biopax-level3-documentation.pdf

http://www.biopax.org/release/biopax-level3-documentation.pdf

Date post:	19-Jan-2015
Category:	Technology
Upload:	intellileaf-ltd
View:	482 times
Download:	1 times

BioPAX (an introduction)

Technology