biopax level 3: an overview of new features -...

BioPAX Level 3:An overview of new features

Emek DemirMemorial Sloan Kettering Cancer Center

AKT1

Physical EntityName,Sequenceetc.

PhysicalEntity Participant

ModificationsCellular locationAndStoichiometry

States in Level 2

States in Level 3

AKT1

InteractionsPhysical Entity

State, location

Physical Entity Reference:Name, Sequence,etc

stoichiometry

Features Entity Feature

− ModificationFeature CovalentBindingFeature

− BindingFeature CovalentBindingFeature

− FragmentFeature

Features and Combinatorial Complexity

AKT1P@308

AKT1

P@308

AKT1

P@308

?@473

P@473

?

Features and Overlapping Pools

AKT1

P@308

P@473

AKT1

P@308

P@473

AKT1

P@308

P@473

AKT1

P@473

AKT1

P@308

AKT1

P@308

P@473

=

=

Features and not Features

AKT1 AKT1P@308

AKT1 AKT1

P@308

P@308

AKT1 AKT1

P@308

P@308

?@473

?@473

P@473

P@473

Binding Feature

HSP90 b@31 AKT1b@Tb@R

HSP90 b@R AKT1b@T

Generics

Generics

rWNT

rWNT1

rWNT2

WNT

rWNT

rWNT1

rWNT2

WNT

WNTP

@x

P@45

P@21

Generics

Gene Regulation

DNARegion Protein

TemplateReaction

Template Product

TF

AS

TemplateReactionRegulation

Genetic Interactions A separate non-causal, non-physical

interaction : GeneticInteraction A separate non-physical entity : Gene Phenotype: e.g. viability InteractionScore: strength of interaction

Controlled Vocabulary subclasses

Cellular Location Vocabulary (GO)

Relationship Type Vocabulary (Orphan)

Sequence Modification Vocabulary(PSI-MI for protein, orphan for others)

Experimental Form Vocabulary (PSI-MI for proteins, orphan for others)

Tissue Vocabulary (BTO)

Controlled Vocabulary subclasses

Cell Vocabulary (CL)

Evidence Code Vocabulary (PSI-MI for proteomics)

Entity Reference Type Vocabulary ( Orphan)

Phenotype Vocabulary ( PATO)

Interaction Vocabulary ( PSI-MI)

Refactorings

All class names are now CamelCase All property names are now singular, lower

case Some classes were renamed to better

reflect biology/common terminology

Refactorings

Better handling of data source, method score, provenance

Name, Standard Name, Display Name Pathways can now control reactions Pathway Step improved to cover context

specific direction of reversible reactions.

Ontology specification

Web Ontology Language (OWL) XML file, developed using free Protégé ontology editor software[57].

Ontology documentation

Explanation of BioPAX entities, example documentation, best practice recommendations, use cases, how to.

Example files Example files for biochemical pathway, protein and genetic interaction, protein phosphorylation, insulin maturation, gene regulation, generic molecules in OWL XML.

Graphical representation

Recommendations for graphical representation using Systems Biology Graphical Notation (SBGN) as a guide.

Paxtools software

Java programming library supporting import/export, conversion, validation. Can be used to add BioPAX support to software.

List of data sources & supporting software

Databases making data available in BioPAX format, software systems for storing, visualizing and analyzing BioPAX pathways.

What is included in the release

BioPAX – A community standard for pathway data sharing

Emek Demir1,2 Michael P. Cary1Suzanne Paley3Ken Fukuda4Christian Lemer5ImreVastrik6Guanming Wu7Peter D'Eustachio8Carl Schaefer9Joanne Luciano10FrankSchacherer11Irma Martinez-Flores12Zhenjun Hu13Veronica Jimenez-Jacinto12GeetaJoshi-Tope14Kumaran Kandasamy15Alejandra C. Lopez-Fuentes16Huaiyu Mi17ElgarPichlerIgor Rodchenkov18Andrea Splendiani19,20Sasha Tkachev21JeremyZucker22Gopal Gopinath23Harsha Rajasimha24,25Ranjani Ramakrishnan26ImranShah27Mustafa Syed28Nadia Anwar1Ozgun Babur1,2Michael Blinov29ErikBrauner30Dan Corwin31Sylva Donaldson18Frank Gibbons30Robert Goldberg32PeterHornbeck21Augustin Luna33Peter Murray-Rust34Eric Neumann35OliverReubenacker36Matthias Samwald37,64Martijn van Iersel38Sarala Wimalaratne39KeithAllen40Burk Braun11Michelle Whirl-Carrillo41Kam Dahlquist 42AndrewFinney43Marc Gillespie44Elizabeth Glass45Li Gong41Robin Haw46MichaelHonig47Olivier Hubaut5David Kane48Shiva Krupa49Martina Kutmon50JulieLeonard40Debbie Marks51David Merberg52Victoria Petri53Alex Pico54DeanRavenscroft55Liya Ren14Nigam Shah56 Margot Sunshine33Rebecca Tang41RyanWhaley41Stan Letovksy57Kenneth H. Buetow58Andrey Rzhetsky59VincentSchachter60Bruno S. Sobral24Ugur Dogrusoz2Shannon McWeeney26MiritAladjem33Ewan Birney6Julio Collado-Vides12Susumu Goto61MichaelHucka62Nicolas Le Novère6Natalia Maltsev45Akhilesh Pandey15Paul Thomas17EdgarWingender63Peter D. Karp3Chris Sander1Gary D. Bader18