biopax level 3: an overview of new features -...
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BioPAX Level 3:An overview of new features
Emek DemirMemorial Sloan Kettering Cancer Center
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AKT1
Physical EntityName,Sequenceetc.
PhysicalEntity Participant
ModificationsCellular locationAndStoichiometry
States in Level 2
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States in Level 3
AKT1
InteractionsPhysical Entity
State, location
Physical Entity Reference:Name, Sequence,etc
stoichiometry
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Features Entity Feature
− ModificationFeature CovalentBindingFeature
− BindingFeature CovalentBindingFeature
− FragmentFeature
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Features and Combinatorial Complexity
AKT1P@308
AKT1
P@308
AKT1
P@308
?@473
P@473
?
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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
=
=
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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
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Binding Feature
HSP90 b@31 AKT1b@Tb@R
HSP90 b@R AKT1b@T
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Generics
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Generics
rWNT
rWNT1
rWNT2
WNT
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rWNT
rWNT1
rWNT2
WNT
WNTP
@x
P@45
P@21
Generics
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Gene Regulation
DNARegion Protein
TemplateReaction
Template Product
TF
AS
TemplateReactionRegulation
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Genetic Interactions A separate non-causal, non-physical
interaction : GeneticInteraction A separate non-physical entity : Gene Phenotype: e.g. viability InteractionScore: strength of interaction
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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)
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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)
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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
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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.
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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
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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