1. A database of biological pathways David Croft
Reactome
A database of biological pathways
David Croft

2. Reaction Example 1: Enzymatic
Reactome: a database of biological pathways

3. Reaction Example 2: Transport
Reactome: a database of biological pathways

4. Reaction Example 3: Signaling
Dimerization
Phosphorylation
Reactome: a database of biological pathways

5. A Reactome Pathway Compartment input output catalyst 11.11.2018
Reactome: a database of biological pathways

6. Reactome Data Model Events: Reactions Pathways Entities: Proteins
Complexes
Small compounds
Modulation:
Inhibition
Activation
Reactome: a database of biological pathways

7. Where Reactome’s Data Comes From
Curator
(staff)
Expert
(recruited)
Reviewer
Expert and curator create outline of new pathway
Expert fills in details
Curator enters information into database
Reviewer (another expert) checks biological correctness
Reactome: a database of biological pathways

8. Projecting Reactions to Other Species I
+ ATP B
+ ADP -P C
Human
Mouse
Drosophila
Reaction not
inferred
Protein not
Reactome: a database of biological pathways

9. Projecting Reactions to Other Species II
Notch signaling
Human - manually curated
Drosophila - electronically inferred
Reactome: a database of biological pathways

10. Coverage - Current Apoptosis Cell cycle DNA repair
Transcription, mRNA processing, translation, post-translational modification
Signaling pathways (insulin, NOTCH, opioid, NGF, EGFR, FGFR)
Hemostasis
Metabolism (energy, amino acid, lipid, nucleotide, xenobiotic)
HIV and Influenza lifecycles
Neurotoxicity of botulinum toxins
Reactome: a database of biological pathways

11. Coverage - Planned Signaling pathways (PDGF, Rho GTPases II)
Due before end-2007
Signaling pathways (PDGF, Rho GTPases II)
Obesity pathways
Cholesterol metabolism
Epigenetics: RNAi pathway
Reactome: a database of biological pathways

12. Reactome by Numbers Pathways 765 Reactions 2241
November 2007
Pathways
Reactions
Proteins (~10% SwissProt human)
Complexes
Literature references
Reactome: a database of biological pathways

13. Reactome APIs Full details of BioMart at: www.biomart.org API
Remote access
Firewall tunneling
Perl
Yes No
Java
BioMart
Web services
Full details of BioMart at:
Reactome: a database of biological pathways

14. BioMart and Reactome: GUI
Reactome: a database of biological pathways

15. BioMart and Reactome: Web Services
<Query virtualSchemaName = "default" >
<Dataset name = “reaction" interface = "default" >
<Attribute name = "stableidentifier_identifier" />
<Attribute name = "_displayname" />
<Attribute name = "referencedatabase_uniprot" />
<Filter name = "referencepeptidesequence_uniprot_id_list" value = “O00311"/>
</Dataset>
</Query>
** Perl API also available **
Reactome: a database of biological pathways

16. Reactome Team Grants www.reactome.org NHGRI # R01 HG002639
Ewan Birney
Imre Vastrik
Esther Schmidt
Bijay Jassal
Bernard de Bono
David Croft
Phani Vijay Garapati
European Bioinformatics Institute
Lincoln Stein
Peter D'Eustachio
Lisa Matthews
Gopal Gopinath
Marc Gillespie
Guanming Wu
Cold Spring Harbor Laboratory
Gene Ontology Consortium
Suzanna Lewis
NHGRI # R01 HG002639
EU STRP, EMI-CD
EBI Industry program
Grants
Reactome: a database of biological pathways

17. Web Page Walkthrough David Croft
Reactome
Web Page Walkthrough
David Croft

18. Front Page Navigator Search Species Starry-sky Top-level pathways
Navigator
Search
Species
Starry-sky
Top-level
pathways
Reactome: a database of biological pathways

19. Pathway Description Event hierarchy Participants Export
Description
Participants
Export
Event
hierarchy
Reactome: a database of biological pathways

20. Pathway Participants Key: ChEBI UniProt Compound Ensembl GO MIM KEGG
UCSC
EntRezMed
Reactome: a database of biological pathways

21. Pathway Data Export
<?xml version="1.0" encoding="UTF-8" ?>
<sbml xmlns=" level="2" version="1" xmlns:html="
<model name="R_109581">
<listOfCompartments>
<compartment name="R_cytosol" id="R_cytosol"/>
<compartment name="R_extracellular_region" id="R_extracellular_region"/>
<compartment name="R_mitochondrial_intermembrane_space" id="R_mitochondrial_intermembrane_space"/>
<compartment name="R_mitochondrial_outer_membrane" id="R_mitochondrial_outer_membrane"/>
<compartment name="R_plasma_membrane" id="R_plasma_membrane"/>
</listOfCompartments>
<listOfSpecies>
<species name="R_114236_Apoptosis_regulator_Bcl_X" compartment="R_mitochondrial_outer_membrane" id="R_114236_Apoptosis_regulator_Bcl_X" />
<species name="R_114240_NOXA_BCL2" compartment="R_mitochondrial_outer_membrane" id="R_114240_NOXA_BCL2" />
<species name="R_114242_BAD_protein" compartment="R_mitochondrial_outer_membrane" id="R_114242_BAD_protein" />
<species name="R_114243_BAD_BCL_xl" compartment="R_mitochondrial_outer_membrane" id="R_114243_BAD_BCL_xl" />
<species name="R_114244_Cytochrome_c" compartment="R_mitochondrial_intermembrane_space" id="R_114244_Cytochrome_c" /> …
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF xmlns:rdf=" xmlns=" xmlns:rdfs=" xmlns:owl=" xmlns:xsd=" xml:base="
<owl:Ontology rdf:about="">
<owl:imports rdf:resource=" />
<rdfs:comment rdf:datatype=" pathway converted from "Apoptosis" in the Reactome database.</rdfs:comment>
</owl:Ontology>
<pathway rdf:ID="Apoptosis">
<PATHWAY-COMPONENTS rdf:resource="#Activation__myristolyation_of_BID_and_translocation_to_mitochondriaStep" />
<PATHWAY-COMPONENTS rdf:resource="#Apoptotic_execution__phaseStep" />
<PATHWAY-COMPONENTS rdf:resource="#Extrinsic_Pathway_for_ApoptosisStep" />
<PATHWAY-COMPONENTS rdf:resource="#Intrinsic_Pathway_for_ApoptosisStep" />
<PATHWAY-COMPONENTS rdf:resource="#Activation_of__Effector_CaspasesStep" />
<ORGANISM rdf:resource="#Homo_sapiens" />
<NAME rdf:datatype="
<SHORT-NAME rdf:datatype="
<XREF rdf:resource="#Reactome109581" /> …
P6316 P98170 Q15628
P55211
P55957
P10415
P19438
P48454
Q9BXH1
O43521
P55210
Q07817
Q96FJ2
P31946
Reactome: a database of biological pathways

22. Reaction Reaction diagram Reactants, products, catalyst.
Reaction
diagram
Reactants,
products,
catalyst.
Reactome: a database of biological pathways

23. Bookmarking and Stable IDs
Get stable ID history:
Use this link to bookmark the reaction
Reactome: a database of biological pathways

24. SkyPainter – Entering a List of Identifiers
Usable identifiers:
UniProt
RefSeq
Ensembl
MIM
Entrez Gene
Affymetrix GO
KEGG COMPOUND
ChEBI
Reactome: a database of biological pathways

25. SkyPainter – Overrepresented Events
Decreasing
significance
Reactome: a database of biological pathways

26. SkyPainter – Numeric Values (e.g. Expression)
#ID value1 P P Q P O P P P P P O Q Q P O P Q P O P O P P P P P P P …
Download:
Reactome: a database of biological pathways

27. SkyPainter - Coloring E.g. zoom in Move focus Broken! Zoom in Zoom out
Reactome: a database of biological pathways

28. Simple Search 11.11.2018 Reactome: a database of biological pathways

29. Download Database “Interactions” “Textbooks” Local installation
Data entry tools
Web services API
Reactome: a database of biological pathways

30. Protein-Protein Interactions
Types of derived interaction:
Direct complex
Indirect complex
Reaction
Neighboring reaction
Reactome: a database of biological pathways