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A database of biological pathways David Croft
Reactome A database of biological pathways David Croft
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Reaction Example 1: Enzymatic
Reactome: a database of biological pathways
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Reaction Example 2: Transport
Reactome: a database of biological pathways
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Reaction Example 3: Signaling
Dimerization Phosphorylation Reactome: a database of biological pathways
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A Reactome Pathway Compartment input output catalyst 11.11.2018
Reactome: a database of biological pathways
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Reactome Data Model Events: Reactions Pathways Entities: Proteins
Complexes Small compounds Modulation: Inhibition Activation Reactome: a database of biological pathways
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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
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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
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Projecting Reactions to Other Species II
Notch signaling Human - manually curated Drosophila - electronically inferred Reactome: a database of biological pathways
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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
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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
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Reactome by Numbers Pathways 765 Reactions 2241
November 2007 Pathways Reactions Proteins (~10% SwissProt human) Complexes Literature references Reactome: a database of biological pathways
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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
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BioMart and Reactome: GUI
Reactome: a database of biological pathways
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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
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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
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Web Page Walkthrough David Croft
Reactome Web Page Walkthrough David Croft
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Front Page Navigator Search Species Starry-sky Top-level pathways
Navigator Search Species Starry-sky Top-level pathways Reactome: a database of biological pathways
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Pathway Description Event hierarchy Participants Export
Description Participants Export Event hierarchy Reactome: a database of biological pathways
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Pathway Participants Key: ChEBI UniProt Compound Ensembl GO MIM KEGG
UCSC EntRezMed Reactome: a database of biological pathways
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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
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Reaction Reaction diagram Reactants, products, catalyst.
Reaction diagram Reactants, products, catalyst. Reactome: a database of biological pathways
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Bookmarking and Stable IDs
Get stable ID history: Use this link to bookmark the reaction Reactome: a database of biological pathways
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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
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SkyPainter – Overrepresented Events
Decreasing significance Reactome: a database of biological pathways
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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
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SkyPainter - Coloring E.g. zoom in Move focus Broken! Zoom in Zoom out
Reactome: a database of biological pathways
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Simple Search 11.11.2018 Reactome: a database of biological pathways
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Download Database “Interactions” “Textbooks” Local installation
Data entry tools Web services API Reactome: a database of biological pathways
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Protein-Protein Interactions
Types of derived interaction: Direct complex Indirect complex Reaction Neighboring reaction Reactome: a database of biological pathways
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