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Structure and function in the Reactome datamodel

Structure and function in the Reactome datamodel. Bernard de Bono. http://brie8.cshl.org/. 1) Data Model 2) Orthology projections 3) Interfacing. HIV life cycle. http://brie8.cshl.org/. http://brie8.cshl.org/cgi-bin/tutorial. Class hierarchy with attributes.

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Structure and function in the Reactome datamodel

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  1. Structure and function in the Reactome datamodel Bernard de Bono

  2. http://brie8.cshl.org/

  3. 1) Data Model2) Orthology projections3) Interfacing

  4. HIV life cycle

  5. http://brie8.cshl.org/ http://brie8.cshl.org/cgi-bin/tutorial

  6. Class hierarchy with attributes EntityWithAccessionedSequence -referenceEntity (ReferenceSequence) -hasModifiedResidue -startCoordinate (default 1, 0 if unknown) -endCoordinate (default -1, 0 if unknown) GenomeEncodedEntity -species SimpleEntity -referenceEntity (ReferenceMolecule) DefinedSet -hasInstance -species UndefinedSet -hasExample -referenceEntity (ReferenceMoleculeClass) -species PhysicalEntity -name -compartment CandidateSet -hasConfirmedMember -hasCandidate -species Complex -hasComponent -species EntityWithRepeatedUnits -repeatedUnit -species -minUnitCount -maxUnitCount Arrows point from super-class to sub-class Note that sub-classes inherit the attributes of the super-class

  7. Collaboration between GO and Reactome Comparison and sharing of annotations between Reactome and GOA • Provides Reactome curated referenced GO annotations where they do not currently exist in GOA • Provides stronger experimental evidence for GOA annotation supported only by computational • inferences. • Improves the accuracy and consistency of the annotations in both databases. Cross-references between Reactome and GO • Reactome pathway --> GO Biological Processes • Reactome catalyst activity --> GO Molecular Function • Cellular location of Reactome reactions --> GO Cellular Compartment • Location of Reactome reaction input/output etc.-->GO Cellular Compartment • The GO consortium will soon cross-reference GO terms back to their • corresponding concepts in Reactome.

  8. http://brie8.cshl.org/ http://brie8.cshl.org/cgi-bin/view

  9. Other species in Reactome • Primary focus: manual curation of human reactions • Some human reactions are (manually) inferred from other species (lack of experimental evidence in human) • For each release a set of electronically inferred reactions is produced based on orthology data (from human to other species)

  10. http://brie8.cshl.org/ http://brie8.cshl.org/cgi-bin/tutorial http://www.reactome.org/

  11. Human - manually curated Notch signaling Drosophila - electronically inferred

  12. Reaction inference • Orthologue mapping based on the OrthoMCL system for a set of diverse, well-annotated species • Includes (recent) paralogues • Complex threshold (not all components of a complex need to have orthologues)

  13. OrthoMCL Flow chart

  14. Mouse C A A + ATP + ADP -P B B Drosophila C A Not inferred B Reaction inference - basic principle Human C A A + ATP + ADP -P B B

  15. Front page

  16. Pathwayevent hierarchy

  17. Pathwaydescription authors summary species GO term other species

  18. ChEBI UniProt Compound Ensembl MIM KEGG UCSC Pathwayparticipants

  19. Pathwaydata export

  20. <?xml version="1.0" encoding="UTF-8" ?> <sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1" xmlns:html="http://www.w3.org/1999/xhtml"> <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="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.biopax.org/release/biopax-level2.owl#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xml:base="http://www.biopax.org/release/biopax-level2.owl#"> <owl:Ontology rdf:about=""> <owl:imports rdf:resource="http://www.biopax.org/Downloads/Level2v0.92/biopax-level2.owl" /> <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BioPAX 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="http://www.w3.org/2001/XMLSchema#string">Apoptosis</NAME> <SHORT-NAME rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Apoptosis</SHORT-NAME> <XREF rdf:resource="#Reactome109581" /> … P63167 P98170 Q15628 P55211 P55957 P10415 P19438 P48454 Q9BXH1 O43521 P55210 Q07817 Q96FJ2 P31946 P45983 P30419 Q13794 P25445 Q12933 Q92934 P42574 P99999 O14727 Q14790 P48023 P31749 P63098 Q13158 P01375 Q13546 Q16611 P50591 Q07812 Q9NR28 O14763 Q96LC9 Q92851 P10144 Pathwaydata export

  21. Skypainter #ID value1 P20248 2.381255 P14635 2.078063 Q01094 1.358003 P08319 1.274531 O95067 1.251352 P12004 1.031162 P30305 1.654142 P16104 1.274092 P33992 1.560363 P35249 1.185243 O94913 2.410139 Q13415 1.085086 Q15054 1.148979 P30307 2.270973 O75496 0.796653 P49736 0.998988 Q13243 2.634955 P50613 1.466119 O75419 1.853295 P30304 0.863513 O96017 0.889464 P38398 1.068929 P06730 1.789461 P15927 0.89531 P30038 0.655572 P51530 1.060222 P17174 1.611088 P35250 0.58771 … • Usable identifiers: • UniProt • RefSeq • Ensembl • MIM • Entrez Gene • KEGG COMPOUND • ChEBI • Affymetrix • GO

  22. Skypaintercoloring according to the numeric values provided

  23. Skypainter 143E_HUMAN 1C06_HUMAN 2AAB_HUMAN 2ABB_HUMAN 2B11_HUMAN 2B14_HUMAN 2B17_HUMAN 2B18_HUMAN 2B19_HUMAN 2B1A_HUMAN 2B1B_HUMAN 3BH2_HUMAN 3BP2_HUMAN 41_HUMAN A1A2_HUMAN A1AT_HUMAN A2AC_HUMAN A2AP_HUMAN A2MG_HUMAN A3B1_HUMAN A4GT_HUMAN A4_HUMAN A8B1_HUMAN AAAS_HUMAN AAC3_HUMAN AAC4_HUMAN AACT_HUMAN …

  24. Skypaintercoloring according to the number of “hits”

  25. Download Database SBML “Interactions” Local installation Data entry tool

  26. Thank You

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