Reactome Pengine

Reactome Pengine is a Prolog based API to the human reactome. It is available at https://apps.nms.kcl.ac.uk/reactome-pengine/. Users can send their own small Prolog programs alongside a query to Reactome Pengine, so that the computation takes place in the cloud. Users send their 'small' program to the 'large' data, rather than sending data to the program as is more typical for a webservice, saving both bandwidth and storage space.

Prolog files

load.plShow source
logging.plShow source
pathway_link.plShow source
ridPathway_link/2Relate each pathway to the links in that pathway.Source
pre_links.plShow source
ridReaction_ridLink_type_ridReaction/4Denotes an edge in the Reaction graph.Source
probes.plShow source
ridProtein_probelist/2Relate a Reactome protein identifier to the list of Affy probes for that Protein.Source
reactome_utility_module.plShow source
allReactions/1Generate a list of of Reaction identifiers in Reactome (or check that a list corresponds to a list of all identifiers).Source
ridComplex_component/2Relate a Reactome identifier of a protein complex to a component.Source
ridComplex_components/2Relate a Reactome identifier of a protein complex to a list of components.Source
ridComponent_child/2Relate either a Reactome protein set identifier or a Reactome complex identifier, to a subcomponent that is one level down.Source
ridComponent_childSimpleProtein/2Relate a protein set or complex idenifier to a subcomponent that is a simple protein (i.e is not a set or complex).Source
ridComponent_descendant/2Relate either a Reactome protein set identifier or a Reactome complex identifier, to a subcomponent any level down.Source
ridComponent_descendantSetOrComplex/2Relate a protein set or complex identifier to a subset or complex.Source
ridComponent_descendants/2Relate a protein set or complex identifier to all subcomponents recursively.Source
ridPathwayAtomic/1Generate or test a pathway that is atomic i.e.Source
ridPathway_component/2Relate a Reactome pathway identifier to a component in the pathway.Source
ridPathway_links/2Relate a Reactome pathway identifier to its constituent links (edges).Source
ridPathway_reactions/2Relate a Reactome pathway identifier to all component reactions.Source
ridProteinSet/1Generate a Reactome identifier that is a protein set, or check that an identifier refers to a protein set.Source
ridProteinSet_component/2Relate a Reactome identifier of a protein set to a component of that protein set.Source
ridProteinSet_components/2Relate a Reactome identifier of a protein set to a list of components.Source
ridProtein_uniprotId/2Convert between Reactome protein identifiers and Uniprot identifiers.Source
ridReaction_controller_type/3Relate a Reactome reaction identifier to its controller and the type of that controller.Source
ridReaction_input/2This finds top level inputs entities to a reaction that are not components of complexes or members of protein sets.Source
ridReaction_inputProbelist/2Relate a Reactome reaction identifer to the set of affymetrix probes that are used for the proteins involved in the inputs to that reaction.Source
ridReaction_inputs/2Relate a Reactome identifier for a reaction to a list of top level inputs (i.e.Source
ridReaction_output/2Finds top level outputs to a reaction but not sub components of complexes or members of protein sets.Source
ridReaction_outputs/2Relate a Reactome identifier for a reaction to a list of top level outputs (i.e these outputs do not include subcomponents of complexes and sets).Source
ridSimpleProtein/1Generate a Reactome identifier that refers to a protein that is not a protein set, or test an identifier to see if it is a protein set.Source
rid_location/2Relate a Reactome identifier to a physical location in the cell.Source
rid_name/2Relate Reactome identifiers to their name.Source
rid_stableid/2Convert between the identifiers used in this version of Reactome and the stable identifiers.Source
rid_type_iri/3Generate Reactome identifiers alongside the type and International Resource Identifiers (IRIs).Source