Reactome

• Get the data releaseGet the Reactome data release both APIs are on, such as release 97, and the day it was published. Record it beside an analysis so the results can be reproduced.
• List speciesList the species Reactome covers, with their taxonomy IDs and common names: the sixteen with pathways of their own, human first, or all of them, viruses and bacteria included.
• List top-level pathwaysList a species' top-level pathways, the top of Reactome's hierarchy, such as Cell Cycle, Immune System and Signal Transduction.
• Get the pathway hierarchyGet a species' pathways as a tree, one row per pathway with its depth, parent, number of molecules and whether it has a diagram: from the top level, or under one pathway, as many levels down as asked.
• Search ReactomeSearch Reactome's pathways, reactions, proteins, complexes, compounds and drugs by words, a gene name or an identifier, best match first, narrowed by species, type and compartment. Counts of the matches by type, species and compartment come back too, for narrowing further.
• Get a pathway, reaction or moleculeGet one Reactome entry by its stable ID: a pathway, reaction, protein, complex, set or compound, with its summary, species, compartments, literature, the pathways and reactions directly in it, a reaction's inputs and outputs, a complex's parts, and the UniProt or ChEBI molecule behind it. An unknown ID comes back with 'found' false.
• List a pathway's eventsList every pathway and reaction inside a pathway, at any depth, with each one's type, species and whether it is a disease or inferred event. Narrow it to pathways or reactions.
• List a pathway's participantsList the proteins, complexes, sets and compounds that take part in a pathway or reaction, each in its compartment, with counts by type.
• List a pathway's genes and moleculesList the genes, proteins, chemicals and drugs behind a pathway's or reaction's participants, each once, with its UniProt, ChEBI, Ensembl or other ID and gene names: a pathway's gene set, ready for another app or an analysis.
• List the pathways an event is inList every path from a pathway or reaction up to its top-level pathways, such as 'Cell Cycle > Cell Cycle Checkpoints > Mitotic Spindle Checkpoint', with the pathways it sits in directly.
• Find pathways for a gene or moleculeFind the pathways a gene, protein or compound takes part in from its UniProt, Ensembl, NCBI Gene, HGNC, OMIM, ChEBI, KEGG or miRBase ID: the lowest-level pathways holding its reactions. An identifier with none comes back with 'found' false.
• Find reactions for a gene or moleculeFind the reactions a gene, protein or compound takes part in from its UniProt, Ensembl, NCBI Gene, HGNC, OMIM, ChEBI, KEGG or miRBase ID, with each reaction's category. An identifier with none comes back with 'found' false.
• Find complexes for a gene or moleculeFind the complexes a protein or compound is part of, at any depth, from its UniProt, Ensembl, ChEBI or other ID, each with its compartment. An identifier in none comes back with 'found' false.
• List a protein's interactorsList the molecules a protein interacts with, from the IntAct database Reactome integrates, best scored first, with each one's confidence score and number of experiments.
• Find the equivalent in another speciesFind the same pathway, reaction or molecule in another species, such as mouse Apoptosis (R-MMU-109581) from human (R-HSA-109581), through Reactome's orthology. One with no equivalent there comes back with 'equivalent_found' false.
• Get a pathway diagramGet a checked link to a pathway's or reaction's diagram image, with a gene or compound highlighted or an analysis overlaid if asked, and links to it as SBGN, SBML and a PDF report and in the Pathway Browser. Diagrams are CC BY 4.0: credit Reactome when you share one.
• Analyse a list of identifiersFind the pathways a list of genes, proteins or compounds is over-represented in (pathway enrichment): each pathway's p-value, false discovery rate and how many of the list it holds, plus the identifiers Reactome didn't recognise and a token for the other analysis steps. Takes gene symbols and UniProt, Ensembl, NCBI, ChEBI and other IDs, mixed.
• Get analysis resultsGet an earlier analysis's pathways again from its token, filtered and sorted afresh: another p-value threshold, species, molecule type, pathway size or page, without running the analysis again.
• List identifiers found in a pathwayList which of an analysis's identifiers were found in one pathway, and what each maps to in UniProt, Ensembl or ChEBI: the genes behind a pathway's p-value.

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