/reactome/pathways/search

POST /api/reactome/pathways/search

Price: 10 credits

Search Reactome for pathways, reactions, proteins, complexes and the other curated entries

How to use it

Results span every kind of Reactome entry, not only pathways, so set `types` when you want one kind - `Pathway` for processes, `Reaction` for single steps, `Protein` for participants. `species` takes the display name such as `Homo sapiens`; a taxonomy id is not a species here, and Reactome carries the same process separately per species, so an unfiltered query returns the same biology many times over. Filters are enforced: a filter value with no hits among the query's own results answers 412 instead of widening back to the unfiltered set, and a query with no hits answers 412 as well, so the two are not told apart by status - drop the filter and repeat to see which it was.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• query string required — Search terms matched against names, identifiers and summaries (examples: "insulin", "apoptosis", "TP53", "glycolysis"; minLength: 1)
• species string nullable — Keep only entries of this species (one of: "Arenicola marina", "Bacillus anthracis", "Bos taurus", "Caenorhabditis elegans", "Candida albicans", "Canis familiaris", "Cavia porcellus", "Cercopithecus aethiops", "Chlamydia trachomatis", "Chlorocebus sabaeus", "Clostridium botulinum", "Clostridium perfringens", "Clostridium tetani", "Corynephage beta", "Cowpox virus", "Cricetulus griseus", "Crithidia fasciculata", "Danio rerio", "Dengue virus type 2", "Dictyostelium discoideum", "Drosophila melanogaster", "Entries without species", "Escherichia coli", "Escherichia coli O127:H6", "Escherichia coli O157:H7", "Escherichia coli O6:K15:H31", "Escherichia coli O78:H11", "Felis catus", "Gallus gallus", "Hepatitis B virus", "Hepatitis C Virus", "Hepatitis C virus genotype 2a", "Hepatitis C virus subtype 1a", "Homarus americanus", "Homo sapiens", "Human SARS coronavirus", "Human alphaherpesvirus 2", "Human cytomegalovirus", "Human gammaherpesvirus 4", "Human herpesvirus 1", "Human herpesvirus 8", "Human immunodeficiency virus 1", "Human papillomavirus type 16", "Human papillomavirus type 18", "Human respiratory syncytial virus A", "Infectious bronchitis virus", "Influenza A virus", "Klebsiella pneumoniae", "Legionella pneumophila", "Leishmania major", "Leishmania mexicana", "Listeria monocytogenes", "Listeria monocytogenes serotype 1/2a", "Listeria monocytogenes serovar 1/2a", "Macaca mulatta", "Measles virus", "Meleagris gallopavo", "Molluscum contagiosum virus subtype 1", "Moloney murine leukemia virus", "Mus musculus", "Mycobacterium tuberculosis", "Mycobacterium tuberculosis H37Rv", "Neisseria gonorrhoeae", "Neisseria meningitidis serogroup B", "Oryctolagus cuniculus", "Ovis aries", "Penicillium chrysogenum", "Plasmodium falciparum", "Rattus norvegicus", "Rotavirus", "Rotavirus A", "Saccharomyces cerevisiae", "Salmonella typhimurium", "Schizosaccharomyces pombe", "Sendai virus", "Severe acute respiratory syndrome coronavirus 2", "Shigella flexneri", "Sindbis virus", "Staphylococcus aureus", "Sus scrofa", "Tick-borne encephalitis virus", "Toxoplasma gondii", "Triticum aestivum", "Vaccinia virus", "Vesicular stomatitis virus", "Vigna radiata var. radiata", "West Nile virus", "Xenopus laevis", "Xenopus tropicalis"; examples: "Homo sapiens", "Mus musculus")
• types string nullable — Keep only entries of this kind (one of: "Cell", "Chemical Compound", "Complex", "DNA Sequence", "Drug", "Entity", "Genes and Transcripts", "Icon", "Interactor", "NegativeRegulation", "OtherEntity", "Pathway", "Polymer", "PositiveRegulation", "Protein", "RNA Sequence", "Reaction", "Set"; examples: "Pathway", "Reaction", "Protein")
• compartments string nullable — Keep only entries located in this cellular compartment (one of: "COPII-coated ER to Golgi transport vesicle", "ER to Golgi transport vesicle membrane", "Golgi lumen", "Golgi membrane", "Golgi-associated vesicle membrane", "apical plasma membrane", "autophagosome membrane", "axonemal microtubule", "azurophil granule lumen", "azurophil granule membrane", "basolateral plasma membrane", "cell junction", "cell outer membrane", "chromosome", "chromosome, centromeric region", "ciliary base", "ciliary membrane", "ciliary tip", "cilium", "clathrin-coated endocytic vesicle", "clathrin-coated endocytic vesicle membrane", "clathrin-sculpted acetylcholine transport vesicle membrane", "clathrin-sculpted gamma-aminobutyric acid transport vesicle", "clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane", "clathrin-sculpted glutamate transport vesicle membrane", "clathrin-sculpted monoamine transport vesicle membrane", "cornified envelope", "cytoplasm", "cytoplasmic side of endoplasmic reticulum membrane", "cytoplasmic side of plasma membrane", "cytoplasmic vesicle lumen", "cytoplasmic vesicle membrane", "cytosol", "double membrane vesicle viral factory outer membrane", "early endosome", "early endosome lumen", "early endosome membrane", "endocytic vesicle lumen", "endocytic vesicle membrane", "endolysosome lumen", "endolysosome membrane", "endoplasmic reticulum lumen", "endoplasmic reticulum membrane", "endoplasmic reticulum quality control compartment", "endoplasmic reticulum-Golgi intermediate compartment", "endoplasmic reticulum-Golgi intermediate compartment membrane", "endosome", "endosome lumen", "endosome membrane", "external side of plasma membrane", "extracellular exosome", "extracellular region", "ficolin-1-rich granule lumen", "ficolin-1-rich granule membrane", "lamellar body", "lamellar body membrane", "late endosome lumen", "late endosome membrane", "lipid droplet", "lumenal side of endoplasmic reticulum membrane", "lysosomal lumen", "lysosomal membrane", "melanosome lumen", "melanosome membrane", "microtubule organizing center", "mitochondrial inner membrane", "mitochondrial intermembrane space", "mitochondrial matrix", "mitochondrial outer membrane", "mitochondrion", "multivesicular body lumen", "multivesicular body, internal vesicle", "multivesicular body, internal vesicle membrane", "nuclear envelope", "nucleolus", "nucleoplasm", "peptidoglycan-based cell wall", "periplasmic space", "peroxisomal matrix", "peroxisomal membrane", "phagocytic vesicle", "phagocytic vesicle lumen", "phagocytic vesicle membrane", "phagolysosome", "phagophore assembly site membrane", "photoreceptor disc membrane", "photoreceptor outer segment membrane", "plasma membrane", "platelet alpha granule lumen", "platelet alpha granule membrane", "platelet dense granule lumen", "platelet dense granule membrane", "platelet dense tubular network membrane", "recycling endosome", "recycling endosome membrane", "sarcoplasmic reticulum membrane", "secretory granule lumen", "secretory granule membrane", "smooth endoplasmic reticulum", "specific granule lumen", "specific granule membrane", "synaptic vesicle membrane", "tertiary granule lumen", "tertiary granule membrane", "trans-Golgi network membrane", "transport vesicle", "transport vesicle membrane", "viral envelope", "viral tegument", "virion membrane"; examples: "cytosol", "nucleoplasm")
• keywords string nullable — Keep only entries carrying this curated keyword (one of: "activates", "binds", "cleaves", "co-transports", "combines", "condenses", "converts", "deacetylates", "deaminates", "decarboxylates", "dehydrates", "dehydrogenates", "demethylates", "dephosphorylates", "desaturates", "deubiquitinates", "dioxygenates", "dismutates", "elongates", "exchanges", "extends", "hydrates", "hydrolyses", "hydroxylates", "inhibits", "initiates", "inserts", "isomerises", "ligates", "lyses", "oxidises", "phosphorylates", "reduces", "regulates", "ribosylates", "signals", "sulfates", "synthesizes", "transaminates", "transfers", "transforms", "translocates", "transports", "ubiquitinates", "unwinds"; examples: "binds", "phosphorylates")
• count integer required — Max number of results (min: 1; max: 40000)

Response

• @type string (default: "ReactomeSearchHit")
• id string required
• db_id integer nullable
• display_name string (default: "")
• record_type string (default: "")
• exact_type string (default: "")
• species array (default: [])
• compartment_names array (default: [])
• compartment_accessions array (default: [])
• summary string (default: "")
• is_disease boolean nullable
• has_reference_entity boolean nullable
• has_ehld boolean nullable
• reference_database string (default: "")
• reference_identifier string (default: "")
• reference_name string (default: "")
• reference_url string (default: "")
• url string (default: "")

Errors

• 422 — Unknown species, type, compartment or keyword Check the fields against this schema. A URN with the wrong prefix is the most common cause.
• 408 — The request ran past its time limit Raise `timeout` in the request body, up to the maximum this endpoint documents. Lowering `count` or turning off the `with_*` flags also helps, because less work finishes sooner.
• 412 — No entries match the query Retrying will not help: either the entity does not exist, or the input points at a different one.
• 429 — Too many requests: a rate limit or a usage window is exhausted When the response carries an X-Retry-After header, wait that many seconds and retry: the same number is in the body as `detail.retry_after`, and the limit clears once that window passes. The message in the body names the limit that was hit.
• 500 — Something broke on our side Retrying will not help. If it keeps happening, send us the X-Request-ID from the response headers.
• 529 — Rate limit reached, or the endpoint is overloaded Wait at least 30 seconds, then retry.

Response headers

• X-Error — Error message text (present only on error)
• X-Request-ID — Unique request identifier
• X-Execution-Time — Execution time in seconds
• X-Result-Count — How many records the body carries. 0 means an empty result, which is a normal answer and not by itself an error. A non-zero count can come back together with X-Error when the failure happened partway through — read this header and X-Error independently.
• X-Total-Available-Results — How many records exist for this query, when the endpoint can say. On a `dry_run` request this is the answer and the body is empty. It saturates: the endpoint's documented maximum means 'at least that many', any smaller number is exact.
• X-Warning — Present when the request body carried keys this endpoint does not document. They were ignored, so any filter you meant to apply through them did not apply. Check the spelling against this schema and retry.
• X-Retry-After — Seconds to wait before retrying. Present only on 429.