WormBase ParaSite REST API Endpoints

Comparative Genomics

ResourceDescription
GET /rest-9/genetree/id/:id Retrieves a gene tree dump for a gene tree stable identifier
GET /rest-9/genetree/member/id/:id Retrieves a gene tree that contains the stable identifier
GET /rest-9/genetree/member/symbol/:species/:symbol Retrieves a gene tree containing the gene identified by a symbol
GET /rest-9/homology/id/:id Retrieves homology information (orthologues) by gene id
GET /rest-9/homology/symbol/:species/:symbol Retrieves homology information (orthologues) by symbol

Cross References

ResourceDescription
GET /rest-9/xrefs/symbol/:species/:symbol Looks up an external symbol and returns all objects linked to it. This can be a display name for a gene/transcript/translation, a synonym or an externally linked reference. If a gene's transcript is linked to the supplied symbol the service will return both gene and transcript (it supports transient links).
GET /rest-9/xrefs/id/:id Perform lookups of identifiers and retrieve their external references in other databases
GET /rest-9/xrefs/name/:species/:name Performs a lookup based upon the primary accession or display label of an external reference and returning the information we hold about the entry

Information

ResourceDescription
GET /rest-9/info/assembly/:species List the currently available assemblies for a species. NOTE: Response may be large
GET /rest-9/info/assembly/:species/:region_name Returns information about the specified toplevel sequence region for the given species.
GET /rest-9/info/genomes/:name Find information about a given genome
GET /rest-9/info/genomes Find information about all genomes. Response may be very large.
GET /rest-9/info/genomes/assembly Find information about a genome with a specified assembly
GET /rest-9/info/genomes/taxonomy Find information about all genomes beneath a given node of the taxonomy
GET /rest-9/info/version Get the WormBase release number for any specified WormBase ParaSite release
GET /rest-9/info/species Lists all available species, their aliases, available adaptor groups and data release.

Lookup

ResourceDescription
GET /rest-9/lookup/id/:id Find the species and database for a single identifier
GET /rest-9/lookup/genome/:name Query for a named genome and retrieve the gene models
POST /rest-9/lookup/id Find the species and database for several identifiers. IDs that are not found are returned with no data.
GET /rest-9/lookup/symbol/:species/:symbol Find the species and database for a symbol in a linked external database
POST /rest-9/lookup/symbol/:species/:symbol Find the species and database for a set of symbols in a linked external database. Unknown symbols are omitted from the response.

Mapping

ResourceDescription
GET /rest-9/map/cdna/:id/:region Convert from cDNA coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the API.
GET /rest-9/map/cds/:id/:region Convert from CDS coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the API.
GET /rest-9/map/translation/:id/:region Convert from protein (translation) coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the API.

Ontologies and Taxonomy

ResourceDescription
GET /rest-9/ontology/ancestors/:id Reconstruct the entire ancestry of a term from is_a and part_of relationships
GET /rest-9/ontology/ancestors/chart/:id Reconstruct the entire ancestry of a term from is_a and part_of relationships.
GET /rest-9/ontology/descendants/:id Find all the terms descended from a given term. By default searches are conducted within the namespace of the given identifier
GET /rest-9/ontology/id/:id Search for an ontological term by its namespaced identifier
GET /rest-9/ontology/name/:name Search for a list of ontological terms by their name

Overlap

ResourceDescription
GET /rest-9/overlap/id/:id Retrieves features (e.g. genes, transcripts etc.) that overlap a region defined by the given identifier.
GET /rest-9/overlap/region/:species/:region Retrieves multiple types of features for a given region.
GET /rest-9/overlap/translation/:id Retrieve features related to a specific Translation as described by its stable ID (e.g. domains).

Sequence

ResourceDescription
GET /rest-9/sequence/id/:id Request multiple types of sequence by stable identifier.
POST /rest-9/sequence/id Request multiple types of sequence by a stable identifier list.
GET /rest-9/sequence/region/:species/:region Returns the genomic sequence of the specified region of the given species.
POST /rest-9/sequence/region/:species Request multiple types of sequence by a list of regions.