WormBase ParaSite REST API Endpoints

Versioning

This is version 10 of the REST API. We maintain both the current and one previous release of the REST service. Versioning is handled by the URL, e.g. /rest-10 will direct to release 10 of the website. To always retrieve the latest data, simply remove the release number from the URL, i.e. /rest.

Comparative Genomics

ResourceDescription
GET /rest-10/genetree/id/:id Retrieves a gene tree dump for a gene tree stable identifier
GET /rest-10/genetree/member/id/:id Retrieves a gene tree that contains the stable identifier
GET /rest-10/genetree/member/symbol/:species/:symbol Retrieves a gene tree containing the gene identified by a symbol
GET /rest-10/homology/id/:id Retrieves homology information (orthologues) by gene id
GET /rest-10/homology/symbol/:species/:symbol Retrieves homology information (orthologues) by symbol

Cross References

ResourceDescription
GET /rest-10/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-10/xrefs/id/:id Perform lookups of identifiers and retrieve their external references in other databases
GET /rest-10/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-10/info/assembly/:species List the currently available assemblies for a species. NOTE: Response may be large
GET /rest-10/info/assembly/:species/:region_name Returns information about the specified toplevel sequence region for the given species.
GET /rest-10/info/genomes/:name Find information about a given genome
GET /rest-10/info/genomes Find information about all genomes. Response may be very large.
GET /rest-10/info/genomes/assembly Find information about a genome with a specified assembly
GET /rest-10/info/genomes/taxonomy Find information about all genomes beneath a given node of the taxonomy
GET /rest-10/info/quality Get the quality (CEGMA and BUSCO) scores for a specific genome in WormBase ParaSite
GET /rest-10/info/version Get the WormBase release number for any specified WormBase ParaSite release
GET /rest-10/info/species Lists all available species, their aliases, available adaptor groups and data release.

Lookup

ResourceDescription
GET /rest-10/lookup/id/:id Find the species and database for a single identifier
GET /rest-10/lookup/genome/:name Query for a named genome and retrieve the gene models
POST /rest-10/lookup/id Find the species and database for several identifiers. IDs that are not found are returned with no data.
GET /rest-10/lookup/symbol/:species/:symbol Find the species and database for a symbol in a linked external database
POST /rest-10/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-10/map/cdna/:id/:region Convert from cDNA coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the API.
GET /rest-10/map/cds/:id/:region Convert from CDS coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the API.
GET /rest-10/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-10/ontology/ancestors/:id Reconstruct the entire ancestry of a term from is_a and part_of relationships
GET /rest-10/ontology/ancestors/chart/:id Reconstruct the entire ancestry of a term from is_a and part_of relationships.
GET /rest-10/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-10/ontology/id/:id Search for an ontological term by its namespaced identifier
GET /rest-10/ontology/name/:name Search for a list of ontological terms by their name

Overlap

ResourceDescription
GET /rest-10/overlap/id/:id Retrieves features (e.g. genes, transcripts etc.) that overlap a region defined by the given identifier.
GET /rest-10/overlap/region/:species/:region Retrieves multiple types of features for a given region.
GET /rest-10/overlap/translation/:id Retrieve features related to a specific Translation as described by its stable ID (e.g. domains).

Sequence

ResourceDescription
GET /rest-10/sequence/id/:id Request multiple types of sequence by stable identifier.
POST /rest-10/sequence/id Request multiple types of sequence by a stable identifier list.
GET /rest-10/sequence/region/:species/:region Returns the genomic sequence of the specified region of the given species.
POST /rest-10/sequence/region/:species Request multiple types of sequence by a list of regions.