WormBase ParaSite REST API Endpoints
Versioning
This is version 19 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-19 will direct to release 19 of the website. To always retrieve the latest data, simply remove the release number from the URL, i.e. /rest.
Comparative Genomics | |
| Resource | Description |
|---|---|
| GET /rest-19/genetree/id/:id | Retrieves a gene tree dump for a gene tree stable identifier |
| GET /rest-19/genetree/member/id/:id | Retrieves a gene tree that contains the stable identifier |
| GET /rest-19/genetree/member/symbol/:species/:symbol | Retrieves a gene tree containing the gene identified by a symbol |
| GET /rest-19/homology/id/:id | Retrieves homology information (orthologues) by gene id |
| GET /rest-19/homology/symbol/:species/:symbol | Retrieves homology information (orthologues) by symbol |
Cross References | |
| Resource | Description |
| GET /rest-19/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-19/xrefs/id/:id | Perform lookups of identifiers and retrieve their external references in other databases |
| GET /rest-19/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 | |
| Resource | Description |
| GET /rest-19/info/assembly/:species | List the currently available assemblies for a species. NOTE: Response may be large |
| GET /rest-19/info/assembly/:species/:region_name | Returns information about the specified toplevel sequence region for the given species. |
| GET /rest-19/info/genomes/:name | Find information about a given genome |
| GET /rest-19/info/genomes | Find information about all genomes. Response may be very large. |
| GET /rest-19/info/genomes/assembly | Find information about a genome with a specified assembly |
| GET /rest-19/info/genomes/taxonomy | Find information about all genomes beneath a given node of the taxonomy |
| GET /rest-19/info/quality | Get the quality (CEGMA and BUSCO) scores for a specific genome in WormBase ParaSite |
| GET /rest-19/info/version | Get the WormBase release number for any specified WormBase ParaSite release |
| GET /rest-19/info/species | Lists all available species, their aliases, available adaptor groups and data release. |
Lookup | |
| Resource | Description |
| GET /rest-19/lookup/id/:id | Find the species and database for a single identifier |
| POST /rest-19/lookup/id | Find the species and database for several identifiers. IDs that are not found are returned with no data. |
| GET /rest-19/lookup/symbol/:species/:symbol | Find the species and database for a symbol in a linked external database |
| POST /rest-19/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 | |
| Resource | Description |
| GET /rest-19/map/cdna/:id/:region | Convert from cDNA coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the API. |
| GET /rest-19/map/cds/:id/:region | Convert from CDS coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the API. |
| GET /rest-19/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 | |
| Resource | Description |
| GET /rest-19/ontology/ancestors/:id | Reconstruct the entire ancestry of a term from is_a and part_of relationships |
| GET /rest-19/ontology/ancestors/chart/:id | Reconstruct the entire ancestry of a term from is_a and part_of relationships. |
| GET /rest-19/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-19/ontology/id/:id | Search for an ontological term by its namespaced identifier |
| GET /rest-19/ontology/name/:name | Search for a list of ontological terms by their name |
Overlap | |
| Resource | Description |
| GET /rest-19/overlap/id/:id | Retrieves features (e.g. genes, transcripts etc.) that overlap a region defined by the given identifier. |
| GET /rest-19/overlap/region/:species/:region | Retrieves multiple types of features for a given region. |
| GET /rest-19/overlap/translation/:id | Retrieve features related to a specific Translation as described by its stable ID (e.g. domains). |
Sequence | |
| Resource | Description |
| GET /rest-19/sequence/id/:id | Request multiple types of sequence by stable identifier. |
| POST /rest-19/sequence/id | Request multiple types of sequence by a stable identifier list. |
| GET /rest-19/sequence/region/:species/:region | Returns the genomic sequence of the specified region of the given species. |
| POST /rest-19/sequence/region/:species | Request multiple types of sequence by a list of regions. |