REST API for the OMA Browser

REST API for the OMA Browser

The OMA Brower now supports its own REST API, which serves as a window into its database. It enables the abstraction of OMA browser’s data which also allows it to be more accessible via other programming languages. Furthermore, due to its RESTful architecture, it allows the users to access the data they need easily through HTTP requests sent to the server which can be found at:

http://omabrowser.org/api

The OMA REST API supports many data formats and its predominant use of the JSON data format makes it very browser-compatible.To further facilitate the ease of access, we have also developed a Python library and R package to serve as user friendly wrappers around the API. The links to their documentation can be found below:

Pagination in the API

Note that some endpoints, such as the list of all Hierarchical Orthologous groups, return a very long list. In order to keep the response size and time manageable the API will take advantage of pagination, which is a mechanism for returning a subset of the results for a request (by default, we return the results in chunks of 100 objects) and allowing for subsequent requests to “page” through the rest of the results until the end is reached. This pagination is implemented with a "page" query parameter and a "per_page" parameter to specify the number of objects per page.

Information about pagination is provided in the Link header of an API call. This is a popular way how to implement pagination for APIs. In essence this strategy includes in the HTTP reply header a "Link" header with the urls to to next, previous, first and last page. Furthermore, we include in the "X-Total-Count" header the total number of objects that the request will return over all pages. Here is an example request:

curl -I "https://omabrowser.org/api/genome/?page=2"
HTTP 200 OK
Allow: GET, HEAD, OPTIONS
Content-Type: application/json
Link: 
 <https://omabrowser.org/api/genomes/>; rel="first",
 <https://omabrowser.org/api/genomes/>; rel="prev",
 <https://omabrowser.org/api/genomes/?page=3>; rel="next",
 <https://omabrowser.org/api/genomes/?page=22>; rel="last"
Vary: Accept
X-Total-Count: 2198

HTTP status codes

Status Code Description
200 OK. All is well.
400Malformed request.
404 Not found.
500 Internal Server Error.

Available API Endpoints

Below we list all the available endpoints together with a brief description of what they return and the parameters they take.

# Install the command line client
$ pip install coreapi-cli

# Install the Python client library
$ pip install coreapi

<!-- Load the JavaScript client library -->
<script src="/static/rest_framework/js/coreapi-0.1.0.js"></script>
<script src="/api/docsschema.js"></script>

function

GET /api/function/

Annotate a sequence with GO functions based on all annotations in OMA.

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
query the sequence to be annotated
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action function list -p query=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["function", "list"]
params = {
    "query": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["function", "list"]
var params = {
    query: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

genome

GET /api/genome/

List of all the genomes present in the current release.

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
pageA page number within the paginated result set.
per_pageNumber of results to return per page.
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action genome list -p page=... -p per_page=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["genome", "list"]
params = {
    "page": ...,
    "per_page": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["genome", "list"]
var params = {
    page: ...,
    per_page: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/genome/{genome_id}/

Retrieve the information available for a given genome.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
genome_id requiredan unique identifier for a genome - either its ncbi taxon id or the UniProt species code
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action genome read -p genome_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["genome", "read"]
params = {
    "genome_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["genome", "read"]
var params = {
    genome_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/genome/{genome_id}/proteins/

Retrieve the list of all the protein entries available for a genome.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
genome_id requiredan unique identifier for a genome - either its ncbi taxon id or the UniProt species code
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action genome proteins -p genome_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["genome", "proteins"]
params = {
    "genome_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["genome", "proteins"]
var params = {
    genome_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

group

GET /api/group/

List of all the OMA Groups in the current release.

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
pageA page number within the paginated result set.
per_pageNumber of results to return per page.
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action group list -p page=... -p per_page=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["group", "list"]
params = {
    "page": ...,
    "per_page": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["group", "list"]
var params = {
    page: ...,
    per_page: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/group/{group_id}/

Retrieve the information available for a given OMA group.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
group_id requiredan unique identifier for an OMA group - either its group number, its fingerprint or an entry id of one of its members
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action group read -p group_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["group", "read"]
params = {
    "group_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["group", "read"]
var params = {
    group_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/group/{group_id}/close_groups/

Retrieve the sorted list of closely related groups for a given OMA group.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
group_id requiredan unique identifier for an OMA group - either its group number, its fingerprint or an entry id of one of its members
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action group close_groups -p group_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["group", "close_groups"]
params = {
    "group_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["group", "close_groups"]
var params = {
    group_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

hog

GET /api/hog/

List of all the HOGs identified by OMA.

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
level allows filtering of the list of HOGs by a specific taxonomic level.
pageA page number within the paginated result set.
per_pageNumber of results to return per page.
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action hog list -p level=... -p page=... -p per_page=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["hog", "list"]
params = {
    "level": ...,
    "page": ...,
    "per_page": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["hog", "list"]
var params = {
    level: ...,
    page: ...,
    per_page: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/hog/{hog_id}/

Retrieve the detail available for a given HOG, along with its deepest level (i.e. root level) as well as the list of all the taxonomic levels that the HOG spans through.

For a given hog_id, the endpoint searches the deepest taxonomic level that has this ID, unless a more recent level has been chosen with the level query parameter in which case the following information is returned for all induced hogs.

The endpoint returns an object per hog with the level, urls to the members and a list of parent and children hogs. The parent and children hogs are more ancient resp. more recent levels that involve at least one duplication event on the lineage from the query hog. So, in the parent_hogs, one can find hogs for which we infer a duplication event to the query hog level, where as for the children_hogs there happened at least one duplication event after the query hog level. In addition, we indicate alternative levels for which we infer that no event happened between those levels for this specific hog.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
hog_id requiredan unique identifier for a hog_group - either its hog id or one of its member proteins

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
level taxonomic level of restriction for a HOG. The special level 'root' can be used to identify the level at the roothog. 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action hog read -p hog_id=... -p level=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["hog", "read"]
params = {
    "hog_id": ...,
    "level": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["hog", "read"]
var params = {
    hog_id: ...,
    level: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/hog/{hog_id}/members/

Retrieve a list of all the protein members for a given hog_id.

The hog_id parameter uses an encoding of the inferred duplication events along the evolution of the family using the LOFT schema (see https://doi.org/10.1186/1471-2105-8-83).

The hog_id changes only after duplication events and hence, the ID remains the same for potentially many taxonomic levels. If no level parameter is provided, this endpoint returns the deepest level that contains this specific ID.

If a level is provided, the endpoint returns the members with respect to this level. Note that if the level is a more ancient taxonomic level than the deepest level for the specified hog_id, the endpoint retuns the members of for that more ancient level (but adjusting the hog_id in the result object). The special level "root" will always return the members of the root HOG together with its deepest level.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
hog_id requiredan unique identifier for a hog_group - either its hog id starting with "HOG:" or one of its member proteins in which case the specific HOG ID of that protein is used.

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
level taxonomic level of restriction for a HOG - default is its deepest level for a given HOG ID. . 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action hog members -p hog_id=... -p level=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["hog", "members"]
params = {
    "hog_id": ...,
    "level": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["hog", "members"]
var params = {
    hog_id: ...,
    level: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

pairs

GET /api/pairs/{genome_id1}/{genome_id2}/

List the pairwise relations among two genomes

The relations are orthologs in case the genomes are different and close paralogs and homoeologs in case they are the same.

By using the query_params 'chr1' and 'chr2', one can limit the relations to a certain chromosome for one or both genomes. The id of the chromosome corresponds to the ids returned by the genome endpoint.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
genome_id1 requiredan unique identifier for the first genome - either its ncbi taxon id or the UniProt species code
genome_id2 requiredan unique identifier for the second genome - either its ncbi taxon id or the UniProt species code

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
chr1 id of the chromosome of interest in the first genome
chr2 id of the chromosome of interest in the second genome
rel_type limit relations to a certain type of relations, e.g. '1:1'. 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action pairs read -p genome_id1=... -p genome_id2=... -p chr1=... -p chr2=... -p rel_type=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["pairs", "read"]
params = {
    "genome_id1": ...,
    "genome_id2": ...,
    "chr1": ...,
    "chr2": ...,
    "rel_type": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["pairs", "read"]
var params = {
    genome_id1: ...,
    genome_id2: ...,
    chr1: ...,
    chr2: ...,
    rel_type: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

protein

POST /api/protein/bulk_retrieve/

Retrieve the information available for multiple protein IDs at once.

The POST request must contain a json-encoded list of IDs of up to 1000 IDs for which the information is returned.

In case the ID is not unique or unknown, an empty element is returned for this query element.

# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action protein bulk_retrieve

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["protein", "bulk_retrieve"]
result = client.action(schema, action)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["protein", "bulk_retrieve"]
client.action(schema, action).then(function(result) {
    // Return value is in 'result'
})
GET /api/protein/{entry_id}/

Retrieve the information available for a protein entry.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
entry_id requiredan unique identifier for a protein - either it entry number, omaid or its canonical id
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action protein read -p entry_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["protein", "read"]
params = {
    "entry_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["protein", "read"]
var params = {
    entry_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/protein/{entry_id}/domains/

List of the domains present in a protein.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
entry_id requiredan unique identifier for a protein - either it entry number, omaid or its canonical id
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action protein domains -p entry_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["protein", "domains"]
params = {
    "entry_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["protein", "domains"]
var params = {
    entry_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/protein/{entry_id}/gene_ontology/

Gene ontology information available for a protein.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
entry_id requiredan unique identifier for a protein - either its entry number, omaid or its canonical id
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action protein gene_ontology -p entry_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["protein", "gene_ontology"]
params = {
    "entry_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["protein", "gene_ontology"]
var params = {
    entry_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/protein/{entry_id}/hog_derived_orthologs/

List of the orthologs derived from the hog for a given protein.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
entry_id requiredan unique identifier for a protein - either it entry number, omaid or its canonical id
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action protein hog_derived_orthologs -p entry_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["protein", "hog_derived_orthologs"]
params = {
    "entry_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["protein", "hog_derived_orthologs"]
var params = {
    entry_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/protein/{entry_id}/homoeologs/

List of all the homoeologs for a given protein.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
entry_id requiredan unique identifier for a protein - either its entry number, omaid or canonical id.
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action protein homoeologs -p entry_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["protein", "homoeologs"]
params = {
    "entry_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["protein", "homoeologs"]
var params = {
    entry_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/protein/{entry_id}/ontology/

Deprecated: use gene_ontology endpoint instead

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
entry_id required
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action protein ontology -p entry_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["protein", "ontology"]
params = {
    "entry_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["protein", "ontology"]
var params = {
    entry_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/protein/{entry_id}/orthologs/

List of all the identified pairwise orthologs for a protein.

Possible to filter out orthologs by specifying the ?rel_type query parameter.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
entry_id requiredan unique identifier for a protein - either it entry number, omaid or its canonical id

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
rel_type allows the user to filter the orthologs for a specific relationship type only 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action protein orthologs -p entry_id=... -p rel_type=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["protein", "orthologs"]
params = {
    "entry_id": ...,
    "rel_type": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["protein", "orthologs"]
var params = {
    entry_id: ...,
    rel_type: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/protein/{entry_id}/xref/

List of cross-references for a protein.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
entry_id requiredan unique identifier for a protein - either it entry number, omaid or its canonical id
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action protein xref -p entry_id=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["protein", "xref"]
params = {
    "entry_id": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["protein", "xref"]
var params = {
    entry_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

sequence

GET /api/sequence/

Identify a protein sequence

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
query the sequence to be searched.
search argument to choose search strategy. Can be set to 'exact', 'approximate' or 'mixed'. Defaults to 'mixed', meaning first tries to find exact match. If no target can be found, uses approximate search strategy to identify query sequence in database.
full_length a boolean indicating whether or not for exact matches, the query sequence must be matching the full target sequence. By default, a partial exact match is also reported as exact match.
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action sequence list -p query=... -p search=... -p full_length=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["sequence", "list"]
params = {
    "query": ...,
    "search": ...,
    "full_length": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["sequence", "list"]
var params = {
    query: ...,
    search: ...,
    full_length: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

taxonomy

GET /api/taxonomy/

Retrieve the taxonomic tree that is available in the current release.

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
type the type of the returned data - either dictionary (default), newick or phyloxml.
members list of members to get the induced taxonomy from. The list is supposed to be a comma-separated list. Member IDs can be either their ncbi taxon IDs or their UniProt species codes - they just have to be consistent.
collapse whether or not taxonomic levels with a single child should be collapsed or not. Defaults to yes. 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action taxonomy list -p type=... -p members=... -p collapse=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["taxonomy", "list"]
params = {
    "type": ...,
    "members": ...,
    "collapse": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["taxonomy", "list"]
var params = {
    type: ...,
    members: ...,
    collapse: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})
GET /api/taxonomy/{root_id}/

Retrieve the subtree rooted at the taxonomic level indicated.

Path Parameters

The following parameters should be included in the URL path.

ParameterDescription
root_id requiredeither the taxon id, species name or the 5 letter UniProt species code for a root taxonomic level

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
type the type of the returned data - either dictionary (default) or newick.
collapse whether or not taxonomic levels with a single child should be collapsed or not. Defaults to yes. 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action taxonomy read -p root_id=... -p type=... -p collapse=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["taxonomy", "read"]
params = {
    "root_id": ...,
    "type": ...,
    "collapse": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["taxonomy", "read"]
var params = {
    root_id: ...,
    type: ...,
    collapse: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

version

GET /api/version/

Returns the version information of the api and the underlying oma browser database release.

# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action version list

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["version", "list"]
result = client.action(schema, action)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["version", "list"]
client.action(schema, action).then(function(result) {
    // Return value is in 'result'
})

xref

GET /api/xref/

List all the crossreferences that match a certain pattern.

Query Parameters

The following parameters should be included as part of a URL query string.

ParameterDescription
search the pattern to be searched for. The pattern must be at least 3 characters long in order to return a hit.
 
# Load the schema document
$ coreapi get https://corona.omabrowser.org/api/docs

# Interact with the API endpoint
$ coreapi action xref list -p search=...

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://corona.omabrowser.org/api/docs")

# Interact with the API endpoint
action = ["xref", "list"]
params = {
    "search": ...,
}
result = client.action(schema, action, params=params)

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["xref", "list"]
var params = {
    search: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})