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:

R package: OmaDB bioconductor package; project repository
Python library: OmaDB python package

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.
400	Malformed 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

<!-- Load the JavaScript client library -->
<script src="/static/rest_framework/js/coreapi-0.1.1.js"></script>
<script src="/api/docsschema.js"></script>

# Install the Python client library
$ pip install coreapi

function

list

GET /api/function/

Annotate a sequence with GO functions based on all annotations in OMA. The sequence is expected to be a simple string of amino acids and can be passed as a query parameter

Query Parameters

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

Parameter	Description
`query` required	the sequence to be annotated

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

genome

list

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.

Parameter	Description
`page`	A page number within the paginated result set.
`per_page`	Number of results to return per page.

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

read

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.

Parameter	Description
`genome_id` required	an unique identifier for a genome - either its ncbi taxon id or the UniProt species code

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

proteins

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.

Parameter	Description
`genome_id` required	an unique identifier for a genome - either its ncbi taxon id or the UniProt species code

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

group

list

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.

Parameter	Description
`page`	A page number within the paginated result set.
`per_page`	Number of results to return per page.

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

read

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.

Parameter	Description
`group_id` required	an 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://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

close_groups

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.

Parameter	Description
`group_id` required	an 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://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

hog

list

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.

Parameter	Description
`level`	filter the list of HOGs by a specific taxonomic level.
`compare_with`	compares the hog at `level` with those passed with this argument (must be a parent level) and annotates all hogs with the evolutionary events that occured between the two points in time.
`page`	A page number within the paginated result set.
`per_page`	Number of results to return per page.

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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: ...,
    compare_with: ...,
    page: ...,
    per_page: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

read

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.

Parameter	Description
`hog_id` required	an 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.

Parameter	Description
`level`	taxonomic level of restriction for a HOG. The special level 'root' can be used to identify the level at the roothog, i.e. the deepest level of that HOG.

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

members

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.

Parameter	Description
`hog_id` required	an 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. (Example: HOG:0001221.1a, P12345)

Query Parameters

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

Parameter	Description
`level`	taxonomic level of restriction for a HOG - default is its deepest level for a given HOG ID. (Example: Mammalia)

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

similar_profile_hogs

GET /api/hog/{hog_id}/similar_profile_hogs/

Returns the HOGs with the most similar phylogenetic profiles.

The profiles are based on the number of duplications, losses and retained genes along the phylogenetic tree. Hence, the profiles are computed on the deepest level only and all sub-hogs ids will return the same similar HOGs.

Similar profile search is only useful for hogs that have a certain size, i.e. 100 species. For smaller query HOGs, the result will simply be empty.

The result contains for both, the query HOG as well as the similar HOGs a field in_species that contains a list of all species in which at least one copy of the gene is present in the HOG.

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`hog_id` required	an 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. (Example: HOG:0450897, P12345)

Query Parameters

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

Parameter	Description
`max_results`	the number of similar profiles to return. Must be a positive number less than 50. By default the 10 most HOGs with the most similar profiles are returned. (Example: 20)

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

# Interact with the API endpoint
$ coreapi action hog similar_profile_hogs -p hog_id=... -p max_results=...

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", "similar_profile_hogs"]
var params = {
    hog_id: ...,
    max_results: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

pairs

read

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.

Parameter	Description
`genome_id1` required	an unique identifier for the first genome - either its ncbi taxon id or the UniProt species code
`genome_id2` required	an 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.

Parameter	Description
`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://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/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)

protein

bulk_retrieve

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.

changed in verison 1.7: the endpoint returns now a list with tuples (query_id, target) instead of a simple list of proteins in the order of the query ids.

Request Body

The request body should be "application/json" encoded, and should contain a single item.

Parameter	Description
`ids` required	A list of ids of proteins to retrieve

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

# Interact with the API endpoint
$ coreapi action protein bulk_retrieve -p ids=...

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"]
var params = {
    ids: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

read

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.

Parameter	Description
`entry_id` required	an unique identifier for a protein - either it entry number, omaid or its canonical id

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

domains

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.

Parameter	Description
`entry_id` required	an unique identifier for a protein - either it entry number, omaid or its canonical id

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

gene_ontology

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.

Parameter	Description
`entry_id` required	an unique identifier for a protein - either its entry number, omaid or its canonical id

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

hog_derived_orthologs

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.

Parameter	Description
`entry_id` required	an unique identifier for a protein - either it entry number, omaid or its canonical id

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

homoeologs

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.

Parameter	Description
`entry_id` required	an unique identifier for a protein - either its entry number, omaid or canonical id.

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

isoforms

GET /api/protein/{entry_id}/isoforms/

List of isoforms for a protein.

The result contains a list of proteins with information on their locus and and exon structure for all the isoforms recored in OMA belonging to the gene of the query protein.

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`entry_id` required	an unique identifier for a protein - either it entry number, omaid or its canonical id

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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", "isoforms"]
var params = {
    entry_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

ontology

GET /api/protein/{entry_id}/ontology/

Deprecated: use gene_ontology endpoint instead

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

# Interact with the API endpoint
$ coreapi action protein ontology

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"]
client.action(schema, action).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

orthologs

GET /api/protein/{entry_id}/orthologs/

List of all the identified pairwise orthologues for a protein. Filtering specific subtypes of orthology is possible by specifying a rel_type query parameter.

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`entry_id` required	an 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.

Parameter	Description
`rel_type`	filter for orthologs of a specific relationship type only (Example: 1:1)

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

xref

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.

Parameter	Description
`entry_id` required	an unique identifier for a protein - either it entry number, omaid or its canonical id

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

sequence

list

GET /api/sequence/

Identify a protein sequence.

Query Parameters

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

Parameter	Description
`query` required	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://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

summary

shared_ancestry > read

GET /api/summary/shared_ancestry/{genome_id1}/{genome_id2}/

Returns the fraction of shared ancestry between to species of interest.

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`genome_id1` required	an unique identifier for the first genome - either its ncbi taxon id or the UniProt species code
`genome_id2` required	an 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.

Parameter	Description
`type`	type of orthology information to compute the fraction of shared ancestry, either 'hogs' (default) or 'vps'.

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

# Interact with the API endpoint
$ coreapi action summary shared_ancestry read -p genome_id1=... -p genome_id2=... -p type=...

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 = ["summary", "shared_ancestry &gt; read"]
var params = {
    genome_id1: ...,
    genome_id2: ...,
    type: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

# Interact with the API endpoint
action = ["summary", "shared_ancestry &gt; read"]
params = {
    "genome_id1": ...,
    "genome_id2": ...,
    "type": ...,
}
result = client.action(schema, action, params=params)

taxonomy

list

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.

Parameter	Description
`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://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

read

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.

Parameter	Description
`root_id` required	either 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.

Parameter	Description
`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://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

version

list

GET /api/version/

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

# Load the schema document
$ coreapi get https://drosoma.unil.ch/api/docs

# Interact with the API endpoint
$ coreapi action version list

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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

xref

list

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.

Parameter	Description
`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://drosoma.unil.ch/api/docs

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

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'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("https://drosoma.unil.ch/api/docs")

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