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 theLink 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 OKAllow: GET, HEAD, OPTIONSContent-Type: application/jsonLink:  <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: AcceptX-Total-Count: 2198

HTTP status codes

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$pipinstallcoreapi-cli

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

# Install the Python client library$pipinstallcoreapi

create

Request Body

The request body should be a"application/json" encoded object, containing the following items.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionenrichmentcreate-ptype=...-pforeground=...-ptaxlevel=...-pname=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["enrichment","create"]varparams={type:...,foreground:...,taxlevel:...,name:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["enrichment","create"]params={"type":...,"foreground":...,"taxlevel":...,"name":...,}result=client.action(schema,action,params=params)

status > read

Path Parameters

The following parameters should be included in the URL path.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionenrichmentstatusread-pid=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["enrichment","status > read"]varparams={id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["enrichment","status > read"]params={"id":...,}result=client.action(schema,action,params=params)

list

Annotate a sequence with GO functions based on allannotations in OMA. The sequence is expected to be asimple string of amino acids and can be passed as aquery parameter

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionfunctionlist-pquery=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["function","list"]varparams={query:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["function","list"]params={"query":...,}result=client.action(schema,action,params=params)

list

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.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactiongenomelist-ppage=...-pper_page=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["genome","list"]varparams={page:...,per_page:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["genome","list"]params={"page":...,"per_page":...,}result=client.action(schema,action,params=params)

read

Retrieve the information available for a given genome.

Path Parameters

The following parameters should be included in the URL path.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactiongenomeread-pgenome_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["genome","read"]varparams={genome_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["genome","read"]params={"genome_id":...,}result=client.action(schema,action,params=params)

genes

Retrieve the list of all the genes available for a genome.

This corresponds to the list of main isoform for genomes withmultiple isoforms, or to all the proteins for the others.

Path Parameters

The following parameters should be included in the URL path.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactiongenomegenes-pgenome_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["genome","genes"]varparams={genome_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["genome","genes"]params={"genome_id":...,}result=client.action(schema,action,params=params)

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.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactiongenomeproteins-pgenome_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["genome","proteins"]varparams={genome_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["genome","proteins"]params={"genome_id":...,}result=client.action(schema,action,params=params)

list

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.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactiongrouplist-ppage=...-pper_page=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["group","list"]varparams={page:...,per_page:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["group","list"]params={"page":...,"per_page":...,}result=client.action(schema,action,params=params)

read

Retrieve the information available for a given OMA group.

Path Parameters

The following parameters should be included in the URL path.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactiongroupread-pgroup_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["group","read"]varparams={group_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["group","read"]params={"group_id":...,}result=client.action(schema,action,params=params)

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.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactiongroupclose_groups-pgroup_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["group","close_groups"]varparams={group_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["group","close_groups"]params={"group_id":...,}result=client.action(schema,action,params=params)

list

List of all the HOGs identified by OMA.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionhoglist-plevel=...-pcompare_with=...-ppage=...-pper_page=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["hog","list"]varparams={level:...,compare_with:...,page:...,per_page:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["hog","list"]params={"level":...,"compare_with":...,"page":...,"per_page":...,}result=client.action(schema,action,params=params)

read

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 HOGspans through.

For a given hog_id, the endpoint searches the deepest taxonomic level thathas this ID, unless a more recent level has been chosen with thelevel queryparameter in which case the following information is returned for all inducedhogs.

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

Path Parameters

The following parameters should be included in the URL path.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionhogread-phog_id=...-plevel=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["hog","read"]varparams={hog_id:...,level:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["hog","read"]params={"hog_id":...,"level":...,}result=client.action(schema,action,params=params)

gene_ontology

Gene ontology annotations for an ancestral gene (i.e. HOG).

If a level is provided, the endpoint returns annotations with respectto this level. Note that if the level is a more ancient taxonomiclevel than the deepest level for the specified hog_id, the endpointreturns the annotations of that more ancient level (but adjusting thehog_id in the result object).The special level "root" will always return the members of the rootHOG together with its deepest level.

Path Parameters

The following parameters should be included in the URL path.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionhoggene_ontology-phog_id=...-plevel=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["hog","gene_ontology"]varparams={hog_id:...,level:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["hog","gene_ontology"]params={"hog_id":...,"level":...,}result=client.action(schema,action,params=params)

members

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

The hog_id parameter uses an encoding of the inferred duplicationevents 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, theID remains the same for potentially many taxonomic levels. Ifno level parameter is provided, this endpoint returns the deepestlevel that contains this specific ID.

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

Path Parameters

The following parameters should be included in the URL path.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionhogmembers-phog_id=...-plevel=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["hog","members"]varparams={hog_id:...,level:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["hog","members"]params={"hog_id":...,"level":...,}result=client.action(schema,action,params=params)

similar_profile_hogs

Returns the HOGs with the most similar phylogenetic profiles.

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

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

The result contains for both, the query HOG as well as the similar HOGsa fieldin_species that contains a list of all species in which atleast one copy of the gene is present in the HOG.

Path Parameters

The following parameters should be included in the URL path.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionhogsimilar_profile_hogs-phog_id=...-pmax_results=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["hog","similar_profile_hogs"]varparams={hog_id:...,max_results:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["hog","similar_profile_hogs"]params={"hog_id":...,"max_results":...,}result=client.action(schema,action,params=params)

read

List the pairwise relations among two genomes

The relations are orthologs in case the genomes aredifferent and close paralogs and homoeologs in casethey are the same.

By using the query_params 'chr1' and 'chr2', one can limitthe relations to a certain chromosome for one or bothgenomes. The id of the chromosome corresponds to the idsreturned by the genome endpoint.

Path Parameters

The following parameters should be included in the URL path.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionpairsread-pgenome_id1=...-pgenome_id2=...-pchr1=...-pchr2=...-ptype=...-pxrefs=...-prel_type=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["pairs","read"]varparams={genome_id1:...,genome_id2:...,chr1:...,chr2:...,type:...,xrefs:...,rel_type:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["pairs","read"]params={"genome_id1":...,"genome_id2":...,"chr1":...,"chr2":...,"type":...,"xrefs":...,"rel_type":...,}result=client.action(schema,action,params=params)

bulk_retrieve

Retrieve the information available for multiple protein IDs at once.

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

In case the ID is not unique or unknown, an empty element isreturned 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.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionproteinbulk_retrieve-pids=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["protein","bulk_retrieve"]varparams={ids:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["protein","bulk_retrieve"]params={"ids":...,}result=client.action(schema,action,params=params)

read

Retrieve the information available for a protein entry.

Path Parameters

The following parameters should be included in the URL path.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionproteinread-pentry_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["protein","read"]varparams={entry_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["protein","read"]params={"entry_id":...,}result=client.action(schema,action,params=params)

domains

List of the domains present in a protein.

Path Parameters

The following parameters should be included in the URL path.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionproteindomains-pentry_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["protein","domains"]varparams={entry_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["protein","domains"]params={"entry_id":...,}result=client.action(schema,action,params=params)

gene_ontology

Gene ontology information available for a protein.

Path Parameters

The following parameters should be included in the URL path.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionproteingene_ontology-pentry_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["protein","gene_ontology"]varparams={entry_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["protein","gene_ontology"]params={"entry_id":...,}result=client.action(schema,action,params=params)

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.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionproteinhog_derived_orthologs-pentry_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["protein","hog_derived_orthologs"]varparams={entry_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["protein","hog_derived_orthologs"]params={"entry_id":...,}result=client.action(schema,action,params=params)

homoeologs

List of all the homoeologs for a given protein.

Path Parameters

The following parameters should be included in the URL path.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionproteinhomoeologs-pentry_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["protein","homoeologs"]varparams={entry_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["protein","homoeologs"]params={"entry_id":...,}result=client.action(schema,action,params=params)

isoforms

List of isoforms for a protein.

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

Path Parameters

The following parameters should be included in the URL path.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionproteinisoforms-pentry_id=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["protein","isoforms"]varparams={entry_id:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["protein","isoforms"]params={"entry_id":...,}result=client.action(schema,action,params=params)

ontology

Deprecated: use gene_ontology endpoint instead

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionproteinontology

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["protein","ontology"]client.action(schema,action).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["protein","ontology"]result=client.action(schema,action)

orthologs

List of all the identified pairwise orthologues for a protein. Filteringspecific subtypes of orthology is possible by specifying a rel_typequery parameter.

Path Parameters

The following parameters should be included in the URL path.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionproteinorthologs-pentry_id=...-prel_type=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["protein","orthologs"]varparams={entry_id:...,rel_type:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["protein","orthologs"]params={"entry_id":...,"rel_type":...,}result=client.action(schema,action,params=params)

xref

List of cross-references for a protein.

Path Parameters

The following parameters should be included in the URL path.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionproteinxref-pentry_id=...-pfilter=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["protein","xref"]varparams={entry_id:...,filter:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["protein","xref"]params={"entry_id":...,"filter":...,}result=client.action(schema,action,params=params)

list

Identify a protein sequence.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionsequencelist-pquery=...-psearch=...-pfull_length=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["sequence","list"]varparams={query:...,search:...,full_length:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["sequence","list"]params={"query":...,"search":...,"full_length":...,}result=client.action(schema,action,params=params)

shared_ancestry > read

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

Path Parameters

The following parameters should be included in the URL path.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionsummaryshared_ancestryread-pgenome_id1=...-pgenome_id2=...-ptype=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["summary","shared_ancestry > read"]varparams={genome_id1:...,genome_id2:...,type:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["summary","shared_ancestry > read"]params={"genome_id1":...,"genome_id2":...,"type":...,}result=client.action(schema,action,params=params)

list

List of all the ancestral / extant "contigs" of an ancestral / extant genome.

Each contig will contain a graph with all the ancestral genes (HOGs) orthe extant genes and their neighbors as edges (order of ancestral/extant geneson "scaffolds/chromosomes")

The return value is a list of graph objects that consist of 'nodes' and'links' attributes.

{"nodes": [{"id":"HOG:C0594134.1a", ...},           {"id":"HOG:C0594135.3c", ...},           {"id":"HOG:C0600830.1c.3b", ...}], "links": [{"weight":15,"source":"HOG:C0594134.1a","target":"HOG:C0594135.3c"},           {"weight":15,"source":"HOG:C0594134.1a","target":"HOG:C0600830.1c.3b"}]}

For extant genes, the gene IDs are the OMA IDs (e.g.HUMAN00007)

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionsyntenylist-plevel=...-pevidence=...-pbreak_circular_contigs=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["synteny","list"]varparams={level:...,evidence:...,break_circular_contigs:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["synteny","list"]params={"level":...,"evidence":...,"break_circular_contigs":...,}result=client.action(schema,action,params=params)

read

Returns the ancestral synteny graph around a reference hog at a given taxonomic level.

Path Parameters

The following parameters should be included in the URL path.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionsyntenyread-phog_id/protein_id=...-plevel=...-pevidence=...-pcontext=...-pbreak_circular_contigs=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["synteny","read"]varparams={hog_id/protein_id:...,level:...,evidence:...,context:...,break_circular_contigs:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["synteny","read"]params={"hog_id / protein_id":...,"level":...,"evidence":...,"context":...,"break_circular_contigs":...,}result=client.action(schema,action,params=params)

list

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.

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactiontaxonomylist-ptype=...-pmembers=...-pcollapse=...-pnewick_leaf_label=...-pnewick_internal_label=...-pnewick_quote_labels=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["taxonomy","list"]varparams={type:...,members:...,collapse:...,newick_leaf_label:...,newick_internal_label:...,newick_quote_labels:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["taxonomy","list"]params={"type":...,"members":...,"collapse":...,"newick_leaf_label":...,"newick_internal_label":...,"newick_quote_labels":...,}result=client.action(schema,action,params=params)

read

Retrieve the subtree rooted at the taxonomic level indicated.

Path Parameters

The following parameters should be included in the URL path.

Query Parameters

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactiontaxonomyread-proot_id=...-ptype=...-pcollapse=...

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["taxonomy","read"]varparams={root_id:...,type:...,collapse:...,}client.action(schema,action,params).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["taxonomy","read"]params={"root_id":...,"type":...,"collapse":...,}result=client.action(schema,action,params=params)

list

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

# Load the schema document$coreapigethttps://omabrowser.org/api/docs# Interact with the API endpoint$coreapiactionversionlist

varcoreapi=window.coreapi// Loaded by `coreapi.js`varschema=window.schema// Loaded by `schema.js`// Initialize a clientvarclient=newcoreapi.Client()// Interact with the API endpointvaraction=["version","list"]client.action(schema,action).then(function(result){// Return value is in 'result'})

importcoreapi# Initialize a client & load the schema documentclient=coreapi.Client()schema=client.get("https://omabrowser.org/api/docs")# Interact with the API endpointaction=["version","list"]result=client.action(schema,action)