Info API

GET /api/info/version

Returns the current version of all the Registry APIs.

If the request is successful, the Response is an hash with one key, version, whose value is a string which identifies the API version.

Resource Information

Parameters

None

Example Request

GET https://trackhubregistry.org/api/info/version

Example Response

HTTP/1.0 200 OK
{
   "version": "0.8.1"
}

HTTP Status Codes

GET /api/info/ping

Checks if the service is alive.

If the request is successful, the response is a hash with one key, ping. If it's value is 1 the service is available.

Resource Information

Parameters

None

Example Request

GET https://trackhubregistry.org/api/info/ping

Example Response

HTTP/1.0 200 OK
{
    "ping": 1
}

HTTP Status Codes

GET /api/info/species

Returns the set of species the track hubs registered in the Registry contain data for.

If the request is successful, the response is an array containing the scientific names of the species.

Resource Information

Parameters

None

Example Request

GET https://trackhubregistry.org/api/info/species

Example Response

HTTP/1.0 200 OK
[
    "Homo sapiens",
    "Phaeodactylum tricornutum CCAP 1055/1",
    "Pythium arrhenomanes ATCC 12531",
    "Colletotrichum graminicola M1.001",
    "Colletotrichum higginsianum",
    "Colletotrichum sublineola",
    "Brassica rapa",
    "Mus musculus",
    "Chlamydomonas reinhardtii",
    "Solanum tuberosum",
    "Zea mays",
    "Arabidopsis thaliana",
    "Brachypodium distachyon",
    "Triticum aestivum",
    ...
]

HTTP Status Codes

GET /api/info/assemblies

Returns the set of assemblies the track hubs registered in the Registry contain data for. The returned assemblies are grouped by their corresponding species.

If the request is successful, the response is a hash where a key is a species scientific name, and whose value is an array of hashes, each one representing an assembly for that species and containing its name, synonyms and accession.

Resource Information

Parameters

None

Example Request

GET https://trackhubregistry.org/api/info/assemblies

Example Response

HTTP/1.0 200 OK
{
    "Homo sapiens": [
        {
            "name": "GRCh38",
            "accession": "GCA_000001405.15",
            "synonyms": [
                "hg38"
            ]
        },
        {
            "name": "GRCh37",
            "accession": "GCA_000001405.1",
            "synonyms": [
                "hg19"
            ]
        },
        {
            "name": "GRCh38.p13",
            "accession": "GCA_000001405.28",
            "synonyms": [
                "hg38"
            ]
        },
        {
            "name": "GRCh38.p12",
            "accession": "GCA_000001405.27",
            "synonyms": [
                "hg38"
            ]
        },
        {
            "name": "T2T-CHM13v2.0",
            "accession": "GCA_009914755.4",
            "synonyms": [
                "GCA_009914755.4"
            ]
        }
    ],
    "Phaeodactylum tricornutum CCAP 1055/1": [
        {
            "name": "ASM15095v2",
            "accession": "GCA_000150955.2",
            "synonyms": [
                "ASM15095v2"
            ]
        }
    ],
    "Pythium arrhenomanes ATCC 12531": [
        {
            "name": "par_scaffolds_v1",
            "accession": "GCA_000387505.2",
            "synonyms": [
                "par_scaffolds_v1"
            ]
        }
    ],
    "Colletotrichum graminicola M1.001": [
        {
            "name": "C_graminicola_M1_001_V1",
            "accession": "GCA_000149035.1",
            "synonyms": [
                "C_graminicola_M1_001_V1"
            ]
        }
    ],
    "Colletotrichum higginsianum": [
        {
            "name": "ASM31379v2",
            "accession": "GCA_000313795.2",
            "synonyms": [
                "GCA_000313795.2"
            ]
        }
    ],
    "Colletotrichum sublineola": [
        {
            "name": "ASM69613v1",
            "accession": "GCA_000696135.1",
            "synonyms": [
                "ASM69613v1"
            ]
        }
    ],
    "Brassica rapa": [
        {
            "name": "Brapa_1.0",
            "accession": "GCA_000309985.1",
            "synonyms": [
                "braRap1"
            ]
        }
    ]
    ...
}

HTTP Status Codes

GET /api/info/hubs_per_assembly/:assembly

Returns the number of hubs for a given assembly, specified either by INSDC name or accession.

If the request is successful, the response is a hash with a key "tot", whose value is the total number of hubs which contains data for the specified assembly.

Resource Information

Parameters

The INSDC name or accession of the assembly

Example Requests

GET https://trackhubregistry.org/api/info/hubs_per_assembly/GRCz10

GET https://trackhubregistry.org/api/info/hubs_per_assembly/GCA_000002035.3

Example Response

HTTP/1.0 200 OK
{
    "tot": 4
}

HTTP Status Codes

GET /api/info/tracks_per_assembly/:assembly

Returns the number of tracks for a given assembly, specified by INSDC name or accession.

If the request is successful, the response is a hash with a key "tot", whose value is the total number of tracks which contains data for the specified assembly.

Resource Information

Parameters

The INSDC name or accession of the assembly

Example Request

GET https://trackhubregistry.org/api/info/tracks_per_assembly/GRCz10

GET https://trackhubregistry.org/api/info/tracks_per_assembly/GCA_000002035.3

Example Response

HTTP/1.0 200 OK
{
    "tot": 19
}

HTTP Status Codes

GET /api/info/trackhubs

Return the list of registered track data hubs.

If the request is successful, the response is an array of hashes identifying trackhubs. Each trackhub hash has the following key/value pairs:

• name: the single-word name of the directory containing the track hub files;
• url: the track hub remote URL;
• shortLabel: the short name for the track hub;
• longLabel: the longer descriptive label for the track hub;
• trackdbs: a list of hashes containing information for each trackDb (i.e. assembly specific data files) registered for the track hub. Each trackDb hash contains the species NCBI tax id and assembly accession, and the URI of the JSON representation of the trackDb which can be retrieved from the Registry.

Resource Information

Parameters

None

Example Request

GET https://trackhubregistry.org/api/info/trackhubs

Example Response

HTTP 200 OK
{
    "count": 8274,
    "next": "https://trackhubregistry.org/api/info/trackhubs?limit=5&offset=5",
    "previous": null,
    "results": [
        {
            "name": "Blueprint_Hub_20160816",
            "shortLabel": "Blueprint Hub",
            "longLabel": "Blueprint Epigenomics Data Hub",
            "url": "http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/current_release/homo_sapiens/hub/hub.txt",
            "trackdbs": [
                {
                    "species": "9606",
                    "uri": "https://trackhubregistry.org/api/search/trackdb/1",
                    "assembly": "GCA_000001405.15"
                }
            ]
        },
        {
            "name": "SRP040703",
            "shortLabel": "RNA-Seq alignment hub SRP040703",
            "longLabel": "Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen",
            "url": "ftp://ftp.ensemblgenomes.org/pub/misc_data/track_hubs/protists//SRP040703/hub.txt",
            "trackdbs": [
                {
                    "species": "556484",
                    "uri": "https://trackhubregistry.org/api/search/trackdb/2",
                    "assembly": "GCA_000150955.2"
                }
            ]
        },
        {
            "name": "SRP006964",
            "shortLabel": "RNA-Seq alignment hub SRP006964",
            "longLabel": "Pythium Comparative Transcriptome Analysis SRP006964",
            "url": "ftp://ftp.ensemblgenomes.org/pub/misc_data/track_hubs/protists//SRP006964/hub.txt",
            "trackdbs": [
                {
                    "species": "1223556",
                    "uri": "https://trackhubregistry.org/api/search/trackdb/3",
                    "assembly": "GCA_000387505.2"
                },
                {
                    "species": "1223557",
                    "uri": "https://trackhubregistry.org/api/search/trackdb/3010",
                    "assembly": "GCA_000387425.2"
                },
                {
                    "species": "1223558",
                    "uri": "https://trackhubregistry.org/api/search/trackdb/6157",
                    "assembly": "GCA_000387465.2"
                },
                {
                    "species": "1223560",
                    "uri": "https://trackhubregistry.org/api/search/trackdb/6482",
                    "assembly": "GCA_000387545.2"
                }
            ]
        },
        {
            "name": "SRP123414",
            "shortLabel": "RNA-Seq alignment hub SRP123414",
            "longLabel": "Colletotrichum graminicola CBS130836 Gene Expression Profiling on Sugar Beet Pulp - 32",
            "url": "ftp://ftp.ensemblgenomes.org/pub/misc_data/track_hubs/fungi/SRP123414/hub.txt",
            "trackdbs": [
                {
                    "species": "645133",
                    "uri": "https://trackhubregistry.org/api/search/trackdb/4",
                    "assembly": "GCA_000149035.1"
                }
            ]
        },
        {
            "name": "SRP123425",
            "shortLabel": "RNA-Seq alignment hub SRP123425",
            "longLabel": "Colletotrichum higginsianum IMI349063 Gene Expression Profiling on MP - 7 SRP123425",
            "url": "ftp://ftp.ensemblgenomes.org/pub/misc_data/track_hubs/fungi/SRP123425/hub.txt",
            "trackdbs": [
                {
                    "species": "80884",
                    "uri": "https://trackhubregistry.org/api/search/trackdb/5",
                    "assembly": "GCA_000313795.2"
                }
            ]
        }
    ]
}

HTTP Status Codes