Search API

POST /api/search

Search track hubs using a query specified in the message body. Read the Search docs for information on how to perform a query.

You may also specify some (optional) filters in the message body:

species: the species scientific name
assembly: the name of the assembly
accession: INSDC accession
hub: the hub name

If the request is successful, the response is formatted as a JSON hash with the following key/value pairs:

total_entries: the total number of search results
items: an array of search results. Each item is a minimal representation of the trackDb matching the query, as stored in the Registry. It contains basic information (species, assembly, hub etc.) plus an id which can used with the /api/search/trackdb/:id endpoint to retrieve the full trackDb document from the Registry.

Resource Information

Response formats	JSON
Authentication	No
Rate Limited	No

Parameters

page: the wanted page of the search results (default: 1)
entries_per_page: the number of search results per page (default: 5)
all: if non-zero, request to return all results with no pagination, page and entries_per_page parameters are ignored (default: 0)

Message

Content-type

application/json

Format

{
    "type": "object",
    "properties": {
        "query": {
            "type": "string"
        },
        "species": {
            "type": "string"
        },
        "assembly": {
            "type": "string"
        },
        "accession": {
            "type": "string",
            "pattern": "^GCA_[0-9]+.[0-9]+$"
        },
        "hub": {
            "type": "string"
        },
        "type": {
            "type": "string",
            "enum": [ "genomics", "epigenomics", "transcriptomics", "proteomics" ]
        }
    }
}

Example

{"query" : "monocyte male", assembly: "ASM107743v1"}

Example Request

    POST https://trackhubregistry.org/api/search?page=1
    {
      "query": "monocyte male",
      "assembly": "ASM107743v1"
    }

Example Response

    HTTP/1.0 200 OK
    {
      "next": null,
      "previous": null,
      "total_entries": 2,
      "items": [
        {
          "trackdb_id": 6503,
          "source": {
            "checksum": "81fd31116605f49853d4d1a5d6c3321e",
            "url": "ftp://ftp.vectorbase.org/public_data/rnaseq_alignments/hubs/glossina_morsitans/VBRNAseq_group_1386/GmorY1/trackdb.txt"
          },
          "hub": {
            "name": "VBRNAseq_group_1386",
            "shortLabel": "SRP063744 Male accessory gland and testes",
            "longLabel": "This collection of datasets are derived from male reproductive tissues from the tsetse fly (Glossina morsitans).",
            "url": "ftp://ftp.vectorbase.org/public_data/rnaseq_alignments/hubs/glossina_morsitans/VBRNAseq_group_1386/hub.txt",
            "description_url": null,
            "email": null
          },
          "version": "v1.0",
          "owner": "vb-trackhub",
          "status": {
            "last_update": 1670865945,
            "tracks": {
              "total": 14,
              "with_data": {
                "total": 12,
                "total_ko": 0
              }
            },
            "message": "All is Well"
          },
          "species": {
            "taxon_id": 37546,
            "scientific_name": "Glossina morsitans morsitans",
            "common_name": null
          },
          "assembly": {
            "accession": "GCA_001077435.1",
            "name": "ASM107743v1",
            "long_name": null,
            "ucsc_synonym": "GmorY1"
          },
          "created": 1513007652,
          "type": "transcriptomics",
        },
        ...
      ]
    }

HTTP Status Codes

Code	Description	Reason
200	OK	Request successful
400	Bad request	Empty request body or unable to perform query
500	Internal Server Error	Request cannot be fulfilled due to unexpected condition
503	Service Unavailable	Request cannot be fulfilled due to temporary overloading or maintenance of the server

GET /api/search/trackdb/:id

Retrieve the document in the Registry representing the trackDb with the given ID.

Resource Information

Response formats	JSON
Authentication	No
Rate Limited	No

Parameters

Name	Type	Description	Example Values
id	`String`	A trackDb document ID	`gOGRzcTSRd2l0LMQTufS4w`

Example Request

GET https://trackhubregistry.org/api/search/trackdb/1

Example Response

HTTP/1.0 200 OK
{
    "source": {
        "checksum": "c70af2c480087b45848d60c9ae76f1ad",
        "url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/trackDb.txt"
    },
    "hub": {
        "shortLabel": "Plants",
        "url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt",
        "name": "cshl2013",
        "longLabel": "CSHL Biology of Genomes meeting 2013 demonstration assembly hub"
    },
    "version": "v1.0",
    "owner": "trackhub1",
    "status": {
        "last_update": 1500768407,
        "message": "All is Well"
    },
    "species": {
        "scientific_name": "Arabidopsis thaliana",
        "common_name": "thale cress",
        "tax_id": "3702"
    },
    "assembly": {
        "synonyms": "araTha1",
        "name": "TAIR10",
        "accession": "GCA_000001735.1"
    },
    "created": 1438615855,
    "type": "genomics",
    "configuration": {
        "repeatMasker_": {
            "priority": "149.1",
            "visibility": "dense",
            "compositeTrack": "on",
            "shortLabel": "RepeatMasker",
            "track": "repeatMasker_",
            "members": {
                "repeatMaskerOther_": {
                    "priority": "9",
                    "spectrum": "on",
                    "colorByStrand": "50,50,150 150,50,50",
                    "parent": "repeatMasker_",
                    "shortLabel": "Other",
                    "track": "repeatMaskerOther_",
                    "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.Other.bb",
                    "additional_fields": 1,
                    "type": "bigbed",
                    "maxWindowToDraw": "10000000",
                    "longLabel": "Other Repeating Elements by RepeatMasker",
                    "standard_fields": "6"
                },
                "repeatMaskerLowComplexity_": {
                    "priority": "6",
                    "spectrum": "on",
                    "colorByStrand": "50,50,150 150,50,50",
                    "parent": "repeatMasker_",
                    "shortLabel": "Low Complexity",
                    "track": "repeatMaskerLowComplexity_",
                    "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.Low_complexity.bb",
                    "additional_fields": 1,
                    "type": "bigbed",
                    "maxWindowToDraw": "10000000",
                    "longLabel": "Low Complexity Repeating Elements by RepeatMasker",
                    "standard_fields": "6"
                },
                "repeatMaskerSimple_": {
                    "priority": "5",
                    "spectrum": "on",
                    "colorByStrand": "50,50,150 150,50,50",
                    "parent": "repeatMasker_",
                    "shortLabel": "Simple",
                    "track": "repeatMaskerSimple_",
                    "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.Simple.bb",
                    "additional_fields": 1,
                    "type": "bigbed",
                    "maxWindowToDraw": "10000000",
                    "longLabel": "Simple Repeating Elements by RepeatMasker",
                    "standard_fields": "6"
                },
                "repeatMaskerSINE_": {
                    "priority": "1",
                    "spectrum": "on",
                    "colorByStrand": "50,50,150 150,50,50",
                    "parent": "repeatMasker_",
                    "shortLabel": "SINE",
                    "track": "repeatMaskerSINE_",
                    "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.SINE.bb",
                    "additional_fields": 1,
                    "type": "bigbed",
                    "maxWindowToDraw": "10000000",
                    "longLabel": "SINE Repeating Elements by RepeatMasker",
                    "standard_fields": "6"
                },
                "repeatMaskerLTR_": {
                    "priority": "3",
                    "spectrum": "on",
                    "colorByStrand": "50,50,150 150,50,50",
                    "parent": "repeatMasker_",
                    "shortLabel": "LTR",
                    "track": "repeatMaskerLTR_",
                    "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.LTR.bb",
                    "additional_fields": 1,
                    "type": "bigbed",
                    "maxWindowToDraw": "10000000",
                    "longLabel": "LTR Repeating Elements by RepeatMasker",
                    "standard_fields": "6"
                },
                "repeatMaskerLINE_": {
                    "priority": "2",
                    "spectrum": "on",
                    "colorByStrand": "50,50,150 150,50,50",
                    "parent": "repeatMasker_",
                    "shortLabel": "LINE",
                    "track": "repeatMaskerLINE_",
                    "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.LINE.bb",
                    "additional_fields": 1,
                    "type": "bigbed",
                    "maxWindowToDraw": "10000000",
                    "longLabel": "LINE Repeating Elements by RepeatMasker",
                    "standard_fields": "6"
                },
                "repeatMaskerRNA_": {
                    "priority": "8",
                    "spectrum": "on",
                    "colorByStrand": "50,50,150 150,50,50",
                    "parent": "repeatMasker_",
                    "shortLabel": "RNA",
                    "track": "repeatMaskerRNA_",
                    "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.RNA.bb",
                    "additional_fields": 1,
                    "type": "bigbed",
                    "maxWindowToDraw": "10000000",
                    "longLabel": "RNA Repeating Elements by RepeatMasker",
                    "standard_fields": "6"
                },
                "repeatMaskerDNA_": {
                    "priority": "4",
                    "spectrum": "on",
                    "colorByStrand": "50,50,150 150,50,50",
                    "parent": "repeatMasker_",
                    "shortLabel": "DNA",
                    "track": "repeatMaskerDNA_",
                    "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.DNA.bb",
                    "additional_fields": 1,
                    "type": "bigbed",
                    "maxWindowToDraw": "10000000",
                    "longLabel": "DNA Repeating Elements by RepeatMasker",
                    "standard_fields": "6"
                },
                "repeatMaskerSatellite_": {
                    "priority": "7",
                    "spectrum": "on",
                    "colorByStrand": "50,50,150 150,50,50",
                    "parent": "repeatMasker_",
                    "shortLabel": "Satellite",
                    "track": "repeatMaskerSatellite_",
                    "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.rmsk.Satellite.bb",
                    "additional_fields": 1,
                    "type": "bigbed",
                    "maxWindowToDraw": "10000000",
                    "longLabel": "Satellite Repeating Elements by RepeatMasker",
                    "standard_fields": "6"
                }
            },
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/repeatMasker_.html",
            "group": "varRep",
            "html": "../trackDescriptions/repeatMasker",
            "noInherit": "on",
            "type": "bed",
            "longLabel": "Repeating Elements by RepeatMasker"
        },
        "windowMasker_": {
            "priority": "149.26",
            "visibility": "dense",
            "shortLabel": "WM + SDust",
            "track": "windowMasker_",
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.windowMasker.bb",
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/windowMasker_.html",
            "group": "varRep",
            "html": "../trackDescriptions/windowMasker",
            "configurable": 1,
            "type": "bigbed",
            "standard_fields": "3",
            "longLabel": "Genomic Intervals Masked by WindowMasker + SDust"
        },
        "ensGene": {
            "priority": "40",
            "visibility": "pack",
            "searchTrix": "ensGene.araTha1.ix",
            "track": "ensGene",
            "shortLabel": "Ensembl genes",
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/ensGene.araTha1.bb",
            "searchIndex": "name",
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/ensGene.html",
            "group": "genes",
            "color": "150,0,0",
            "configurable": 1,
            "type": "bigbed",
            "standard_fields": "12",
            "longLabel": "Ensembl genes from Arabidopsis_thaliana.TAIR10.18.gtf.gz"
        },
        "assembly_": {
            "priority": "10",
            "colorByStrand": "150,100,30 230,170,40",
            "visibility": "pack",
            "track": "assembly_",
            "shortLabel": "Assembly",
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.assembly.bb",
            "altColor": "230,170,40",
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/assembly_.html",
            "group": "map",
            "color": "150,100,30",
            "html": "assembly",
            "type": "bigbed",
            "standard_fields": "6",
            "longLabel": "Assembly"
        },
        "simpleRepeat_": {
            "priority": "149.3",
            "visibility": "dense",
            "shortLabel": "Simple Repeats",
            "track": "simpleRepeat_",
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.simpleRepeat.bb",
            "additional_fields": 1,
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/simpleRepeat_.html",
            "group": "varRep",
            "html": "../trackDescriptions/simpleRepeat",
            "type": "bigbed",
            "standard_fields": "4",
            "longLabel": "Simple Tandem Repeats by TRF"
        },
        "blatBraRap1": {
            "priority": "160",
            "visibility": "dense",
            "shortLabel": "blat braRap1",
            "track": "blatBraRap1",
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/blatAraTha1ToBraRap1.bb",
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/blatBraRap1.html",
            "group": "compGeno",
            "configurable": 1,
            "type": "bigbed",
            "longLabel": "lift-over blat to braRap1",
            "standard_fields": "12"
        },
        "gap_": {
            "priority": "11",
            "visibility": "dense",
            "shortLabel": "Gap",
            "track": "gap_",
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gap.bb",
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/gap_.html",
            "group": "map",
            "color": "0,0,0",
            "html": "gap",
            "type": "bigbed",
            "standard_fields": "4",
            "longLabel": "Gap"
        },
        "blatRicCom1": {
            "priority": "170",
            "visibility": "dense",
            "shortLabel": "blat ricCom1",
            "track": "blatRicCom1",
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1ToRicCom1.bb",
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/blatRicCom1.html",
            "group": "compGeno",
            "configurable": 1,
            "type": "bigbed",
            "longLabel": "lift-over blat to ricCom1",
            "standard_fields": "12"
        },
        "lastzBraRap1": {
            "priority": "150",
            "visibility": "dense",
            "shortLabel": "lastz braRap1",
            "track": "lastzBraRap1",
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/lastzAraTha1ToBraRap1.bb",
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/lastzBraRap1.html",
            "group": "compGeno",
            "configurable": 1,
            "type": "bigbed",
            "longLabel": "lastz chain to braRap1",
            "standard_fields": "12"
        },
        "gc5Base_": {
            "priority": "23.5",
            "visibility": "full",
            "shortLabel": "GC Percent",
            "signal_range": [
                "0",
                "100"
            ],
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.gc5Base.bw",
            "maxHeightPixels": "128:36:16",
            "color": "0,0,0",
            "group": "map",
            "autoScale": "Off",
            "html": "../trackDescriptions/gc5Base",
            "graphTypeDefault": "Bar",
            "longLabel": "GC Percent in 5-Base Windows",
            "viewLimits": "30:70",
            "track": "gc5Base_",
            "gridDefault": "OFF",
            "altColor": "128,128,128",
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/gc5Base_.html",
            "type": "bigwig",
            "windowingFunction": "Mean"
        },
        "genscan_": {
            "priority": "50",
            "visibility": "pack",
            "shortLabel": "Genscan Genes",
            "track": "genscan_",
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.genscan.bb",
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/genscan_.html",
            "group": "genes",
            "color": "170,100,0",
            "configurable": 1,
            "html": "../trackDescriptions/genscan",
            "type": "bigbed",
            "standard_fields": "12",
            "longLabel": "Genscan Gene Predictions"
        },
        "cpgIslandExt_": {
            "priority": "90",
            "visibility": "pack",
            "track": "cpgIslandExt_",
            "shortLabel": "CpG Islands",
            "bigDataUrl": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/bbi/araTha1.cpgIslandExt.bb",
            "altColor": "128,228,128",
            "additional_fields": 1,
            "description_url": "http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/cpgIslandExt_.html",
            "group": "regulation",
            "color": "0,100,0",
            "html": "../trackDescriptions/cpgIslandExt",
            "type": "bigbed",
            "standard_fields": "4",
            "longLabel": "CpG Islands (Islands < 300 Bases are Light Green)"
        }
    }
}

HTTP Status Codes

Code	Description	Reason
200	OK	Request successful
404	Not found	Couldn't find trackDb document with the given ID
500	Internal Server Error	Request cannot be fulfilled due to unexpected condition
503	Service Unavailable	Request cannot be fulfilled due to temporary overloading or maintenance of the server