Metagenome BIN API

The API is only using GET request:

• One IMG bin id:

  • curl https://img.jgi.doe.gov/cgi-bin/binMetadata.cgi?ids=3300061477_13

• Two or more IMG bin ids: The URL should be quoted when using multiple ids separated by a space. Or ids can be separated by comma or a "%20" which is a "space" character for URLs.

  • The GET is URL quoted:

    • curl "https://img.jgi.doe.gov/cgi-bin/binMetadata.cgi?ids=3300061477_13 3300061477_18"

  • The bin ids are separated by a comma:

    • curl https://img.jgi.doe.gov/cgi-bin/binMetadata.cgi?ids=3300061477_13,3300061477_18

  • The bin ids separated by a space. The space should be the "%20" characters (without the double quotes)

    • curl https://img.jgi.doe.gov/cgi-bin/binMetadata.cgi?ids=3300061477_13%203300061477_18

• Search by IMG taxon ids

  • • curl https://img.jgi.doe.gov/cgi-bin/binMetadata.cgi?ids=3300054958

• One found bin and one failed search

  • • curl https://img.jgi.doe.gov/cgi-bin/binMetadata.cgi?ids=3300061477_13,123

{

   "123" : {

      "error" : "id not found"

   },

   "MetaBAT_3300061477_13" : {...}

}

• A failed search will return a JSON object with an error message.

  • curl https://img.jgi.doe.gov/cgi-bin/binMetadata.cgi?ids=33_1

{

   "error" : "2 - No bin found"

}

{

   "EukCC_3300061477_18" : {

      "avg_coverage" : 276.94,

      "completeness" : 58.27,

      "contamination" : 0,

      "ebin_class" : "Dothideomycetes",

      "ebin_domain" : "Eukaryota",

      "ebin_family" : "Teratosphaeriaceae",

      "ebin_genus" : "",

      "ebin_oid" : "3300061477_18",

      "ebin_order" : "Mycosphaerellales",

      "ebin_phylum" : "Ascomycota",

      "methods" : "EukCC version 2.1.2, eukcc2_db_ver_1.2",

      "num_18s" : 0,

      "num_28s" : 0,

      "num_5s" : 35,

      "processed_by" : 1000,

      "processed_date" : "2024-05-08",

      "scaffold_count" : 862,

      "taxon_oid" : "3300061477",

      "total_bases" : 17434901

   },

   "MetaBAT_3300061477_13" : {

      "avg_coverage" : 13.36,

      "bin_add_date" : "2023-05-03",

      "bin_class" : "Sphingobacteriia",

      "bin_created_by" : 1000,

      "bin_domain" : "Bacteria",

      "bin_family" : "Sphingobacteriaceae",

      "bin_genus" : "Pedobacter",

      "bin_methods" : "MetaBAT v2:2.15, CheckM v1.2.1, GTDB-tk v2.1.1, GTDB database release R207_v2",

      "bin_oid" : "3300061477_13",

      "bin_order" : "Sphingobacteriales",

      "bin_phylum" : "Bacteroidota",

      "bin_quality" : "MQ",

      "bin_species" : "",

      "completeness" : 72.7,

      "contamination" : 0.48,

      "gene_count" : 2681,

      "gtdb_class" : "Bacteroidia",

      "gtdb_domain" : "Bacteria",

      "gtdb_family" : "Sphingobacteriaceae",

      "gtdb_genus" : "Pedobacter",

      "gtdb_order" : "Sphingobacteriales",

      "gtdb_phylum" : "Bacteroidota",

      "gtdb_species" : "",

      "num_16s" : 0,

      "num_23s" : 0,

      "num_5s" : 2,

      "num_trna" : 20,

      "scaffold_count" : 195,

      "taxon_oid" : "3300061477",

      "total_base" : 2853963

   }

}