How to get IMG's metagenome BIN metadata via Web API. See examples using CURL in the section below.
The API only supports public IMG data sets. Private data set are not supported yet. It will be coming soon.
The API is only using GET request:
One IMG bin id:
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:
The bin ids are separated by a comma:
The bin ids separated by a space. The space should be the "%20" characters (without the double quotes)
Search by IMG taxon ids
One found bin and one failed search
{
"123" : {
"error" : "id not found"
},
"MetaBAT_3300061477_13" : {...}
}
A failed search will return a JSON object with an error message.
{
"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
}
}
See Google Sheet: Metagenome BIN Metadata definitions