How to get IMG's genome or metagenome metadata via Web API. See examples using CURL in the section below.
The metadata provided is similar to the metadata selection in the IMG's Genome Cart.
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 taxon id:
Two or more IMG taxon 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 taxon ids are separated by a comma:
The taxon ids separated by a space. The space should be the "%20" characters (without the double quotes)
One found taxon and one failed search
{
"123" : {
"error" : "id not found"
},
"646311906" : {...}
}
A failed search will return a JSON object with an error message.
{
"error" : "1 - No taxon found"
}
{
"3300046527" : {
"add_date" : "2021-08-01",
"analysis_project_id" : "Ga0499340",
"checkm2_completeness" : "",
"checkm2_contamination" : "",
"comments" : "released by JGI data releasing policy",
"domain" : "*Microbiome",
"family" : "Unclassified",
"funding_agency" : "",
"genus" : "Unclassified",
"gtdbtk_class" : "",
"gtdbtk_domain" : "",
"gtdbtk_family" : "",
"gtdbtk_genus" : "",
"gtdbtk_order" : "",
"gtdbtk_phylum" : "",
"gtdbtk_species" : "",
"has_coverage" : "No",
"high_quality_flag" : "",
"img_version" : "IMG Annotation Pipeline v.5.0.23",
"ir_class" : "Porifera",
"ir_order" : "Sponge",
"is_public" : "Yes",
"metadata" : {
"alternative2_contact_emails" : "s.campana@uva.nl",
"alternative2_contact_names" : "Sara Campana",
"alternative_contact_email" : "s.campana@uva.nl",
"alternative_contact_name" : "Sara Campana",
"altitude_in_meters" : "",
"award_doi" : "",
"biotic_relationships" : "",
"cell_arrangement" : "",
"cell_shape" : "",
"chlorophyll_concentration" : "",
"contact_email" : "s.campana@uva.nl",
"contact_name" : "Sara Campana",
"culture_type" : "",
"cultured" : "No",
"depth_in_meters" : "",
"diseases" : "",
"ecosystem" : "Host-associated",
"ecosystem_category" : "Porifera",
"ecosystem_subtype" : "Unclassified",
"ecosystem_type" : "Sponge",
"elevation_in_meters" : "",
"energy_source" : "",
"funding_program" : "",
"funding_year" : "",
"ga" : "Ga0499340",
"genbank_anomalous_assembly" : "",
"genbank_anomalous_reason" : "",
"geographic_location" : "Curacao",
"gpts_proposal_id" : "",
"gram_staining" : "",
"habitat" : "Marine sponge tissue",
"hmp_id" : "",
"hospital_visits" : "",
"host_gender" : "",
"host_name" : "Plakortis angulospiculatus",
"is_published" : "No",
"isolation" : "sponge tissue",
"isolation_country" : "Curacao",
"its_proposal_id" : "",
"its_proposal_name" : "",
"its_sp_id" : "",
"jgi_data_utilization_status" : "",
"latitude" : "n/a",
"longhurst_code" : "",
"longhurst_description" : "",
"longitude" : "n/a",
"medical_record_number" : "",
"metabolism" : "",
"motility" : "",
"ncbi_assembly_accession" : "",
"ncbi_bioproject_accession" : "",
"ncbi_biosample_accession" : "",
"ncbi_genbank_id" : "",
"nitrate_concentration" : "",
"oxygen_concentration" : "",
"oxygen_requirement" : "",
"ph" : "",
"phenotype" : "",
"pmo_project_id" : "",
"pressure" : "",
"proportal_ecotype" : "",
"proportal_isolation" : "",
"proportal_ocean" : "",
"proportal_station" : "",
"proportal_woa_dissolved_oxygen" : "",
"proportal_woa_nitrate" : "",
"proportal_woa_phosphate" : "",
"proportal_woa_salinity" : "",
"proportal_woa_silicate" : "",
"proportal_woa_temperature" : "",
"pubmed_id" : "",
"relevance" : "",
"salinity" : "",
"salinity_concentration" : "",
"sample_body_site" : "",
"sample_body_subsite" : "",
"sample_collection_date" : "2017/12",
"sample_collection_temperature" : "",
"sequencing_depth" : "",
"sequencing_method" : "Illumina NovaSeq",
"sequencing_quality" : "Level 2: High-Quality Draft",
"sequencing_status" : "Complete",
"sequencing_strategy" : "Metatranscriptome",
"specific_ecosystem" : "Unclassified",
"sporulation" : "",
"sra_id" : "",
"sra_run" : "",
"subsurface_in_meters" : "",
"temperature_range" : "",
"type_strain" : "",
"uncultured_type" : ""
},
"ncbi_taxon_id" : "",
"phylum" : "Host-associated",
"proposal_name" : "Marine sponges tissue microbial communities from Caribbean Sea near Curacao",
"release_date" : "2024-03-11",
"seq_center" : "Christian-Albrechts University of Kiel",
"seq_status" : "Permanent Draft",
"sequencing_gold_id" : "Gp0575361",
"species" : "Marine sponges tissue microbial communities from Caribbean Sea near Curacao",
"statistics" : {
"cds_genes" : 1125783,
"cds_genes_pc" : 99.58,
"cog_clusters" : 4203,
"crispr_count" : 421,
"gc_percent" : 49.73,
"genes_hor_transfer" : "",
"genes_hor_transfer_pc" : "",
"genes_in_cog" : 471880,
"genes_in_cog_pc" : 41.74,
"genes_in_enzymes" : 171471,
"genes_in_enzymes_pc" : 15.17,
"genes_in_kegg" : 193846,
"genes_in_kegg_pc" : 17.15,
"genes_in_ko" : 314961,
"genes_in_ko_pc" : 27.86,
"genes_in_kog" : "",
"genes_in_kog_pc" : "",
"genes_in_metacyc" : 104983,
"genes_in_metacyc_pc" : 9.29,
"genes_in_paralogs" : "",
"genes_in_paralogs_pc" : "",
"genes_in_pfam" : 571110,
"genes_in_pfam_pc" : 50.52,
"genes_in_tigrfam" : 101931,
"genes_in_tigrfam_pc" : 9.02,
"genes_not_in_kegg" : 931937,
"genes_not_in_kegg_pc" : 82.43,
"genes_not_in_ko" : 810822,
"genes_not_in_ko_pc" : 71.72,
"genes_not_in_metacyc" : 1020800,
"genes_not_in_metacyc_pc" : 90.29,
"genes_signalp" : "",
"genes_signalp_pc" : "",
"genes_transmembrane" : "",
"genes_transmembrane_pc" : "",
"genes_w_func_pred" : 46.94,
"genes_wo_func_pred" : 595077,
"genes_wo_func_pred_pc" : 52.64,
"kog_clusters" : "",
"n_scaffolds" : 404751,
"other_rna_genes" : 0,
"paralog_groups" : "",
"pfam_clusters" : 7676,
"predicted_plasmid_contigs" : 0,
"predicted_viral_contigs" : "",
"pseudo_genes" : "",
"rna_genes" : 4769,
"rna_genes_pc" : 0.42,
"rrna16s_genes" : 4,
"rrna18s_genes" : 0,
"rrna23s_genes" : 7,
"rrna28s_genes" : 19,
"rrna5s_genes" : 0,
"rrna_genes" : 30,
"smc_bcgs" : "",
"tigrfam_clusters" : 2330,
"total_bases" : 1026931826,
"total_coding_bases" : 1026544506,
"total_coding_bases_pc" : "",
"total_gc" : 510681295,
"total_gene_count" : 1130552,
"trna_genes" : 4739,
"uncharacterized_genes" : "",
"uncharacterized_genes_pc" : ""
},
"statistics_metagenome_assembled" : {
"cds_genes" : 1125783,
"cds_genes_pc" : 99.58,
"cog_clusters" : 4203,
"crispr_count" : 421,
"gc_percent" : 49.73,
"genes_in_cog" : 471880,
"genes_in_cog_pc" : 41.74,
"genes_in_enzymes" : 171471,
"genes_in_enzymes_pc" : 15.17,
"genes_in_kegg" : 193846,
"genes_in_kegg_pc" : 17.15,
"genes_in_ko" : 314961,
"genes_in_ko_pc" : 27.86,
"genes_in_metacyc" : 104983,
"genes_in_metacyc_pc" : 9.29,
"genes_in_pfam" : 571110,
"genes_in_pfam_pc" : 50.52,
"genes_in_tigrfam" : 101931,
"genes_in_tigrfam_pc" : 9,
"genes_not_in_kegg" : 931937,
"genes_not_in_kegg_pc" : 82.43,
"genes_not_in_ko" : 810822,
"genes_not_in_ko_pc" : 71.72,
"genes_not_in_metacyc" : 1020800,
"genes_not_in_metacyc_pc" : 90.29,
"genes_w_func_pred" : 530706,
"genes_wo_func_pred" : 595077,
"kog_clusters" : 7676,
"n_scaffolds" : 404751,
"other_rna_genes" : 0,
"pfam_clusters" : 2330,
"rna_genes" : 4769,
"rna_genes_pc" : 0.42,
"rrna16s_genes" : 4,
"rrna18s_genes" : 0,
"rrna23s_genes" : 7,
"rrna28s_genes" : 19,
"rrna5s_genes" : 0,
"rrna_genes" : 30,
"smc_bcgs" : "",
"tigrfam_clusters" : "",
"total_bases" : 1026931826,
"total_coding_bases" : 1026544506,
"total_gc" : 510681295,
"total_gene_count" : 1130552,
"trna_genes" : 4739
},
"statistics_metagenome_estimated" : {
"average_coverage_of_assembled_sequences" : "",
"estimated_average_genome_size" : 5970533,
"estimated_number_of_genomes" : 172,
"estimated_number_of_genomes_marker_genes_average" : 169.24,
"estimated_number_of_genomes_marker_genes_median" : 172,
"estimated_number_of_genomes_marker_genes_mode" : "",
"number_of_filtered_reads" : "",
"number_of_mapped_reads" : "",
"percent_assembled_reads" : "",
"standard_deviation_of_marker_gene_counts" : 61.38,
"total_filtered_bases" : "",
"total_mapped_bases" : ""
},
"statistics_metagenome_unassembled" : {},
"strain" : "",
"study_gold_id" : "Gs0154195",
"submission_id" : "254323",
"taxon_display_name" : "Combined Assembly of Marine sponge associated microbial communities from Caribbean Sea near Curacao - Plakortis angulospiculatus"
}
}
See Google Sheet: Genome Metadata definitions