Genome Metadata API

The API is only using GET request:

• One IMG taxon id:

  • curl https://img.jgi.doe.gov/cgi-bin/genomesMetadata.cgi?ids=646311906

• 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.

  • • curl "https://img.jgi.doe.gov/cgi-bin/genomesMetadata.cgi?ids=646311906 3300008418"

  • The taxon ids are separated by a comma:

    • curl https://img.jgi.doe.gov/cgi-bin/genomesMetadata.cgi?ids=646311906,3300008418

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

    • curl https://img.jgi.doe.gov/cgi-bin/genomesMetadata.cgi?ids=646311906%203300008418

• One found taxon and one failed search

  • curl https://img.jgi.doe.gov/cgi-bin/genomesMetadata.cgi?ids=646311906,123

{

   "123" : {

      "error" : "id not found"

   },

   "646311906" : {...}

}

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

  • curl https://img.jgi.doe.gov/cgi-bin/genomesMetadata.cgi?ids=123

{

   "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"

   }

}