Mgnify Expanded Tools

Configuration File: mgnify_expanded_tools.json Tool Type: Local Tools Count: 9

This page contains all tools defined in the mgnify_expanded_tools.json configuration file.

Available Tools

MGnify_get_genome (Type: MGnifyExpandedTool)

Get detailed genome information from the MGnify genome catalog. Returns assembly quality metrics …

MGnify_get_genome tool specification

Tool Information:

• Name: MGnify_get_genome

• Type: MGnifyExpandedTool

• Description: Get detailed genome information from the MGnify genome catalog. Returns assembly quality metrics (completeness, contamination, N50), taxonomy, geographic origin, rRNA counts, protein count, pangenome statistics, and cross-references to ENA. Example: MGYG000000001 returns a high-quality Firmicutes isolate genome with 98.6% completeness.

Parameters:

• genome_id (string) (required) MGnify genome accession. Examples: ‘MGYG000000001’, ‘MGYG000535630’.

Example Usage:

query = {
    "name": "MGnify_get_genome",
    "arguments": {
        "genome_id": "example_value"
    }
}
result = tu.run(query)

MGnify_get_go_terms (Type: MGnifyExpandedTool)

Get Gene Ontology (GO) functional annotations from a MGnify metagenomics analysis. Returns GO ter…

MGnify_get_go_terms tool specification

Tool Information:

• Name: MGnify_get_go_terms

• Type: MGnifyExpandedTool

• Description: Get Gene Ontology (GO) functional annotations from a MGnify metagenomics analysis. Returns GO terms with their accession, description, gene count, and category (biological_process, molecular_function, or cellular_component). Use to understand the functional capacity of a microbial community. Example: MGYA00585482 returns GO:0055114 oxidation-reduction process (count=1507).

Parameters:

• analysis_id (string) (required) MGnify analysis accession (e.g., ‘MGYA00585482’). Find IDs via MGnify_list_analyses.

• page_size (integer) (optional) Number of GO terms to return per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_get_go_terms",
    "arguments": {
        "analysis_id": "example_value"
    }
}
result = tu.run(query)

MGnify_get_interpro (Type: MGnifyExpandedTool)

Get InterPro protein domain annotations from a MGnify metagenomics analysis. Returns InterPro ide…

MGnify_get_interpro tool specification

Tool Information:

• Name: MGnify_get_interpro

• Type: MGnifyExpandedTool

• Description: Get InterPro protein domain annotations from a MGnify metagenomics analysis. Returns InterPro identifiers with description and gene counts, ranked by abundance. Useful for understanding the protein family composition of a microbial community. Example: MGYA00585482 returns IPR036388 Winged helix-like DNA-binding domain (count=360).

Parameters:

• analysis_id (string) (required) MGnify analysis accession (e.g., ‘MGYA00585482’). Find IDs via MGnify_list_analyses.

• page_size (integer) (optional) Number of InterPro entries to return per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_get_interpro",
    "arguments": {
        "analysis_id": "example_value"
    }
}
result = tu.run(query)

MGnify_get_samples (Type: MGnifyExpandedTool)

List biological SAMPLES in MGnify (EBI Metagenomics) with full geographic/host/environment proven…

MGnify_get_samples tool specification

Tool Information:

• Name: MGnify_get_samples

• Type: MGnifyExpandedTool

• Description: List biological SAMPLES in MGnify (EBI Metagenomics) with full geographic/host/environment provenance. Returns each sample’s accession, BioSample id, latitude, longitude, geo-loc-name, collection-date, host-tax-id, species, and ENVO environment biome/feature/material - the sample-level metadata table that the study, analysis, genome, and biome tools never expose. Pass a single ‘sample_accession’ (e.g. ‘SRS10016989’) to fetch one sample, or omit it to page through samples optionally filtered by ‘study_accession’ or ‘biome’. No API key required.

Parameters:

• sample_accession ([‘string’, ‘null’]) (optional) Fetch a single sample by its MGnify/ENA accession (e.g., ‘SRS10016989’). If provided, study_accession/biome/page are ignored.

• study_accession ([‘string’, ‘null’]) (optional) Filter samples belonging to a study (e.g., ‘MGYS00002008’).

• biome ([‘string’, ‘null’]) (optional) Filter by biome name lineage (e.g., ‘root:Host-associated:Human:Digestive system’).

• page ([‘integer’, ‘null’]) (optional) Page number (default 1).

• page_size ([‘integer’, ‘null’]) (optional) Samples per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_get_samples",
    "arguments": {
    }
}
result = tu.run(query)

MGnify_get_study_detail (Type: MGnifyExpandedTool)

Get detailed information about a specific MGnify metagenomics study. Returns study name, abstract…

MGnify_get_study_detail tool specification

Tool Information:

• Name: MGnify_get_study_detail

• Type: MGnifyExpandedTool

• Description: Get detailed information about a specific MGnify metagenomics study. Returns study name, abstract, associated BioProject, centre, biomes, and counts of analyses/downloads. Complementary to MGnify_search_studies which lists studies. Example: MGYS00002008 is a Tara Oceans marine metagenomics study.

Parameters:

• study_accession (string) (required) MGnify study accession. Examples: ‘MGYS00002008’, ‘MGYS00005292’.

Example Usage:

query = {
    "name": "MGnify_get_study_detail",
    "arguments": {
        "study_accession": "example_value"
    }
}
result = tu.run(query)

MGnify_get_taxonomy (Type: MGnifyExpandedTool)

Get taxonomic composition from a MGnify metagenomics analysis. Returns organisms detected with th…

MGnify_get_taxonomy tool specification

Tool Information:

• Name: MGnify_get_taxonomy

• Type: MGnifyExpandedTool

• Description: Get taxonomic composition from a MGnify metagenomics analysis. Returns organisms detected with their abundance counts, taxonomic lineage (domain/phylum/class/order/family/genus/species), and rank. Supports SSU (16S/18S) and LSU (23S/28S) rRNA marker genes. Use MGnify_list_analyses to find analysis IDs for a study. Example: MGYA00585482 returns Bacteria, Proteobacteria, Firmicutes lineages with counts.

Parameters:

• analysis_id (string) (required) MGnify analysis accession (e.g., ‘MGYA00585482’). Find IDs via MGnify_list_analyses.

• rna_type (string) (optional) rRNA marker type: ‘ssu’ for 16S/18S (default) or ‘lsu’ for 23S/28S.

• page_size (integer) (optional) Number of taxa to return per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_get_taxonomy",
    "arguments": {
        "analysis_id": "example_value"
    }
}
result = tu.run(query)

MGnify_list_analysis_downloads (Type: MGnifyExpandedTool)

List the downloadable result files produced by a MGnify analysis. Returns each output file’s id, …

MGnify_list_analysis_downloads tool specification

Tool Information:

• Name: MGnify_list_analysis_downloads

• Type: MGnifyExpandedTool

• Description: List the downloadable result files produced by a MGnify analysis. Returns each output file’s id, label/description, file format, compression, group type, and a direct download URL - covering taxonomy and functional outputs such as predicted CDS (.faa), predicted ORF (.ffn), processed contigs (.fasta), combined eggNOG/InterPro/antiSMASH annotation GFF, eggNOG (emapper) TSV, and Diamond TSV. The parsed-annotation tools (taxonomy, GO, InterPro) summarize content but cannot enumerate or point to the actual files; this tool does. No API key required.

Parameters:

• analysis_id (string) (required) MGnify analysis accession (e.g., ‘MGYA00585482’). Find IDs via MGnify_list_analyses.

• page_size ([‘integer’, ‘null’]) (optional) Number of download entries to return (default 100, max 100).

Example Usage:

query = {
    "name": "MGnify_list_analysis_downloads",
    "arguments": {
        "analysis_id": "example_value"
    }
}
result = tu.run(query)

MGnify_list_biomes (Type: MGnifyExpandedTool)

Browse the MGnify biome hierarchy. Returns biome identifiers, names, and sample counts. Biomes ra…

MGnify_list_biomes tool specification

Tool Information:

• Name: MGnify_list_biomes

• Type: MGnifyExpandedTool

• Description: Browse the MGnify biome hierarchy. Returns biome identifiers, names, and sample counts. Biomes range from engineered environments (bioreactors) to natural habitats (ocean, soil, host-associated). Useful for discovering what metagenomic data is available for specific environments.

Parameters:

• depth (integer) (optional) Hierarchy depth to filter by (1=root, 2=second level, etc.).

• page (integer) (optional) Page number (default 1).

• page_size (integer) (optional) Results per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_list_biomes",
    "arguments": {
    }
}
result = tu.run(query)

MGnify_search_genomes (Type: MGnifyExpandedTool)

Search the MGnify genome catalog for metagenome-assembled genomes (MAGs) and isolate genomes. Fil…

MGnify_search_genomes tool specification

Tool Information:

• Name: MGnify_search_genomes

• Type: MGnifyExpandedTool

• Description: Search the MGnify genome catalog for metagenome-assembled genomes (MAGs) and isolate genomes. Filter by taxonomy lineage or genome type. Returns quality metrics, taxonomy, and protein counts. Useful for finding reference genomes from specific microbial lineages.

Parameters:

• taxonomy (string) (optional) Taxonomy lineage filter. Examples: ‘Firmicutes’, ‘Bacteroidetes’, ‘Proteobacteria’.

• genome_type (string) (optional) Filter by genome source type. Options: ‘Isolate’, ‘MAG’.

• page (integer) (optional) Page number (default 1).

• page_size (integer) (optional) Results per page (default 25, max 100).

Example Usage:

query = {
    "name": "MGnify_search_genomes",
    "arguments": {
    }
}
result = tu.run(query)

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