Ampsphere Tools#

Configuration File: ampsphere_tools.json Tool Type: Local Tools Count: 7

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

Available Tools#

AMPSphere_get_amp_coprediction (Type: AMPSphereCopredictionTool)#

Get the per-predictor antimicrobial scores for one AMPSphere peptide: how each of the seven indep…

AMPSphere_get_amp_coprediction tool specification

Tool Information:

  • Name: AMPSphere_get_amp_coprediction

  • Type: AMPSphereCopredictionTool

  • Description: Get the per-predictor antimicrobial scores for one AMPSphere peptide: how each of the seven independent AMP predictors scored it (APIN, AI4AMP, AMPScanner2, AMPlify, ampir, Macrel, amPEPpy). AMPSphere’s own membership is a Macrel call, and the predictors DISAGREE – AMP10.000_000 reads 1.0 from APIN and 0.989 from AI4AMP but 0.604 from Macrel and 0.601 from amPEPpy – so this is the evidence for the question the resource exists to answer, and it was not reachable from any tool. Treat a peptide scored high by one predictor and low by six as weakly supported. Keyless AMPSphere REST API (/v1/amps/{accession}/coprediction).

Parameters:

  • accession (string) (required) AMPSphere AMP accession. Example: ‘AMP10.000_000’.

Example Usage:

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

AMPSphere_get_amp_distributions (Type: AMPSphereGetAmpDistributionsTool)#

Retrieve the ecological and geographic distribution of a single AMPSphere AMP by accession (e.g. …

AMPSphere_get_amp_distributions tool specification

Tool Information:

  • Name: AMPSphere_get_amp_distributions

  • Type: AMPSphereGetAmpDistributionsTool

  • Description: Retrieve the ecological and geographic distribution of a single AMPSphere AMP by accession (e.g. ‘AMP10.000_000’): where it has been observed as a bubble-map of lat/lon coordinates with sample counts, across which habitats, and from which microbial taxonomic sources. Returns three blocks: geo (type=’bubble map’ with parallel lat/lon/size arrays), habitat (labels + values), and microbial_source (labels + values). Keyless AMPSphere REST API (/v1/amps/{accession}/distributions).

Parameters:

  • accession (string) (required) AMPSphere AMP accession. Example: ‘AMP10.000_000’.

Example Usage:

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

AMPSphere_get_amp_features (Type: AMPSphereGetAmpFeaturesTool)#

Retrieve the full physicochemical feature profile of a single AMPSphere AMP by accession (e.g. ‘A…

AMPSphere_get_amp_features tool specification

Tool Information:

  • Name: AMPSphere_get_amp_features

  • Type: AMPSphereGetAmpFeaturesTool

  • Description: Retrieve the full physicochemical feature profile of a single AMPSphere AMP by accession (e.g. ‘AMP10.000_000’): molecular weight, length, molar extinction (reduced cysteines / cystine residues), aromaticity, GRAVY hydrophobicity, instability index, isoelectric point, net charge at pH 7, and predicted secondary-structure fractions (helix / turn / sheet). The same GRAVY / instability / pI / charge values are also available as fields on AMPSphere_search_amps; this tool adds molar extinction and secondary-structure fractions. Keyless AMPSphere REST API (/v1/amps/{accession}/features).

Parameters:

  • accession (string) (required) AMPSphere AMP accession. Example: ‘AMP10.000_000’.

Example Usage:

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

AMPSphere_get_amp_metadata (Type: AMPSphereAmpMetadataTool)#

Page through the samples one AMPSphere peptide was observed in: per sample, the GMSC gene accessi…

AMPSphere_get_amp_metadata tool specification

Tool Information:

  • Name: AMPSphere_get_amp_metadata

  • Type: AMPSphereAmpMetadataTool

  • Description: Page through the samples one AMPSphere peptide was observed in: per sample, the GMSC gene accession and gene sequence, the sample id, whether it is metagenomic, the geographic location with latitude/longitude, the habitat (general_envo_name, environment_material) and the microbial source resolved down the taxonomy (domain to species). This is where a peptide’s ecology and host range live, and nothing reached it: AMP10.000_000 has 15,523 such rows and AMPSphere_get_amp embeds five. Returns one page plus the totals, so a page is never mistaken for the set. Keyless AMPSphere REST API (/v1/amps/{accession}/metadata).

Parameters:

  • accession (string) (required) AMPSphere AMP accession. Example: ‘AMP10.000_000’.

  • page (integer) (optional) Zero-based page number.

  • page_size (integer) (optional) Rows per page (upstream default 20).

Example Usage:

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

AMPSphere_get_family (Type: AMPSphereGetFamilyTool)#

Retrieve full detail for an AMPSphere protein family (SPHERE cluster) by accession (e.g. ‘SPHERE-…

AMPSphere_get_family tool specification

Tool Information:

  • Name: AMPSphere_get_family

  • Type: AMPSphereGetFamilyTool

  • Description: Retrieve full detail for an AMPSphere protein family (SPHERE cluster) by accession (e.g. ‘SPHERE-III.001_396’): the consensus sequence, member count, the full member-AMP accession list, per-member feature statistics, geographic / habitat / microbial-source distributions, and ready-to-use download URLs for the family’s alignment (.aln), member sequences (.faa), HMM profile (.hmm), and phylogenetic tree (.nwk / ASCII figure). Keyless AMPSphere REST API (/v1/families/{accession}).

Parameters:

  • accession (string) (required) SPHERE family accession. Example: ‘SPHERE-III.001_396’ (23 member AMPs, consensus ‘GDKLXXXXXVDXXXXGGLIVKXGSRMXDXSLXXKLXXLXXAMKXXG’).

Example Usage:

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

AMPSphere_get_statistics (Type: AMPSphereStatisticsTool)#

Get AMPSphere’s catalogue-wide totals from /v1/statistics: how many AMPs the resource holds (num_…

AMPSphere_get_statistics tool specification

Tool Information:

  • Name: AMPSphere_get_statistics

  • Type: AMPSphereStatisticsTool

  • Description: Get AMPSphere’s catalogue-wide totals from /v1/statistics: how many AMPs the resource holds (num_amps), how many predicted smORF genes they were called from (num_genes), how many SPHERE families they cluster into (num_families), and how many habitats, genomes and metagenomes they were surveyed across. Use it to size the resource before a filtered search, to report a denominator alongside a hit count, or to check whether a cached figure is still current – the other AMPSphere tools quote 863,498 AMPs in their descriptions and that number comes from here. Takes no parameters. Keyless AMPSphere REST API.

Parameters:

No parameters required.

Example Usage:

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

AMPSphere_search_amps (Type: AMPSphereSearchAmpsTool)#

Filter/search the AMPSphere catalogue (863,498 prokaryotic smORF antimicrobial peptides from the …

AMPSphere_search_amps tool specification

Tool Information:

  • Name: AMPSphere_search_amps

  • Type: AMPSphereSearchAmpsTool

  • Description: Filter/search the AMPSphere catalogue (863,498 prokaryotic smORF antimicrobial peptides from the 2024 Global Microbial smORF Catalogue, Big Data Biology Lab) by habitat, SPHERE family, microbial source, peptide length, molecular weight, isoelectric point, charge, and quality-control flags (exp_evidence, antifam, RNAcode, coordinates), with pagination. Returns a paginated list of AMPs, each with its accession, amino-acid sequence, physicochemical properties (length, MW, pI, charge, aromaticity, instability index, GRAVY) and quality flags. Interval filters use a ‘min,max’ string (e.g. pep_length_interval=’8,20’). Set list_options=true to instead return the valid filter values (habitats, microbial sources, quality labels, and min/max ranges) from /v1/all_available_options. Keyless AMPSphere REST API.

Parameters:

  • list_options (boolean) (optional) If true, ignore all other filters and return the valid filter enumerations from /v1/all_available_options (quality labels, habitat list, microbial_source list, and min/max ranges for pep_length, molecular_weight, isoelectric_point, charge_at_pH_7). Use this first to discover valid habitat / microbial_source values.

  • habitat (string) (optional) Environmental habitat filter, e.g. ‘human gut’, ‘soil’, ‘marine’. Must match an AMPSphere habitat label (see list_options).

  • family (string) (optional) SPHERE family accession filter, e.g. ‘SPHERE-III.001_396’. Returns the AMPs in that family.

  • microbial_source (string) (optional) Microbial taxonomic source filter (GTDB-style name), e.g. ‘Faecalibacterium’. See list_options for valid values.

  • exp_evidence (string) (optional) Experimental-evidence quality flag filter: ‘Passed’, ‘Failed’, or ‘Not tested’.

  • antifam (string) (optional) Antifam quality flag filter: ‘Passed’, ‘Failed’, or ‘Not tested’ (Antifam = not a spurious/false ORF).

  • RNAcode (string) (optional) RNAcode coding-potential quality flag filter: ‘Passed’, ‘Failed’, or ‘Not tested’.

  • coordinates (string) (optional) Genomic-coordinates quality flag filter: ‘Passed’, ‘Failed’, or ‘Not tested’.

  • pep_length_interval (string) (optional) Peptide-length range as ‘min,max’ (residues), e.g. ‘8,20’. Catalogue range is 8-99.

  • mw_interval (string) (optional) Molecular-weight range as ‘min,max’ (Da), e.g. ‘800,3000’. Catalogue range is ~813-12286.

  • pI_interval (string) (optional) Isoelectric-point range as ‘min,max’, e.g. ‘9,12’. Catalogue range is ~4-12.

  • charge_interval (string) (optional) Net-charge-at-pH-7 range as ‘min,max’, e.g. ‘0,10’. Catalogue range is ~-57 to 44.

  • page_size ([‘integer’, ‘string’]) (optional) Results per page (default 20).

  • page ([‘integer’, ‘string’]) (optional) Zero-based page index (default 0).

Example Usage:

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