Ebi Proteins Ext Tools

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

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

Available Tools

EBIProteins_get_antigen (Type: EBIProteinsExtTool)

Get predicted antigenic regions for a protein from the EBI Proteins API. Returns regions of the p…

EBIProteins_get_antigen tool specification

Tool Information:

  • Name: EBIProteins_get_antigen

  • Type: EBIProteinsExtTool

  • Description: Get predicted antigenic regions for a protein from the EBI Proteins API. Returns regions of the protein sequence predicted to be immunogenic and suitable for antibody generation. Includes match scores indicating prediction confidence. Critical for antibody design, vaccine development, and immunology research. Example: P04637 (TP53) returns 2 antigenic regions at positions 291-379 and 5-64 with 100% match scores.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P01308’ (Insulin).

Example Usage:

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

EBIProteins_get_coordinates (Type: EBIProteinsExtTool)

Get genomic coordinate mappings for a protein from the EBI Proteins API. Maps UniProt protein to …

EBIProteins_get_coordinates tool specification

Tool Information:

  • Name: EBIProteins_get_coordinates

  • Type: EBIProteinsExtTool

  • Description: Get genomic coordinate mappings for a protein from the EBI Proteins API. Maps UniProt protein to genomic coordinates including Ensembl gene/transcript IDs, chromosome location, strand, and exon structure. Essential for cross-referencing protein features with genomic data, variant mapping between coordinate systems, and genome browser integration. Example: P04637 (TP53) maps to ENSG00000141510 on chr17.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P38398’ (BRCA1).

Example Usage:

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

EBIProteins_get_features (Type: EBIProteinsExtTool)

Get protein features filtered by category from the EBI Proteins API. Categories include DOMAINS_A…

EBIProteins_get_features tool specification

Tool Information:

  • Name: EBIProteins_get_features

  • Type: EBIProteinsExtTool

  • Description: Get protein features filtered by category from the EBI Proteins API. Categories include DOMAINS_AND_SITES (domains, binding sites, active sites, motifs), MOLECULE_PROCESSING (signal peptides, transit peptides, chains), PTM (glycosylation, phosphorylation, disulfide bonds), STRUCTURAL (helices, strands, turns), TOPOLOGY (transmembrane, extracellular, cytoplasmic), and VARIANTS. Provides a consolidated view of all UniProt-annotated features. Example: P04637 (TP53) with DOMAINS_AND_SITES returns 31 features including DNA-binding domain, transactivation regions.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P01308’ (Insulin).

  • category (string) (optional) Feature category. Options: ‘DOMAINS_AND_SITES’, ‘MOLECULE_PROCESSING’, ‘PTM’, ‘STRUCTURAL’, ‘TOPOLOGY’, ‘VARIANTS’, ‘MUTAGENESIS’. Default: ‘DOMAINS_AND_SITES’.

Example Usage:

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

EBIProteins_get_mutagenesis (Type: EBIProteinsExtTool)

Get mutagenesis experiment data for a protein from the EBI Proteins API. Returns experimentally c…

EBIProteins_get_mutagenesis tool specification

Tool Information:

  • Name: EBIProteins_get_mutagenesis

  • Type: EBIProteinsExtTool

  • Description: Get mutagenesis experiment data for a protein from the EBI Proteins API. Returns experimentally characterized mutations with their functional effects, including gain/loss of function, binding changes, and structural impacts. Data is curated from UniProtKB with literature evidence. Essential for understanding structure-function relationships. Example: P04637 (TP53) returns 651 mutagenesis annotations showing effects of each mutation on p53 function.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P04637’ (TP53/p53), ‘P38398’ (BRCA1), ‘P00533’ (EGFR), ‘P01308’ (Insulin).

Example Usage:

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

EBIProteins_get_proteomics_peptides (Type: EBIProteinsExtTool)

Get mass spectrometry proteomics peptide evidence for a protein from the EBI Proteins API. Return…

EBIProteins_get_proteomics_peptides tool specification

Tool Information:

  • Name: EBIProteins_get_proteomics_peptides

  • Type: EBIProteinsExtTool

  • Description: Get mass spectrometry proteomics peptide evidence for a protein from the EBI Proteins API. Returns detected peptides with their positions, uniqueness status, and source databases (PeptideAtlas, ProteomicsDB, MaxQB, EPD). Shows which parts of the protein have been experimentally confirmed by mass spectrometry. Useful for validating protein expression and mapping coverage. Example: P04637 (TP53) returns 64 detected peptides, P00533 (EGFR) returns 241 peptides.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P38398’ (BRCA1).

Example Usage:

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

EBIProteins_get_proteomics_ptm (Type: EBIProteinsExtTool)

Get post-translational modification (PTM) evidence from mass spectrometry proteomics for a protei…

EBIProteins_get_proteomics_ptm tool specification

Tool Information:

  • Name: EBIProteins_get_proteomics_ptm

  • Type: EBIProteinsExtTool

  • Description: Get post-translational modification (PTM) evidence from mass spectrometry proteomics for a protein from the EBI Proteins API. Returns experimentally detected PTMs (phosphorylation, acetylation, ubiquitination, etc.) with evidence from PeptideAtlas, ProteomicsDB, MaxQB, and EPD proteomics repositories. Shows modification positions, types, and detection confidence. Example: P04637 (TP53) returns 101 PTM features including phosphorylation sites critical for p53 regulation.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P04637’ (TP53/p53), ‘P38398’ (BRCA1), ‘P00533’ (EGFR), ‘P31749’ (AKT1).

Example Usage:

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

EBIProteins_get_variation (Type: EBIProteinsExtTool)

Get all known protein sequence variants for a UniProt protein from the EBI Proteins API. Returns …

EBIProteins_get_variation tool specification

Tool Information:

  • Name: EBIProteins_get_variation

  • Type: EBIProteinsExtTool

  • Description: Get all known protein sequence variants for a UniProt protein from the EBI Proteins API. Returns variants from multiple sources including COSMIC (somatic mutations in cancer), ClinVar (clinical significance), gnomAD/ExAC (population frequencies), and UniProt (curated). Includes disease associations, clinical significance classifications, and cross-references. Essential for variant impact analysis and clinical interpretation. Example: P04637 (TP53) returns 3469 variants with cancer associations and clinical classifications.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P38398’ (BRCA1).

  • source_type ([‘string’, ‘null’]) (optional) Filter by variant source. Options: ‘large_scale_study’ (COSMIC, gnomAD), ‘mixed’ (multiple sources), ‘uniprot’ (curated). Null returns all.

  • disease_only (boolean) (optional) If true, return only variants with disease associations. Default: false.

Example Usage:

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