Ebi Proteins Ext Tools

Configuration File: ebi_proteins_ext_tools.json Tool Type: Local Tools Count: 11

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_hpp_peptides (Type: EBIProteinsExtTool)

Get Human Proteome Project (HPP) peptide-level mass-spectrometry evidence mapped to a protein fro…

EBIProteins_get_hpp_peptides tool specification

Tool Information:

• Name: EBIProteins_get_hpp_peptides

• Type: EBIProteinsExtTool

• Description: Get Human Proteome Project (HPP) peptide-level mass-spectrometry evidence mapped to a protein from the EBI Proteins API. Returns HPP-curated peptides that confirm protein expression, each with sequence, start/end position, uniqueness flag, and source (e.g. HppPeptideAtlas). This is the stringent HPP evidence set, distinct from and larger than the generic proteomics peptide set for the same protein. Example: P04637 (TP53) returns 237 HPP features (vs 82 from generic /proteomics), e.g. peptide ‘SDSDGLAPPQHLI’ at residues 183-195, unique.

Parameters:

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

Example Usage:

query = {
    "name": "EBIProteins_get_hpp_peptides",
    "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_rna_editing (Type: EBIProteinsExtTool)

Get RNA editing annotations (A-to-I / Q->R recoding sites) for a UniProt protein from the EBI Pro…

EBIProteins_get_rna_editing tool specification

Tool Information:

• Name: EBIProteins_get_rna_editing

• Type: EBIProteinsExtTool

• Description: Get RNA editing annotations (A-to-I / Q->R recoding sites) for a UniProt protein from the EBI Proteins API. Returns post-transcriptional RNA editing sites where a genomic adenosine is read as guanosine, recoding the protein. Each site includes the protein position, genomic location, codon, consequence type, wild-type and edited amino acid, and tissue/sample editing statistics. Distinct from DNA-level variation. Example: P42262 (GRIA2) returns 3 sites including the canonical Q/R site at residue 607 (Q->R, genomic NC_000004.12:g.157336723A>G, missense). P28335 (HTR2C) returns 5 sites.

Parameters:

• accession (string) (required) UniProt accession. Examples: ‘P42262’ (GRIA2, canonical Q/R editing site), ‘P28335’ (HTR2C, 5 editing sites).

Example Usage:

query = {
    "name": "EBIProteins_get_rna_editing",
    "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)

EBIProteins_get_variation_by_dbsnp (Type: EBIProteinsExtTool)

Reverse variation lookup by dbSNP rsID from the EBI Proteins API. Given a dbSNP rsID, returns eve…

EBIProteins_get_variation_by_dbsnp tool specification

Tool Information:

• Name: EBIProteins_get_variation_by_dbsnp

• Type: EBIProteinsExtTool

• Description: Reverse variation lookup by dbSNP rsID from the EBI Proteins API. Given a dbSNP rsID, returns every UniProt protein (including isoforms) that carries that variant, each with the mapped natural-variant features (wild-type and alternative residue, protein position, genomic location, clinical significances, cross-references to ClinVar/COSMIC/dbSNP). Inverse of looking up variants by protein accession. Example: ‘rs1042522’ (TP53 codon 72 Pro/Arg) returns 11 UniProt entries including TP53 isoforms and A0AAQ5BHX5, each with the position-72 variant feature.

Parameters:

• dbsnp_id (string) (required) dbSNP reference SNP ID (rsID). Examples: ‘rs1042522’ (TP53 Pro72Arg), ‘rs429358’ (APOE).

Example Usage:

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

EBIProteins_get_variation_by_hgvs (Type: EBIProteinsExtTool)

Reverse variation lookup by HGVS genomic expression from the EBI Proteins API. Given an HGVS geno…

EBIProteins_get_variation_by_hgvs tool specification

Tool Information:

• Name: EBIProteins_get_variation_by_hgvs

• Type: EBIProteinsExtTool

• Description: Reverse variation lookup by HGVS genomic expression from the EBI Proteins API. Given an HGVS genomic-level expression (e.g. ‘NC_000017.11:g.7676154G>A’), returns every overlapping UniProt protein with the resulting variant consequence projected onto the protein sequence (wild-type and alternative residue, protein position, genomic location). Use to translate a genomic DNA change into its protein consequence across all affected UniProt entries. Example: ‘NC_000017.11:g.7676154G>A’ returns 4 UniProt entries; the TP53 (P04637) entry reports VARIANT P->L at residue 72 (the Pro72Leu protein consequence).

Parameters:

• hgvs (string) (required) HGVS genomic expression using a RefSeq NC_ accession. Example: ‘NC_000017.11:g.7676154G>A’ (TP53 region).

Example Usage:

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

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