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 by category from the EBI Proteins API with limit/offset pagination and expli…

EBIProteins_get_features tool specification

Tool Information:

• Name: EBIProteins_get_features

• Type: EBIProteinsExtTool

• Description: Get protein features by category from the EBI Proteins API with limit/offset pagination and explicit completeness metadata. Preserves every evidence record supplied for each feature. Categories include DOMAINS_AND_SITES, MOLECULE_PROCESSING, PTM, STRUCTURAL, TOPOLOGY, VARIANTS, and MUTAGENESIS. Example: P04637 has 31 domain/site features but more than 1,000 VARIANTS features.

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’.

• limit (integer) (optional) Maximum number of category features to return in this page.

• offset (integer) (optional) Zero-based feature offset. Use data.next_offset for the next page.

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 with sequence, positions, uniqueness, and supporting source, with complete limit/offset pagination and explicit total/has_more metadata. This is the stringent HPP evidence set, distinct from the generic proteomics peptide set. Example: P04637 (TP53) has 237 HPP features; use next_offset to retrieve pages after the first 100.

Parameters:

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

• limit (integer) (optional) Maximum number of HPP peptides to return in this page.

• offset (integer) (optional) Zero-based peptide offset. Use data.next_offset to retrieve the next page.

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 with limit/offset paginat…

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 with limit/offset pagination and explicit completeness metadata. Returns experimentally characterized mutations, functional effects, and all supplied literature evidence. Example: P04637 (TP53) has 651 annotations; use next_offset to retrieve pages after the first 100.

Parameters:

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

• limit (integer) (optional) Maximum number of mutagenesis features to return in this page.

• offset (integer) (optional) Zero-based feature offset. Use data.next_offset for the next page.

Example Usage:

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

EBIProteins_get_proteomics_peptides (Type: EBIProteinsExtTool)

Get mass-spectrometry peptide evidence from the EBI Proteins API with limit/offset pagination and…

EBIProteins_get_proteomics_peptides tool specification

Tool Information:

• Name: EBIProteins_get_proteomics_peptides

• Type: EBIProteinsExtTool

• Description: Get mass-spectrometry peptide evidence from the EBI Proteins API with limit/offset pagination and explicit completeness metadata. Returns peptide positions, uniqueness, and all supplied source records from PeptideAtlas, ProteomicsDB, MaxQB, and EPD. Example: P00533 (EGFR) currently has more than 300 peptides and requires multiple pages.

Parameters:

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

• limit (integer) (optional) Maximum number of proteomics peptides to return in this page.

• offset (integer) (optional) Zero-based peptide offset. Use data.next_offset for the next page.

Example Usage:

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

EBIProteins_get_proteomics_ptm (Type: EBIProteinsExtTool)

Get mass-spectrometry PTM evidence from the EBI Proteins API with limit/offset pagination and exp…

EBIProteins_get_proteomics_ptm tool specification

Tool Information:

• Name: EBIProteins_get_proteomics_ptm

• Type: EBIProteinsExtTool

• Description: Get mass-spectrometry PTM evidence from the EBI Proteins API with limit/offset pagination and explicit completeness metadata. Returns modification positions, types, and all supplied evidence from PeptideAtlas, ProteomicsDB, MaxQB, and EPD. Example: P04637 (TP53) has 101 PTM features, so the second page is required with the default limit.

Parameters:

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

• limit (integer) (optional) Maximum number of proteomics PTM features to return in this page.

• offset (integer) (optional) Zero-based feature offset. Use data.next_offset for the next page.

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. NOTE (checked 2026-09-20): the upstream rna-editing dataset currently returns no features for any accession tried (GRIA2 P42262, HTR2C P28335), and a taxid=9606 query returns an empty list, so this tool returns an error until EBI restores the data. It previously returned e.g. the canonical GRIA2 Q/R site at residue 607.

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 known protein sequence variants from the EBI Proteins API with source/disease filters, limit/…

EBIProteins_get_variation tool specification

Tool Information:

• Name: EBIProteins_get_variation

• Type: EBIProteinsExtTool

• Description: Get known protein sequence variants from the EBI Proteins API with source/disease filters, limit/offset pagination, and explicit completeness metadata. Preserves all supplied COSMIC, ClinVar, dbSNP, gnomAD/ExAC, and UniProt cross-references rather than only the first three. Example: P04637 (TP53) currently has more than 3,000 variants and requires multiple pages.

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.

• limit (integer) (optional) Maximum number of filtered variants to return in this page.

• offset (integer) (optional) Zero-based offset after source_type and disease_only filtering. Use data.next_offset for the next page.

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. Returns every affected UniProt …

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. Returns every affected UniProt entry and feature. Cross-references within every feature are independently paginated with xref_offset/xref_limit; inspect xrefs_total, xrefs_truncated, and next_xref_offset to retain all ClinVar/COSMIC/dbSNP evidence.

Parameters:

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

• xref_offset (integer) (optional) Zero-based xref offset applied within every returned variant feature.

• xref_limit (integer) (optional) Cross-references returned per feature (default 5, maximum 500).

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. Returns every proj…

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. Returns every projected protein consequence. Cross-references within every feature are independently paginated with xref_offset/xref_limit; inspect xrefs_total, xrefs_truncated, and next_xref_offset for completeness.

Parameters:

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

• xref_offset (integer) (optional) Zero-based xref offset applied within every returned variant feature.

• xref_limit (integer) (optional) Cross-references returned per feature (default 5, maximum 500).

Example Usage:

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

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