Ebi Proteins Coordinates Tools

Configuration File: ebi_proteins_coordinates_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

EBIProteins_get_coordinate_mapping (Type: EBIProteinsCoordinatesTool)

Map UniProt protein positions to genomic coordinates at exon-level resolution. Returns chromosome…

EBIProteins_get_coordinate_mapping tool specification

Tool Information:

  • Name: EBIProteins_get_coordinate_mapping

  • Type: EBIProteinsCoordinatesTool

  • Description: Map UniProt protein positions to genomic coordinates at exon-level resolution. Returns chromosome, strand, and per-exon mappings between protein residue positions and chromosomal coordinates for all transcript isoforms. Essential for translating protein variant positions (e.g., ‘p.R273H at position 273’) to genomic coordinates for variant analysis, connecting protein annotations to genome browsers, or understanding exon-intron structure at the protein level. Example: ‘P04637’ (TP53) returns 6 transcript mappings on chromosome 17 (reverse strand) with 10 exons spanning positions 7669612-7676594; ‘P00533’ (EGFR) maps to chromosome 7.

Parameters:

  • accession (string) (required) UniProt accession. Examples: ‘P04637’ (TP53), ‘P00533’ (EGFR), ‘P38398’ (BRCA1), ‘P01308’ (Insulin), ‘P69905’ (HBA1 hemoglobin alpha).

Example Usage:

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

EBIProteins_get_proteins_by_genomic_loc (Type: EBIProteinsCoordinatesTool)

Reverse genome-to-protein coordinate lookup from the EBI Proteins API: given a genomic position (…

EBIProteins_get_proteins_by_genomic_loc tool specification

Tool Information:

  • Name: EBIProteins_get_proteins_by_genomic_loc

  • Type: EBIProteinsCoordinatesTool

  • Description: Reverse genome-to-protein coordinate lookup from the EBI Proteins API: given a genomic position (taxonomy + chromosome:position), return all UniProt proteins whose coding sequence overlaps that position, with exon-level mapping (accession, Ensembl gene/transcript/translation IDs, protein start/end residue, amino acid, chromosome, strand, assembly). Inverse of EBIProteins_get_coordinate_mapping. Use to find which proteins a chromosomal variant affects and at which residue. Example: taxonomy 9606, location ‘17:7676154’ returns 18 entries including TP53 (P04637) at protein residue 72 (Pro) on ENST00000923569.

Parameters:

  • taxonomy ([‘string’, ‘integer’]) (optional) NCBI taxonomy ID. Default ‘9606’ (human). Example: 9606 (Homo sapiens), 10090 (mouse).

  • location ([‘string’, ‘null’]) (optional) Genomic location as ‘chromosome:position’ (1-based). Example: ‘17:7676154’. Provide this OR both ‘chromosome’ and ‘position’.

  • chromosome ([‘string’, ‘integer’, ‘null’]) (optional) Chromosome (used with ‘position’ if ‘location’ not given). Example: ‘17’, ‘X’.

  • position ([‘string’, ‘integer’, ‘null’]) (optional) 1-based genomic position (used with ‘chromosome’ if ‘location’ not given). Example: 7676154.

Example Usage:

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