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. Transcript coordin…

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. Transcript coordinate mappings and exons within every mapping are independently paginated. Inspect total/returned/truncated/next-offset fields at both levels; proteins such as CACNA1C have dozens of mappings and TTN has hundreds of exons.

Parameters:

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

  • coordinate_offset (integer) (optional) Zero-based transcript coordinate-mapping offset.

  • coordinate_limit (integer) (optional) Coordinate mappings returned per page (default 10, maximum 500).

  • exon_offset (integer) (optional) Zero-based exon offset applied within every returned coordinate mapping.

  • exon_limit (integer) (optional) Exons returned per coordinate mapping (default 20, maximum 1000).

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)