Hlaligandatlas Tools#

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

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

Available Tools#

HLALigandAtlas_get_benign_peptides (Type: HLALigandAtlasTool)#

Retrieve benign-tissue HLA-presented peptides from the complete HLA Ligand Atlas 2020.12 aggregat…

HLALigandAtlas_get_benign_peptides tool specification

Tool Information:

  • Name: HLALigandAtlas_get_benign_peptides

  • Type: HLALigandAtlasTool

  • Description: Retrieve benign-tissue HLA-presented peptides from the complete HLA Ligand Atlas 2020.12 aggregated table with exact local pagination. metadata.total_matches is exact; continue with next_offset while has_more is true. Filter by exact peptide, HLA class, donor allele substring and/or tissue. Donor allele flags use ‘s/’ = strong binder, ‘w/’ = weak binder, and ‘n/’ = NON-binder; a bare allele substring matches all three, so use s/A*02:01 when only predicted presentation should count.

Parameters:

  • peptide (string) (optional) Exact peptide sequence (single-letter amino acids) to match, e.g. ‘LLPKKTESHHKAKGK’. Case-insensitive. Leave empty to return any peptide matching the other filters.

  • hla_class ([‘string’, ‘null’]) (optional) HLA class filter: ‘HLA-I’ or ‘HLA-II’. Leave empty for both.

  • allele (string) (optional) Substring of a presenting allele to match within the donor_alleles list, e.g. ‘DRB1*01:01’ or ‘DQA1*01:03-DQB1*06:02’. Case-sensitive. NOTE: this is a plain substring match, so a bare allele such as ‘A*02:01’ also matches the ‘s/’, ‘w/’ AND ‘n/’ prefixed entries – including peptides that allele is predicted NOT to present. To restrict to peptides genuinely presented by the allele, include the strong-binder prefix: ‘s/A*02:01’.

  • tissue (string) (optional) Tissue of origin substring to match, e.g. ‘Lung’, ‘Brain’, ‘Spleen’. Case-insensitive.

  • limit (integer) (optional) Maximum rows on this page, 1-500. Defaults to 50; invalid values are rejected.

  • offset (integer) (optional) Zero-based offset into the exact filtered match set; continue with metadata.next_offset.

Example Usage:

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

HLALigandAtlas_get_donors (Type: HLALigandAtlasTool)#

Retrieve the donor-to-HLA-allele mapping table from the HLA Ligand Atlas (hla-ligand-atlas.org, r…

HLALigandAtlas_get_donors tool specification

Tool Information:

  • Name: HLALigandAtlas_get_donors

  • Type: HLALigandAtlasTool

  • Description: Retrieve the donor-to-HLA-allele mapping table from the HLA Ligand Atlas (hla-ligand-atlas.org, release 2020.12). Each row pairs a benign-tissue donor identifier (e.g. ‘AUT01-DN13’) with one of that donor’s typed HLA alleles (e.g. ‘A*11:01’). Use this to find which donors carry a given allele, or which alleles a donor carries, when interpreting the benign immunopeptidome.

Parameters:

  • donor (string) (optional) Donor identifier substring to match, e.g. ‘AUT01’ or ‘AUT01-DN13’. Leave empty for all donors.

  • allele (string) (optional) HLA allele substring to match, e.g. ‘A*11:01’ or ‘A*11’. Leave empty for all alleles.

Example Usage:

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