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 (immunopeptidome) from the HLA Ligand Atlas (hla-li…

HLALigandAtlas_get_benign_peptides tool specification

Tool Information:

  • Name: HLALigandAtlas_get_benign_peptides

  • Type: HLALigandAtlasTool

  • Description: Retrieve benign-tissue HLA-presented peptides (immunopeptidome) from the HLA Ligand Atlas (hla-ligand-atlas.org, release 2020.12) - the curated reference of self-peptides eluted from non-malignant human tissues, used to filter self-peptides during cancer neoantigen discovery. Filter the aggregated table by peptide sequence, HLA class (HLA-I or HLA-II), presenting donor allele, and/or tissue of origin. Each row reports the peptide, HLA class, the donor-allele presentation flags (strong ‘n/’ or weak ‘w/’), and the tissues in which it was detected. Filtering by an exact peptide sequence or a specific tissue/allele is recommended because the aggregated table is large.

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.

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

  • limit (integer) (optional) Maximum number of peptide rows to return (1-500). Default 50.

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)