Glygen Tools

Configuration File: glygen_tools.json Tool Type: Local Tools Count: 5

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

Available Tools

GlyGen_get_glycan (Type: GlyGenTool)

Get detailed glycan structure information from GlyGen by GlyTouCan accession. Returns mass, monos…

GlyGen_get_glycan tool specification

Tool Information:

  • Name: GlyGen_get_glycan

  • Type: GlyGenTool

  • Description: Get detailed glycan structure information from GlyGen by GlyTouCan accession. Returns mass, monosaccharide count, IUPAC/WURCS representations, species, glycoprotein associations, and publications. Essential for glycomics research. Example: G17689DH returns a 12-monosaccharide biantennary N-glycan found in human and hamster.

Parameters:

  • glytoucan_ac (string) (required) GlyTouCan accession ID for the glycan. Examples: ‘G17689DH’, ‘G62765YT’, ‘G00055MO’.

Example Usage:

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

GlyGen_get_glycoprotein (Type: GlyGenTool)

Get detailed glycoprotein information from GlyGen by UniProt accession. Returns protein name, gly…

GlyGen_get_glycoprotein tool specification

Tool Information:

  • Name: GlyGen_get_glycoprotein

  • Type: GlyGenTool

  • Description: Get detailed glycoprotein information from GlyGen by UniProt accession. Returns protein name, glycosylation sites (N-linked, O-linked), site positions, attached glycan structures, and associated diseases/pathways. Essential for studying protein glycosylation. Example: P14210 (Hepatocyte Growth Factor) has 77 glycosylation annotations.

Parameters:

  • uniprot_ac (string) (required) UniProt accession ID. Examples: ‘P14210’ (HGF), ‘P02724’ (Glycophorin A), ‘P01857’ (IgG1).

Example Usage:

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

GlyGen_get_site (Type: GlyGenTool)

Get detailed information about a specific glycosylation site from GlyGen. Returns the amino acid …

GlyGen_get_site tool specification

Tool Information:

  • Name: GlyGen_get_site

  • Type: GlyGenTool

  • Description: Get detailed information about a specific glycosylation site from GlyGen. Returns the amino acid position, flanking sequences, attached glycans, SNVs at the site, phosphorylation, and mutagenesis data. Useful for studying site-specific glycosylation and its biological consequences.

Parameters:

  • site_id (string) (required) Glycosylation site identifier in format UniProtAC.start_pos.end_pos. Examples: ‘P02724-1.52.52’, ‘P14210-1.294.294’.

Example Usage:

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

GlyGen_search_glycans (Type: GlyGenTool)

Search GlyGen for glycans by mass range, monosaccharide count, organism, or glycan type. Returns …

GlyGen_search_glycans tool specification

Tool Information:

  • Name: GlyGen_search_glycans

  • Type: GlyGenTool

  • Description: Search GlyGen for glycans by mass range, monosaccharide count, organism, or glycan type. Returns matching glycan accessions with mass, protein counts, and relevance scores. Use for finding glycans within specific structural or biological criteria.

Parameters:

  • mass_min (number) (optional) Minimum molecular mass in Daltons. Example: 1000.

  • mass_max (number) (optional) Maximum molecular mass in Daltons. Example: 3000.

  • monosaccharide_min (integer) (optional) Minimum number of monosaccharide residues.

  • monosaccharide_max (integer) (optional) Maximum number of monosaccharide residues.

  • glycan_type (string) (optional) Glycan type filter. Examples: ‘N-linked’, ‘O-linked’.

  • limit (integer) (optional) Maximum results to return (default 20, max 50).

  • offset (integer) (optional) Pagination offset (1-indexed, default 1).

Example Usage:

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

GlyGen_search_glycoproteins (Type: GlyGenTool)

Search GlyGen for glycoproteins by organism, glycosylation evidence type, protein name, or gene n…

GlyGen_search_glycoproteins tool specification

Tool Information:

  • Name: GlyGen_search_glycoproteins

  • Type: GlyGenTool

  • Description: Search GlyGen for glycoproteins by organism, glycosylation evidence type, protein name, or gene name. Returns matching proteins with glycosylation site counts and relevance scores. Useful for finding glycosylated proteins in specific organisms or pathways.

Parameters:

  • organism_id (integer) (optional) NCBI taxonomy ID. Examples: 9606 (human), 10090 (mouse), 10029 (Chinese hamster).

  • glycosylation_evidence (string) (optional) Evidence level filter. Options: ‘reported’ (experimentally confirmed).

  • glycosylation_type (string) (optional) Type of glycosylation. Examples: ‘N-linked’, ‘O-linked’.

  • protein_name (string) (optional) Protein name to search. Example: ‘transferrin’.

  • gene_name (string) (optional) Gene name to search. Example: ‘EGFR’.

  • limit (integer) (optional) Maximum results to return (default 20, max 50).

  • offset (integer) (optional) Pagination offset (1-indexed, default 1).

Example Usage:

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