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, and the complete species and glycoprotein association records with positions, taxonomy, and evidence. Also reports the publication count. 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 all gene names wi…

GlyGen_get_glycoprotein tool specification

Tool Information:

  • Name: GlyGen_get_glycoprotein

  • Type: GlyGenTool

  • Description: Get detailed glycoprotein information from GlyGen by UniProt accession. Returns all gene names with evidence and all glycosylation annotations, preserving subtype, site, attached glycan, and evidence qualifiers; also reports associated disease/pathway/SNV/publication counts. 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, or glycan type with one-based offs…

GlyGen_search_glycans tool specification

Tool Information:

  • Name: GlyGen_search_glycans

  • Type: GlyGenTool

  • Description: Search GlyGen for glycans by mass range, monosaccharide count, or glycan type with one-based offset pagination. Returns accessions, mass, association counts, and relevance scores. Response metadata exposes total_results, returned_count, has_more, and next_offset; follow next_offset to retrieve the complete search result.

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) Results per request (default 20, range 1-50).

  • offset (integer) (optional) One-based first result (default 1). Continue with metadata.next_offset.

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 with one-based offset pagination. Returns matching proteins with glycosylation-site counts and relevance scores. Response metadata exposes total_results, returned_count, has_more, and next_offset; follow next_offset for complete retrieval.

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) Results per request (default 20, range 1-50).

  • offset (integer) (optional) One-based first result (default 1). Continue with metadata.next_offset.

Example Usage:

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