GlycoNAVI Documment
Text Search
Typing your search query into the text box and pushing the search button.
The results of the text search will be displayed in a table.
You can refine your search by using the search box on the upper right.
Browse the table and click on the TCarp ID link to go to the details page of TCarp.
Glycan Structure
Go to the search site of SugarDrawer.
Drawing the glycan structures to be searched for using SugarDrawer.
pushing the search button.
The searched glycan structure and the accession number of GlyTouCan are displayed below the search button.
A list of entries containing glycan structures will be displayed.
Browse the table and click on the TCarp ID link to go to the details page of TCarp.
Click the Common Name Search image.
Typing your search query into the text box.
Clicking on CommonName or WURCS will display a list of entries containing that glycan structure. (If no entry is found, “No data available in table” is displayed.)
Browse the table and click on the TCarp ID link to go to the details page of TCarp.
Click the Motif Search image.
Enter your search query in the text box or browse the table to find the motif structure.
Clicking on Motif or WURCS will display a list of entries containing that glycan structure. (If no entry is found, “No data available in table” is displayed.)
Browse the table and click on the TCarp ID link to go to the details page of TCarp.
1. Click on an image of the categories and search using the displayed table.
The TCarp entry page contains information on the three-dimensional structure of the glycans and proteins, structural information near the glycans, information on the glycosylation sites of the glycoproteins, citation information, and a structure validation report.
GlycoNAVI-SPARQList
SPARQList is a REST API server which executes a SPARQL query.
This is a web interface designed to access RDF-encoded GlycoNAVI-TCarp data.
SPARQL Endpoint URL: https://sparql.glyconavi.org/sparql
Graph: http://glyconavi.org/tcarp
Example of SPARQL Query
DEFINE sql:select-option "order"
prefix xsd: <http://www.w3.org/2001/XMLSchema#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix glycan: <http://purl.jp/bio/12/glyco/glycan#>
prefix pdbo: <https://rdf.wwpdb.org/schema/pdbx-v50.owl#>
prefix dcterms: <http://purl.org/dc/terms/>
prefix glyconavi: <http://glyconavi.org/ontology/pdb#>
SELECT DISTINCT ?id ?model_num ?protein_db ?db_name
?strand_id as ?mod_chain ?mod_comp_id as ?mod_aa ?sequon ?neighboring_sequence
?glycan_type_label as ?gtype ?mod_pos ?gtc ?wurcs #?ctfile
FROM <http://glyconavi.org/tcarp>
WHERE {
?TcarpEntry a glyconavi:TCarpEntry ;
dcterms:identifier ?id .
FILTER ( ?id = "1CKL" )
# Strand
?TcarpEntry glyconavi:has_strand ?strand .
?strand dcterms:identifier ?protein_db ;
a ?strand_type ;
glyconavi:has_strand_id ?strand_id ;
glyconavi:has_db_name ?db_name ;
glyconavi:has_entity_id ?entity_id ;
glyconavi:has_sequence ?aa_seq .
# PDBModel
?TcarpEntry glyconavi:has_PDB_model_glycan ?model_glycan .
?model_glycan glyconavi:has_model ?model .
?model a glyconavi:PDBModel ;
#glyconavi:has_ctfile ?ctfile ;
glyconavi:has_pdbx_PDB_model_num ?model_num .
# Interaction (optional)
# OPTIONAL { ?model glyconavi:has_interaction ?interaction . }
# Glycan and Glycosequence
?model glycan:has_glycan ?glycan .
?glycan ?a glyconavi:WURCSStandard ;
glycan:has_glycosequence ?glycosequence .
?glycosequence a glycan:Glycosequence ;
glycan:has_sequence ?wurcs ;
glycan:in_carbohydrate_format glycan:carbohydrate_format_wurcs .
OPTIONAL { ?glycan glyconavi:has_glytoucan_id ?gtc . }
# GlycosylationSite
?model_glycan glyconavi:has_glycosylation_site ?ptm_site .
?ptm_site a glyconavi:GlycosylationSite ;
glyconavi:is_on_strand ?strand ;
glyconavi:has_one_letter_code ?one_letter_code ;
glyconavi:has_sequence_before ?sequence_before ;
glyconavi:has_sequence_after ?sequence_after ;
glyconavi:has_asym_id ?mod_asym_id ;
glyconavi:has_entity_id ?mod_entity_id ;
glyconavi:has_seq_id ?mod_pos ;
glyconavi:has_asym_id ?mod_asym_id ;
glyconavi:has_comp_id ?mod_comp_id ;
glyconavi:has_atom_id ?mod_atom_id ;
glyconavi:has_glycan_type ?glycan_type .
# URI for pdbx_struct_mod_residue (optional)
OPTIONAL { ?ptm_site glyconavi:is_mod_residue ?mod_residue . }
FILTER (STRLEN(?sequence_after) = 3)
BIND (CONCAT(?one_letter_code, substr(?sequence_after, 1, 2)) as ?sequon)
BIND (CONCAT(?sequence_before,?sequon) as ?neighboring_sequence)
OPTIONAL { ?ptm_site glyconavi:has_helix_info ?helix_info . }
OPTIONAL { ?ptm_site glyconavi:has_sheet_info ?sheet_info . }
?glycan_type a glyconavi:GlycanType;
rdfs:label ?glycan_type_label .
}
ORDER BY ?protein_db ?db_name ?mod_chain ?mod_pos
RDF Schema
Statistics related to glycans in the Protein Data Bank
Statistics on glycan-containing proteins in the Protein Data Bank
Statistics of protein structures around carbohydrates in the Protein Data Bank
Helix structures of proteins around glycan structures
Sheet structures of proteins around glycan structures
Statistics of the sequon
Statistics of amino acid residues
Statistics of the paired structure of glycans and amino acid residues
Statistics of the experimental methods
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