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GlycoNAVI Documment


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GlycoNAVI TCarp Documantation

About GlycoNAVI TCarp

How to use

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  1. Click the Common Name Search image.

  2. Typing your search query into the text box.

  3. 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.)

  4. Browse the table and click on the TCarp ID link to go to the details page of TCarp.

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  1. Click the Motif Search image.

  2. Enter your search query in the text box or browse the table to find the motif structure.

  3. 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.)

  4. Browse the table and click on the TCarp ID link to go to the details page of TCarp.

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 1. Click on an image of the categories and search using the displayed table.

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Entry Page

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Programmatic Access

Web Service Interface

SPARQL Endpoint

  1. Glycosylation site information
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

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