Overview

This document will cover the trivial name processing when registering a new glycan. It is very similar to a technical tutorial explaining how the glytoucan client can be used to not only retrieve data from GlyTouCan but also from other known public databases such as monosaccharideDB.

Monosaccharides

As of this writing, the monosaccharideDB1 database is the main resource for trivial names of monosaccharides. The composition paper explains in more detail the system flow of how this works when broken down from a larger glycan.

Sequential flow

The following is a sequence flow diagram explaining the roles and communication made within this process. To simplify this will be for a singular monosaccharide.

Created with Raphaël 2.1.2UserUserGlyTouCanGlyTouCanmonosaccharideDBmonosaccharideDBRDF DatastoreRDF Datastoreregister glycan Xvarious processing for a glycanrequest names of RDF for monosaccharides in glycan Xprocess request and return RDF with trivial namesvarious post-processing for a glycanregister glycan information including contributor datadisplay new accession numberrequest glycan entry page of glycan Xretrieve RDFs including data from monosaccharideDB contributiondisplay trivial names

Remote Access

Remote access to monosaccharideDB2 is a web service providing conversion routines via http protocol.

Here is an example of a remote access request using the WURCS residue code:

http://www.monosaccharidedb.org/rdf/monosaccharide.action?name=Aad211d2h-2a_2-6_5%2ANCC%2F3%3DO

link

Example result, with unused parts such as glycan:has_external_substituent removed

<http://www.monosaccharidedb.org/rdf/monosaccharide_alias.action?scheme=BCSDB&name=aD3,7dgalNonp5N-ulosonic&substName=Ac&substPos=5&substLink=o>
      a       glycan:monosaccharide_alias ;
      glycan:has_alias_name
              "aD3,7dgalNonp5N-ulosonic" ;
      glycan:has_monosaccharide_notation_scheme glycan:monosaccharide_notation_scheme_bcsdb ;

This data will be converted as contributor data using the trivial name contributor submission webservice:

Admin access
MonoDB partner
aD3,7dgalNonp5N-ulosonic
bcsdb

This is executed by the AliasRegisterRequest client api.

Which essentially executes the following SPARQL:

    PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
    INSERT DATA { 
      GRAPH <http://rdf.glytoucan.org/contributor/monosaccharidedb> { 
        <http://rdf.glytoucan.org/contributor/trivialname?scheme=BCSDB&name=aD3,7dgalNonp5N-ulosonic>
          a       glycan:monosaccharide_alias ;
          glycan:has_alias_name "aD3,7dgalNonp5N-ulosonic" ;
          glycan:has_monosaccharide_notation_scheme glycan:monosaccharide_notation_scheme_bcsdb .
      }
    }

As this is a GlyTouCan specific entry, the URI is different from what monosaccharide DB utilizes.

http://rdf.glytoucan.org/contributor/trivialname?scheme=BCSDB&name=aD3,7dgalNonp5N-ulosonic

It will then be retrievable using the trivial name architecture.

Written with StackEdit.

  1. monosaccharideDB ↩
  2. monosaccharideDB ↩