Breaking Down a Glycan

糖鎖の分解

Registration

登録時

When a new glycan structure is registered, one fairly complex process that occurs is the breaking down of the components. Components in this case can be any unit piece of a Glycan, such as a monosaccharide. These can include substituents as well as the linkage information.

GlyTouCanに糖鎖構造を登録する時のコンポーネント分解フローの詳細を説明します。

Flow

新規登録のフロー

新規登録
- シーケンスの分解WFW(converter)から取得＊
  - 現時点、WurcsRDFを利用して担当データ（MS）を生成します。＊
- 単糖別
  - 単糖のタイプをSPARQLで取得し分解
    - monosaccharideタイプ別のReadableNameを取得
      - monosaccharideDB
      - [土屋くんのIUPAC]
    - aglyconのクラスも作成＊＊

＊開発済み＊＊現時点スコープ外

新しいGlycoRDFの変更点

<Saccharide or Glycoconjugate>
	a	glycan:saccharide or glycoconjugate
<Saccharide>
	a	glycan:saccharide
	glytoucan:has_primary_id	"accession number"  ## もう使わないけど、とりあえず残す
	glycan:has_component	<Component>
	glycan:has_resource_entry	<Resource entry>
	glycan:has_glycosequence	<Glycosequence>

Glycoconjugateの場合のみ

glycan:has_glycoconjugate_sequence	<Glycoconjugate_Sequence>
	glycan:has_attached_glycan	<Saccharide> # GlycoconjugateのWURCSからSaccharideのWURCSを取得
	glycan:has_aglycon <Aglycon>

Resource Entry dcterms:identifier “GXXXXYZ” glycan:in_glycan_database “GlyTouCan”

WURCSのGlycoSequenceは、WURCS-RDFを利用している

<Aglycon>
	foaf:name	“trivial name”  # WFW?

<Glycoconjugate_Sequence>
	a	glycan:glycocojugate_sequence
	glycan:has_sequence		“WURCS=2.0/”
	glycan:in_carbohydrate_format	glycan:carbohydrate_format_wurcs

<Component>
	a	glycan:component
	glycan:has_cardinality	integer
	glycan:has_monosaccharide	<glycoRDF:Monosaccharide>
	or 
	glycan:has_aglycon	<Aglycon>

WURCS-MS-RDF - WURCSから生成したもの

<http://rdf.glycoinfo.org/glycan/wurcs/2.0/Monosaccharide/Aad211d2h-2a_2-6_5%2ANCC%2F3%3DO>
<wurcs:Monosaccharide> #monosaccharide residue
	a          wurcs:Monosaccharide
	noc:is_type	2
	noc:is_modified	false

Relation of MS

ここまでが、gs2virtで生成したRDF

ここからが、http://rdf.glytoucan.org/ms/carbbankに含まれるRDF コンストラクトで生成（手動）していたが、WURCSベースにしますので、

# < http://www.monosaccharidedb.org/rdf/monosaccharide.action?name=o-xgal-HEX-0:0|1:aldi>
# <glycoRDF:Monosaccharide> => wurcsの文字列が入るURI
# ComponentGenerator:
# <http://www.monosaccharidedb.org/rdf/monosaccharide.action?name=Aad211d2h-2a_2-6_5%2ANCC%2F3%3DO>
<glycoRDF:Monosaccharide>
	a	glycan:monosaccharide
	glycan:has_alias	<Monosaccharide alias>
# new alias graph:
# <http://www.monosaccharidedb.org/rdf/monosaccharide_alias.action?scheme=IUPAC&name=Gal-ol>
#
# <http://www.monosaccharidedb.org/rdf/monosaccharide_alias.action?scheme=CARBBANK&name=Gal-ol>
<Monosaccharide alias>
	a	glycan:monosaccharide_alias
	glycan:has_monosaccharide_notation_scheme glycan:monosaccharide_notation_scheme_carbbank 
	glycan:has_alias_name "monosaccharide alias name"
"# "monosaccharide alias name" => Gal-ol"

<Aglycon>
	a	glycan:aglycon
案１
<saccharide or glycoconjugate>
           a  saccharide, glycoconjugate
<saccharide>
           a  saccharide
	has_component <Component>

<Component>
	is_monosaccharide <Monosaccharide>

<Monosaccharide>
	is_type1 true/false
　　　rdfs:label “ReadableName”

<Component>
	is_aglycon <Aglycon>

Glycan Composition Process