rdf.glytoucan.org(from gs2virt)をバラす

Target GRAPH

From
http://rdf.glytoucan.org (made by gs2virt)

To
http://rdf.glytoucan.org/core
http://rdf.glytoucan.org/sequence/glycoct
http://rdf.glytoucan.org/motif
http://rdf.glytoucan.org/ms/carbbank

#http://rdf.glytoucan.org/image は作っていない
# massは、gs2virtでは扱っていない。http://rdf.glytoucan.org/massで記述されている。
# クラス名を大文字から始めることは、この時点では行わない。登録システムの変更も行わなければならないため。
# 現在本番環境で利用されているRDFモデルに準じて、gs2virtを各graphに分割する。

Saccharide & Resource entry

<http://rdf.glytoucan.org/core>

Saccharide class
Resource entry class
glycan:has_componentは、/ms/carbankの方に移す
Accession numberは、has_primary_idを利用してる
</core>に、has_componentが元々入っている糖鎖もある

INSERT SPARQL

Saccharide

log_enable(2,1);
sparql
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>
INSERT
{ GRAPH <http://rdf.glytoucan.org/core> {
    ?Saccharide
        a glycan:saccharide ;
        glytoucan:has_primary_id ?AccessionNumber ;
        glycan:has_resource_entry ?ResourceEntry .
  }
}
USING <http://rdf.glytoucan.org>
WHERE {
    # Saccharide
    ?Saccharide a glycan:saccharide .
    ?Saccharide glytoucan:has_primary_id ?AccessionNumber .
    ?Saccharide glycan:has_resource_entry ?Entry .
    BIND(STR(?Entry) AS ?strEntry)
    BIND(STRAFTER(?strEntry, "http://glytoucan.org/Structures/Glycans/") AS ?AccNum)
    BIND(IRI(CONCAT("http://rdf.glycoinfo.org/resource-entry/", ?AccNum)) AS ?ResourceEntry)
};
checkpoint;
commit WORK;

Resource Entry

log_enable(2,1);
sparql
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>
PREFIX dcterms: <http://purl.org/dc/terms/>

INSERT
{ GRAPH <http://rdf.glytoucan.org/core> {
    ?ResourceEntry
        a glycan:resource_entry ;
        glytoucan:contributor ?Contributor ;
        glytoucan:date_registered ?Date ;
        glycan:in_glycan_database ?DB ;
        dcterms:identifier ?AccessionNumber ;
        rdfs:seeAlso ?Entry .
  }
}
USING <http://rdf.glytoucan.org>
WHERE {
    # Resource entry
    ?Saccharide glytoucan:has_primary_id ?AccessionNumber .
    ?Saccharide glycan:has_resource_entry ?Entry .
    ?Entry a glycan:resource_entry .
    ?Entry glytoucan:contributor ?Contributor .
    ?Entry glytoucan:date_registered ?Date .
    ?Entry glycan:in_glycan_database ?DB .
    BIND(STR(?Entry) AS ?strEntry)
    BIND(STRAFTER(?strEntry, "http://glytoucan.org/Structures/Glycans/") AS ?AccNum)
    BIND(IRI(CONCAT("http://rdf.glycoinfo.org/resource-entry/", ?AccNum)) AS ?ResourceEntry)
};
checkpoint;
commit WORK;

confirm query

Saccharide class

# Saccharide
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>

SELECT ?ResourceEntry
#SELECT count(?ResourceEntry)
#SELECT count(?Saccharide)
#FROM <http://rdf.glytoucan.org>
FROM <http://rdf.glytoucan.org/core>
WHERE {
    # Saccharide
    #?Saccharide a ?Class .
    #?Saccharide glytoucan:has_primary_id ?AccessionNumber .
    #?Saccharide glycan:has_resource_entry ?ResourceEntry .
    #?Saccharide glycan:has_resource_entry ?ResourceEntry .
}
limit 200

Resource Entry class

# Resource entry
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>
PREFIX dcterms: <http://purl.org/dc/terms/>

SELECT *
#SELECT COUNT(?AccessionNumber)
#SELECT COUNT(?DB)
#SELECT COUNT(?Date)
#SELECT COUNT(?Contributor)
#SELECT COUNT(?ResourceEntry)
#FROM <http://rdf.glytoucan.org>
FROM <http://rdf.glytoucan.org/core>
WHERE {
    # New Resource entry
    #?ResourceEntry a ?Class .
    #?ResourceEntry glytoucan:contributor ?Contributor .
    #?ResourceEntry glytoucan:date_registered ?Date .
    #?ResourceEntry glycan:in_glycan_database ?DB .
    #?ResourceEntry dcterms:identifier ?AccessionNumber .
    #?ResourceEntry rdfs:seeAlso ?Entry .
}
limit 200

Glycosequence

<http://rdf.glytoucan.org/sequence/glycoct>

Glycosequence class
http://rdf.glytoucan.org/sequence/glycoctのGRAPHについて
- 登録時のGlycoCTを記述している
- Property
  - rdfs:label, glycan:has_glycosequence, glycan:has_sequence, glycan:in_carbohydrate_format
  - 今のところ、glycan:glycosequenceのタイプ付けはされていない
  - rdfs:labelとglycan:has_sequenceが同じデータタイプ
    - rdfs:labeは、,Stanzaでは使われていなかった

INSERT SPARQL

log_enable(2,1);
sparql
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
INSERT
{ GRAPH <http://rdf.glytoucan.org/sequence/glycoct> {
    ?Saccharide
        glycan:has_glycosequence ?GSequence .
    ?GSequence
        glycan:has_sequence ?Sequence ;
        glycan:in_carbohydrate_format ?Format ;
        rdfs:label ?Sequence .
  }
}
USING <http://rdf.glytoucan.org>
WHERE {
    # Glycosequence
    ?Saccharide glycan:has_glycosequence ?GSequence .
    ?GSequence glycan:has_sequence ?Sequence .
    ?GSequence glycan:in_carbohydrate_format ?Format .
};
checkpoint;
commit WORK;

Confirm query

PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>

SELECT *
#SELECT COUNT(?label)
#SELECT COUNT(?Format)
#SELECT COUNT(?Sequence)
#SELECT COUNT(?GSequence)
#FROM <http://rdf.glytoucan.org>
FROM <http://rdf.glytoucan.org/sequence/glycoct>
WHERE {
    # Glycosequence
    ?Saccharide glycan:has_glycosequence ?GSequence .
    ?GSequence glycan:has_sequence ?Sequence .
    ?GSequence glycan:in_carbohydrate_format ?Format .
    ?GSequence rdfs:label ?label .
}
limit 100

Glycan motf

<http://rdf.glytoucan.org/motif>

以前の</motif>には、glycan:has_motifのみだった

</motif>に、以下の要素を追加する

rdf:type
glycan:has_glycosequence
rdfs:label
glytoucan:is_reducing_end

INSERT query

log_enable(2,1);
sparql
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>

INSERT
{ GRAPH <http://rdf.glytoucan.org/motif> {
   # Motif
    ?Saccharide
        glycan:has_motif ?Motif .
    ?Motif
        a glycan:glycan_motif ;
        glycan:has_glycosequence ?GSequence ;
        rdfs:label ?MotifName ;
        glytoucan:is_reducing_end ?ReducingEnd .
  }
}
USING <http://rdf.glytoucan.org>
WHERE {
    # Motif
    ?Saccharide glycan:has_motif ?Motif .
    ?Motif a glycan:glycan_motif .
    ?Motif glycan:has_glycosequence ?GSequence .
    ?Motif rdfs:label ?MotifName .
    ?Motif glytoucan:is_reducing_end ?ReducingEnd .
};
checkpoint;
commit WORK;

Confirm query

PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>

SELECT *
#SELECT COUNT(?MotifName)
#SELECT COUNT(?GlycanMotifAlias)
#SELECT COUNT(?ReducingEnd)
#SELECT COUNT(?GSequence)
#SELECT COUNT(?GlycanMotif)
#FROM <http://rdf.glytoucan.org>
FROM <http://rdf.glytoucan.org/motif/test>
WHERE {
    # Motif
    #?Saccharide glycan:has_motif ?GlycanMotif.
    #?GlycanMotif a glycan:glycan_motif .
    #?GlycanMotif glycan:has_glycosequence ?GSequence .
    #?GlycanMotif glytoucan:is_reducing_end ?ReducingEnd .
    #?GlycanMotif rdfs:label ?MotifName .
}
limit 100

Component

Component情報がgs2virtからなくなると、Glycan listおよびGlycan entryが表示されなくなる glycan:Componentも追加する
そのため、/ms/carbbankにComponent情報を追加する

Target GRAPH
<http://rdf.glytoucan.org/ms/carbbank>

INSERT query

log_enable(2,1);
sparql
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>

INSERT
{ GRAPH <http://rdf.glytoucan.org/ms/carbbank> {
   # Component
    ?saccharide
        glycan:has_component ?component .
    ?component
        a glycan:componentt ;
        glycan:has_cardinality ?cardinality ;
        glycan:has_monosaccharide ?mono .
  }
}
USING <http://rdf.glytoucan.org>
WHERE {
    # Component
    ?saccharide glycan:has_component ?component .
    ?component a glycan:component .
    ?component glycan:has_cardinality ?cardinality .
    ?component glycan:has_monosaccharide ?mono .
};
checkpoint;
commit WORK;

Confirm query

## Monosaccharide
SELECT DISTINCT *
#SELECT DISTINCT ?ComponentName ?cardinality
#FROM <http://rdf.glytoucan.org>
FROM <http://rdf.glytoucan.org/core>
FROM <http://rdf.glytoucan.org/ms/carbbank>
WHERE{
    # Accession Number
    ?glycan glytoucan:has_primary_id "G00051MO" .
    OPTIONAL{
        ?glycan glycan:has_component ?comp .
        ?comp glycan:has_cardinality ?cardinality .
        ?comp glycan:has_monosaccharide ?mono .
        ?mono glycan:has_alias ?msdb .
        ?mono a ?class.
        ?msdb glycan:has_alias_name ?ComponentName .
    }
}

Image class

<http://rdf.glytoucan.org/image>

GRAPHは作っていない(今のところ必要な場面が無いため)

* GlyTouCanでは、RDFで記述されているImageのURIは利用していない
* JavascriptでイメージのURLを作っている
* 念のためにやり方を残す

Instance URI	property	Class	Literal	Individual
saccharide instance	glycan:has_image	image instance
image instance	a	glycan:image
	dc:format		image/pingxsd:string
	glycan:has_symbol_format			glycan:symbol_format_cfg
				glycan:symbol_format_uoxf
				glycan:symbol_format_text
				glycan:symbol_format_uoxf_color
				glycan:symbol_format_cfg_uoxf
				glycan:symbol_format_cfg_bw

INSERT query

log_enable(2,1);
sparql
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>
INSERT
{ GRAPH <http://rdf.glytoucan.org/image> {
  ?Saccharide glycan:has_image ?Image .
    ?Image a glycan:image, glycan:Image .
    ?Image dc:format ?Format .
    ?Image glycan:has_symbol_format ?Symbol .
  }
}
FROM <http://rdf.glytoucan.org>
WHERE {
    # Image
  ?Saccharide glycan:has_image ?Image .
    ?Image a glycan:image .
    ?Image dc:format ?Format .
    ?Image glycan:has_symbol_format ?Symbol .
}

Confirm query

PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX glytoucan:  <http://www.glytoucan.org/glyco/owl/glytoucan#>

SELECT *
#SELECT COUNT(?Symbol)
#SELECT COUNT(?Format)
#SELECT COUNT(?Image)
#FROM <http://rdf.glytoucan.org>
FROM <http://rdf.glytoucan.org/image/test>
WHERE {
    # Image
    #?Sacc glycan:has_image ?Image .
    #?Image a ?Class .
    #?Image dc:format ?Format .
    #?Image glycan:has_symbol_format ?Symbol .

}
limit 100

RDF model

各GRAPHに記述されているRDF model

Saccharide RDF

?Saccharide a glycan:saccharide .
?Saccharide glycan:has_resource_entry ?ResourceEntry .
?Saccharide glytoucan:has_primary_id ?AccessionNumber .

Resource entry RDF

?ResourceEntry a glycan:resource_entry, glycan:Resource_entry .
?ResourceEntry glytoucan:contributor ?Person .
?ResourceEntry glytoucan:date_registered ?dateTimeStanp .
?ResourceEntry dcterms:identifier ?AccessionNumber .
?ResourceEntry rdfs:seeAlso ?GlyTouCanURL .
?ResourceEntry glycan:in_glycan_database glytoucan:database_glytoucan .

2017/11/17

glycan:resource_entryと glycan:Resource_entryの混在が確認された。

Glycosequence RDF

?Saccharide glycan:has_glycosequence ?Glycosequence .
?Glycosequence glycan:has_sequence ?GlycoCT_Sequence .
?Glycosequence glycan:in_carbohydrate_format glycan:carbohydrate_format_glycoct .
?Glycosequence rdfs:label ?GlycoCT_String .

2017/11/17

glycan:glycosequenceが記述されていないことが確認された。

Glycan motif RDF

?Saccharide glycan:has_motif ?GlycanMotif .
?GlycanMotif a glycan:glycan_motif .
?GlycanMotif glycan:has_glycosequence ?Glycosequence .
?GlycanMotif rdfs:label ?MotifName .
?GlycanMotif glytoucan:is_reducing_end ?Boolean .

Component RDF

Before RDF

# Monosaccharide
?mono a glycan:monosaccharide .
?mono glycan:has_alias ?msdb .
?msdb a glycan:monosaccharide_alias .
?msdb glycan:has_alias_name ?ComponentName .
?msdb glycan:has_monosaccharide_notation_scheme glycan:monosaccharide_notation_scheme_carbbank  .

After RDF

# Component
?saccharide glycan:has_component ?component .
?component a glycan:component, glycan:Component .
?component glycan:has_cardinality ?cardinality .
?component glycan:has_monosaccharide ?mono .

# Monosaccharide
?mono a glycan:monosaccharide .
?mono glycan:has_alias ?msdb .
?msdb a glycan:monosaccharide_alias .
?msdb glycan:has_alias_name ?ComponentName .
?msdb glycan:has_monosaccharide_notation_scheme glycan:monosaccharide_notation_scheme_carbbank  .

Note

http://test.ts.glytoucan.org/sparql
- このテスト環境のエンドポイントでコンストラクトすると、 glytoucan:is_reducing_endのbooleanが数字の０と１になる
https://ts.glytoucan.org/sparql
- 本番環境のエンドポイントでコンストラクトをすると、glytoucan:is_reducing_endのbooleanが”true”^^xsd:booleanと”false”^^xsd:boolean になる
テスト環境にTTLをアップロードしても、Virtuosoの状態により、0と1になってしまう。
テスト環境、本番環境、共にINSERTクエリを利用する

Split GlyTouCan RDF GRAPH

rdf.glytoucan.org(from gs2virt)をバラす

Target GRAPH

Saccharide & Resource entry

Glycosequence

Glycan motf

Component

Image class

RDF model

Note