RDF/KazusaAnnotation – BioHackathon 2010

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KazusaAnnoation? RDF

KazusaAnnotation is a social genome annotation tool.

KazusaAnnotation? SPARQL endpoint: http://beta.dbcls.jp/4store/ka/test/

Turtle sample

<http://a.kazusa.or.jp/bookmarks/136848>        <http://purl.org/dc/elements/1.1/date>  "2008-01-15T16:23:42+09:00"^^<http://www.w3.org/2001/XMLSchema#:datetime> .
<http://a.kazusa.or.jp/bookmarks/136848>        <http://purl.org/dc/elements/1.1/creator>       "yoshimura_h" .
<http://a.kazusa.or.jp/bookmarks/136848>        gi:annotate     <http://a.kazusa.or.jp/pages/54> .
<http://a.kazusa.or.jp/pages/54>        <http://purl.org/dc/elements/1.1/title> "CyanoBase/Synechocystis - syn:sll0821" .
<http://a.kazusa.or.jp/pages/54>        <http://purl.org/dc/elements/1.1/uri>   <http://genome.kazusa.or.jp/cyanobase/Synechocystis/genes/sll0821> .
<http://genome.kazusa.or.jp/cyanobase/Synechocystis/genes/sll0821>      <http://purl.org/dc/elements/1.1/title> "CyanoBase/Synechocystis - syn:sll0821" .
<http://a.kazusa.or.jp/pages/54>        <http://www.w3.org/2000/01/rdf-schema#label>    "sll0821" .
<http://a.kazusa.or.jp/pages/54>        gi:gene <http://genome.kazusa.or.jp/cyanobase/Synechocystis/genes/sll0821> .
<http://a.kazusa.or.jp/pages/54>        gi:aspect       "genes" .
<http://a.kazusa.or.jp/pages/54>        gi:dsn  <http://genome.kazusa.or.jp/cyanobase/Synechocystis> .
<http://a.kazusa.or.jp/pages/54>        gi:dataset      <http://genome.kazusa.or.jp/cyanobase/> .
<http://a.kazusa.or.jp/pages/54>        gi:species      "Synechocystis" .
<http://a.kazusa.or.jp/bookmarks/136848>        gi:comment      "[pmid:15641769][Discussion]" .
<http://a.kazusa.or.jp/bookmarks/136848>        gi:tag  "pmid:15641769" .
<http://a.kazusa.or.jp/bookmarks/136848>        gi:tag  "pmid" .
<http://a.kazusa.or.jp/bookmarks/136848>        gi:tag  "Discussion" .

vocabulary

http://a.kazusa.or.jp/core/1.0/ (image)

Sample queries

Bookmarks and tags annotated with gene "slr1311"

SELECT ?b ?tag WHERE {
 ?page <http://www.w3.org/2000/01/rdf-schema#label> "slr1311" .
 ?b ?p ?page . 
 ?b <http://a.kazusa.or.jp/core/1.0/tag> ?tag
} LIMIT 1000

bookmarks and predicates of a page

select * where {?s ?p <http://a.kazusa.or.jp/pages/23> } limit 10

bookmarks and tags of page 23

select ?s ?tag where {
?s ?p <http://a.kazusa.or.jp/pages/23> . 
?s <http://a.kazusa.or.jp/core/1.0/tag> ?tag 
} limit 10

pages and labels

select * WHERE {
?s <http://www.w3.org/2000/01/rdf-schema#label> ?o 
} limit 10

slr1311 page

select * WHERE {
?s <http://www.w3.org/2000/01/rdf-schema#label> "slr1311" 
} limit 10

bookmarks annotated with slr1311 page

select * WHERE {
?page <http://www.w3.org/2000/01/rdf-schema#label> "slr1311" . 
?b <http://a.kazusa.or.jp/core/1.0/annotate> ?page . 
} limit 10

bookmarks and tags annotated with slr1311 page

select * WHERE {
?page <http://www.w3.org/2000/01/rdf-schema#label> "slr1311" . 
?b <http://a.kazusa.or.jp/core/1.0/annotate> ?page . 
?b <http://a.kazusa.or.jp/core/1.0/tag> ?tag .
}

bookmarks to have "title" tag

select * where {?s <http://a.kazusa.or.jp/core/1.0/tag> "title" }

bookmarks and genes in article pmid:8193127

select * where {
?b <http://a.kazusa.or.jp/core/1.0/tag> "pmid:8193127" . 
?b <http://a.kazusa.or.jp/core/1.0/annotate> ?page . 
?page <http://a.kazusa.or.jp/core/1.0/gene> ?gene 
}

tags of article pmid:8193127

select ?tag where {
?b <http://a.kazusa.or.jp/core/1.0/tag> "pmid:8193127" . 
?b <http://a.kazusa.or.jp/core/1.0/annotate> ?page .  
?c <http://a.kazusa.or.jp/core/1.0/annotate> ?page . 
?c <http://a.kazusa.or.jp/core/1.0/tag> ?tag
}

generic guery

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ka: <http://a.kazusa.or.jp/core/1.0/>
PREFIX mb: <http://genome.kazusa.or.jp/ns#>
PREFIX togo: <http://togows.dbcls.jp/ns/ncbi-pubmed#>
SELECT * WHERE {
 ?s ?p ?o
} LIMIT 10

"slr1485"

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ka: <http://a.kazusa.or.jp/core/1.0/>
PREFIX mb: <http://genome.kazusa.or.jp/ns#>
PREFIX togo: <http://togows.dbcls.jp/ns/ncbi-pubmed#>
SELECT * WHERE {
 ?s ?p "slr1485"
} LIMIT 10

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ka: <http://a.kazusa.or.jp/core/1.0/>
PREFIX mb: <http://genome.kazusa.or.jp/ns#>
PREFIX togo: <http://togows.dbcls.jp/ns/ncbi-pubmed#>
CONSTRUCT 
{
?s ?p "slr1485"
}
WHERE {
 ?s ?p "slr1485"
} LIMIT 10

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ka: <http://a.kazusa.or.jp/core/1.0/>
PREFIX mb: <http://genome.kazusa.or.jp/ns#>
PREFIX togo: <http://togows.dbcls.jp/ns/ncbi-pubmed#>
SELECT * WHERE {
<http://a.kazusa.or.jp/pages/83> ?p ?o
} LIMIT 10

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ka: <http://a.kazusa.or.jp/core/1.0/>
PREFIX mb: <http://genome.kazusa.or.jp/ns#>
PREFIX togo: <http://togows.dbcls.jp/ns/ncbi-pubmed#>
CONSTRUCT
{
<http://a.kazusa.or.jp/pages/83> ?p ?o
}
WHERE {
<http://a.kazusa.or.jp/pages/83> ?p ?o
} LIMIT 10

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ka: <http://a.kazusa.or.jp/core/1.0/>
PREFIX mb: <http://genome.kazusa.or.jp/ns#>
PREFIX togo: <http://togows.dbcls.jp/ns/ncbi-pubmed#>
SELECT * WHERE {
?s ?p <http://a.kazusa.or.jp/pages/83>
} LIMIT 10

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ka: <http://a.kazusa.or.jp/core/1.0/>
PREFIX mb: <http://genome.kazusa.or.jp/ns#>
PREFIX togo: <http://togows.dbcls.jp/ns/ncbi-pubmed#>
CONSTRUCT
{
?s ?p <http://a.kazusa.or.jp/pages/83>
}
WHERE {
?s ?p <http://a.kazusa.or.jp/pages/83>
} LIMIT 10

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