LinkDB RDF

LinkDB SPARQL endpoint

If you are familiar with the SPARQL language, use this. SPARQL Querie Examples below may be helpful. See also API section.

LinkDB STANZA

If you are not familiar with the SPARQL language, use this. In LinkDB STANZA, some typical queries are prepared and all you need is specifing some parameters.

In the following examples, you can modify sparql query and execute it.

1. Retrieve information on KEGG GENES entry T01001:5621

   SELECT * WHERE {values ?s {<https://www.genome.jp/linkdb/T01001/5621>} ?s ?p ?o}

   
   

   Related STANZA:

   Entry

   
   
2. Retrieve link data of KEGG GENES entry T01001:5621

   BASE <https://www.genome.jp/linkdb/> SELECT * WHERE { ?from ?link ?to . ?from rdf:type <entry> . ?link rdf:type <link> . ?to rdf:type <entry> . FILTER (?from = <T01001/5621>) . } ORDER BY ?to

   
   Show results of above SPARQL query in LinkDB API form.

   BASE <https://www.genome.jp/linkdb/> SELECT ?fromlabel ?tolabel ?linklabel WHERE { ?from ?link ?to . ?from rdf:type <entry> . ?link rdf:type <link> . ?to rdf:type <entry> . FILTER (?from = <T01001/5621>) . ?from rdfs:label ?fromlabel . ?to rdfs:label ?tolabel . ?link rdfs:label ?linklabel . } ORDER BY ?tolabel

   
   

   Related STANZA:

   Link From An Entry

3. DBLABEL
   Some abbreviated name and group of databases are defined by dblabel predicate.
   
   Search canonical name of KEGG GENES hsa

   BASE <https://www.genome.jp/linkdb/> SELECT ?db WHERE { ?db rdf:type <database> . ?db <core/dblabel> "hsa" . }

   
   Show all dblabels defined to KEGG GENES T01001

   BASE <https://www.genome.jp/linkdb/> SELECT ?dblabel WHERE { <database/T01001> <core/dblabel> ?dblabel } ORDER BY ?dblabel

   
   

   Related STANZA:

   Search Database

   dblabel List

4. Retrieve equivalent link information between two databases (from compound to 3dmet)

   BASE <https://www.genome.jp/linkdb/> SELECT ?fromlabel ?tolabel WHERE { ?from <equivalent> ?to . ?from <core/database> ?fromdb . ?to <core/database> ?todb . ?fromdb <core/dblabel> "compound" . ?todb <core/dblabel> "3dmet" . ?from rdfs:label ?fromlabel . ?to rdfs:label ?tolabel . } ORDER BY ?fromlabel ?tolabel

   
   

   Related STANZA:

   DB2DB Equivalent Link

   DB2DB Link

5. Retrieve indirect link of KEGG GENES entry hsa:5621

   BASE <https://www.genome.jp/linkdb/> SELECT DISTINCT ?fromlabel ?vialabel ?tolabel WHERE { ?from <original> ?via . ?via <original> ?to . ?from rdfs:label ?fromlabel . ?via rdfs:label ?vialabel . ?to rdfs:label ?tolabel . FILTER (?fromlabel = "hsa:5621") . FILTER (?fromlabel != ?tolabel) . } ORDER BY ?tolabel ?vialabel

   
   

   Related STANZA:

   Indirect Link From An Entry

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API

Using LinkDB SPARQL Endpoint API, you can directly download results of your SPARQL query.

URL

Parameter

Example

https://www.genome.jp/sparql/linkdb?default-graph-uri=https://linkdb&query=SELECT%20*%20WHERE%20%7B%3Fp%20%3Fo%20%3Fs%7D%20LIMIT%20100&format=text/html&timeout=10000

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Last updated: June 18, 2014