Version 39 (modified by shuichi, 9 years ago)

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URL

PDB things

where {PDBID} should be something like "1a00" (in lowercase).

DDBJ things

e.g.  http://xml.nig.ac.jp/rest/Invoke?service=DDBJ&method=getXMLEntry&accession=AL121903

e.g.  http://sabi.ddbj.nig.ac.jp/ddbj/data/Z48241

e.g.  http://sabi.ddbj.nig.ac.jp/ddbj/Z48241

e.g.  http://sabi.ddbj.nig.ac.jp/ddbj/html/Z48241

KEGG things

Reflect for pubmed

To use reflect on pubmed:  http://reflect.cbs.dtu.dk/TEST/GetEntities?uri=http://www.ncbi.nlm.nih.gov/pubmed/20146332&entity_types=9606

The result will contain XML code like seen at  http://reflect.cbs.dtu.dk/restAPI.html

SPARQL endpoint

Room 415 network

Facet

Validating RDF/XML format

How to load data to virtuoso

First, in the virtuoso.ini file, set the following parameter

DirsAllowed                     = ., /usr/local/virtuoso-opensource/share/virtuoso/vad, /tmp

So the directory /tmp is allowed to have data to be loaded.

Then put the data file in /tmp (e.g., all.ttl, ddbj.rdf).

% cat load.isql
DB.DBA.TTLP_MT(file_to_string_output('/tmp/all.ttl'), '' ,'http://www.pdbj.org');
checkpoint;

DB.DBA.RDF_LOAD_RDFXML(file_to_string_output('/tmp/lala.rdf'), '' ,'http://www.pdbj.org');
checkpoint;

% isql 1111 dba dba < load.isql

Here the third argument for the functions TTLP_MT and RDF_LOAD_RDFXML is the name of the graph (in this case, it's  http://www.pdbj.org).

Results?

[DDBJ-KEGG-PDBj/Results]

Developed the following on-the-fly DDBJ interface of RDF, Web API and HTML page

e.g.  http://sabi.ddbj.nig.ac.jp/ddbj/data/Z48241

e.g.  http://sabi.ddbj.nig.ac.jp/ddbj/Z48241

e.g.  http://sabi.ddbj.nig.ac.jp/ddbj/html/Z48241

Installed the following virtuoso at DDBJ site

Attachments