Version 48 (modified by hhorn, 9 years ago)



PDB things

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

Converting PDBML to RDF

tore.eriksson has made a tentative XSL stylesheet to convert PDBMLplus (some selected elements) into RDF. (but when I checked the output RDF with raptor converter (rapper), it had some errors...)

While I (akinjo) was in Shinkansen from Tokyo to Osaka, I wrote an XSL stylesheet that convert the whole PDBML file into RDF (files attached). I noticed one good thing about PDBML.

Some examples of the triples are:

<> <> "1A00" .
<> <> <[4]> .

(Predicate URI's are not valid at present.)

To do

  • Currently, PDBML files converted by using PDBMLplus2rdf.xsl and PDBML2rdf.xsl do not contain any links to other databases. For that we need to write other XSL stylesheets.
  • There are also cross references within PDB, but these are not handled yet. To do so requires some analysis of the PDBML schema.

DDBJ things





KEGG things

Reflect for pubmed

To use reflect on pubmed:

The result will contain XML code like seen at

SPARQL endpoint

Room 415 network


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'), '' ,'');

DB.DBA.RDF_LOAD_RDFXML(file_to_string_output('/tmp/lala.rdf'), '' ,'');

% 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



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




Installed the following virtuoso at DDBJ site

FAQ: How many triples ?

mnmq:pdbj bh10$ wc -l *.ttl
 1018388 all.ttl
   25991 ddbj.ttl
  730602 kegg-genes2pdb.ttl
   18988 kegg-hsa2kegg-ko.ttl
   51438 kegg-hsa2ncbi-gene_id.ttl
   22774 kegg-ko2kegg-pathway.ttl
 15048785 kegg.ttl
   61208 pubmed.ttl
  831951 struct_title.ttl
   57943 taxonomy.ttl
   67286 uniprot.ttl