Follwo-up meetings held during 2011/01-2011/03 at DBCLS.

  1. URL
    1. BioMart? RDF integration via SPARQL
      1. To do
    2. 2010-02-15: PDBML schema to OWL
      1. To do
  2. DDBJ things
  3. KEGG things
  4. Reflect for pubmed
  5. SPARQL endpoint
  6. Validating RDF/XML format
  7. How to load data to virtuoso
  8. Results?
    1. PDBML2RDF

URL

BioMart? RDF integration via SPARQL

The work on this page is in progress. Whatever is below is not yet edited properly

Some examples of the triples are: 

<http://service.pdbj.org/mine/xpath/1A00> <http://www.w3.org/2000/01/rdf-schema#label> "1A00" .
<http://service.pdbj.org/mine/xpath/1A00/PDBx:datablock/PDBx:entityCategory/PDBx:entity[1]> <http://mmcif.pdbj.org/XML/pdbmlplus/pdbMLplus_v32.xsd/_entity.pdbx_description> "HEMOGLOBIN (ALPHA CHAIN)" .
<http://service.pdbj.org/mine/xpath/1A00/PDBx:datablock/PDBx:entityCategory> <http://mmcif.pdbj.org/XML/pdbmlplus/pdbMLplus_v32.xsd/entity> <http://service.pdbj.org/mine/xpath/1A00/PDBx:datablock/PDBx:entityCategory/PDBx:entity[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.

2010-02-15: PDBML schema to OWL

I succeeded converting PDBML schema into OWL/RDF using XSLT. The resulting OWL file was validated as OWL/Full-compatible by WonderWeb OWL Ontology validator (  http://www.mygrid.org.uk/OWL/Validator )!

To do

  • Writing a XSL stylesheet that write another XSL stylesheet for converting PDBML files into RDF.

That is, 

PDBML Schema (pdbx-v32.xsd) --(pdbx2pdbml2rdf.xsl)--> XSL Stylesheet (pdbml2rdf.xsl)
PDBML file --(pdbml2rdf.xsl)--> PDBML/RDF

One big advantage of translating PDBML schema is that it contains cross-references to many items within a PDBML file.

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

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

PDBML2RDF

  • The XSL stylesheet for converting PDBML Schema (pdbx-v32.xsd) to an OWL ontology is completed (pdbx2owl.xsl).
  • The XSL stylesheet for converting PDBML Schema (pdbx-v32.xsd) to the XSL stylesheet that converts PDBML files to RDF files is completed (pdbx2pdbml2rdf.xsl).
    • This converter generator also make internal cross-references within each PDB entry. However, there are a number of errors in the definition of cross-references in the PDBML Schema (using xsd:key and xsd:keyref), thus, the resulting cross-references are significantly flawed.

Example of using the stylesheets 

# creating OWL ontology
% xsltproc pdbx2owl.xsl pdbx-v32.xsd > pdbx-v32.owl

# creating PDBML-> RDF converter
% xsltproc pdbx2pdbml2rdf.xsl pdbx-v32.xsd > PDBML2rdf.xsl

# converting a PDBML file to RDF.
% xsltproc PDBML2rdf.xsl 1a00-noatom.xml > 1a00-noatom.rdf