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

[[PageOutline]] 
= URL =
 * BioMart http://www.biomart.org
 * ICGC Data Portal http://dcc.icgc.org 


== BioMart RDF integration via SPARQL ==

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


 * PDBML is based on mmCIF (PDB's original format)
 * mmCIF is actually defined as an ontology.
 * So, we can use mmCIF categories and items as predicates.
 * An xpath REST interface for PDBMLplus is available at pdbj: e.g., http://service.pdbj.org/mine/xpath/1a00/PDBx:datablock/PDBx:entityCategory
 * Thus, we can use xpaths as subjects and objects in RDF.

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 =
 * http://xml.nig.ac.jp/rest/Invoke?service=DDBJ&method=getXMLEntry&accession=<ACCESSION>
    e.g. http://xml.nig.ac.jp/rest/Invoke?service=DDBJ&method=getXMLEntry&accession=AL121903
 * URL which returns prototype RDF
 * http://sabi.ddbj.nig.ac.jp/ddbj/data/<ACCESSION>
    e.g. http://sabi.ddbj.nig.ac.jp/ddbj/data/Z48241
 * URL which returns in flatfile format
 * http://sabi.ddbj.nig.ac.jp/ddbj/<ACCESSION>
    e.g. http://sabi.ddbj.nig.ac.jp/ddbj/Z48241
 * URL which redirects HTML page
 * http://sabi.ddbj.nig.ac.jp/ddbj/html/<ACCESSION>
    e.g. http://sabi.ddbj.nig.ac.jp/ddbj/html/Z48241

= KEGG things =
 * Draft KEGG RDF download site (temporal) : http://www.hgc.jp/~shuichi/biohack2010/

 * Note: I wouldn't recommend to display the following files in your web browsers because it's large text file.
 * http://www.hgc.jp/~shuichi/biohack2010/kegg-genes2pdb.ttl (KEGG GENES2PDB / PDB2KEGG GENES turtle: 730,602 triples)
 * http://www.hgc.jp/~shuichi/biohack2010/kegg-genes2kegg-ko.ttl (KEGG GENES2KO / KEGG KO2GENES turtle: 3,687,074 triples)
 * http://www.hgc.jp/~shuichi/biohack2010/kegg-ko2kegg-pathway.ttl (KEGG KO2PATHWAY / KEGG PATHWAY2KO turtle: 22,774 triples)
 * http://www.hgc.jp/~shuichi/biohack2010/kegg-genes2kegg-ko.ttl (KEGG GENES2NCBI GENE-ID / NCBI GENE-ID2KEGG GENES turtle: 3,687,074 triples)
 * http://www.hgc.jp/~shuichi/biohack2010/kegg-ko2definition.ttl (KEGG KO2KO definition turtle: 13,211 triples)
 * Total 14,391,245 triples

= 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 http://reflect.cbs.dtu.dk/restAPI.html]


= SPARQL endpoint =

Room 415 network
 * Bio2RDF KEGG - http://192.168.11.61:8890/sparql/
 * Bio2RDF PDB - http://192.168.11.61:8891/sparql/
 * DDBJ+KEGG-PDBj -  http://192.168.11.61:8892/sparql/
 * PDBj -
 * KEGG - 
 * DDBJ - 

Facet
 * Bio2RDF KEGG - http://192.168.11.61:8890/fct/
 * Bio2RDF PDB - http://192.168.11.61:8891/fct/
 * DDBJ-KEGG-PDBj -  http://192.168.11.61:8892/fct/
 * PDBj - 
 * KEGG - 
 * DDBJ - 

= Validating RDF/XML format =
 * http://librdf.org/parse

= 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? =
[[wiki:DDBJ-KEGG-PDBj/Results]]

Developed the following on-the-fly DDBJ interface of RDF, Web API and HTML page
 * URL which returns prototype RDF
 * http://sabi.ddbj.nig.ac.jp/ddbj/data/<ACCESSION>
    e.g. http://sabi.ddbj.nig.ac.jp/ddbj/data/Z48241
 * URL which returns in flatfile format (URI?)
 * http://sabi.ddbj.nig.ac.jp/ddbj/<ACCESSION>
    e.g. http://sabi.ddbj.nig.ac.jp/ddbj/Z48241
 * URL which redirects HTML page
 * http://sabi.ddbj.nig.ac.jp/ddbj/html/<ACCESSION>
    e.g. http://sabi.ddbj.nig.ac.jp/ddbj/html/Z48241

Installed the following virtuoso at DDBJ site
 * http://sabi.ddbj.nig.ac.jp:8080/sparql

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
}}}