URL

• PDBj  http://www.pdbj.org/PDBID (PDBID = 1gof, 1a00, ...) This is a fake URL.
• KEGG  http://togows.dbcls.jp/entry/kegg-DBNAME/ENTRYID
• DDBJ  http://togows.dbcls.jp/entry/ddbj/ENTRYID
• UniProt  http://www.uniprot.org/uniprot/ENTRYID
• PubMed  http://www.ncbi.nlm.nih.gov/pubmed/ENTRYID
• Taxonomy  http://www.ncbi.nlm.nih.gov/Taxonomy/TAXID (this is invalid URL)
• HapMap?  http://www.khapmap.org/ENTRYID (this is invalid URL)
• gene_id  http://www.ncbi.nlm.nih.gov/gene/ENTRYID (NCBI gene ID)

PDB things

•  ftp://ftp.protein.osaka-u.ac.jp/pub/pdb/data/structures/all/XML-noatom/{PDBID}-noatom.xml.gz
• /PDBx:datablock/PDBx:entity_src_genCategory/PDBx:entity_src_gen/PDBx:pdbx_gene_src_ncbi_taxonomy_id

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.

• 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.)

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

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?

[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