CodeFest 2010

 http://www.open-bio.org/wiki/Codefest_2010

•  http://www.open-bio.org/wiki/SemWeb:PDB2RDF

Ontology for PDB

•  http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Index/index.html (mmCIF PDB exchange dictionary)
•  http://www.pdbj.org/schema/pdbx-v32.owl (not completely complete yet)

!Bio2RDF

 http://quebec.pdb.bio2rdf.org/fct/

•  http://bio2rdf.org/pdb:1GOF

PDBj URL Examples

Entry

•  http://www.pdbj.org/pdb/1gof
•  http://www.pdbj.org/pdb/1a00
•  http://www.pdbj.org/pdb/100d

XPath (contents of an entry)

•  http://www.pdbj.org/xpath/1GOF/PDBx:datablock/PDBx:atom_sitesCategory/PDBx:atom_sites%5b@entry_id=%271GOF%27%5d
•  http://www.pdbj.org/xpath/1GOF/PDBx:datablock/PDBx:entityCategory/PDBx:entity%5b@id=%271%27%5d

Making URL short (not implemented)

•  http://www.pdbj.org/xpath/1GOF/PDBx:datablock/PDBx:atom_sitesCategory/PDBx:atom_sites%5b@entry_id=%271GOF%27%5d -->  http://www.pdbj.org/xpath/1GOF/atom_sites/@entry_id=%271GOF%27

Each single-quote (') must be uri-encoded (%27) for Virtuoso to work properly.