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URL: http://rdf.wwpdb.org/pdb

PDB/RDF is a collection of PDB data in the Resource Description Framework (RDF) format. The RDF format is the standard format for the Semantic Web. An ontology defined in the Web Ontology Language (OWL) is also provided for the PDB/RDF, which is a straightforward translation of the PDB mmCIF Exchange Dictionary.

[Usage]

The PDB/RDF is designed primarily for software agents. That is, programs can download specific elements of PDB entries by accessing specific URLs. For example,

  1. by accessing http://rdf.wwpdb.org/pdb/1GOF, a list of category holders for the PDB entry 1GOF can be retrieved in the RDF/XML format.
  2. By following the link for the object, e.g., http://rdf.wwpdb.org/pdb/1GOF/entityCategory, a list of category elements can be retrieved (again in the RDF/XML format).
  3. Then, by following a link for an object, the a particular category element, e.g., http://rdf.wwpdb.org/pdb/1GOF/entity/1, the list of properties of that element is retrieved.

Below is an example of an RDF/XML file obtained from http://rdf.wwpdb.org/pdb/1GOF/entity/1 :

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="http://rdf.wwpdb.org/pdb-rdf.xsl" ?>
<rdf:RDF xmlns:PDBo="http://rdf.wwpdb.org/schema/pdbx-v40.owl#" 
         xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" 
         xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
  <PDBo:PDBID rdf:about="http://pdbj.org/pdb/1GOF">
    <rdfs:label>1GOF</rdfs:label>
  </PDBo:PDBID>
  <rdf:Description rdf:about="http://rdf.wwpdb.org/pdb/1GOF/entity/1">
    <PDBo:of_datablock rdf:resource="http://rdf.wwpdb.org/pdb/1GOF"/>
    <PDBo:entity.formula_weight>68579.250</PDBo:entity.formula_weight>
    <PDBo:entity.id>1</PDBo:entity.id>
    <PDBo:entity.pdbx_description>GALACTOSE OXIDASE</PDBo:entity.pdbx_description>
    <PDBo:entity.pdbx_ec>1.1.3.9</PDBo:entity.pdbx_ec>
    <PDBo:entity.pdbx_number_of_molecules>1</PDBo:entity.pdbx_number_of_molecules>
    <PDBo:entity.src_method>man</PDBo:entity.src_method>
    <PDBo:entity.type>polymer</PDBo:entity.type>
    <PDBo:link_to_enzyme rdf:resource="http://purl.uniprot.org/enzyme/1.1.3.9"/>
    <PDBo:referenced_by_entity_keywords rdf:resource="http://rdf.wwpdb.org/pdb/1GOF/entity_keywords/1"/>
    <PDBo:referenced_by_entity_poly rdf:resource="http://rdf.wwpdb.org/pdb/1GOF/entity_poly/1"/>
    <PDBo:referenced_by_entity_src_gen rdf:resource="http://rdf.wwpdb.org/pdb/1GOF/entity_src_gen/1"/>
    <PDBo:referenced_by_struct_asym rdf:resource="http://rdf.wwpdb.org/pdb/1GOF/struct_asym/A"/>
    <PDBo:referenced_by_struct_ref rdf:resource="http://rdf.wwpdb.org/pdb/1GOF/struct_ref/1"/>
    <rdf:type rdf:resource="http://rdf.wwpdb.org/schema/pdbx-v40.owl#entity"/>
  </rdf:Description>
</rdf:RDF>

[Human interface]

Although wwPDB/RDF is designed for software agents, it is also useful for human users to understand the relationship between various category elements in the PDB. Simply accessing the URL resources for the PDB/RDF with any modern Web browsers will display the RDF/XML files rendered in HTML (some browsers that cannot handle XSLT will display the plain XML file).

In addition, a simple search interface is available at http://rdf.wwpdb.org/pdb where the user can search RDF entries by specifying PDB ID, properties (predicates) or keywords.

Limitations

  • Currently, simple keyword and property searches returns only up to 200 triples, even when there are more matching triples.

[Ontology]

The ontology for wwPDB/RDF is semi-automatically generated from the PDBML Schema which in turn is derived from the PDB mmCIF Exchange Dictionary. The OWL ontology file is available at

For the definitions of classes and properties, please refer to this OWL file.

[Bulk download]

All RDF files are available at our FTP site: ftp://ftp.pdbj.org/RDF/pdb.

2012-07-13 (last edited: more than 1 year ago)2013-10-31
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