Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Jan;40(Database issue):D453-60.
doi: 10.1093/nar/gkr811. Epub 2011 Oct 5.

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

Akira R Kinjo  1 , Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Daron M Standley, Atsushi Nakagawa, Haruki Nakamura
Affiliations

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

Akira R Kinjo et al. Nucleic Acids Res. 2012 Jan.

Abstract

The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Example of PDB/RDF pages. (A) The PDB/RDF page for the PDB entry 1GOF (http://pdbj.org/rdf/1GOF) displays a list of RDF triples whose subject is the URL itself and objects are mostly the links to the category element holders. (B) The PDB/RDF page for the ‘entity’ category element holder (http://pdbj.org/rdf/1GOF/entityCategory) of the same entry displays a list of entity category elements. (C) The PDB/RDF page for the entity category with entity.id = 1 (http://pdbj.org/rdf/1GOF/entity/1) displays the properties (category items) of the element as well as to links to external resources and cross-references within the entry. The source files of these pages are in the RDF/XML format.
Figure 2.
Figure 2.
Example of an RDF graph for PDB entry 1GOF. (A) The network of RDF resources for the PDB entry 1GOF. Nodes in magenta represent dereferenceable RDF resources within the PDB entry, nodes in green represent external resources; edges represent links between nodes. (B) A subgraph of (A) augmented with literal objects (orange rectangles). Nodes are labeled with simplified URL or literal values and edges with predicates defined in the OWL ontology (‘r:’ and ‘o:’ are short-hands for http://pdbj.org/rdf/ and http://pdbj.org/schema/pdbx-v40.owl#, respectively; ‘UP:’ and ‘Enzyme:’ indicate http://purl.uniprot.org/uniprot/ and http:/purl.uniprot.org/enzyme/, respectively). Diagrams were created using Cytoscape (21).
Figure 3.
Figure 3.
Yorodumi and EM Navigator. (A) Yorodumi displaying an EMDB-PDB hybrid data, EMDB-5168 and PDB 3MFP (helical assembly) (40). (B) EM Navigator gallery page.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 2007;35:D301–D303. - PMC - PubMed
    1. Standley DM, Kinjo AR, Kinoshita K, Nakamura H. Protein structure databases with new web services for structural biology and biomedical research. Brief. Bioinformatics. 2008;9:276–285. - PubMed
    1. Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlić A, Quesada M, Quinn GB, Westbrook JD, et al. The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 2011;39:D392–D401. - PMC - PubMed
    1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, et al. BioMagResBank. Nuleic Acids Res. 2008;36:D402–D408. - PMC - PubMed
    1. Velankar S, Alhroub Y, lle Alili A, Best C, Boutselakis HC, Caboche S, Conroy MJ, Dana JM, van Ginkel G, Golovin A, et al. PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2011;39:D402–D410. - PMC - PubMed

Publication types