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

By Akira R. Kinjo, Hirofumi Suzuki, R. Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Daron M. Standley, A. Nakagawa and 1 more. 2011

130 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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In Molecular Biology

1. S. Velankar
2. Gerard J. Kleywegt
3. John L. Markley
4. Stephen K. Burley
5. Haruki Nakamura
6. John D. Westbrook
7. Helen M. Berman
8. David S. Goodsell

Citations in the corpus

• PubChem Substance and Compound databases (2015, neutral): “org/help/rdf) (37); biosystem to Reactome RDF (https://www.”
• SIFTS: Structure Integration with Function, Taxonomy and Sequences resource (2012, methodology): “SIFTS data are also used by major bioinformatics resources such as UniProt, Pfam, CATH, SCOP, InterPro, RCSB (26), PDBj (27) and DAS-clients such as Spice (28) use these data.”
• Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB (2013, unknown): “Other efforts to visualise archived EM data include PDBj’s EM Navigator (http://pdbj.org/emnavi; Kinjo et al., 2012) and Pepper (Macias et al., 2007).”
• Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (2017, methodology): “PDBML, an XML format based on PDBx/mmCIF [38] and the requisite RDF (Resource Description Framework) conversion have also been developed to facilitate integration of structural biology data with other life sciences data resources [39].”
• The RCSB Protein Data Bank: new resources for research and education (2012, unknown): “org) (5) and BioMagResBank (http:// bmrb.”
• The RCSB protein data bank: integrative view of protein, gene and 3D structural information (2016, background): “org) (4) and Europe (Protein Data Bank in Europe or PDBe; http://pdbe.”