Tools that enhance interoperability:

BMRBxTool

BMRBoTool

BMRBxTool converts NMR-STAR data into XML format (BMRB/XML). Schema of the BMRB/XML (BMRB/XML Schema) has been translated from the current dictionary provided by BMRB (NMR-STAR v3.2.0.2) using “MMCIF Dictionary Suite” provided by RCSB PDB.

BMRBxTool generates qualified XML documents by programmed remediation, and reports validation errors against the XML schema. By using scripts bundled with the tool, XML documents can be updated for both new entries and revised ones.

Please refer to the README file for installation and usage.

Download

BMRB/XML & BMRB/RDF Data Server

A portal site has opened for publishing BMRB/XML and BMRB/RDF.
Available web services are as follows:

Validated BMRB/XML documents

BMRB/XML archival data is available from the server.

References

  1. Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Linvy, John L. Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara, J. Biomed. Semantics, 7, 1-4 (2016).
  2. Eldon L. Ulrich, Hideo Akutsu, Jurgen F. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F. Schulte, David E. Tolmie, R. Kent Wenger, Hongyang Yao, John L. Markley, Nucleic Acids Research, 36, D402-D408 (2008).
  3. John Wesbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman, Bioinformatics, 21(7), 988-992 (2005).