Tools that enhance interoperability:
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
v184.108.40.206) 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.
BMRB/XML & BMRB/RDF Data Server
A portal site has opened for publishing BMRB/XML and BMRB/RDF.
Available web services are as follows:
- Updating information content.
- File download service via HTTP and rsync protocols.
- One-stop search service for NMR-STAR v3, BMRB/XML and BMRB/RDF.
- Advanced search services using XQuery and SPARQL.
Validated BMRB/XML documents
BMRB/XML archival data is available from the server.
- 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).
- 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).
- John Wesbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, Helen M. Berman, Bioinformatics, 21(7), 988-992 (2005).