The BMRBxTool converts NMR-STAR data into XML format, BMRB/XML
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
bmr_src
bmrb
bmrb_plus_pdb_ext
bms_src
cs_complete
extlibs
lacs_ext
ligand_expo
pb_ext
queries
schema
scripts
taxonomy
xsd_ann/src
CHANGELOG
INSTALL
LICENSE
NMR-STAR.dic
NOTICE
README.md
VERSION
bmr-util.jar
bmr2basex.sh
bmr2existdb.sh
bmr2xml.sh
bmrb-plus-pdb-ext.jar
bmrchk_xml.sh
bmrrep_log.sh
bmrunzip_json.sh
bmrunzip_xml.sh
bmrxml2json.sh
bms-util.jar
bms2basex.sh
bms2existdb.sh
bms2xml.sh
bmschk_xml.sh
bmsrep_log.sh
bmsunzip_json.sh
bmsunzip_xml.sh
bmsxml2json.sh
clean_all.sh
clone_bmrb.sh
cs-complete.jar
index_bmrb_clone.sh
index_bmrb_clone.sql
index_metabolomics_clone.sh
index_metabolomics_clone.sql
lacs-ext.jar
lucene_dic.sh
lucene_ftxt.sh
lucene_index.sh
lucene_infix.sh
lucene_shard.sh
pb-ext.jar
run_all.sh
run_sparql.sh
run_xquery.sh
sphinx.conf
sphinx_index.sh
start_pgschema_serv.sh
status_pgschema_serv.sh
stop_pgschema_serv.sh
update_rsrc.sh
xsd-ann.jar

README.md

BMRBxTool

The BMRBxTool converts NMR-STAR data into XML format (BMRB/XML) and JSON format (BMRB/JSON). The schema of the BMRB/XML has been translated from the current NMR-STAR dictionary using mmCIF Dictionary Suite. BMRBxTool generates qualified XML files by programmed remediation and reports validation errors against the XML schema. By using scripts bundled with the tool, XML and JSON documents can be updated. BMRBxTool uses a extended NMR-STAR dictionary, derived from the original NMR-STAR v3.2 Dictionary, to pass XML schema validation and accomodate extra data; the difference between the dictionaries is minimal.
The PDBj-BMRB Data Server has opened for publishing these alternative representations of NMR-STAR data.

Usage

Please refer to INSTALL.

References

  • 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.
    "Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins", J. Biomed. Semantics, 7, 1-4 (2016)
  • Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata, Naohiro Kobayashi, Toshimichi Fujiwara, Genji Kurisu, Haruki Nakamura,
    "New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)", Protein Science, 27(1), 95-102 (2018)