PDBj-BMRB Data Server:

common open representations of BMRB NMR-STAR data in XML, RDF and JSON formats

The article about data-out activity of PDBj-BMRB group has been published in Protein Science.

BMRB/XML, BMRB/RDF and BMRB/JSON archives are now based on NMR-STAR v3.2.0.9 Dictionary.

We updated conversion tools (v1.24.0) based on NMR-STAR v3.2.0.9 Dictionary.

NMR-STAR v3.2.0.9 Dictionary is available now.

BMRB/XML, BMRB/RDF and BMRB/JSON archives are now based on NMR-STAR v3.2.0.7 Dictionary.

We updated conversion tools (v1.23.0) based on NMR-STAR v3.2.0.7 Dictionary.

We withdrew BMRB/JSON (complete) archive.
NMR-STAR v3.2.0.7 Dictionary is available now.
NMR-STAR v3.2.0.5 Dictionary is available now.
NMR-STAR v3.2.0.4 Dictionary is available now.
NMR-STAR v3.2.0.2 Dictionary is available now.

We have released BMSxNmrML, an nmrML converter for BMRB metabolomics entries based on BMRB/XML. nmrML is an open mark-up language for NMR data (FID). Generated nmrML documents are available via either HTTP or rsync protcol.

NMR-STAR v3.2.0.1 Dictionary is available now.

BMRB/XML, BMRB/RDF and BMRB/JSON archives are now based on NMR-STAR v3.1.2.6 Dictionary.

We updated conversion tools (v1.22.0) based on NMR-STAR v3.1.2.6 Dictionary.

BMRB/JSON Schema is available.

We have added BMRB/JSON archive, which is converted from BMRB/XML like PDBx/mmJSON.

We updated conversion tools (v1.21.0). Released for generation of BMRB/JSON archive.

We have changed directory name and rsync module name for BMRB/RDF (N-Triples) archive.

We made a presentation at The 5th Informatics in Biology, Medicine and Pharmacology. Thank you for your attention.

We added PostgreSQL dump file for BMRB entries in rsync download service.

We made a presentation at The 27th International Conference on Magnetic Resonance in Biological Systems. Thank you for your attention.

We added MolProbity structure validation reports for all PDB entries generated by BMRB, Wisconsin-Madison. They are identical resource available at BMRB mirror sites.

NMR-STAR v3.1.2.6 Dictionary is available now.

We are now distributing BLAST seuquence alignment results queried by EMDB sequqnces.

We are now distributing FASTA sequence files, which were carefully extracted from EMDB entities and BLAST database for EMDB protein/nucleotide sequences (emdbaa.tar.gz or emdbnt.tar.gz) as well.

The article about BMRB/XML and BMRB/RDF has been published in Journal of Biomedical Semantics.

We have updated index page adding SANS as an NMR-STAR parser library, detailed descriptions about information contents and a relating image.

We replaced SPARQL based simple search service by integrated search service of PDBj-BMRB portal site

We updated conversion tools (v1.20.0). Released for re-integration of BMRB+PDB archive, performance improvement and experimental support for full-text search via Sphinx.

We made a presentation at The 2015 Annual Conference of the Japanease Society for Bioinformatics. Thank you for your attention.

"BMRBo:link_to" RDF property and relating sub-properties in BMRB/OWL were no longer used. All external links starting with "BMRBo:link_to_" in BMRB/RDF were simply replaced by rdfs:seeAlso though users can still distinguish data resources by following either "info" URI scheme or URN scheme. Namespaces of the "info" URI scheme are compatible with registry in http://identifiers.org/. We have added RDF links to Identifier.org for redundancy.

We have added a page for testing various SPARQL queries.

We updated conversion tools (v1.19.0). Released for enhanced agreements with Linked Data. Exactly, almost all RDF data properties have direct links to counterparts of NMR-STAR Dictionary's items and counterparts in PDBx OWL document by appending rdfs:seeAlso or owl:equivalentProperty properties.

We have added external RDF links pointing to PubChem SID (chem_comp.pubchem_code, chem_comp_db_link.accession_code) and CID (chem_comp_db_link.accession_code) in BMRB/RDF dataset.

BMRB/XML and BMRB/RDF are now available from all BMRB sites: BMRB at Wisconsin-Madison, PDBj-BMRB at Osaka and CERM-BMRB at Florence.

We are now distributing FASTA sequence files, which were carefully extracted from PDB entities and BLAST database for PDB protein/nucleotide sequences (pdbaa.tar.gz or pdbnt.tar.gz) as well.

We are now distributing BLAST seuquence alignment results queried by PDB sequqnces and UniProtKB sequences. We added Archive page, which summarized available contents produced by PDBj-BMRB.

We are now distributing validation reports about completeness of assigned chemical shifts. Excluded atoms in calculation of the completeness are listed here.
We updated conversion tools (v1.18.0). Released for supporting the validation reports about completeness.

We updated conversion tools (v1.17.0). Released for recent Metabolomics update.

We have added following items expressing PDBx compatible author's name: entry_author.pdbx_name, entry_editor.pdbx_name and citation_author.pdbx_name, respectively.

We are now distributing BLAST output files queried against BMRB protein (bmrbaa) database and BLAST output files queried against BMRB nucleotide database (bmrbnt).

We are now distributing FASTA sequence files, which were carefully extracted from entities of NMR-STAR data, BLAST output files queried against UniProtKB (swissprot) database and BLAST output files queried against PDB nucleotide database (pdbnt).

We are now distributing BLAST output files queried against PDB protein database (pdbaa) using the condition that sequence coverage is greater than 80%.

We are now distributing BLAST database for BMRB protein/nucleotide sequences (bmrbaa.tar.gz or bmrbnt.tar.gz).

We are now distributing structural annotation files using Protein Blocks for matched NMR structures and matched X-ray structures.

We updated conversion tools (v1.16.0), which remediate entity.polymer_seq_one_letter_code, entity.polymer_seq_one_letter_code_can and entity.number_of_monomers.

We added N-Triples format as BMRB/RDF data collection.

We updated conversion tools (v1.15.0), which support making search index via Apache Lucene and N-Triples in addtion with RDF/XML.

We made a presentation at The 53rd Annual Meeting of the NMR Society of Japan. Thank you for your attention.

We updated conversion tools (v1.14.0), which remediate information about formula weight using RCSB Ligand Expo database (entity.formula_weight and chem_comp.formula_weight).

We updated conversion tools (v1.13.0), which revive primary PDB reference (entry.assigned_pdb_id and entry.assigned_pdb_deposition_code).

We updated conversion tools (v1.12.0), which include RDB cloner tools.

We updated conversion tools (v1.11.1).

We updated conversion tools (v1.11.0), which support LACS validation reports.

We updated conversion tools (v1.10.0) based on NMR-STAR v3.1.1.65 Dictionary.

We updated conversion tools (v1.9.4).

NMR-STAR v3.1.1.65 Dictionary is available now.

XQuery REST service is fully functionalized.

We updated conversion tools (v1.9.3).

We updated conversion tools (v1.9.2).

We updated conversion tools (v1.9.1).

File name pattern of BMRB/XML ("noatom" version) was changed from "entry_id".xml.gz to "entry_id"-noatom.xml.gz.

We updated conversion tools (v1.9.0).

We will make a presentation at The 36th Annual Meeting of the Molecular Biology Society of Japan.

We updated conversion tools (v1.8.0).

We updated data set and conversion tools (v1.7.0) based on NMR-STAR v3.1.1.53 Dictionary.

SPARQL endpoint is fully functionalized.

We will make a presentation about BMRB/XML and BMRB/RDF at The 51st Annual Meeting of the Biophysical Society.

NMR-STAR v3.1.1.53 Dictionary is available now.

Initial release date.