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CHANGELOG
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CHANGELOG
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Changes in BMRBxTool 1.35.0 (release 2021-09-24)
Changed namespace URI to http://bmrbpub.pdbj.org/schema/mmcif_nmr-star.xsd. (BMRBx)
Updated enumerations of _entity_natural_src.kingdom.
Changes in BMRBxTool 1.34.0 (release 2021-08-25)
Updated dictionary NMR-STAR v3.2.1.15 to v3.2.1.18.
Updated xsd2pgschema to 4.2.1.
Added remediation for '_chem_comp_identifier.type' for bmr archive.
Updated dictionary and translation profiles for processing entries released on 2019-03-13, 2019-05-15, 2019-05-29, 2019-08-28, 2019-12-04, 2020-01-15, 2020-02-05, 2020-07-15, 2020-07-22, 2020-09-02, 2020-09-23, 2020-09-30, 2021-08-25.
Fixed definition of backbone atoms of GLY.
Added remediation for database accesion code and EC number.
Added remediation for '_heteronucl_t1rho_list.temp_control_method'.
Added remediation for '_heteronucl_t1rho_list.temp_calibration_method'.
Added remediation for '_theoretical_heteronucl_t1_list.t1_coherence_type'.
Added remediation for '_theoretical_heteronucl_t2_list.temp_calibration_method'.
Added remediation for '_theoretical_heteronucl_t2_list.temp_control_method'.
Added remediation for '_entry.type'.
Added remediation for '_chem_comp_bond.aromatic_flag'.
Updated BMRB/JSON Schema.
Updated scripts for Ligand Expo.
Changes in BMRBxTool 1.33.0 (release 2019-02-01)
Updated dictionary NMR-STAR v3.2.1.12 to v3.2.1.15.
Changes in BMRBxTool 1.32.0 (release 2018-11-26)
Updated dictionary NMR-STAR v3.2.1.9 to v3.2.1.12.
Updated xsd2pgschema to 3.0.8.
Changes in BMRBxTool 1.31.0 (release 2018-11-08)
Updated xsd2pgschema to 3.0.7.
Changed all item with xsd:integer to xsd:int.
Updated dictionary and translation profiles for processing entries released on 2018-10-24.
Added 'NSC NUMBER' of enumeration of '_chem_comp_identifer.type'.
Added remediation for '_chem_comp.image_file_format', '_chem_comp_identifier.type'.
Changes in BMRBxTool 1.30.0 (release 2018-10-22)
Updated dictionary NMR-STAR v3.2.1.5 to v3.2.1.9.
Updated xsd2pgschema to 3.0.4.
Changed PDBML Schema for ligand expo database from v50 to v40.
Changes in BMRBxTool 1.29.0 (release 2018-08-07)
Changed namespace URI from http://bmrbpub.protein.osaka-u.ac.jp/schema/mmcif_nmr-star.xsd to https://bmrbpub.pdbj.org/schema/mmcif_nmr-star.xsd.
Changed package name from jp.ac.osakaU.protein.schema.mmcifNmrStar to org.pdbj.bmrbpub.schema.mmcifNmrStar.
Updated xsd2pgschema to 2.12.7.
Changes in BMRBxTool 1.28.0 (release 2018-06-22)
Updated dictionary NMR-STAR v3.2.1.2 to v3.2.1.5.
Updated xsd2pgschema to 2.12.2.
Updated dictionary and translation profiles for processing entries released on 2018-05-23.
Updated BMRB/JSON Schema.
Fixed key constraint in BMRB/XML Schema.
Changes in BMRBxTool 1.27.0 (release 2018-04-15)
Updated dictionary NMR-STAR v3.2.0.15 to v3.2.1.2.
Added to support for refreshed relational tables (since Apr-05-2018).
Improved overall performance.
Changed package name from org.pdb.pdbml.schema.mmcifNmrStar to jp.ac.osakaU.protein.schema.mmcifNmrStar.
Fixed SQL exception in metabolomics database.
Changes in BMRBxTool 1.26.0 (release 2018-03-30)
Updated dictionary from NMR-STAR v3.2.0.11 to v3.2.0.15 (2018-02-27 version).
Apache License V2.0 branding.
Renamed script: do_all.sh -> run_all.sh
Appended _pdbx_item_linked_group loop and _pdbx_item_linked_group_list loop in NMR-STAR Dictionary.
Updated xsd2pgschema to 2.8.5.
Updated scripts for differential update.
Changes in BMRBxTool 1.25.0 (release 2018-01-24)
Updated dictionary from NMR-STAR v3.2.0.9 to v3.2.0.11.
Updated dictionary and translation profiles for processing entries released on 2017-09-28 and 2017-10-26.
Preserved item order of original NMR-STAR format.
Updated xsd2pgschema from 2.6.3 to 2.7.7.
Fixed invalid release date.
Removed JSON array whose all objects are either null or empty.
Changes in BMRBxTool 1.24.0 (release 2017-09-25)
Updated dictionary from NMR-STAR v3.2.0.7 to v3.2.0.9.
Updated xsd2pgschema from 2.4.1 to 2.6.3.
Updated dictionary and translation profiles for processing entries released on 2017-04-06, 2017-04-13, 2017-06-01, 2017-06-08 and 2017-08-31.
Changed PubMed RESTful service to HTTPS protocol.
Updated PDBML Schema from pdbx-v40.xsd to pdbx-v50.xsd.
Changes in BMRBxTool 1.23.0 (release 2017-04-10)
Updated dictionary from NMR-STAR v3.1.2.6 to v3.2.0.7.
Updated SCOPe data from 2.05 to 2.06.
Updated dictionary and translation profiles for processing entries released on 2017-01-26, 2017-02-09, 2017-02-23, 2017-03-10 and 2017-03-30.
Updated xsd2pgschema from 1.13.4 to 2.4.1.
Changes in BMRBxTool 1.22.0 (release 2017-01-11)
Updated dictionary from NMR-STAR v3.1.1.65 to v3.1.2.6.
Updated xsd2pgschema to 1.13.4 and revised sphinx_index.sh script.
Changes in BMRBxTool 1.21.0 (release 2016-11-29)
Added BMRB/XML -> BMRB/JSON conversion.
Updated xsd2pgschema to 1.13.1.
Updated dictionary and translation profiles for processing entries released on 2016-11-10.
Changed schemaLocation to public XML Schema (http://bmrbpub.protein.osaka-u.ac.jp/schema/mmcif_nmr-star.xsd).
Updated Xerces from 2.7.0 to 2.11.0.
Revised parser for PubMed eutils APIs.
Revised NCBI Taxonomy ID remediation chasing merged taxnomy ID.
Added BMRB/XML Schema -> BMRB/JSON Schema mapping (schema/bmrb_clone.json).
Changed BMRB/JSON format from relational- to column-oriented.
Changes in BMRBxTool 1.20.0 (release 2016-10-21)
Added bmrb_plus_pdb_ext directory with bmrb_plus_pdb-ext.jar and executable script for integrating BMRB+PDB archive.
Updated dictionary and translation profiles for processing entries released on 2015-12-09, 2015-12-25, 2016-02-10, 2016-02-25, 2016-03-18, 2016-04-21, 2016-05-05, 2016-06-09, 2016-07-07, 2016-07-21, 2016-07-28, 2016-09-22, 2016-09-29, 2016-10-06 and 2016-10-20.
Updated xsd2pgschema to 1.10.5.
Added full-text search feature via Sphinx (sphinx_index.sh and xsd2pgschema-min.jar).
Intruduced relaxed schema, in which minOccurs=0 attribute is added to pointer IDs, which reduces substitutions of meaningless zero value.
Resolved network latency by caching results obtained through remote web APIs and resolving BMRB Ligand Expo's URL.
Added automated remediation about *.id (xsd:integer).
Fixed formula weight calculator.
Revised automated remediation about entry.assigned_pdb_id based on sharing primary citation.
Added automated remediation about entry.original_release_date and entry.last_release_date.
Revised data item name 'cross_correlation_list_id' in NMR-STAR Dictionary, they are splitted into 'cross_correlation_dd_list_id' and 'cross_correlation_d_csa_list_id'.
Added automated remediation about entry.accession_date and entry.submission_date.
Changes in BMRBxTool 1.19.0 (release 2015-10-16)
Added xsd-ann.jar and updated schema/update_schema.sh for appending reference links to NMR-STAR Dictionary from categories and items in BMRB/XML Schema.
Updated xsd2pgschema to 1.8.0.
Revised source code of BMRxTool and BMSxTool to reduce redundancy and to improve network stability.
Updated dictionary and translation profiles for processing entries released on 2015-10-02 and 2015-10-08.
Updated automated remediation about journal citation using PubMed RESTful service (splitting title header by semicolon).
Added struct_classification.sunid for storing SCOP unique identifier (sunid).
Changes in BMRBxTool 1.18.0 (release 2015-09-25)
Extended dictionary to support validation reports about completeness of assigned chemical shifts.
Added cs_complete directory with cs-complete.jar and executable script for supporting the validation reports.
Updated xsd2pgschema to 1.7.3.
Revised dictionary about chem_shift_completeness_list and chem_shift_completeness_char categories.
Updated dictionary and translation profiles for processing entries released on 2015-09-25.
Dropped run_sparql.sh dependency, curl command instead.
Revived bmrchk_xml.sh and bmschk_xml.sh scripts utilizing XMLStarlet for validating well-formed XML documents.
Rescued PACSY relational database which have been unintentionally dropped because of change of schema.
Eliminated entity_natural_src.organism_name_scientific and citation.journal_abbrev, they are automatically remediated.
Added --user-bmrb, --user-tax and --user-le options for authentication.
Fixed remediation against enity.formula_weight for older entries.
Added indexing script for clone DB (index_metabolomics_clone.sh and index_metabolomics_clone.sql).
Revised source code to drop null XML elements but required by schema.
Changes in BMRBxTool 1.17.0 (release 2015-05-18)
Revised master source code, which allowed '.' and '?' codes as empty data that solved critical errors against recent Metabolomics update.
Updated dictionary and translation profiles for processing entries released on 2015-05-11 and 2015-05-18.
Changes in BMRBxTool 1.16.0 (release 2015-04-21)
Added automated remediation about entity.polymer_seq_one_letter_code, entity.polymer_seq_one_letter_code_can and entity.number_of_monomers.
Extended dictionary to support Protein Blocks annotation.
Added pb_ext directory with pb-ext.jar and executable script for supporting Protein Blocks annotation.
Added automated remediation for replacing obsolete PDB IDs.
Droped not-informative LACS_output and PB_annotation categories and revised LACS_plot and PB_list categories.
Revised management tools for LACS validation report and PB annotation (lacs-ext.jar and pb-ext.jar).
Updated xsd2pgschema to 1.5.0.
Revised BMRB/XML Schema (xsd:decimal -> xsd:double @ entity_db_link.seq_homology_expectation_val).
Revised default timezone (from local to UTC).
Added citation_author.pdbx_name, citation_editor.pdbx_name and entry_author.pdbx_name tags for storing pdbx-style author name (e.g. O'Neil, F.K.).
Shrinked XML documents by dropping xsd:nil="true" elements.
Enforced remediation against enity.formula_weight and chem_comp.formula_weight.
Added extlibs directory, which includes external jar libraries.
Revised automated remediation about journal citation using PubMed RESTful service (checked vilidity of pubmed_id).
Revised DB cloner script (clone_bmrb.sh), which supports metabolomics too.
Revised update script for Ligand Expo.
Revised automated remediation about citation title using PubMed RESTful service (first author family name).
Added automated remediation about DOI using CrossRef RESTful service (http://search.crossref.org/).
Updated dictionary and translation profiles for processing entries released on 2015-04-14.
Changes in BMRBxTool 1.15.0 (release 2014-11-28)
Added full-text search feature via Apache Lucene (lucene_index.sh and xsd2pgschema.jar).
Revised scripts (clone_bmrb.sh and lunece_index.sh) and xsd2pgschema.jar that improve processing speed.
Updated dictionary and translation profiles for processing entries released on 2014-11-09, 2014-11-18, 2014-12-03 and 2014-12-16.
Added indexing script for clone DB (index_bmrb_clone.sh and index_bmrb_clone.sql).
Changes in BMRBxTool 1.14.0 (release 2014-10-14)
Updated dictionary and translation profiles for processing entries released on 2014-09-25, 2014-09-30 and 2014-10-14.
Added automated remediation about entity.formula_weight and chem_comp.formula_weight data items using RCSB Ligand Expo database.
Revised PDB primary referencing by addtion of citation authors' matching.
Changes in BMRBxTool 1.13.0 (release 2014-09-18)
Updated dictionary and translation profiles for processing entries released on 2014-09-11 and 2014-09-18.
Revived entry.assigned_pdb_id and entry.assigned_pdb_deposition_id for primary reference to PDB.
Added run_sparql.sh for SPARQL query to complement the primary reference to PDB.
Revised automated remediation about journal citation using PubMed RESTful service (first author family name).
Changes in BMRBxTool 1.12.0 (release 2014-09-04)
Updated dictionary and translation profiles for processing entries released on 2014-08-14 and 2014-09-04.
Added RDB cloner tools (xsd2pgschema.jar and clone_bmrb.sh files) for cloning BMRB RDB from BMRB/XML.
Revised source code for excluding duplicated contents in XML document.
Revised source code and do_all.sh script for more seamless update.
Added PostgreSQL DDL based on BMRB/XML Schema.
Changes in BMRBxTool 1.11.1 (release 2014-07-04)
Updated dictionary and translation profiles for processing entries released 2014-07-01.
Updated remediation report scripts.
Changes in BMRBxTool 1.11.0 (release 2014-06-17)
Extended dictionary to support LACS validation reports.
Added lacs_ext directory with lacs-ext.jar and executable script for supporting LACS validation reports.
Changes in BMRBxTool 1.10.0 (release 2014-06-05)
Updated dictionary from NMR-STAR v3.1.1.53 to v3.1.1.65.
Changes in BMRBxTool 1.9.4 (release 2014-06-04)
Disable certificate validation in SSL connection to BMRB Ligand Expo.
Updated dictionary and translation profiles for processing entries released 2014-06-01.
Changes in BMRBxTool 1.9.3 (release 2014-05-15)
Updated dictionary and translation profiles for processing entries released 2014-05-01.
Revised run_xquery.sh and queries directory.
Changes in BMRBxTool 1.9.2 (release 2014-04-15)
Updated dictionary and several fixes for processing entries released 2014-03-26.
Replacing 'not reported' values to 'na'.
Changed maximum heap memory size from 2GB to 4GB for validation of bmr18978 entry.
Fixed bmrrep_log.sh and bmsrep_log.sh that report total amount of remediated items.
Added bmrstat_log.sh and bmsstat_log.sh that report statistics on non-trivial data remediations.
Changes in BMRBxTool 1.9.1 (release 2014-02-12)
Updated dictionary and several fixes for processing entries released 2014-02-10.
Changes in BMRBxTool 1.9.0 (release 2013-12-20)
Resolved unlinked relations (structure_annotation, struct_anno_char, struct_anno_software and struct_classification).
Revised property file names in the schema directory.
Revised scripts and added scripts to upload XML documents into eXist-db (XML Database).
Added automated remediation about chem_comp category (chem_comp.bmrb_id and chem_comp.pdb_id).
Added run_xquery.sh script and queries directory.
Changes in BMRBxTool 1.8.0 (release 2013-12-06)
Added automated remediation about journal citation using PubMed RESTful service (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/).
Added automated remediation about enzyme commission number in entity.ec_number and assembly.enzyme_commission_number tags.
Changes in BMRBxTool 1.7.0 (release 2013-11-12)
Updated dictionary from NMR-STAR v3.1.1.38 to v3.1.1.53.
Revised resource update scripts that allow user to select BMRB mirror sites.
Fixed XML conversion scripts.
Package now includes Java Archive files (bmr-util.jar and bms-util.jar).
Added do_all.sh script.
Changes in BMRBxTool 1.6.0 (internal version)
Added a "no-remediate" option that turns off programmed remediation.
Added remediation log output function.
Changes in BMRBxTool 1.5.0 (internal version)
Updated dictionary from NMR-STAR v3.1.1.29 to v3.1.1.38.
Changes in BMRBxTool 1.4.0 (release 2013-09-28)
Revised scripts and document.
Fixed invalid DB name matching.
Changes in BMRBxTool 1.4.0 (release 2013-07-10)
XML Schema location is changed from pdbml.pdb.org to bmrbpub.protein.osaka-u.ac.jp.
Added a "max-thrds" option that allows user to change the number of threads.
Added scripts to manage corrupted XML documents.
Added scripts to upload XML documents into BaseX (XML Database).
Changes in BMRBxTool 1.3.0 (release 2013-06-26)
Updated dictionary for processing entries released 2013-06-18.
Fixed null pointer exception issue at processing atom_chem_shift.ambiguity_code.
Fixed revision date invalid issue.
Added a "well-formed" option to validate XML format, which is turned off by default.
Changed to exclude atomic coordinates, restraints and peak lists categories if the "noatom" option was selected.
Changes in BMRBxTool 1.2.4 (release 2013-06-17)
Added a "noatom" option to generate reduced XML document (excl. Atom_site category) for RDFization.
Changes in BMRBxTool 1.2.3 (release 2013-06-11)
Changed directory name of metabolomics associated with the BMRBoTool.
Changes in BMRBxTool 1.2.2 (release 2013-06-05)
Revised scripts to support XML->RDF conversion tool; BMRBoTool.
Changes in BMRBxTool 1.2.1 (release 2013-05-30)
Updated dictionary and text conversion tables for processing entries released 2013-05-20.
1. Sanitized database accession codes which were related to database names; 'NDB' and 'NCBI'.
2. Remediated items of the following categories;
Constraint_file, Gen_dist_constraint and Conformer_stat_list.
Changes in BMRBxTool 1.2.0 (release 2013-05-23)
Changed QName from nmrstar to BMRBx.
Updated dictionary and text conversion tables for processing entries released 2013-05-06.
Changes in BMRBxTool 1.1.0 (release 2013-04-26)
Improved efficiency in parallel processing.
Changes in BMRBxTool 1.0.0 (release 2013-04-12)
First release.