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CHANGELOG
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CHANGELOG
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Changes in BMRBoTool 1.35.0 (release 2023-07-24)
Synchronus update with BMRBxTool.
Changed namespace URI to http://bmrbpub.pdbj.org/schema/mmcif_nmr-star.xsd. (BMRBx)
Changed namespace URI to http://bmrbpub.pdbj.org/schema/mmcif_nmr-star.owl. (BMRBo)
Changed namespace URI of PDB/RDF to http://rdf.wwpdb.org/schema/pdbx-v50.owl. (PDBo)
Updated enumerations of _entity_natural_src.kingdom.
Utilize xsltproc for generation of BMRB/RDF.
Revert RDF link pattern to identifiers.org.
Fix invalid code of RDF resource URI.
Strip carriage return codes from BMRBo:entity.polymer_seq_one_letter_code_can and BMRBo:polymer_seq_one_letter_code.
Changes in BMRBoTool 1.34.0 (release 2021-05-17)
Updated dictionary NMR-STAR v3.2.1.15 to v3.2.1.18.
Fixed invalid whitespace in URI.
Updated BMRB/JSON Schema.
Updated PostgreSQL DDL.
Revised XML->RDF XSLT code (PDBj-BMRB to BMRBj).
Changes in BMRBoTool 1.33.0 (release 2019-01-23)
Updated dictionary NMR-STAR v3.2.1.12 to v3.2.1.15.
Changes in BMRBoTool 1.32.0 (release 2018-11-26)
Updated dictionary NMR-STAR v3.2.1.9 to v3.2.1.12.
Changes in BMRBoTool 1.31.0 (release 2018-11-08)
Synchronus update with BMRBxTool.
Added 'NSC NUMBER' of enumeration of '_chem_comp_identifer.type'.
Changes in BMRBoTool 1.30.0 (release 2018-08-24)
Updated dictionary NMR-STAR v3.2.1.5 to v3.2.1.9.
Changes in BMRBoTool 1.29.0 (release 2018-06-29)
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.
XML Schema location is changed from bmrbpub.protein.osaka-u.ac.jp to bmrbpub.pdbj.org.
Changes in BMRBoTool 1.28.0 (release 2018-06-13)
Updated dictionary NMR-STAR v3.2.1.2 to v3.2.1.5.
Changed protocol of wwPDB/RDF from http://rdf.wwpdb.org/pdb to https://rdf.wwpdb.org/pdb.
Updated BMRB/JSON Schema.
Fixed key constraint in BMRB/XML Schema.
Changes in BMRBoTool 1.27.0 (release 2018-04-13)
Updated dictionary NMR-STAR v3.2.0.15 to v3.2.1.2.
Added to support for refreshed relational tables (since Apr-05-2018).
XML Schema location is changed from pdbml.pdb.org to bmrbpub.protein.osaka-u.ac.jp.
Changes in BMRBoTool 1.26.0 (release 2018-03-29)
Updated dictionary from NMR-STAR v3.2.0.11 to v3.2.0.15.
Apache License V2.0 branding.
Added ontology relationship between BMRB/OWL and PDBx ontology.
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.
Added delay time after virtuoso starts.
Changes in BMRBoTool 1.25.0 (release 2018-02-02)
Synchronus update with BMRBxTool.
Updated dictionary from NMR-STAR v3.2.0.9 to v3.2.0.11.
Added xml:base attribute in BMRB/OWL.
Added exclude-result-prefixes="BMRBx" in XML->RDF XSLT code.
Updated saxon9he.jar.
Add object property "datablock_of" in BMRB/OWL.
Changes in BMRBoTool 1.24.0 (release 2017-09-08)
Synchronus update with BMRBxTool.
Updated dictionary from NMR-STAR v3.2.0.7 to v3.2.0.9.
Used Dublin Core Terms in BMRB/OWL.
Updated PDBx Ontology from v42 to v50.
Changes in BMRBoTool 1.23.0 (release 2017-03-31)
Synchronus update with BMRBxTool.
Updated dictionary from NMR-STAR v3.1.2.6 to v3.2.0.7.
Revised XML->RDF XSLT code (entry.doi, auxiliary_files.doi, entry_author.orcid, citation_author.orcid).
Changes in BMRBoTool 1.22.0 (release 2016-12-13)
Synchronus update with BMRBxTool.
Updated dictionary from NMR-STAR v3.1.1.65 to v3.1.2.6.
Fixed XML->RDF XSLT code to support matched_entries, which is introduced from v3.1.2.6.
Changes in BMRBoTool 1.21.0 (release 2016-11-24)
Synchronus update with BMRBxTool.
Changed directory name for N-Triples (rdf_*_ntz -> nt_*_doc).
Updated Xerces from 2.7.0 to 2.11.0.
Added JSON Schema for BMRB/JSON.
Changes in BMRBoTool 1.20.0 (release 2016-07-22)
Synchronus update with BMRBxTool.
Revised BMRB/XML Schema and BMRB/OWL, which reduces substitutions of meaningless zero value.
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'.
Revised stylesheet bmrb-rdf.xsl to redirect integrated search service of PDBj-BMRB.
Revised XML->RDF XSLT code (pdbj-bmrbdep integrated search).
Changes in BMRBoTool 1.19.0 (release 2015-10-16)
Synchronus update with BMRBxTool.
Revised BMRB/XML Schema and BMRB/OWL to support reference pointers to NMR-STAR Dictionary.
Fixed RDF link properties of BMRB/OWL to PubChem SID and CID.
Added owl-ann.jar to append owl:equivalentProperty and rdfs:seeAlso referring to equivalent properties in PDBx OWL.
Changed PubMed link pattern to http://rdf.ncbi.nlm.nih.gov/pubmed/{pmid}.
Replaced BMRBo:link_to by rdfs:seeAlso in BMRB/OWL.
Changed "info" URI to use info:ddbj-embl-genbank instead of info:ddbj, info:embl and info:genbank, respectively.
Added many SPARQL query examples in queries directory.
Revised namespace of "info" URI scheme to fit with registry name in http://identifiers.org/.
Added cross references to http://identifiers.org/{db_namespace}/{db_id}.
Added struct_classification.sunid for storing SCOP unique identifier (sunid).
Changes in BMRBoTool 1.18.0 (release 2015-09-18)
Extended dictionary to support validation reports about completeness of assigned chemical shifts.
Synchronus update with BMRBxTool.
Fixed stylesheet (bmrb-rdf.xsl).
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).
Changes in BMRBoTool 1.17.0 (release 2015-05-18)
Synchronus update with BMRBxTool.
Changes in BMRBoTool 1.16.0 (release 2015-04-15)
Extended dictionary to support Protein Blocks annotation.
Revised BMRB/XML Schema (xsd:decimal -> xsd:double @ entity_db_link.seq_homology_expectation_val).
Fixed XML->RDF XSLT code (assembly_db_link.accession_code).
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.).
Synchronus update with BMRBxTool.
Added extlibs directory, which includes external jar libraries.
Revised RDF validation script.
Changes in BMRBoTool 1.15.0 (release 2014-11-19)
Synchronus update with BMRBxTool.
Added RDF/XML -> N-Triples conversion script (bmr2nt.sh and bms2n.sh).
Revised stylesheet (bmrb-rdf.xsl) to support N-Triples format.
Changes in BMRBoTool 1.14.0 (release 2014-09-30)
Synchronus update with BMRBxTool.
Changes in BMRBoTool 1.13.0 (release 2014-09-12)
Revived entry.assigned_pdb_id and entry.assigned_pdb_deposition_id for primary reference to PDB.
Revised XML->RDF XSLT code (entry.assigned_pdb_id).
Changes in BMRBoTool 1.12.0 (release 2014-09-03)
Synchronus update with BMRBxTool.
Dropped FUSEKI relating scripts.
Added PostgreSQL DDL generated from BMRB/XML Schema.
Dropped GRAPH URIs for each of BMRB entries and Metabolomics entries.
GRAPH URI for OMIM is updated.
Updated owl2xhtml.xsl.
Changes in BMRBoTool 1.11.1 (release 2014-07-04)
Synchronus update with BMRBxTool.
Added chkrdflinks.sh, which returns statitics on external RDF links.
Changes in BMRBoTool 1.11.0 (release 2014-06-17)
Extended dictionary to support LACS validation reports.
Synchronus update with BMRBxTool.
Changes in BMRBoTool 1.10.0 (release 2014-06-12)
Updated dictionary from NMR-STAR v3.1.1.53 to v3.1.1.65.
Removed bmrb-owl.xsl, which was replaced by owl2xhtml.xsl.
Added stylesheets xs3p.xsl (for BMRB/XML Schema) and owl2xhtml.xsl (for BMRB/OWL).
Changes in BMRBoTool 1.9.4 (release 2014-06-04)
Synchronus update with BMRBxTool.
Changes in BMRBoTool 1.9.3 (release 2014-05-02)
Synchronus update with BMRBxTool.
Changes in BMRBoTool 1.9.2 (release 2014-04-15)
Fixed update script for the NMR-STAR dictionary.
Fixed reference_to property of BMRB/OWL.
Revised comment of BMRB/OWL.
Changes in BMRBoTool 1.9.1 (release 2014-03-19)
Added federated SPARQL queries that span PDB.
Added GRAPH URIs for each of BMRB entries and Metabolomics entries (e.g. http://bmrbpub.protein.osaka-u.ac.jp/rdf/bmr[0-9]+ or http://bmrbpub.protein.osaka-u.ac.jp/rdf/bms[et][0-9]{6}).
Changes in BMRBoTool 1.9.0 (release 2014-02-07)
Revised ontology to support SCOP (Structural Classification of Proteins).
Changed URL from bmrb.protein.osaka-u.ac.jp to bmrb.pdbj.org.
Fixed invalid chem_comp.id.
Revised ontology to support chem_comp and ligand_expo.
Added run_sparql.sh, collect_cs_all.sh, collect_cs_sel.sh, count_comp_id.sh,
average_cs.sh, variance_cs.sh and relating SPARQL templates.
Added federated SPARQL queries that span BMRB, UniProt, OMIM and PubMed.
Changed GRAPH URI from http://bmrbpub.protein.osaka-u.ac.jp/search/rdf/bm[rs] to http://bmrbpub.protein.osaka-u.ac.jp/rdf/bm[rs]. (Canceled in v1.12.0 or later)
Changes in BMRBoTool 1.8.0 (release 2013-12-06)
Revised ontology to support both ISSN and ISBN.
Revised base of URLs linking UniProt ID, NCBI Taxonomy ID and enzyme commission number.
Changes in BMRBoTool 1.7.0 (release 2013-11-12)
Updated dictionary from NMR-STAR v3.1.1.38 to v3.1.1.53.
Added do_all.sh script.
Changes in BMRBoTool 1.6.0 (internal version)
Updated dictionary from NMR-STAR v3.1.1.29 to v3.1.1.38.
Changes in BMRBoTool 1.4.0 (release 2013-10-25)
Revised TDB bulk loader and removed FUSEKI bulk loader.
Revised FUSEKI start script.
Added Virtuoso bulk loader.
Revised XML->RDF XSLT code (linked data).
Revised BMRB/RDF->HTML XSLT codes used in bmrbpub.protein.osaka-u.ac.jp.
Changes in BMRBoTool 1.4.0 (release 2013-07-10)
First release.