pdbx-validation

The pdbx-validation is a generation tool of alternative wwPDB validation reports where validation metrics are reorganized using the familiar mmCIF naming scheme and categories. It includes PDBx/mmCIF compatible versions of validation reports (VRPT mmCIF and VRPT PDBML), RDF version of validation reports (VRPT/RDF), and a series of ontologies; wwPDB Validation Information Dictionary, VRPT PDBML Schema, and VRPT/OWL.

Usage

To generate the alternative wwPDB validation report of some PDB entries,
./run_vrpt_test.sh 5b1l 5u9b 5h0s ...
To update the alternative wwPDB validation report of the entire PDB entry,
./run_vrpt_all.sh
Here is a map of the program.

File path	Document
schema/mmcif_pdbx_validation_v4.dic	wwPDB Validation Information Dictionary (v4.389)
schema/pdbx-validation-v4.xsd	VRPT PDBML Schema (v4.389)
schema/pdbx-validation-v4.owl	VRPT/OWL (v4.389)
schema/mmcif_ddl.dic	extended mmCIF DDL Core Dictionary (dubbed as v2.4.2)
resource/mmcif_pdbx_v50.dic	PDB Exchange Data Dictionary (v5.389)
resource/pdbx-v50.xsd	PDBML Schema (v5.389)
resource/pdbx-v50.owl	PDBx ontology, ontology for PDB/RDF (v5.389)
resource/wwpdb_validation_v6.01.xsd	XML Schema for wwPDB validation reports (v6.01, rev 2022-09-20)
scripts	a directory contains scripts invoked by the 'run_vrpt_all.sh' script
virtuoso_scripts	a directory contains scripts for uploading VRPT/RDF to local SPARQL endpoint
stylesheet	a directory contains XSL style sheets for generation of alternative wwPDB validation reports
test	a directory contains resource files for test on several PDB entries

References

Gert-Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, Takeshi Iwata, Takahiro Kudou, Kei Yura, Toshimichi Fujiwara, Takeshi Kawabata, Genji Kurisu.
"Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data", Protein Science, 31(1), 173-186 (2022)

Examples of alternative wwPDB validation reports

PDB ID: 5B1L, Exptl. method: X-RAY DIFFRACTION
- PDBx/mmCIF format
  - VRPT mmCIF: 5b1l-validation-full.cif
  - VRPT mmCIF-alt: 5b1l-validation-alt.cif
- PDBML format
  - VRPT PDBML: 5b1l-validation-full.xml
  - VRPT PDBML-alt: 5b1l-validation-alt.xml
- PDB/RDF format
  - VRPT/RDF: 5b1l-validation-full.rdf
  - VRPT/RDF-alt: 5b1l-validation-alt.rdf
- wwPDB validation report (XML format)
  - Original source: 5b1l_validation.xml
  - Reverted from VRPT PDBML: 5b1l_validation.xml
  - Reverted from VRPT PDBML-alt and PDBML-noatom: 5b1l_validation.xml
PDB ID: 5U9B, Exptl. method: SOLUTION NMR
- PDBx/mmCIF format
  - VRPT mmCIF: 5u9b-validation-full.cif
  - VRPT mmCIF-alt: 5u9b-validation-alt.cif
- PDBML format
  - VRPT PDBML: 5u9b-validation-full.xml
  - VRPT PDBML-alt: 5u9b-validation-alt.xml
- PDB/RDF format
  - VRPT/RDF: 5u9b-validation-full.rdf
  - VRPT/RDF-alt: 5u9b-validation-alt.rdf
- wwPDB validation report (XML format)
  - Original source: 5u9b_validation.xml
  - Reverted from VRPT PDBML: 5u9b_validation.xml
  - Reverted from VRPT PDBML-alt and PDBML-noatom: 5u9b_validation.xml
PDB ID: 2LOY, Exptl. method: SOLUTION NMR with NMR restraint validation (v6.00, 2021-01-22)
- PDBx/mmCIF format
  - VRPT mmCIF: 2loy-validation-full.cif
  - VRPT mmCIF-alt: 2loy-validation-alt.cif
- PDBML format
  - VRPT PDBML: 2loy-validation-full.xml
  - VRPT PDBML-alt: 2loy-validation-alt.xml
- PDB/RDF format
  - VRPT/RDF: 2loy-validation-full.rdf
  - VRPT/RDF-alt: 2loy-validation-alt.rdf
- wwPDB validation report (XML format)
  - Original source: 2loy_validation.xml
  - Reverted from VRPT PDBML: 2loy_validation.xml
  - Reverted from VRPT PDBML-alt and PDBML-noatom: 2loy_validation.xml
PDB ID: 5H0S, Exptl. method: ELECTRON MICROSCOPY
- PDBx/mmCIF format
  - VRPT mmCIF: 5h0s-validation-full.cif
  - VRPT mmCIF-alt: 5h0s-validation-alt.cif
- PDBML format
  - VRPT PDBML: 5h0s-validation-full.xml
  - VRPT PDBML-alt: 5h0s-validation-alt.xml
- PDB/RDF format
  - VRPT/RDF: 5h0s-validation-full.rdf
  - VRPT/RDF-alt: 5h0s-validation-alt.rdf
- wwPDB validation report (XML format)
  - Original source: 5h0s_validation.xml
  - Reverted from VRPT PDBML: 5h0s_validation.xml
  - Reverted from VRPT PDBML-alt and PDBML-noatom: 5h0s_validation.xml
PDB ID: 6RJH, Exptl. method: ELECTRON MICROSCOPY with EM map/model validation (v004, 2019-11-18)
- PDBx/mmCIF format
  - VRPT mmCIF: 6rjh-validation-full.cif
  - VRPT mmCIF-alt: 6rjh-validation-alt.cif
- PDBML format
  - VRPT PDBML: 6rjh-validation-full.xml
  - VRPT PDBML-alt: 6rjh-validation-alt.xml
- PDB/RDF format
  - VRPT/RDF: 6rjh-validation-full.rdf
  - VRPT/RDF-alt: 6rjh-validation-alt.rdf
- wwPDB validation report (XML format)
  - Original source: 6rjh_validation.xml
  - Reverted from VRPT PDBML: 6rjh_validation.xml
  - Reverted from VRPT PDBML-alt and PDBML-noatom: 6rjh_validation.xml
PDB ID: 6XEY, Exptl. method: ELECTRON MICROSCOPY with EM map/model validation (v004, 2020-02-18)
- PDBx/mmCIF format
  - VRPT mmCIF: 6xey-validation-full.cif
  - VRPT mmCIF-alt: 6xey-validation-alt.cif
- PDBML format
  - VRPT PDBML: 6xey-validation-full.xml
  - VRPT PDBML-alt: 6xey-validation-alt.xml
- PDB/RDF format
  - VRPT/RDF: 6xey-validation-full.rdf
  - VRPT/RDF-alt: 6xey-validation-alt.rdf
- wwPDB validation report (XML format)
  - Original source: 6xey_validation.xml
  - Reverted from VRPT PDBML: 6xey_validation.xml
  - Reverted from VRPT PDBML-alt and PDBML-noatom: 6xey_validation.xml

Bulk download service of full specification or lightweight alternative version of wwPDB validation reports

Bulk download via HTTP protocol
Bulk download via rsync protocol
- VRPT mmCIF (full specification):
  % rsync -av --delete rsync://bmrbpub.pdbj.org/mmcif-vrpt .
- VRPT PDBML (full specification):
  % rsync -av --delete rsync://bmrbpub.pdbj.org/pdbml-vrpt .
- VRPT/RDF (full specification):
  % rsync -av --delete rsync://bmrbpub.pdbj.org/rdf-vrpt .
- VRPT mmCIF (lightweight alternative version):
  % rsync -av --delete rsync://bmrbpub.pdbj.org/mmcif-vrpt-alt .
- VRPT PDBML (lightweight alternative version):
  % rsync -av --delete rsync://bmrbpub.pdbj.org/pdbml-vrpt-alt .
- VRPT/RDF (lightweight alternative version):
  % rsync -av --delete rsync://bmrbpub.pdbj.org/rdf-vrpt-alt .
VRPT PDBML-alt PostgreSQL dump file

Other wwPDB Core Archives in RDF format that have been generated by this tool

Bulk download via HTTP protocol
Bulk download via rsync protocol
- PDB/RDF:
  % rsync -av --delete rsync://bmrbpub.pdbj.org/rdf-pdb .
- chem_comp/RDF:
  % rsync -av --delete rsync://bmrbpub.pdbj.org/rdf-cc .
- BIRD/RDF:
  % rsync -av --delete rsync://bmrbpub.pdbj.org/rdf-bird .
SPARQL endpoint for BMRB/RDF, PDB/RDF, chem_comp/RDF, PRD/RDF, and FAM/RDF
NBDC RDF Portal

Software requirements

Java 8 or later.
Apache Maven (mvn), used to install external libraries.
Git (git), used to install external libraries.
xsltproc, used to XSL translation v1.0.
mmCIF Dictionary Suite, optionally used to generate VRPT PDBML Schema from the wwPDB Validation Information Dictionary.
PDBML2CIF, optionally, used to generate mmCIF version of wwPDB validation reports.
Raptor RDF Syntax Library, optionally, used to validate RDF syntax.
libxml2, optionally, used to post XML beutification (xmllint).
PostgreSQL, optionally used to import XML contents to relational database.
Virtuoso, oprionally used as SPARQL endpoint of VRPT/RDF.

Release notes

Mar 27, 2024: Release v4.4.39
- Update wwPDB Validation Information Dictionary to 4.389.
Mar 27, 2024: Release v4.4.38
- Update wwPDB Validation Information Dictionary to 4.388.
Feb 21, 2024: Release v4.4.37
- Update wwPDB Validation Information Dictionary to 4.387.
Feb 21, 2024: Release v4.4.36
- Update wwPDB Validation Information Dictionary to 4.386.
Feb 21, 2024: Release v4.4.35
- Update wwPDB Validation Information Dictionary to 4.385.
Feb 21, 2024: Release v4.4.34
- Update wwPDB Validation Information Dictionary to 4.384.
Feb 21, 2024: Release v4.4.33
- Update wwPDB Validation Information Dictionary to 4.383.
Feb 21, 2024: Release v4.4.32
- Update wwPDB Validation Information Dictionary to 4.382.
Oct 24, 2023: Release v4.4.31
- Update wwPDB Validation Information Dictionary to 4.381.
Oct 19, 2023: Release v4.4.30
- Update wwPDB Validation Information Dictionary to 4.380.
Sep 06, 2023: Release v4.4.29
- Update wwPDB Validation Information Dictionary to 4.379.
Aug 25, 2023: Release v4.4.28
- Update wwPDB Validation Information Dictionary to 4.378.
- Minor fix to support UNNAMED dihedral angle.
Aug 18, 2023: Release v4.4.27
- Update wwPDB Validation Information Dictionary to 4.377.
Aug 18, 2023: Release v4.4.26
- Update wwPDB Validation Information Dictionary to 4.376.
- Fix invalid IRI codes.
- Added RDF uploader scripts for Oxigraph Server, oxigraph_scripts. Oxigraph Server is still under evaluations.
Jul 27, 2023: Release v4.4.25
- Update wwPDB Validation Information Dictionary to 4.375.
- Performance improvement of extract_info.xsl (XSLT 2.0 -> 1.0, though SAXON is required)
Jul 24, 2023: Release v4.4.24
- Update wwPDB Validation Information Dictionary to 4.374.
Jul 14, 2023: Release v4.4.23
- Update wwPDB Validation Information Dictionary to 4.373.
- Support NMR restraint remediation.
- Set _diffrn.pdbx_serial_crystal_experiment is not mandatory.
- Fix clean-up scripts.
- Fix invalid code of RDF resource URI.
- Strip carriage return codes from PDBo:entity_poly.pdbx_seq_one_letter_code and PDBo:entity_poly.pdbx_seq_one_letter_code_can.
- Enable to switch SIFTS resource from original SIFTS or PDB NextGen Archive.
- Use rsync service to retrieve SIFTS resource. 'aria2c' is not necessary.
- Mitigate validation report data issue, aka. DAOTHER-8001: Atom names containing '_' character are unexpectedly converted to name with comma character in Mogul outliers of XML validation report.
- Include 0.0 in the range for the following data items:
  - _pdbx_nmr_distance_violation_model.maximum_violation
  - _pdbx_nmr_distance_violation_model.average_violation
  - _pdbx_nmr_distance_violation_model.median_violation
  - _pdbx_nmr_dihedral_angle_violation_model.maximum_violation
  - _pdbx_nmr_dihedral_angle_violation_model.average_violation
  - _pdbx_nmr_dihedral_angle_violation_model.median_violation
- Improve performane of translation/validation scripts.
- Add XSD datatype of RDF literals, except for xsd:string.
Jun 21, 2023: Release v4.4.22
- Update wwPDB Validation Information Dictionary to 4.372.
Jun 21, 2023: Release v4.4.21
- Update wwPDB Validation Information Dictionary to 4.371.
Jun 21, 2023: Release v4.4.20
- Update wwPDB Validation Information Dictionary to 4.370.
Jun 21, 2023: Release v4.4.22
- Update wwPDB Validation Information Dictionary to 4.372.
Jun 21, 2023: Release v4.4.21
- Update wwPDB Validation Information Dictionary to 4.371.
Jun 21, 2023: Release v4.4.20
- Update wwPDB Validation Information Dictionary to 4.370.
Apr 13, 2023: Release v4.4.19
- Update wwPDB Validation Information Dictionary to 4.369.
Mar 20, 2023: Release v4.4.18
- Update wwPDB Validation Information Dictionary to 4.368.
- Update URL template for source PDBML.
Mar 7, 2023: Release v4.4.17
- Update wwPDB Validation Information Dictionary to 4.367.
Mar 6, 2023: Release v4.4.16
- Update wwPDB Validation Information Dictionary to 4.366.
- Support for wwpdb_validation_v6.02.xsd (/wwPDB-validation-information/Entry/@bmrb_id).
- Improve performace of SIFTS XML file validation script.
Mar 6, 2023: Release v4.4.15
- Update wwPDB Validation Information Dictionary to 4.365.
Dec 20, 2022: Release v4.4.14
- Update wwPDB Validation Information Dictionary to 4.364.
Dec 20, 2022: Release v4.4.13
- Update wwPDB Validation Information Dictionary to 4.363.
Dec 20, 2022: Release v4.4.12
- Update wwPDB Validation Information Dictionary to 4.362.
Oct 5, 2022: Release v4.4.11
- Update wwPDB Validation Information Dictionary to 4.361.
- Support for Q-score metric of EM map-model validation (wwpdb_validation_v6.01.xsd).
Aug 2, 2022: Release v4.4.10
- Update wwPDB Validation Information Dictionary to 4.360.
Jun 7, 2022: Release v4.4.9
- Update wwPDB Validation Information Dictionary to 4.359.
Jun 7, 2022: Release v4.4.8
- Update wwPDB Validation Information Dictionary to 4.358.
Mar 31, 2022: Release v4.4.7
- Update wwPDB Validation Information Dictionary to 4.357.
Mar 31, 2022: Release v4.4.6
- Update wwPDB Validation Information Dictionary to 4.355.
Jan 18, 2022: Release v4.4.5
- Update wwPDB Validation Information Dictionary to 4.354.
Dec 17, 2021: Release v4.4.4
- Update wwPDB Validation Information Dictionary to 4.353.
Nov 26, 2021: Release v4.4.3
- Update RDF URIs to GO and ChEBI resources.
Nov 4, 2021: Release v4.4.2
- Update wwPDB Validation Information Dictionary to 4.352.
- Revert RDF URI patterns to identifiers.org.
Oct 21, 2021: Release v4.4.1
- Update wwPDB Validation Information Dictionary to 4.351.
Sep 30, 2021: Release v4.4.0
- Add resources for FAM/RDF.
  - Update PDB/OWL, VRPT/OWL, XSLT codes to support external databases: CCDC, PubChem-Substance, ChemSpider, CAS, ChEBI, MeSH, ChEMBL, BindingDB, DrugBank, ChemDB.
Sep 24, 2021: Release v4.3.0
- Change namespace URIs:
  - xmlns:PDBo="http://rdf.wwpdb.org/schema/pdbx-v50.owl#"
  - xmlns:VRPTo="http://rdf.wwpdb.org/schema/pdbx-validation-v4.owl#"
- Revise RDF links.
- Revise RDF directory trees.
- Add resources for PRD/RDF.
- Fix stylesheets to remove category element that has no children. (PDB ID: 7lqs)
- Fix XSD data type of '_pdbx_em_volume_estimate_marker.enclosed_volume' and '_pdbx_em_density_distribution_marker.map_value' (xsd:double).
- Update Virtuoso data upload scripts for PDF/RDF, chem_comp/RDF, PRD/RDF, and VRPT/RDF(-alt).
Sep 17, 2021: Release v4.2.0
- Integration of SIFTS into PDB/RDF that includes HTML links to GO, InterPro, Pfam, CATH domain, SCOP/SCOP2/SCOP2B, and Ensembl from '_pdbx_sifts_xref_db_segments' category.
- Add HTML links to EMDB and SASBDB entries from '_pdbx_database_related' category.
Sep 13, 2021: Release v4.1.1
- Update wwPDB Validation Information Dictionary to 4.350.
Sep 9, 2021: Release v4.1.0
- Change prefixes as follows.
  - xmlns:VRPTx="http://pdbml.pdb.org/schema/pdbx-validation-v4.xsd"
  - xmlns:VRPTo="https://rdf.wwpdb.org/schema/pdbx-validation-v4.owl#"
- Add supports for '_pdbx_sifts_xref_db', '_pdbx_sifts_xref_db_segments', and '_pdbx_sifts_unp_segments' categories of PDBx/mmCIF Dictionary (v5.349).
  - Update PDB/OWL, VRPT/OWL, XSLT codes to support external databases: GO, InterPro, Pfam, CATH domain, SCOP/SCOP2/SCOP2B, and Ensembl.
- Change software requirement of mmCIF Dictionary Suite.
- Add RDF link to Peptide Reference Dictionary (PRD) in BIRD (Biologically Interesting molecule Reference Dictionary).
- Add supports for '_struct_ref.pdbx_db_code'.
  - Update PDB/OWL, VRPT/OWL, XSLT codes to support external databases: GenBank, EMBL, PIR, RefSeq, and Norine.
Sep 2, 2021: Release v4.0.8
- Update wwPDB Validation Information Dictionary to 4.349.
- Update PDBj's data server URLs (data.pdbj.org).
Aug 4, 2021: Release v4.0.7
- Update wwPDB Validation Information Dictionary to 4.348.
Aug 3, 2021: Release v4.0.6
- Update wwPDB Validation Information Dictionary to 4.347.
- Update extended mmCIF DDL Core Dictionary to v2.4.1.
Apr 29, 2021: Release v4.0.5
- Update wwPDB Validation Information Dictionary to 4.342.
- Update extended mmCIF DDL Core Dictionary to v2.3.1.
Apr 6, 2021: Release v4.0.4
- Modify XSLT to handle multiple enzyme commission numbers.
Mar 16, 2021: Release v4.0.3
- Update wwPDB Validation Information Dictionary to 4.341.
Mar 15, 2021: Release v4.0.2
- Update wwPDB Validation Information Dictionary to 4.340.
Feb 19, 2021: Release v4.0.1
- Update wwPDB Validation Information Dictionary to 4.339.
Jan 26, 2021: Release v4.0.0
- Support XML Schema for wwPDB validation report (wwpdb_validation_v6.00.xsd).
Jan 21, 2021: Release v3.0.2
- Update wwPDB Validation Information Dictionary to 3.338.
Jan 8, 2021: Release v3.0.1
- Update wwPDB Validation Information Dictionary to 3.337.
Dec 16, 2020: Release v3.0.0
- Support XML Schema for wwPDB validation report (wwpdb_validation_v5.01.xsd).
  - Add '_pdbx_nmr_restraint_list' category that records list of NMR restraints.
  - Add '_pdbx_nmr_restraint_summary' category that records sumarry of conformationally restricting restraints.
  - Add '_pdbx_nmr_restraint_violation' category that records residual violations of conformationally restricting restraints in different bins.
  - Add '_pdbx_nmr_distance_violation_summary' category that records violations of distance restraints.
  - Add '_pdbx_nmr_distance_violation_model' category that records violations of distance restraints for each model.
  - Add '_pdbx_nmr_distance_violation_ensemble' category that records violations of distance restraints for each virtual ensemble alternating the size of an ensemble.
  - Add '_pdbx_nmr_distance_violation_plural' category that records potentially severe violations of distance restraints, which occurred in multiple coordinate models of the ensemble.
  - Add '_pdbx_nmr_distance_violation' category that records all distance restraint violations of the ensemble.
  - Add '_pdbx_nmr_dihedral_angle_violation_summary' category that records violations of dihedral angle restraints.
  - Add '_pdbx_nmr_dihedral_angle_violation_model' category that records violations of dihedral angle restraints for each model.
  - Add '_pdbx_nmr_dihedral_angle_violation_ensemble' category that records violations of dihedral angle restraints for each virtual ensemble alternating the size of an ensemble.
  - Add '_pdbx_nmr_dihedral_angle_violation_plural' category that records potentially severe violations of dihedral angle restraints, which occurred in multiple coordinate models of the ensemble.
  - Add '_pdbx_nmr_dihedral_angle_violation' category that records all dihedral angle restraint violations of the ensemble.
Nov 27, 2020: Release v2.0.16
- Update wwPDB Validation Information Dictionary to 2.336.
- Add support for wwPDB validation report (wwpdb_validation_v004.xsd, 2020-10-16)
Oct 28, 2020: Release v2.0.15
- Update wwPDB Validation Information Dictionary to 2.335.
Sep 24, 2020: Release v2.0.13
- Update wwPDB Validation Information Dictionary to 2.333.
Aug 24, 2020: Release v2.0.12
- Update wwPDB Validation Information Dictionary to 2.332.
- Add '_pdbx_percentile_view.conditions_label' and '_pdbx_percentile_entity_view.conditions_label' that provides short descriptive label about conditions applied for percentile calculation.
Aug 19, 2020: Release v2.0.11
- Update wwPDB Validation Information Dictionary to 2.331-3.
- Add resources for PDB/RDF and chem_comp/RDF (stylesheet/pdbml2rdf.xsl, stylesheet/cc2rdf.xsl).
- Add RDF link to rdf.glycoinfo.org and GlyTouCan.
- Add support for wwPDB validation report (wwpdb_validation_v004.xsd, 2020-02-18)
- Fix XSL version number of stylesheets and use xsltproc for XSL translation v1.0, instead of SAXON.
- Restore 'em_admin' category.
  - Link '_em_admin.entry_id' and /wwPDB-validation-information/Entry/@emdb_id.
  - Link '_em_admin.deposition_date' and /wwPDB-validation-information/Entry/@EMDB-deposition-date.
Jul 13, 2020: Release v2.0.10
- Update wwPDB Validation Information Dictionary to 2.330.
Jun 24, 2020: Release v2.0.9
- Update wwPDB Validation Information Dictionary to 2.329.
Jun 23, 2020: Release v2.0.8
- Update wwPDB Validation Information Dictionary to 2.328.
Jun 23, 2020: Release v2.0.7
- Update wwPDB Validation Information Dictionary to 2.327.
May 29, 2020: Release v2.0.6
- Update wwPDB Validation Information Dictionary to 2.326 (incorpoate branch chain dictionary extension).
May 26, 2020: Release v2.0.5
- Update wwPDB Validation Information Dictionary to 2.325.
Mar 31, 2020: Release v2.0.4
- Update wwPDB Validation Information Dictionary to 2.324.
Feb 10, 2020: Release v2.0.3
- Update wwPDB Validation Information Dictionary to 2.323.
Feb 4, 2020: Release v2.0.2
- Update wwPDB Validation Information Dictionary to 2.322.
Dec 25, 2019: Release v2.0.1
- Update wwPDB Validation Information Dictionary to 2.321.
- Add URLs for PDBj's FTP and PDBj Mine2 SQL search services.
Dec 10, 2019: Release v2.0.0
- Support XML Schema for wwPDB validation report (wwpdb_validation_v004.xsd).
  - Add '_pdbx_em_density_distribution' category that records map-value distribution of the primary EM volume.
  - Add '_pdbx_em_density_distribution_marker' category that records map-value distribution plot of the primary EM volume.
  - Add '_pdbx_em_volume_estimate' category that records volume estimation of the primary EM volume.
  - Add '_pdbx_em_volume_estimate_marker' category that records volume estimation plot of the primary EM volume.
  - Add '_pdbx_em_raps' category that records Rotationally Averaged Power Spectrum (RAPS).
  - Add '_pdbx_em_raps_marker' category that records Rotationally Averaged Power Spectrum (RAPS) plot.
  - Add '_pdbx_em_fsc_resolution' category that records estimated global resolutions from Fourier-Shell Correlation (FSC) curve using various criteria
  - Add '_pdbx_em_fsc_curve' category that records Fourier-Shell Correlation (FSC) curve.
  - Add '_pdbx_em_fsc_curve_marker' category that records row data to plot Fourier-Shell Correlation (FSC) curve.
  - Add '_pdbx_em_fsc_cutoff_curve' category that records Fourier-Shell Correlation (FSC) cut-off curve that represents a given criterion.
  - Add '_pdbx_em_fsc_cutoff_curve_marker' category that records row data to plot Fourier-Shell Correlation (FSC) cut-off curve that represents a given criterion.
  - Add '_pdbx_em_atom_inclusion' category that records fraction of atoms that are inside the surface.
  - Add '_pdbx_em_atom_inclusion_marker' category that records atom inclusion plot.
  - Add '_pdbx_em_validate_map_model_overall' category that records overall EM map-model validation of each entry.
  - Add '_pdbx_em_validate_map_model' category that records EM map-model validation of each residue.
  - Add '_pdbx_em_validate_map_model_entity' category that records EM map-model validation of each entity.
Nov 19, 2019: Release v1.6.5
- Fix typo of '_pdbx_validate_rmsd_torsion.percent_dihedral_angles_fitted_to_kb'.
- Partial support XML Schema for wwPDB validation report (wwpdb_validation_v004.xsd).
  - Fix typo in style sheet.
  - Add '_pdbx_database_related' category.
  - Update PostgreSQL DDLs (wwpdb_validation_v004.sql) enabling relational model extension.
Nov 14, 2019: Release v1.6.4
- Update wwPDB Validation Information Dictionary from v1.318 to 1.319.
Nov 5, 2019: Release v1.6.3
- Update wwPDB Validation Information Dictionary from v1.315 to 1.318.
- Update PostgreSQL DDLs.
Sep 18, 2019: Release v1.6.2
- Update wwPDB Validation Information Dictionary from v1.314 to 1.315.
  - Add '_refine.pdbx_R_complete' and '_refine_ls_shell.pdbx_R_complete'.
Aug 23, 2019: Release v1.6.1
- Update wwPDB Validation Information Dictionary from v1.313 to 1.314.
Aug 21, 2019: Release v1.6.0
- Update wwPDB Validation Information Dictionary from v1.311 to 1.313.
- Support XML Schema for wwPDB validation report (wwpdb_validation_v003.xsd).
  - Add '_pdbx_validate_rmsd_torsion.percent_dihedral_angles_fitted_to_kb' with link to /wwPDB-validation-information/ModelledSubgroup/mog-torsion-outlier/@local_density.
- Add null check for /wwPDB-validation-information/ModelledSubgroup/@mogul_angles_rmsz | @mogul_bonds_rmsz.
Jun 3, 2019: Release v1.5.5
- Update wwPDB Validation Information Dictionary from v1.309 to 1.311.
May 8, 2019: Release v1.5.4
- Update wwPDB Validation Information Dictionary from v1.307 to 1.309.
- Update extended mmCIF DDL Core Dictionary from v2.2.1 to v2.2.2.
Apl 10, 2019: Release v1.5.3
- Update wwPDB Validation Information Dictionary from v1.306 to 1.307.
Mar 19, 2019: Release v1.5.2
- Update wwPDB Validation Information Dictionary from v1.305 to 1.306.
Feb 23, 2019: Release v1.5.1
- Rename 'revert_info.xsl' to 'revert_info_from_full.xsl'.
- Enable mutual transformation between VRPT PDBML-alt and wwPDB Validation Reports (XML).
  - Add 'revert_info_from_alt_noatom.xsl', 'validation_created_date.xsl', and 'nmr_atom_consistency.xsl' style sheets for the translation.
- Enable parallel mmCIF and RDF syntax validation with check sum calculation.
- Add script 'calc_schema_stat.sh', which reports statistics of wwPDB Validation Information Dictionary and difference with PDB Exchange Data Dictionary.
- Fix typographical errors in item description. (pdbx_nmr_chem_shift_list.id -> pdbx_nmr_assigned_chem_shift_list.id)
- Change '_pdbx_missing_nmr_star_item.name' type to line
- Add '_pdbx_audit_revision_history.major_version' with link to /wwPDB-validation-information/Entry/@PDB-revision-number, which was formerly linked to '_pdbx_audit_revision_history.ordinal'
- Change '_pdbx_validate_rmsd_ring.dihedral_angle_standard_deviation' unit to degrees
- Change '_pdbx_validate_rmsd_torsion.dihedral_angle_standard_deviation' unit to degrees
- Change '_pdbx_dcc_map.LLDFZ_outlier_flag' type to uchar1
- Change '_pdbx_dcc_mon_geometry.LLDFZ_outlier_flag' type to uchar1
Feb 6, 2019: Release v1.5.0
- Add/Revise the following data items in relation with wwPDB validation information XSD.
  - Add '_pdbx_dcc_density.ls_d_res_low' with link to /wwPDB-validation-information/Entry/@PDB-resolution-low
  - Add '_pdbx_dcc_density.reflns_number_obs' with link to /wwPDB-validation-information/Entry/@numMillerIndices, which was formerly linked to '_reflns.number_all'
  - Add '_pdbx_dcc_density.ls_number_reflns_R_free' with link to /wwPDB-validation-information/Entry/@num-free-reflections, which was formerly linked to '_refine.ls_number_reflns_R_free'
  - Add '_pdbx_dcc_density.ls_percent_reflns_obs' with link to /wwPDB-validation-information/Entry/@DataCompleteness, which was formerly linked to '_refine.ls_percent_reflns_obs'
  - Add '_pdbx_dcc_density.ls_percent_reflns_R_free' and '_pdbx_dcc_density_corr.ls_percent_reflns_R_free' with link to /wwPDB-validation-information/Entry/@percent-free-reflections, which was formerly linked to '_refine.ls_percent_reflns_R_free'
- Add the following relationships to wwPDB validation information XSD.
  - Link '_pdbx_dcc_density_corr.ls_d_res_high' and /wwPDB-validation-information/Entry/@EDS_resolution
  - Link '_pdbx_dcc_density_corr.ls_d_res_high' and /wwPDB-validation-information/Entry/@EDS_resolution_low
  - Link '_pdbx_dcc_density_corr.ls_R_factor_R_work' and /wwPDB-validation-information/Entry/@EDS_R
  - Link '_pdbx_dcc_density_corr.ls_number_reflns_obs' and /wwPDB-validation-information/Entry/@numMillerIndices
  - Link '_pdbx_dcc_density_corr.ls_percent_reflns_obs' and /wwPDB-validation-information/Entry/@DataCompleteness
  - Link '_pdbx_dcc_density_corr.correlation_coeff_Fo_to_Fc' and /wwPDB-validation-information/Entry/@Fo_Fc_correlation
- Add '_struct_mon_prot.PDB_model_num' with link to /wwPDB-validation-information/ModelledSubgroup/@model
- Add '_struct_mon_nucl.PDB_model_num' with link to /wwPDB-validation-information/ModelledSubgroup/@model
- Add the following data items in relation with wwPDB validation information XSD.
  - Add '_pdbx_validate_rmsd_bond.bond_minimum_diff_to_kb' with link to /wwPDB-validation-information/ModelledSubgroup/mog-bond-outlier/@mindiff
  - Add '_pdbx_validate_rmsd_bond.number_bonds_in_kb' with link to /wwPDB-validation-information/ModelledSubgroup/mog-bond-outlier/@numobs
  - Add '_pdbx_validate_rmsd_angle.angle_minimum_diff_to_kb' with link to /wwPDB-validation-information/ModelledSubgroup/mog-angle-outlier/@mindiff
  - Add '_pdbx_validate_rmsd_angle.number_angles_in_kb' with link to /wwPDB-validation-information/ModelledSubgroup/mog-angle-outlier/@numobs
  - Add '_pdbx_validate_rmsd_torsion.dihedral_angle_minimum_diff_to_kb' with link to /wwPDB-validation-information/ModelledSubgroup/mog-torsion-outlier/@mindiff
  - Add '_pdbx_validate_rmsd_torsion.number_dihedral_angles_in_kb' with link to /wwPDB-validation-information/ModelledSubgroup/mog-torsion-outlier/@numobs
  - Add '_pdbx_validate_rmsd_ring.dihedral_angle_minimum_diff_to_kb' with link to /wwPDB-validation-information/ModelledSubgroup/mog-ring-outlier/@mindiff
  - Add '_pdbx_validate_rmsd_ring.number_dihedral_angles_in_kb' with link to /wwPDB-validation-information/ModelledSubgroup/mog-ring-outlier/@numobs
- Revise dictionary link of '_pdbx_validate_rmsd_bond.bond_deviation'.
- Revise dictionary link of '_pdbx_validate_rmsd_angle.angle_deviation'.
- Add the following data items in relation with wwPDB validation information XSD.
  - Add '_pdbx_validate_rmsd_bond.Zscore' with link to /wwPDB-validation-information/ModelledSubgroup/bond-outlier/@z
  - Add '_pdbx_validate_rmsd_angle.Zscore' with link to /wwPDB-validation-information/ModelledSubgroup/angle-outlier/@z
  - Add '_pdbx_dcc_mon_geometry.number_angles' with link to /wwPDB-validation-information/ModelledSubgroup/@mogul_rmsz_numangles
  - Add '_pdbx_dcc_mon_geometry.number_bonds' with link to /wwPDB-validation-information/ModelledSubgroup/@mogul_rmsz_numbonds
  - Add '_pdbx_struct_nmr_ens_dom.percent_of_core' with link to /wwPDB-validation-information/cyrange_domain/@percentage_of_core
  - Add '_pdbx_dcc_entity_geometry.number_angles' with link to /wwPDB-validation-information/ModelledEntityInstance/@num_bonds_rmsz
  - Add '_pdbx_dcc_entity_geometry.number_bonds' with link to /wwPDB-validation-information/ModelledEntityInstance/@num_angles_rmsz
  - Add '_pdbx_dcc_geometry.number_angles' with link to /wwPDB-validation-information/Entry/@num_bonds_rmsz
  - Add '_pdbx_dcc_geometry.number_bonds' with link to /wwPDB-validation-information/Entry/@num_angles_rmsz
- Enable mutual transformation between VRPT PDBML and wwPDB Validation Reports (XML).
  - Add 'revert_info.xsl' style sheet for the translation.
  - Modify 'run_test.sh' script which include translation from VRPT PDBML to wwPDB Validation Reports (XML).
- Update wwPDB Validation Information Dictionary from v1.303 to 1.305.
- Apply XML beautifier using xmllint command, if possible.
Jan 8, 2019: Release v1.4.1
- Ensure identity of chemical_shift_list/@list_id.
- Set category key for '_pdbx_missing_nmr_star_item' category.
- Fix style sheet to escape validtion error occurs for empty data in 'pdbx_nmr_unmapped_chem_shift.val_err' and 'pdbx_nmr_unmapped_chem_shift.ambiguity_code'.
- Revise style sheet to support unpaired steric clash (a solo clash/@cid).
- Change directory name containing uncompressed validation reports from validation_info to validation-info.
- Add mmCIF syntax validation when mmCIF Dictionary Suite is available (CifCheck).
- Validate ambiguity code while translation of VRPT PDBML.
Dec 19, 2018: Release v1.4.0
- Add '_pdbx_nmr_chem_shift_annotation.id' and set category key along with '_pdbx_nmr_chem_shift_annotation.list_id'.
- Set '_pdbx_nmr_unmapped_chem_shift.id' as category key along with '_pdbx_nmr_unmapped_chem_shift.list_id'.
- Set '_pdbx_nmr_unparsed_chem_shift.id' as category key along with '_pdbx_nmr_unparsed_chem_shift.list_id'.
- Update 'extract_info.xsl' style sheet which caused translation errors of NMR structure entries.
- Add support for mmCIF version of wwPDB validation reports using PDBML2CIF command.
- Change file extension of VRPT/RDF form validation.rdf to validation-full.rdf.
- Add RDF syntax validation when Raptor RDF Syntax Library is available (rapper).
Dec 4, 2018: Release v1.3.11
- Update wwPDB Validation Information Dictionary from v1.302 to 1.303.
Nov 26, 2018: Release v1.3.10
- Update wwPDB Validation Information Dictionary from v1.301 to 1.302.
Nov 12, 2018: Release v1.3.9
- Update wwPDB Validation Information Dictionary from v1.300 to 1.301.
- Update units for _em_imaging.c2_aperture_diameter from millimeters to micrometres.
Nov 8, 2018: Release v1.3.8
- Update wwPDB Validation Information Dictionary from v1.299 to 1.300.
- Replace all xsd:integer of PDBML Schema and VRPT PDBML Schema by xsd:int.
- Retrieve '_pdbx_audit_revision_category', 'pdbx_audit_revision_item' categories.
- Retrieve '_diffrn_detector.pdbx_frequency'.
- Add XML Schema validation script 'run_valid.sh'.
- Update extended mmCIF DDL Core Dictionary from v2.2.0 to v2.2.1.
- Add PDBML Schema generation script, 'resource/update_pdbx_xsd.sh'.
Sep 5, 2018: Release v1.3.7
- Update wwPDB Validation Information Dictionary from v1.298 to 1.299.
- Add _diffrn.pdbx_serial_crystal_experiment.
- Remove categories of xfel_group defined by PDB Exchange Data Dictionary V5.299.
Aug 3, 2018: Release v1.3.6
- Update wwPDB Validation Information Dictionary from v1.297 to 1.298.
Jul 24, 2018: Release v1.3.5
- Update wwPDB Validation Information Dictionary from v1.296 to 1.297.
Jul 18, 2018: Release v1.3.4
- Change check sum directory name from chk_sum_pdbx_valid to chk_sum_pdbml_valid.
- Add VRPT PDBML-alt, which is a lightweight version of VRPT PDBML by omitting PDBML-noatom content.
- Add PDB/validation-alt, which is a lightweight version of VRPT/RDF by omitting PDBML-noatom content.
- Add PostgreSQL data migration script for VRPT PDBML-alt.
- Add Virtuoso data upload script for VRPT/RDF-alt.
- Add PostgreSQL data migration script for PDBML-noatom.
Jul 10, 2018: Release v1.3.3
- Update wwPDB Validation Information Dictionary from v1.295 to 1.296.
- Change domain name of bulk download service (from bmrbpub.protein.osaka-u.ac.jp to bmrbpub.pdbj.org).
- Revise PostgreSQL data migration scripts.
Jun 13, 2018: Release v1.3.2
- Update wwPDB Validation Information Dictionary from v1.294 to 1.295.
May 23, 2018: Release v1.3.1
- Update wwPDB Validation Information Dictionary from v1.293 to 1.294.
May 11, 2018: Release v1.3.0
- More efficient update scripts using check sum.
- Fix PostgreSQL data migration scripts.
Apr 18, 2018: Release v1.2.3
- Update wwPDB Validation Information Dictionary from v1.292 to 1.293.
Apr 9, 2018: Release v1.2.2
- Add description of bulk download service of the alternative wwPDB validation reports.
Apr 5, 2018: Release v1.2.1
- Fix style sheet to handle null RSR value, null medoid model number.
- Enable differential XML Schema validation of compressed VRPT PDBML.
Mar 23, 2018: Release v1.2.0
- Update PostgreSQL data migration scripts, in which differential update is enabled.
- Update wwPDB Validation Information Dictionary from v1.291 to 1.292.
Mar 14, 2018: Release v1.1.0
- Added RDF uploader scripts, virtuoso_scripts.
- Update wwPDB Validation Information Dictionary from v0.290 to 1.291.
- Fix translation of _pdbx_dcc_map.LLDFZ from @ligRSRZ.
- Fix translation of _pdbx_dcc_map.LLDF from @ligRSRnbrMean.
Feb 20, 2018: Release v1.0.0
- Changed dictionary version from v0 to v1.
Feb 16, 2018: Release v0.1.0
- Revise VRPT PDBML Schema using xsd:minInclusive and xsd:maxExclusive without xsd:union.
- Fix VRPT/OWL lacking XSD data type definition.
- Add validate_all_gz.sh script to perform XML Schema validation of compressed VRPT PDBML.
Feb 15, 2018: Release v0.0.9
- Add ontology relationship between VRPT/OWL and PDBx ontology.
- Add ontology relationship between VRPT/OWL and BMRB/OWL.
- Update ontology mapping between PDBx/mmCIF and NMR-STAR data items.
- PDB mirror server is selectable from rsync.rcsb.org, ftp.pdbj.org, rsync.ebi.ac.uk based on network response.
Feb 13, 2018: Release v0.0.8
- Change directory: from pdbml-validtion to XML-validation, which contains compressed VRPT PDBML.
- Change directory: from rdf-validation to RDF-validation, which contains compressed VRPT/RDF.
- Add source URL in VRPT PDBML Schema pointing PDBx/mmCIF dictionary browser.
Feb 9, 2018: Release v0.0.7
- Add gzip compression scripts: compress_pdbml_validation.sh and compress_rdf_validation.sh
- Update wwPDB Validation Information Dictionary from v0.289 to 0.290.
Feb 8, 2018: Release v0.0.6
- Fix scripts: merge_pdbml_info_worker.sh and validate_all.sh
- Fix update_pdbml.sh and update_validation.sh scripts to support deleted or revised PDB entries.
- Add scripts: sync_delete_with_pdbml.sh and sync_delete_with_info.sh
Feb 7, 2018: Release v0.0.5
- Add null value check for pdbx_dcc_geometry.all_atom_clashscore data item.
Feb 6, 2018: Release v0.0.4
- Update wwPDB Validation Information Dictionary.
- Add null value check for pdbx_dcc_geometry.*_nmr_well_formed data items.
- Support @no-percentile-property="true" case for pdbx_percentile_entity_view.
- Reject multiple omega values for struct_mon_prot.omega since multi conformer occurs.
- Fix parser for @residue_string where negative auth_seq_id prevents delimitation such as "A:-1-A:-1".
- Fix parser for @atoms that involves null atom name such as "C5,,C6,", "C6,,N1,,C2,".
Feb 5, 2018: Release v0.0.3
- Update wwPDB Validation Information Dictionary.
- Update 'extract_info.xsl' style sheet which caused validation errors.
- Update 'run_test.sh' script which allows to add PDB IDs.
Feb 2, 2018: Release v0.0.2
- Change directory names and file extension of VRPT PDBML.
- Implement consistency checker about entry ID in XSL style sheet.
- Avoid XSLT error for entries used other experimental method such as NEUTRON DIFFRACTION.
- Add 'clean_all.sh' script.
- Append current PDBx Ontology (pdbx-v50.owl) in resource directory.
- Append PostgreSQL DDL for wwPDB validation (resource/wwpdb_validation_v002.sql) information and VRPT PDBML (schema/pdbx-validation-v0.sql).
- Add VRPT/OWL, ontology for VRPT/RDF.
- Add script 'scripts/translate_to_rdf.sh' for generation of VRPT/RDF.
Feb 1, 2018: Release v0.0.1
- Generate VRPT PDBML from PDBML-noatom and wwPDB Validation Information.

Name		Name	Last commit message	Last commit date
Latest commit History 1,056 Commits
oxigraph_scripts		oxigraph_scripts
resource		resource
schema		schema
scripts		scripts
stylesheet		stylesheet
test		test
virtuoso_scripts		virtuoso_scripts
wurcs2glytoucan		wurcs2glytoucan
LICENSE		LICENSE
NOTICE		NOTICE
README.md		README.md
clean_cc_all.sh		clean_cc_all.sh
clean_cc_test.sh		clean_cc_test.sh
clean_fam_all.sh		clean_fam_all.sh
clean_fam_test.sh		clean_fam_test.sh
clean_pdb_all.sh		clean_pdb_all.sh
clean_pdb_test.sh		clean_pdb_test.sh
clean_prd_all.sh		clean_prd_all.sh
clean_prd_test.sh		clean_prd_test.sh
clean_vrpt_all.sh		clean_vrpt_all.sh
clean_vrpt_test.sh		clean_vrpt_test.sh
run_cc_all.sh		run_cc_all.sh
run_cc_test.sh		run_cc_test.sh
run_cc_valid.sh		run_cc_valid.sh
run_fam_all.sh		run_fam_all.sh
run_fam_test.sh		run_fam_test.sh
run_fam_valid.sh		run_fam_valid.sh
run_pdb_all.sh		run_pdb_all.sh
run_pdb_test.sh		run_pdb_test.sh
run_pdb_valid.sh		run_pdb_valid.sh
run_prd_all.sh		run_prd_all.sh
run_prd_test.sh		run_prd_test.sh
run_prd_valid.sh		run_prd_valid.sh
run_vrpt_all.sh		run_vrpt_all.sh
run_vrpt_init.sh		run_vrpt_init.sh
run_vrpt_test.sh		run_vrpt_test.sh
run_vrpt_valid.sh		run_vrpt_valid.sh

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pdbx-validation

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