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 (mmCIF-validation and PDBML-validation), RDF version of validation reports (wwPDB/RDF-validation), and a series of ontologies; wwPDB Validation Information Dictionary, PDBML-validation Schema, and wwPDB/OWL-validation.
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To generate the alternative wwPDB validation report of some PDB entries,
./run_test.sh 5b1l 5u9b 5h0s ... -
To update the alternative wwPDB validation report of the entire PDB entry,
./run_all.sh -
Here is a map of the program.
| File path | Document |
|---|---|
| schema/mmcif_pdbx_validation_v2.dic | wwPDB Validation Information Dictionary (v2.331) |
| schema/pdbx-validation-v2.xsd | PDBML-validation Schema (v2.331) |
| schema/pdbx-validation-v2.owl | wwPDB/OWL-validation (v2.331) |
| schema/mmcif_ddl.dic | extended mmCIF DDL Core Dictionary (dubbed as v2.3.0) |
| resource/mmcif_pdbx_v50.dic | PDB Exchange Data Dictionary (v5.331) |
| resource/pdbx-v50.xsd | PDBML Schema (v5.331) |
| resource/pdbx-v50.owl | PDBx ontology, ontology for wwPDB/RDF (v5.331) |
| resource/wwpdb_validation_v004.xsd | XML Schema for wwPDB validation reports (v004, rev n/a) |
| scripts | a directory contains scripts invoked by the 'run_all.sh' script |
| virtuoso_scripts | a directory contains scripts for uploading wwPDB/RDF-validation 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 |
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PDB ID: 5B1L, Exptl. method: X-RAY DIFFRACTION
- PDBx/mmCIF format
- mmCIF-validation: 5b1l-validation-full.cif
- mmCIF-validation-alt: 5b1l-validation-alt.cif
- PDBML format
- PDBML-validation: 5b1l-validation-full.xml
- PDBML-validation-alt: 5b1l-validation-alt.xml
- wwPDB/RDF format
- wwPDB/RDF-validation: 5b1l-validation-full.rdf
- wwPDB/RDF-validation-alt: 5b1l-validation-alt.rdf
- wwPDB validation report (XML format)
- Original source: 5b1l_validation.xml
- Reverted from PDBML-validation: 5b1l_validation.xml
- Reverted from PDBML-validation-alt and PDBML-noatom: 5b1l_validation.xml
- PDBx/mmCIF format
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PDB ID: 5U9B, Exptl. method: SOLUTION NMR
- PDBx/mmCIF format
- mmCIF-validation: 5u9b-validation-full.cif
- mmCIF-validation-alt: 5u9b-validation-alt.cif
- PDBML format
- PDBML-validation: 5u9b-validation-full.xml
- PDBML-validation-alt: 5u9b-validation-alt.xml
- wwPDB/RDF format
- wwPDB/RDF-validation: 5u9b-validation-full.rdf
- wwPDB/RDF-validation-alt: 5u9b-validation-alt.rdf
- wwPDB validation report (XML format)
- Original source: 5u9b_validation.xml
- Reverted from PDBML-validation: 5u9b_validation.xml
- Reverted from PDBML-validation-alt and PDBML-noatom: 5u9b_validation.xml
- PDBx/mmCIF format
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PDB ID: 5H0S, Exptl. method: ELECTRON MICROSCOPY
- PDBx/mmCIF format
- mmCIF-validation: 5h0s-validation-full.cif
- mmCIF-validation-alt: 5h0s-validation-alt.cif
- PDBML format
- PDBML-validation: 5h0s-validation-full.xml
- PDBML-validation-alt: 5h0s-validation-alt.xml
- wwPDB/RDF format
- wwPDB/RDF-validation: 5h0s-validation-full.rdf
- wwPDB/RDF-validation-alt: 5h0s-validation-alt.rdf
- wwPDB validation report (XML format)
- Original source: 5h0s_validation.xml
- Reverted from PDBML-validation: 5h0s_validation.xml
- Reverted from PDBML-validation-alt and PDBML-noatom: 5h0s_validation.xml
- PDBx/mmCIF format
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PDB ID: 6RJH, Exptl. method: ELECTRON MICROSCOPY with EM map/model validation (v004)
- PDBx/mmCIF format
- mmCIF-validation: 6rjh-validation-full.cif
- mmCIF-validation-alt: 6rjh-validation-alt.cif
- PDBML format
- PDBML-validation: 6rjh-validation-full.xml
- PDBML-validation-alt: 6rjh-validation-alt.xml
- wwPDB/RDF format
- wwPDB/RDF-validation: 6rjh-validation-full.rdf
- wwPDB/RDF-validation-alt: 6rjh-validation-alt.rdf
- wwPDB validation report (XML format)
- Original source: 6rjh_validation.xml
- Reverted from PDBML-validation: 6rjh_validation.xml
- Reverted from PDBML-validation-alt and PDBML-noatom: 6rjh_validation.xml
- PDBx/mmCIF format
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Bulk download via HTTP protocol
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Bulk download via rsync protocol
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mmCIF-validation (full specification):
% rsync -av --delete rsync://bmrbpub.pdbj.org/mmcif-valid . -
mmCIF-validation-alt (lightweight version):
% rsync -av --delete rsync://bmrbpub.pdbj.org/mmcif-valid-alt . -
PDBML-validation (full specification):
% rsync -av --delete rsync://bmrbpub.pdbj.org/pdbml-valid . -
PDBML-validation-alt (lightweight version):
% rsync -av --delete rsync://bmrbpub.pdbj.org/pdbml-valid-alt . -
wwPDB/RDF-validation (full specification):
% rsync -av --delete rsync://bmrbpub.pdbj.org/wwpdb-rdf-valid . -
wwPDB/RDF-validation-alt (lightweight version):
% rsync -av --delete rsync://bmrbpub.pdbj.org/wwpdb-rdf-valid-alt .
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- Java 8 or later.
- Apache Maven (mvn), used to install external libraries.
- Git (git), used to install external libraries.
- mmCIF Dictionary Suite, optionally used to generate XML Schema from the wwPDB Validation Information Dictionary. (it is recommend to use mmCIF Dictionary Suite v2.250 instead of v2.300)
- 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 wwPDB/RDF-validation.
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Jul 22, 2020: Release v2.0.11
- Update wwPDB Validation Information Dictionary to 2.331
- Add resources for wwPDB/RDF
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Jul 13, 2020: Release v2.0.10
- Update wwPDB Validation Information Dictionary to 2.330
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Jun 24, 2020: Release v2.0.9
- Update wwPDB Validation Information Dictionary to 2.329
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Jun 23, 2020: Release v2.0.8
- Update wwPDB Validation Information Dictionary to 2.328
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Jun 23, 2020: Release v2.0.7
- Update wwPDB Validation Information Dictionary to 2.327
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May 29, 2020: Release v2.0.6
- Update wwPDB Validation Information Dictionary to 2.326 (incorpoate branch chain dictionary extension)
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May 26, 2020: Release v2.0.5
- Update wwPDB Validation Information Dictionary to 2.325.
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Mar 31, 2020: Release v2.0.4
- Update wwPDB Validation Information Dictionary to 2.324.
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Feb 10, 2020: Release v2.0.3
- Update wwPDB Validation Information Dictionary to 2.323.
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Feb 4, 2020: Release v2.0.2
- Update wwPDB Validation Information Dictionary to 2.322.
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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.
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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.
- Support XML Schema for wwPDB validation report (wwpdb_validation_v004.xsd).
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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.
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Nov 14, 2019: Release v1.6.4
- Update wwPDB Validation Information Dictionary from v1.318 to 1.319.
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Nov 5, 2019: Release v1.6.3
- Update wwPDB Validation Information Dictionary from v1.315 to 1.318.
- Update PostgreSQL DDLs.
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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'.
- Update wwPDB Validation Information Dictionary from v1.314 to 1.315.
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Aug 23, 2019: Release v1.6.1
- Update wwPDB Validation Information Dictionary from v1.313 to 1.314.
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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.
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Jun 3, 2019: Release v1.5.5
- Update wwPDB Validation Information Dictionary from v1.309 to 1.311.
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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.
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Apl 10, 2019: Release v1.5.3
- Update wwPDB Validation Information Dictionary from v1.306 to 1.307.
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Mar 19, 2019: Release v1.5.2
- Update wwPDB Validation Information Dictionary from v1.305 to 1.306.
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Feb 23, 2019: Release v1.5.1
- Rename 'revert_info.xsl' to 'revert_info_from_full.xsl'.
- Enable mutual transformation between PDBML-validation-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
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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 PDBML-validation and wwPDB Validation Reports (XML).
- Add 'revert_info.xsl' style sheet for the translation.
- Modify 'run_test.sh' script which include translation from PDBML-validation to wwPDB Validation Reports (XML).
- Update wwPDB Validation Information Dictionary from v1.303 to 1.305.
- Apply XML beautifier using xmllint command, if possible.
- Add/Revise the following data items in relation with wwPDB validation information XSD.
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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 PDBML-validation.
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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 wwPDB/RDF-validation form validation.rdf to validation-full.rdf.
- Add RDF syntax validation when Raptor RDF Syntax Library is available (rapper).
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Dec 4, 2018: Release v1.3.11
- Update wwPDB Validation Information Dictionary from v1.302 to 1.303.
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Nov 26, 2018: Release v1.3.10
- Update wwPDB Validation Information Dictionary from v1.301 to 1.302.
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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.
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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 PDBML-validation 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'.
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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.
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Aug 3, 2018: Release v1.3.6
- Update wwPDB Validation Information Dictionary from v1.297 to 1.298.
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Jul 24, 2018: Release v1.3.5
- Update wwPDB Validation Information Dictionary from v1.296 to 1.297.
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Jul 18, 2018: Release v1.3.4
- Change check sum directory name from chk_sum_pdbx_valid to chk_sum_pdbml_valid.
- Add PDBML-validation-alt, which is a lightweight version of PDBML-validation by omitting PDBML-noatom content.
- Add wwPDB/validation-alt, which is a lightweight version of wwPDB/RDF-validation by omitting PDBML-noatom content.
- Add PostgreSQL data migration script for PDBML-validation-alt.
- Add Virtuoso data upload script for wwPDB/RDF-validation-alt.
- Add PostgreSQL data migration script for PDBML-noatom.
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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.
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Jun 13, 2018: Release v1.3.2
- Update wwPDB Validation Information Dictionary from v1.294 to 1.295.
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May 23, 2018: Release v1.3.1
- Update wwPDB Validation Information Dictionary from v1.293 to 1.294.
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May 11, 2018: Release v1.3.0
- More efficient update scripts using check sum.
- Fix PostgreSQL data migration scripts.
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Apr 18, 2018: Release v1.2.3
- Update wwPDB Validation Information Dictionary from v1.292 to 1.293.
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Apr 9, 2018: Release v1.2.2
- Add description of bulk download service of the alternative wwPDB validation reports.
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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 PDBML-validation.
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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.
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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.
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Feb 20, 2018: Release v1.0.0
- Changed dictionary version from v0 to v1.
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Feb 16, 2018: Release v0.1.0
- Revise PDBML-validation Schema using xsd:minInclusive and xsd:maxExclusive without xsd:union.
- Fix wwPDB/OWL-validation lacking XSD data type definition.
- Add validate_all_gz.sh script to perform XML Schema validation of compressed PDBML-validation.
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Feb 15, 2018: Release v0.0.9
- Add ontology relationship between wwPDB/OWL-validation and PDBx ontology.
- Add ontology relationship between wwPDB/OWL-validation 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.
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Feb 13, 2018: Release v0.0.8
- Change directory: from pdbml-validtion to XML-validation, which contains compressed PDBML-validation.
- Change directory: from rdf-validation to RDF-validation, which contains compressed wwPDB/RDF-validation.
- Add source URL in PDBML-validation Schema pointing PDBx/mmCIF dictionary browser.
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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.
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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
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Feb 7, 2018: Release v0.0.5
- Add null value check for pdbx_dcc_geometry.all_atom_clashscore data item.
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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,".
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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.
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Feb 2, 2018: Release v0.0.2
- Change directory names and file extension of PDBML-validation.
- 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 PDBML-validation (schema/pdbx-validation-v0.sql).
- Add wwPDB/OWL-validation, ontology for wwPDB/RDF-validation.
- Add script 'scripts/translate_to_rdf.sh' for generation of wwPDB/RDF-validation.
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Feb 1, 2018: Release v0.0.1
- Generate PDBML-validation from PDBML-noatom and wwPDB Validation Information.