diff --git a/config-scripts/annotations/annotation_config.cpp b/config-scripts/annotations/annotation_config.cpp index 3cf5a80..f0e92f7 100644 --- a/config-scripts/annotations/annotation_config.cpp +++ b/config-scripts/annotations/annotation_config.cpp @@ -132,6 +132,44 @@ "url_pattern": "//WWW/Page_Asset/{{{MD5}}}.{{#encode}}{{{Filename}}}{{/encode}}" } }, +#if defined(dev) + { + "column": "Current_File_Holdings_URL", + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:isrd.isi.edu,2017:asset", + "value": { + "byte_count_column": "Current_File_Holdings_Bytes", + "filename_column": "Current_File_Holdings_Name", + "md5": "Current_File_Holdings_MD5", + "url_pattern": "//pdb/archive/holdings/{{{Current_File_Holdings_Name}}}" + } + }, + { + "column": "Released_Structures_LMD_URL", + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:isrd.isi.edu,2017:asset", + "value": { + "byte_count_column": "Released_Structures_LMD_Bytes", + "filename_column": "Released_Structures_LMD_Name", + "md5": "Released_Structures_LMD_MD5", + "url_pattern": "//pdb/archive/holdings/{{{Released_Structures_LMD_Name}}}" + } + }, + { + "column": "Unreleased_Entries_URL", + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:isrd.isi.edu,2017:asset", + "value": { + "byte_count_column": "Unreleased_Entries_Bytes", + "filename_column": "Unreleased_Entries_Name", + "md5": "Unreleased_Entries_MD5", + "url_pattern": "//pdb/archive/holdings/{{{Unreleased_Entries_Name}}}" + } + }, +#endif { "column": "Image_File_URL", "schema": "PDB", @@ -366,6 +404,100 @@ "uri": "tag:isrd.isi.edu,2018:required", "value": {} }, +#if defined(dev) + { + "column": "Archive_Category", + "schema": "Vocab", + "table": "System_Generated_File_Type", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Archive Category" + } + }, + { + "column": "Current_File_Holdings_URL", + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Current File Holdings" + } + }, + { + "column": "Released_Structures_LMD_URL", + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Released Structures LMD" + } + }, + { + "column": "Unreleased_Entries_URL", + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Unreleased Entries" + } + }, + { + "column": "Current_File_Holdings_MD5", + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Current File Holdings MD5" + } + }, + { + "column": "Unreleased_Entries_MD5", + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Unreleased Entries MD5" + } + }, + { + "column": "Released_Structures_LMD_MD5", + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Released Structures LMD MD5" + } + }, + { + "column": "mmCIF_URL", + "schema": "PDB", + "table": "Entry_Latest_Archive", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "mmCIF" + } + }, + { + "column": "mmCIF_URL", + "schema": "PDB", + "table": "Entry_Latest_Archive", + "uri": "tag:isrd.isi.edu,2016:column-display", + "value": { + "*": { + "markdown_pattern": "[{{Entry}}]({{#encode}}{{{mmCIF_URL}}}{{/encode}})" + } + } + }, + { + "column": "Released_Structures_LMD_Name", + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Released Structures LMD Name" + } + }, +#endif { "column": "pdbx_descriptor", "schema": "PDB", @@ -1521,6 +1653,21 @@ } } }, +#if defined(dev) + { + "schema": "PDB", + "table": "PDB_Archive", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "PDB Archive", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, +#endif { "schema": "PDB", "table": "ihm_localization_density_files", @@ -4467,12 +4614,194 @@ ] } }, +#if 1 + { + "schema": "PDB", + "table": "ihm_ordered_model", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Ordered Models", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_ordered_model", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_ordered_model_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment": "Model group id corresponding to the node at the origin of the directed edge", + "markdown_name": "Model Group Id Begin", + "source": [ + { + "outbound": [ + "PDB", + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "Model group id corresponding to the node at the end of the directed edge", + "markdown_name": "Model Group Id End", + "source": [ + { + "outbound": [ + "PDB", + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" + ] + }, + "RID" + ] + } + ], + "detailed": [ + "RID", + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_ordered_model_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment": "Model group id corresponding to the node at the origin of the directed edge", + "markdown_name": "Model Group Id Begin", + "source": [ + { + "outbound": [ + "PDB", + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "Model group id corresponding to the node at the end of the directed edge", + "markdown_name": "Model Group Id End", + "source": [ + { + "outbound": [ + "PDB", + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" + ] + }, + "RID" + ] + }, + [ + "PDB", + "ihm_ordered_model_RCB_fkey" + ], + [ + "PDB", + "ihm_ordered_model_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_ordered_model_Owner_fkey" + ] + ], + "entry": [ + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_ordered_model_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment": "Model group id corresponding to the node at the origin of the directed edge", + "markdown_name": "Model Group Id Begin", + "source": [ + { + "outbound": [ + "PDB", + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "Model group id corresponding to the node at the end of the directed edge", + "markdown_name": "Model Group Id End", + "source": [ + { + "outbound": [ + "PDB", + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" + ] + }, + "RID" + ] + } + ] + } + }, +#endif { "schema": "PDB", "table": "ihm_ordered_ensemble", "uri": "tag:misd.isi.edu,2015:display", "value": { - "name": "Ordered States", + "name": "Ordered Ensembles (to be deprecated and superseded by Ordered Models)", "comment_display": { "*": { "table_comment_display" : "inline" @@ -6063,6 +6392,10 @@ [ "PDB", "ihm_multi_state_model_group_link_state_id_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" ] ], "filter": "detailed" @@ -6197,6 +6530,18 @@ [ "PDB", "ihm_modeling_post_process_dataset_group_id_fkey" + ], + [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" ] ], "filter": "detailed" @@ -6878,476 +7223,1334 @@ ] } }, -#if 1 - { - "schema" : "PDB", - "table" : "entry", - "uri" : "tag:isrd.isi.edu,2019:export", - "value": { - "compact" : - { - "templates" : - [ - { - "displayname":"BDBag", - "type":"BAG", - "outputs": - [ - { - "source": - { - "api": "entity", - "table": "PDB:entry" - }, - "destination": - { - "name": "entry", - "type": "csv" - } - }, - { - "source": - { - "api": "attribute", - "path": "PDB:Entry_Generated_File/url:=File_URL" - }, - "destination": - { - "name": "Entry_Generated_File", - "type": "download" - } - } - ] - } - ] - } - } - }, -#endif +#if defined(dev) { "schema": "PDB", - "table": "entry", - "uri": "tag:isrd.isi.edu,2016:visible-foreign-keys", + "table": "PDB_Archive", + "uri": "tag:isrd.isi.edu,2016:visible-columns", "value": { + "*": [ + "RID", + "Submission_Time", + "Submitted_Entries", + "Current_File_Holdings_URL", + "Released_Structures_LMD_URL", + "Unreleased_Entries_URL", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "PDB", + "PDB_Archive_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "PDB", + "PDB_Archive_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT" + ], + "filter": { + "and": + [ + { + "markdown_name" : "Submission Date", + "source" : "Submission_Time" + }, + { + "markdown_name" : "Submitted Entries", + "source" : "Submitted_Entries" + } + ] + }, "detailed": [ - [ - "PDB", - "Entry_Generated_File_Structure_Id_fkey" - ], - [ - "PDB", - "struct_entry_id_fkey" - ], - [ - "PDB", - "audit_author_structure_id_fkey" - ], - [ - "PDB", - "citation_structure_id_fkey" - ], - [ - "PDB", - "citation_author_structure_id_fkey" - ], - [ - "PDB", - "software_structure_id_fkey" - ], - [ - "PDB", - "chem_comp_structure_id_fkey" - ], - [ - "PDB", - "entity_structure_id_fkey" - ], - [ - "PDB", - "entity_name_com_structure_id_fkey" - ], - [ - "PDB", - "entity_name_sys_structure_id_fkey" - ], - [ - "PDB", - "entity_src_gen_structure_id_fkey" - ], -#if 1 - [ - "PDB", - "struct_ref_structure_id_fkey" - ], - [ - "PDB", - "struct_ref_seq_structure_id_fkey" - ], - [ - "PDB", - "struct_ref_seq_dif_structure_id_fkey" - ], -#endif - [ - "PDB", - "entity_poly_structure_id_fkey" - ], - [ - "PDB", - "pdbx_entity_nonpoly_structure_id_fkey" - ], - [ - "PDB", - "entity_poly_seq_structure_id_fkey" - ], - [ - "PDB", - "atom_type_structure_id_fkey" - ], - [ - "PDB", - "struct_asym_structure_id_fkey" - ], - [ - "PDB", - "ihm_dataset_list_structure_id_fkey" - ], - [ - "PDB", - "ihm_dataset_group_structure_id_fkey" - ], - [ - "PDB", - "ihm_dataset_group_link_structure_id_fkey" - ], -#if 1 - [ - "PDB", - "ihm_data_transformation_structure_id_fkey" - ], -#endif - [ - "PDB", - "ihm_related_datasets_structure_id_fkey" - ], - [ - "PDB", - "ihm_dataset_related_db_reference_structure_id_fkey" - ], - [ - "PDB", - "ihm_external_reference_info_structure_id_fkey" - ], - [ - "PDB", - "ihm_external_files_structure_id_fkey" - ], - [ - "PDB", - "ihm_dataset_external_reference_structure_id_fkey" - ], - [ - "PDB", - "ihm_entity_poly_segment_structure_id_fkey" - ], - [ - "PDB", - "ihm_struct_assembly_structure_id_fkey" - ], - [ - "PDB", - "ihm_struct_assembly_details_structure_id_fkey" - ], - [ - "PDB", - "ihm_struct_assembly_class_structure_id_fkey" - ], - [ - "PDB", - "ihm_struct_assembly_class_link_structure_id_fkey" - ], - [ - "PDB", - "ihm_starting_model_details_structure_id_fkey" - ], - [ - "PDB", - "ihm_starting_comparative_models_structure_id_fkey" - ], - [ - "PDB", - "ihm_starting_computational_models_structure_id_fkey" - ], - [ - "PDB", - "ihm_starting_model_seq_dif_structure_id_fkey" - ], - [ - "PDB", - "ihm_model_representation_structure_id_fkey" - ], - [ - "PDB", - "ihm_model_representation_details_structure_id_fkey" + "RID", + "Submission_Time", + "Submitted_Entries", + "Current_File_Holdings_URL", + { + "markdown_name": "Current File Holdings Size (Bytes)", + "source": "Current_File_Holdings_Bytes" + }, + "Released_Structures_LMD_URL", + { + "markdown_name": "Released Structures LMD Size (Bytes)", + "source": "Released_Structures_LMD_Bytes" + }, + "Unreleased_Entries_URL", + { + "markdown_name": "Unreleased Entries Bytes Size (Bytes)", + "source": "Unreleased_Entries_Bytes" + }, + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "PDB", + "PDB_Archive_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "PDB", + "PDB_Archive_RMB_fkey" + ] + }, + "Full_Name" + ] + } + ], + "entry/edit": [ + "Submission_Time", + "Submitted_Entries", + "Current_File_Holdings_URL", + "Released_Structures_LMD_URL", + "Unreleased_Entries_URL" + ], + "entry": [ + "Submission_Time", + "Submitted_Entries", + "Current_File_Holdings_URL", + "Released_Structures_LMD_URL", + "Unreleased_Entries_URL" + ] + } + }, + { + "schema": "PDB", + "table": "Entry_Latest_Archive", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "RID" + ] + }, + { + "markdown_name" : "Archive", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Archive_Submission_Time_fkey" + ] + }, + "RID" + ] + }, + "mmCIF_URL", + { + "markdown_name" : "Accession Code", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "Accession_Code" + ] + }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "Workflow_Status" + ] + }, + "Submitted_Files", + "Submission_Time", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT" + ], + "filter": { + "and": + [ + { + "markdown_name" : "Submission Date", + "source" : "Submission_Time" + } + ] + }, + "detailed": [ + "RID", + "Submission_Time", + { + "markdown_name" : "Accession Code", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "Accession_Code" + ] + }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "Workflow_Status" + ] + }, + "Submitted_Files", + "mmCIF_URL", + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "RID" + ] + }, + { + "markdown_name" : "Archive", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Archive_Submission_Time_fkey" + ] + }, + "RID" + ] + }, + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_RMB_fkey" + ] + }, + "Full_Name" + ] + } + ], + "entry/edit": [ + "Submission_Time", + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "RID" + ] + }, + { + "markdown_name" : "Archive", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Archive_Submission_Time_fkey" + ] + }, + "RID" + ] + } + ], + "entry": [ + "Submission_Time", + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "RID" + ] + }, + { + "markdown_name" : "Archive", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Archive_Submission_Time_fkey" + ] + }, + "RID" + ] + } + ] + } + }, +#endif +#if 1 + { + "schema" : "PDB", + "table" : "entry", + "uri" : "tag:isrd.isi.edu,2019:export", + "value": { + "compact" : + { + "templates" : + [ + { + "displayname":"BDBag", + "type":"BAG", + "outputs": + [ + { + "source": + { + "api": "entity", + "table": "PDB:entry" + }, + "destination": + { + "name": "entry", + "type": "csv" + } + }, + { + "source": + { + "api": "attribute", + "path": "PDB:Entry_Generated_File/url:=File_URL" + }, + "destination": + { + "name": "Entry_Generated_File", + "type": "download" + } + } + ] + } + ] + } + } + }, +#endif + { + "schema": "PDB", + "table": "entry", + "uri": "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value": { + "detailed": [ + [ + "PDB", + "Entry_Generated_File_Structure_Id_fkey" + ], + [ + "PDB", + "struct_entry_id_fkey" + ], + [ + "PDB", + "audit_author_structure_id_fkey" + ], + [ + "PDB", + "citation_structure_id_fkey" + ], + [ + "PDB", + "citation_author_structure_id_fkey" + ], + [ + "PDB", + "software_structure_id_fkey" + ], + [ + "PDB", + "chem_comp_structure_id_fkey" + ], + [ + "PDB", + "entity_structure_id_fkey" + ], + [ + "PDB", + "entity_name_com_structure_id_fkey" + ], + [ + "PDB", + "entity_name_sys_structure_id_fkey" + ], + [ + "PDB", + "entity_src_gen_structure_id_fkey" + ], +#if 1 + [ + "PDB", + "struct_ref_structure_id_fkey" + ], + [ + "PDB", + "struct_ref_seq_structure_id_fkey" + ], + [ + "PDB", + "struct_ref_seq_dif_structure_id_fkey" + ], +#endif + [ + "PDB", + "entity_poly_structure_id_fkey" + ], + [ + "PDB", + "pdbx_entity_nonpoly_structure_id_fkey" + ], + [ + "PDB", + "entity_poly_seq_structure_id_fkey" + ], + [ + "PDB", + "atom_type_structure_id_fkey" + ], + [ + "PDB", + "struct_asym_structure_id_fkey" + ], + [ + "PDB", + "ihm_dataset_list_structure_id_fkey" + ], + [ + "PDB", + "ihm_dataset_group_structure_id_fkey" + ], + [ + "PDB", + "ihm_dataset_group_link_structure_id_fkey" + ], +#if 1 + [ + "PDB", + "ihm_data_transformation_structure_id_fkey" + ], +#endif + [ + "PDB", + "ihm_related_datasets_structure_id_fkey" + ], + [ + "PDB", + "ihm_dataset_related_db_reference_structure_id_fkey" + ], + [ + "PDB", + "ihm_external_reference_info_structure_id_fkey" + ], + [ + "PDB", + "ihm_external_files_structure_id_fkey" + ], + [ + "PDB", + "ihm_dataset_external_reference_structure_id_fkey" + ], + [ + "PDB", + "ihm_entity_poly_segment_structure_id_fkey" + ], + [ + "PDB", + "ihm_struct_assembly_structure_id_fkey" + ], + [ + "PDB", + "ihm_struct_assembly_details_structure_id_fkey" + ], + [ + "PDB", + "ihm_struct_assembly_class_structure_id_fkey" + ], + [ + "PDB", + "ihm_struct_assembly_class_link_structure_id_fkey" + ], + [ + "PDB", + "ihm_starting_model_details_structure_id_fkey" + ], + [ + "PDB", + "ihm_starting_comparative_models_structure_id_fkey" + ], + [ + "PDB", + "ihm_starting_computational_models_structure_id_fkey" + ], + [ + "PDB", + "ihm_starting_model_seq_dif_structure_id_fkey" + ], + [ + "PDB", + "ihm_model_representation_structure_id_fkey" + ], + [ + "PDB", + "ihm_model_representation_details_structure_id_fkey" + ], + [ + "PDB", + "ihm_modeling_protocol_structure_id_fkey" + ], + [ + "PDB", + "ihm_modeling_protocol_details_structure_id_fkey" + ], + [ + "PDB", + "ihm_modeling_post_process_structure_id_fkey" + ], + [ + "PDB", + "ihm_model_list_structure_id_fkey" + ], + [ + "PDB", + "ihm_model_group_structure_id_fkey" + ], + [ + "PDB", + "ihm_model_group_link_structure_id_fkey" + ], + [ + "PDB", + "ihm_model_representative_structure_id_fkey" + ], + [ + "PDB", + "ihm_residues_not_modeled_structure_id_fkey" + ], + [ + "PDB", + "ihm_multi_state_modeling_structure_id_fkey" + ], + [ + "PDB", + "ihm_multi_state_model_group_link_structure_id_fkey" + ], + [ + "PDB", + "ihm_ordered_model_structure_id_fkey" + ], + [ + "PDB", + "ihm_ordered_ensemble_structure_id_fkey" + ], + [ + "PDB", + "ihm_ensemble_info_structure_id_fkey" + ], +#if 1 + [ + "PDB", + "ihm_ensemble_sub_sample_structure_id_fkey" + ], +#endif + [ + "PDB", + "ihm_localization_density_files_structure_id_fkey" + ], + [ + "PDB", + "ihm_2dem_class_average_restraint_structure_id_fkey" + ], + [ + "PDB", + "ihm_2dem_class_average_fitting_structure_id_fkey" + ], + [ + "PDB", + "ihm_3dem_restraint_structure_id_fkey" + ], + [ + "PDB", + "ihm_sas_restraint_structure_id_fkey" + ], + [ + "PDB", + "ihm_epr_restraint_structure_id_fkey" + ], + [ + "PDB", + "ihm_chemical_component_descriptor_structure_id_fkey" + ], + [ + "PDB", + "ihm_probe_list_structure_id_fkey" + ], + [ + "PDB", + "ihm_poly_probe_position_structure_id_fkey" + ], + [ + "PDB", + "ihm_poly_probe_conjugate_structure_id_fkey" + ], + [ + "PDB", + "ihm_ligand_probe_structure_id_fkey" + ], + [ + "PDB", + "ihm_geometric_object_list_structure_id_fkey" + ], + [ + "PDB", + "ihm_geometric_object_center_structure_id_fkey" + ], + [ + "PDB", + "ihm_geometric_object_transformation_structure_id_fkey" + ], + [ + "PDB", + "ihm_geometric_object_sphere_structure_id_fkey" + ], + [ + "PDB", + "ihm_geometric_object_torus_structure_id_fkey" + ], + [ + "PDB", + "ihm_geometric_object_half_torus_structure_id_fkey" + ], + [ + "PDB", + "ihm_geometric_object_axis_structure_id_fkey" + ], + [ + "PDB", + "ihm_geometric_object_plane_structure_id_fkey" + ], + [ + "PDB", + "Entry_Related_File_entry_id_fkey" + ], +#if 1 + [ + "PDB", + "ihm_pseudo_site_structure_id_fkey" + ], +#endif + [ + "PDB", + "ihm_cross_link_list_structure_id_fkey" + ], + [ + "PDB", + "ihm_cross_link_restraint_structure_id_fkey" + ], +#if 1 + [ + "PDB", + "ihm_cross_link_pseudo_site_structure_id_fkey" + ], +#endif + [ + "PDB", + "ihm_cross_link_result_structure_id_fkey" + ], + [ + "PDB", + "ihm_cross_link_result_parameters_structure_id_fkey" + ], + [ + "PDB", + "ihm_predicted_contact_restraint_structure_id_fkey" + ], + [ + "PDB", + "ihm_hydroxyl_radical_fp_restraint_structure_id_fkey" + ], +#if 1 + [ + "PDB", + "ihm_hdx_restraint_structure_id_fkey" ], +#endif [ "PDB", - "ihm_modeling_protocol_structure_id_fkey" + "ihm_feature_list_structure_id_fkey" ], [ "PDB", - "ihm_modeling_protocol_details_structure_id_fkey" + "ihm_poly_atom_feature_structure_id_fkey" ], [ "PDB", - "ihm_modeling_post_process_structure_id_fkey" + "ihm_poly_residue_feature_structure_id_fkey" ], [ "PDB", - "ihm_model_list_structure_id_fkey" + "ihm_non_poly_feature_structure_id_fkey" ], [ "PDB", - "ihm_model_group_structure_id_fkey" + "ihm_interface_residue_feature_structure_id_fkey" ], [ "PDB", - "ihm_model_group_link_structure_id_fkey" + "ihm_pseudo_site_feature_structure_id_fkey" ], [ "PDB", - "ihm_model_representative_structure_id_fkey" + "ihm_derived_distance_restraint_structure_id_fkey" ], +#if 1 [ "PDB", - "ihm_residues_not_modeled_structure_id_fkey" + "ihm_derived_angle_restraint_structure_id_fkey" ], [ "PDB", - "ihm_multi_state_modeling_structure_id_fkey" + "ihm_derived_dihedral_restraint_structure_id_fkey" ], +#endif [ "PDB", - "ihm_multi_state_model_group_link_structure_id_fkey" + "ihm_geometric_object_distance_restraint_structure_id_fkey" ], [ "PDB", - "ihm_ordered_ensemble_structure_id_fkey" + "ihm_multi_state_scheme_structure_id_fkey" ], [ "PDB", - "ihm_ensemble_info_structure_id_fkey" + "ihm_multi_state_scheme_connectivity_structure_id_fkey" ], -#if 1 [ "PDB", - "ihm_ensemble_sub_sample_structure_id_fkey" + "ihm_kinetic_rate_structure_id_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" ], +#if 1 + { + "comment": "Collections to which the entry belongs", + "markdown_name": "Entry Collections", + "source": [ + { + "inbound": [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + { + "outbound": [ + "PDB", + "ihm_entry_collection_mapping_collection_id_fkey" + ] + }, + "RID" + ] + }, #endif + { + "markdown_name": "Curation Log", + "source": [ + { + "inbound": [ + "PDB", + "Curation_Log_Entry_fkey" + ] + }, + "RID" + ] + }, [ "PDB", - "ihm_localization_density_files_structure_id_fkey" + "audit_conform_structure_id_fkey" ], [ "PDB", - "ihm_2dem_class_average_restraint_structure_id_fkey" + "pdbx_entity_poly_na_type_structure_id_fkey" + ] + ], + "filter": "detailed" + } + }, + { + "schema": "PDB", + "table": "ihm_interface_residue_feature", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Molecular Features - Interface Residues", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_interface_residue_feature", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_structure_id_fkey" + ] + }, + "RID" + ] + }, + "ordinal_id", + { + "comment": "A reference to table ihm_feature_list.feature_id.", + "markdown_name": "Feature Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_feature_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to table entity.id.", + "markdown_name": "Binding Partner Entity Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_binding_partner_entity_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to table struct_asym.id.", + "markdown_name": "Binding Partner Asym Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_binding_partner_asym_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to table ihm_dataset_list.id.", + "markdown_name": "Dataset List Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_dataset_list_id_fkey" + ] + }, + "RID" + ] + }, + "details", + { + "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", + "markdown_name": "Uploaded Restraint File", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_Entry_Related_File_fkey" + ] + }, + "RID" + ] + } + ], + "detailed": [ + "RID", + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_structure_id_fkey" + ] + }, + "RID" + ] + }, + "ordinal_id", + { + "comment": "A reference to table ihm_feature_list.feature_id.", + "markdown_name": "Feature Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_feature_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to table entity.id.", + "markdown_name": "Binding Partner Entity Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_binding_partner_entity_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to table struct_asym.id.", + "markdown_name": "Binding Partner Asym Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_binding_partner_asym_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to table ihm_dataset_list.id.", + "markdown_name": "Dataset List Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_dataset_list_id_fkey" + ] + }, + "RID" + ] + }, + "details", + { + "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", + "markdown_name": "Uploaded Restraint File", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_Entry_Related_File_fkey" + ] + }, + "RID" + ] + }, + [ + "PDB", + "ihm_interface_residue_feature_RCB_fkey" ], [ "PDB", - "ihm_2dem_class_average_fitting_structure_id_fkey" + "ihm_interface_residue_feature_RMB_fkey" ], + "RCT", + "RMT", [ "PDB", - "ihm_3dem_restraint_structure_id_fkey" - ], + "ihm_interface_residue_feature_Owner_fkey" + ] + ], + "entry": [ + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_structure_id_fkey" + ] + }, + "RID" + ] + }, + "ordinal_id", + { + "comment": "A reference to table ihm_feature_list.feature_id.", + "markdown_name": "Feature Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_feature_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to table entity.id.", + "markdown_name": "Binding Partner Entity Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_binding_partner_entity_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to table struct_asym.id.", + "markdown_name": "Binding Partner Asym Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_binding_partner_asym_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to table ihm_dataset_list.id.", + "markdown_name": "Dataset List Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_interface_residue_feature_dataset_list_id_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema": "PDB", + "table": "ihm_dataset_list", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "markdown_name": "Input Datasets^*^", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_dataset_list", + "uri": "tag:isrd.isi.edu,2016:table-display", + "value": { + "row_name": { + "row_markdown_pattern": "{{{id}}}" + } + } + }, + { + "schema": "PDB", + "table": "ihm_dataset_list", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_dataset_list_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", [ "PDB", - "ihm_sas_restraint_structure_id_fkey" + "ihm_dataset_list_data_type_fkey" ], [ "PDB", - "ihm_epr_restraint_structure_id_fkey" + "ihm_dataset_list_database_hosted_fkey" ], + "details" + ], + "detailed": [ + "RID", + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_dataset_list_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", [ "PDB", - "ihm_chemical_component_descriptor_structure_id_fkey" + "ihm_dataset_list_data_type_fkey" ], [ "PDB", - "ihm_probe_list_structure_id_fkey" + "ihm_dataset_list_database_hosted_fkey" ], + "details", [ "PDB", - "ihm_poly_probe_position_structure_id_fkey" + "ihm_dataset_list_RCB_fkey" ], [ "PDB", - "ihm_poly_probe_conjugate_structure_id_fkey" + "ihm_dataset_list_RMB_fkey" ], + "RCT", + "RMT", [ "PDB", - "ihm_ligand_probe_structure_id_fkey" - ], + "ihm_dataset_list_Owner_fkey" + ] + ], + "entry": [ + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_dataset_list_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", [ "PDB", - "ihm_geometric_object_list_structure_id_fkey" + "ihm_dataset_list_data_type_fkey" ], [ "PDB", - "ihm_geometric_object_center_structure_id_fkey" + "ihm_dataset_list_database_hosted_fkey" ], + "details" + ] + } + }, + { + "schema": "PDB", + "table": "ihm_dataset_list", + "uri": "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value": { + "detailed": [ [ "PDB", - "ihm_geometric_object_transformation_structure_id_fkey" + "ihm_dataset_group_link_dataset_list_id_fkey" ], [ "PDB", - "ihm_geometric_object_sphere_structure_id_fkey" + "ihm_dataset_related_db_reference_dataset_list_id_fkey" ], [ "PDB", - "ihm_geometric_object_torus_structure_id_fkey" + "ihm_dataset_external_reference_dataset_list_id_fkey" ], [ "PDB", - "ihm_geometric_object_half_torus_structure_id_fkey" + "ihm_related_datasets_dataset_list_id_derived_fkey" ], [ "PDB", - "ihm_geometric_object_axis_structure_id_fkey" + "ihm_related_datasets_dataset_list_id_primary_fkey" ], [ "PDB", - "ihm_geometric_object_plane_structure_id_fkey" + "ihm_starting_model_details_dataset_list_id_fkey" ], [ "PDB", - "Entry_Related_File_entry_id_fkey" + "ihm_starting_comparative_models_template_dataset_list_id_fkey" ], -#if 1 [ "PDB", - "ihm_pseudo_site_structure_id_fkey" + "ihm_poly_probe_conjugate_dataset_list_id_fkey" ], -#endif [ "PDB", - "ihm_cross_link_list_structure_id_fkey" + "ihm_ligand_probe_dataset_list_id_fkey" ], [ "PDB", - "ihm_cross_link_restraint_structure_id_fkey" + "ihm_cross_link_list_dataset_list_id_fkey" ], -#if 1 [ "PDB", - "ihm_cross_link_pseudo_site_structure_id_fkey" + "ihm_2dem_class_average_restraint_dataset_list_id_fkey" ], -#endif [ "PDB", - "ihm_cross_link_result_structure_id_fkey" + "ihm_3dem_restraint_dataset_list_id_fkey" ], [ "PDB", - "ihm_cross_link_result_parameters_structure_id_fkey" + "ihm_sas_restraint_dataset_list_id_fkey" ], [ "PDB", - "ihm_predicted_contact_restraint_structure_id_fkey" + "ihm_epr_restraint_dataset_list_id_fkey" ], +#if 1 [ "PDB", - "ihm_hydroxyl_radical_fp_restraint_structure_id_fkey" - ], -#if 1 - [ - "PDB", - "ihm_hdx_restraint_structure_id_fkey" + "ihm_hdx_restraint_ihm_dataset_list_combo1_fkey" ], #endif [ "PDB", - "ihm_feature_list_structure_id_fkey" - ], - [ - "PDB", - "ihm_poly_atom_feature_structure_id_fkey" - ], - [ - "PDB", - "ihm_poly_residue_feature_structure_id_fkey" - ], - [ - "PDB", - "ihm_non_poly_feature_structure_id_fkey" - ], - [ - "PDB", - "ihm_interface_residue_feature_structure_id_fkey" - ], - [ - "PDB", - "ihm_pseudo_site_feature_structure_id_fkey" + "ihm_hydroxyl_radical_fp_restraint_dataset_list_id_fkey" ], [ "PDB", - "ihm_derived_distance_restraint_structure_id_fkey" + "ihm_predicted_contact_restraint_dataset_list_id_fkey" ], -#if 1 [ "PDB", - "ihm_derived_angle_restraint_structure_id_fkey" + "ihm_interface_residue_feature_dataset_list_id_fkey" ], [ "PDB", - "ihm_derived_dihedral_restraint_structure_id_fkey" + "ihm_derived_distance_restraint_dataset_list_id_fkey" ], -#endif +#if 1 [ "PDB", - "ihm_geometric_object_distance_restraint_structure_id_fkey" + "ihm_derived_angle_restraint_ihm_dataset_list_combo1_fkey" ], -#if 1 - { - "comment": "Collections to which the entry belongs", - "markdown_name": "Entry Collections", - "source": [ - { - "inbound": [ - "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" - ] - }, - { - "outbound": [ - "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" - ] - }, - "RID" - ] - }, -#endif - { - "markdown_name": "Curation Log", - "source": [ - { - "inbound": [ - "PDB", - "Curation_Log_Entry_fkey" - ] - }, - "RID" - ] - }, [ "PDB", - "audit_conform_structure_id_fkey" + "ihm_derived_dihedral_restraint_ihm_dataset_list_combo1_fkey" ], +#endif [ "PDB", - "pdbx_entity_poly_na_type_structure_id_fkey" + "ihm_geometric_object_distance_restraint_dataset_list_id_fkey" ] ], "filter": "detailed" @@ -7355,10 +8558,10 @@ }, { "schema": "PDB", - "table": "ihm_interface_residue_feature", + "table": "audit_author", "uri": "tag:misd.isi.edu,2015:display", "value": { - "name": "Molecular Features - Interface Residues", + "markdown_name": "Authors^*^", "comment_display": { "*": { "table_comment_display" : "inline" @@ -7368,7 +8571,7 @@ }, { "schema": "PDB", - "table": "ihm_interface_residue_feature", + "table": "audit_author", "uri": "tag:isrd.isi.edu,2016:visible-columns", "value": { "*": [ @@ -7380,74 +8583,124 @@ { "outbound": [ "PDB", - "ihm_interface_residue_feature_structure_id_fkey" + "audit_author_structure_id_fkey" ] }, "RID" ] }, - "ordinal_id", + "pdbx_ordinal", + "name" + ], + "detailed": [ + "RID", { - "comment": "A reference to table ihm_feature_list.feature_id.", - "markdown_name": "Feature Id", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_feature_id_fkey" + "audit_author_structure_id_fkey" ] }, "RID" ] }, + "pdbx_ordinal", + "name", + [ + "PDB", + "audit_author_RCB_fkey" + ], + [ + "PDB", + "audit_author_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "audit_author_Owner_fkey" + ] + ], + "entry": [ { - "comment": "A reference to table entity.id.", - "markdown_name": "Binding Partner Entity Id", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_binding_partner_entity_id_fkey" + "audit_author_structure_id_fkey" ] }, "RID" ] }, + "pdbx_ordinal", + "name" + ] + } + }, + { + "schema": "PDB", + "table": "ihm_geometric_object_plane", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Plane Geometric Objects", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_geometric_object_plane", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", { - "comment": "A reference to table struct_asym.id.", - "markdown_name": "Binding Partner Asym Id", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_binding_partner_asym_id_fkey" + "ihm_geometric_object_plane_structure_id_fkey" ] }, "RID" ] }, { - "comment": "A reference to table ihm_dataset_list.id.", - "markdown_name": "Dataset List Id", + "comment": "A reference to table ihm_geometric_object_list.object_id.", + "markdown_name": "Object Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_dataset_list_id_fkey" + "ihm_geometric_object_plane_object_id_fkey" ] }, "RID" ] }, - "details", + [ + "PDB", + "ihm_geometric_object_plane_plane_type_fkey" + ], { - "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", - "markdown_name": "Uploaded Restraint File", + "comment": "A reference to table ihm_geometric_object_transformation.id.", + "markdown_name": "Transformation Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_Entry_Related_File_fkey" + "ihm_geometric_object_plane_transformation_id_fkey" ] }, "RID" @@ -7463,74 +8716,79 @@ { "outbound": [ "PDB", - "ihm_interface_residue_feature_structure_id_fkey" - ] - }, - "RID" - ] - }, - "ordinal_id", - { - "comment": "A reference to table ihm_feature_list.feature_id.", - "markdown_name": "Feature Id", - "source": [ - { - "outbound": [ - "PDB", - "ihm_interface_residue_feature_feature_id_fkey" + "ihm_geometric_object_plane_structure_id_fkey" ] }, "RID" ] }, { - "comment": "A reference to table entity.id.", - "markdown_name": "Binding Partner Entity Id", + "comment": "A reference to table ihm_geometric_object_list.object_id.", + "markdown_name": "Object Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_binding_partner_entity_id_fkey" + "ihm_geometric_object_plane_object_id_fkey" ] }, "RID" ] }, + [ + "PDB", + "ihm_geometric_object_plane_plane_type_fkey" + ], { - "comment": "A reference to table struct_asym.id.", - "markdown_name": "Binding Partner Asym Id", + "comment": "A reference to table ihm_geometric_object_transformation.id.", + "markdown_name": "Transformation Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_binding_partner_asym_id_fkey" + "ihm_geometric_object_plane_transformation_id_fkey" ] }, "RID" ] }, + [ + "PDB", + "ihm_geometric_object_plane_RCB_fkey" + ], + [ + "PDB", + "ihm_geometric_object_plane_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_geometric_object_plane_Owner_fkey" + ] + ], + "entry": [ { - "comment": "A reference to table ihm_dataset_list.id.", - "markdown_name": "Dataset List Id", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_dataset_list_id_fkey" + "ihm_geometric_object_plane_structure_id_fkey" ] }, "RID" ] }, - "details", { - "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", - "markdown_name": "Uploaded Restraint File", + "comment": "A reference to table ihm_geometric_object_list.object_id.", + "markdown_name": "Object Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_Entry_Related_File_fkey" + "ihm_geometric_object_plane_object_id_fkey" ] }, "RID" @@ -7538,458 +8796,244 @@ }, [ "PDB", - "ihm_interface_residue_feature_RCB_fkey" - ], - [ - "PDB", - "ihm_interface_residue_feature_RMB_fkey" + "ihm_geometric_object_plane_plane_type_fkey" ], - "RCT", - "RMT", - [ - "PDB", - "ihm_interface_residue_feature_Owner_fkey" - ] - ], - "entry": [ { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table ihm_geometric_object_transformation.id.", + "markdown_name": "Transformation Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_structure_id_fkey" + "ihm_geometric_object_plane_transformation_id_fkey" ] }, "RID" ] - }, - "ordinal_id", + } + ] + } + }, + { + "schema": "PDB", + "table": "ihm_predicted_contact_restraint", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Predicted Contact Restraints", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_predicted_contact_restraint", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", { - "comment": "A reference to table ihm_feature_list.feature_id.", - "markdown_name": "Feature Id", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_feature_id_fkey" + "ihm_predicted_contact_restraint_structure_id_fkey" ] }, "RID" ] }, + "id", + "group_id", + "entity_description_1", { - "comment": "A reference to table entity.id.", - "markdown_name": "Binding Partner Entity Id", + "comment": "A reference to table entity_poly_seq.entity_id.", + "markdown_name": "Entity Id 1", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_binding_partner_entity_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" ] }, - "RID" + "entity_id" ] }, { "comment": "A reference to table struct_asym.id.", - "markdown_name": "Binding Partner Asym Id", + "markdown_name": "Asym Id 1", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_binding_partner_asym_id_fkey" + "ihm_predicted_contact_restraint_asym_id_1_fkey" ] }, "RID" ] }, { - "comment": "A reference to table ihm_dataset_list.id.", - "markdown_name": "Dataset List Id", + "comment": "A reference to table entity_poly_seq.mon_id", + "markdown_name": "Component Id 1", "source": [ { "outbound": [ "PDB", - "ihm_interface_residue_feature_dataset_list_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" ] }, - "RID" + "mon_id" ] }, - "details" - ] - } - }, - { - "schema": "PDB", - "table": "ihm_dataset_list", - "uri": "tag:misd.isi.edu,2015:display", - "value": { - "markdown_name": "Input Datasets^*^", - "comment_display": { - "*": { - "table_comment_display" : "inline" - } - } - } - }, - { - "schema": "PDB", - "table": "ihm_dataset_list", - "uri": "tag:isrd.isi.edu,2016:table-display", - "value": { - "row_name": { - "row_markdown_pattern": "{{{id}}}" - } - } - }, - { - "schema": "PDB", - "table": "ihm_dataset_list", - "uri": "tag:isrd.isi.edu,2016:visible-columns", - "value": { - "*": [ - "RID", { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table entity_poly_seq.num", + "markdown_name": "Sequence Id 1", "source": [ { "outbound": [ "PDB", - "ihm_dataset_list_structure_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" ] }, - "RID" + "num" ] }, - "id", - [ - "PDB", - "ihm_dataset_list_data_type_fkey" - ], [ "PDB", - "ihm_dataset_list_database_hosted_fkey" + "ihm_predicted_contact_restraint_rep_atom_1_fkey" ], - "details" - ], - "detailed": [ - "RID", + "entity_description_2", { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table entity_poly_seq.entity_id", + "markdown_name": "Entity Id 2", "source": [ { "outbound": [ "PDB", - "ihm_dataset_list_structure_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" ] }, - "RID" + "entity_id" ] }, - "id", - [ - "PDB", - "ihm_dataset_list_data_type_fkey" - ], - [ - "PDB", - "ihm_dataset_list_database_hosted_fkey" - ], - "details", - [ - "PDB", - "ihm_dataset_list_RCB_fkey" - ], - [ - "PDB", - "ihm_dataset_list_RMB_fkey" - ], - "RCT", - "RMT", - [ - "PDB", - "ihm_dataset_list_Owner_fkey" - ] - ], - "entry": [ { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table struct_asym.id.", + "markdown_name": "Asym Id 2", "source": [ { "outbound": [ "PDB", - "ihm_dataset_list_structure_id_fkey" + "ihm_predicted_contact_restraint_asym_id_2_fkey" ] - }, - "RID" - ] - }, - "id", - [ - "PDB", - "ihm_dataset_list_data_type_fkey" - ], - [ - "PDB", - "ihm_dataset_list_database_hosted_fkey" - ], - "details" - ] - } - }, - { - "schema": "PDB", - "table": "ihm_dataset_list", - "uri": "tag:isrd.isi.edu,2016:visible-foreign-keys", - "value": { - "detailed": [ - [ - "PDB", - "ihm_dataset_group_link_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_dataset_related_db_reference_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_dataset_external_reference_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_related_datasets_dataset_list_id_derived_fkey" - ], - [ - "PDB", - "ihm_related_datasets_dataset_list_id_primary_fkey" - ], - [ - "PDB", - "ihm_starting_model_details_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_starting_comparative_models_template_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_poly_probe_conjugate_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_ligand_probe_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_cross_link_list_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_2dem_class_average_restraint_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_3dem_restraint_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_sas_restraint_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_epr_restraint_dataset_list_id_fkey" - ], -#if 1 - [ - "PDB", - "ihm_hdx_restraint_ihm_dataset_list_combo1_fkey" - ], -#endif - [ - "PDB", - "ihm_hydroxyl_radical_fp_restraint_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_predicted_contact_restraint_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_interface_residue_feature_dataset_list_id_fkey" - ], - [ - "PDB", - "ihm_derived_distance_restraint_dataset_list_id_fkey" - ], -#if 1 - [ - "PDB", - "ihm_derived_angle_restraint_ihm_dataset_list_combo1_fkey" - ], - [ - "PDB", - "ihm_derived_dihedral_restraint_ihm_dataset_list_combo1_fkey" - ], -#endif - [ - "PDB", - "ihm_geometric_object_distance_restraint_dataset_list_id_fkey" - ] - ], - "filter": "detailed" - } - }, - { - "schema": "PDB", - "table": "audit_author", - "uri": "tag:misd.isi.edu,2015:display", - "value": { - "markdown_name": "Authors^*^", - "comment_display": { - "*": { - "table_comment_display" : "inline" - } - } - } - }, - { - "schema": "PDB", - "table": "audit_author", - "uri": "tag:isrd.isi.edu,2016:visible-columns", - "value": { - "*": [ - "RID", + }, + "RID" + ] + }, { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table entity_poly_seq.mon_id", + "markdown_name": "Component Id 2", "source": [ { "outbound": [ "PDB", - "audit_author_structure_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" ] }, - "RID" + "mon_id" ] }, - "pdbx_ordinal", - "name" - ], - "detailed": [ - "RID", { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table entity_poly_seq.num", + "markdown_name": "Sequence Id 2", "source": [ { "outbound": [ "PDB", - "audit_author_structure_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" ] }, - "RID" + "num" ] }, - "pdbx_ordinal", - "name", [ "PDB", - "audit_author_RCB_fkey" + "ihm_predicted_contact_restraint_rep_atom_2_fkey" ], [ "PDB", - "audit_author_RMB_fkey" + "ihm_predicted_contact_restraint_restraint_type_fkey" ], - "RCT", - "RMT", + "distance_lower_limit", + "distance_upper_limit", + "probability", [ "PDB", - "audit_author_Owner_fkey" - ] - ], - "entry": [ + "ihm_predicted_contact_restraint_model_granularity_fkey" + ], { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table software.pdbx_ordinal.", + "markdown_name": "Software Id", "source": [ { "outbound": [ "PDB", - "audit_author_structure_id_fkey" + "ihm_predicted_contact_restraint_software_id_fkey" ] }, "RID" ] }, - "pdbx_ordinal", - "name" - ] - } - }, - { - "schema": "PDB", - "table": "ihm_geometric_object_plane", - "uri": "tag:misd.isi.edu,2015:display", - "value": { - "name": "Plane Geometric Objects", - "comment_display": { - "*": { - "table_comment_display" : "inline" - } - } - } - }, - { - "schema": "PDB", - "table": "ihm_geometric_object_plane", - "uri": "tag:isrd.isi.edu,2016:visible-columns", - "value": { - "*": [ - "RID", { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table ihm_dataset_list.id.", + "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_geometric_object_plane_structure_id_fkey" + "ihm_predicted_contact_restraint_dataset_list_id_fkey" ] }, "RID" ] }, { - "comment": "A reference to table ihm_geometric_object_list.object_id.", - "markdown_name": "Object Id", + "comment": "Refers to a combination of Entity Id, Sequence Id and Component Id in the entity_poly_seq table.", + "markdown_name": "Polymeric Residue 1", "source": [ { "outbound": [ "PDB", - "ihm_geometric_object_plane_object_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" ] }, "RID" ] }, - [ - "PDB", - "ihm_geometric_object_plane_plane_type_fkey" - ], { - "comment": "A reference to table ihm_geometric_object_transformation.id.", - "markdown_name": "Transformation Id", + "comment": "Refers to a combination of Entity Id, Sequence Id and Component Id in the entity_poly_seq table.", + "markdown_name": "Polymeric Residue 2", "source": [ { "outbound": [ "PDB", - "ihm_geometric_object_plane_transformation_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", + "markdown_name": "Uploaded Restraint File", + "source": [ + { + "outbound": [ + "PDB", + "ihm_predicted_contact_restraint_Entry_Related_File_fkey" ] }, "RID" @@ -8005,124 +9049,220 @@ { "outbound": [ "PDB", - "ihm_geometric_object_plane_structure_id_fkey" + "ihm_predicted_contact_restraint_structure_id_fkey" ] }, "RID" ] }, + "id", + "group_id", + "entity_description_1", { - "comment": "A reference to table ihm_geometric_object_list.object_id.", - "markdown_name": "Object Id", + "comment": "A reference to table entity_poly_seq.entity_id.", + "markdown_name": "Entity Id 1", "source": [ { "outbound": [ "PDB", - "ihm_geometric_object_plane_object_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + ] + }, + "entity_id" + ] + }, + { + "comment": "A reference to table struct_asym.id.", + "markdown_name": "Asym Id 1", + "source": [ + { + "outbound": [ + "PDB", + "ihm_predicted_contact_restraint_asym_id_1_fkey" ] }, "RID" ] }, + { + "comment": "A reference to table entity_poly_seq.mon_id", + "markdown_name": "Component Id 1", + "source": [ + { + "outbound": [ + "PDB", + "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + ] + }, + "mon_id" + ] + }, + { + "comment": "A reference to table entity_poly_seq.num", + "markdown_name": "Sequence Id 1", + "source": [ + { + "outbound": [ + "PDB", + "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + ] + }, + "num" + ] + }, [ "PDB", - "ihm_geometric_object_plane_plane_type_fkey" + "ihm_predicted_contact_restraint_rep_atom_1_fkey" ], + "entity_description_2", { - "comment": "A reference to table ihm_geometric_object_transformation.id.", - "markdown_name": "Transformation Id", + "comment": "A reference to table entity_poly_seq.entity_id", + "markdown_name": "Entity Id 2", "source": [ { "outbound": [ "PDB", - "ihm_geometric_object_plane_transformation_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" + ] + }, + "entity_id" + ] + }, + { + "comment": "A reference to table struct_asym.id.", + "markdown_name": "Asym Id 2", + "source": [ + { + "outbound": [ + "PDB", + "ihm_predicted_contact_restraint_asym_id_2_fkey" ] }, "RID" ] }, + { + "comment": "A reference to table entity_poly_seq.mon_id", + "markdown_name": "Component Id 2", + "source": [ + { + "outbound": [ + "PDB", + "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" + ] + }, + "mon_id" + ] + }, + { + "comment": "A reference to table entity_poly_seq.num", + "markdown_name": "Sequence Id 2", + "source": [ + { + "outbound": [ + "PDB", + "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" + ] + }, + "mon_id" + ] + }, [ "PDB", - "ihm_geometric_object_plane_RCB_fkey" + "ihm_predicted_contact_restraint_rep_atom_2_fkey" ], [ "PDB", - "ihm_geometric_object_plane_RMB_fkey" + "ihm_predicted_contact_restraint_restraint_type_fkey" ], - "RCT", - "RMT", + "distance_lower_limit", + "distance_upper_limit", + "probability", [ "PDB", - "ihm_geometric_object_plane_Owner_fkey" - ] - ], - "entry": [ + "ihm_predicted_contact_restraint_model_granularity_fkey" + ], { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table software.pdbx_ordinal.", + "markdown_name": "Software Id", "source": [ { "outbound": [ "PDB", - "ihm_geometric_object_plane_structure_id_fkey" + "ihm_predicted_contact_restraint_software_id_fkey" ] }, "RID" ] }, { - "comment": "A reference to table ihm_geometric_object_list.object_id.", - "markdown_name": "Object Id", + "comment": "A reference to table ihm_dataset_list.id.", + "markdown_name": "Dataset List Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_predicted_contact_restraint_dataset_list_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "Refers to a combination of Entity Id, Sequence Id and Component Id in the entity_poly_seq table.", + "markdown_name": "Polymeric Residue 1", + "source": [ + { + "outbound": [ + "PDB", + "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "Refers to a combination of Entity Id, Sequence Id and Component Id in the entity_poly_seq table.", + "markdown_name": "Polymeric Residue 2", "source": [ { "outbound": [ "PDB", - "ihm_geometric_object_plane_object_id_fkey" + "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" ] }, "RID" ] }, - [ - "PDB", - "ihm_geometric_object_plane_plane_type_fkey" - ], { - "comment": "A reference to table ihm_geometric_object_transformation.id.", - "markdown_name": "Transformation Id", + "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", + "markdown_name": "Uploaded Restraint File", "source": [ { "outbound": [ "PDB", - "ihm_geometric_object_plane_transformation_id_fkey" + "ihm_predicted_contact_restraint_Entry_Related_File_fkey" ] }, "RID" ] - } - ] - } - }, - { - "schema": "PDB", - "table": "ihm_predicted_contact_restraint", - "uri": "tag:misd.isi.edu,2015:display", - "value": { - "name": "Predicted Contact Restraints", - "comment_display": { - "*": { - "table_comment_display" : "inline" - } - } - } - }, - { - "schema": "PDB", - "table": "ihm_predicted_contact_restraint", - "uri": "tag:isrd.isi.edu,2016:visible-columns", - "value": { - "*": [ - "RID", + }, + [ + "PDB", + "ihm_predicted_contact_restraint_RCB_fkey" + ], + [ + "PDB", + "ihm_predicted_contact_restraint_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_predicted_contact_restraint_Owner_fkey" + ] + ], + "entry": [ { "comment": "A reference to table entry.id.", "markdown_name": "Structure Id", @@ -8245,7 +9385,7 @@ "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" ] }, - "num" + "mon_id" ] }, [ @@ -8314,176 +9454,258 @@ }, "RID" ] - }, + } + ] + } + }, + { + "schema": "PDB", + "table": "ihm_3dem_restraint", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "3DEM Restraints", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_3dem_restraint", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", { - "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", - "markdown_name": "Uploaded Restraint File", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_Entry_Related_File_fkey" + "ihm_3dem_restraint_structure_id_fkey" ] }, "RID" ] - } - ], - "detailed": [ - "RID", + }, + "id", { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table ihm_model_list.model_id.", + "markdown_name": "Model Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_structure_id_fkey" + "ihm_3dem_restraint_model_id_fkey" ] }, "RID" ] }, - "id", - "group_id", - "entity_description_1", { - "comment": "A reference to table entity_poly_seq.entity_id.", - "markdown_name": "Entity Id 1", + "comment": "A reference to table ihm_struct_assembly.id.", + "markdown_name": "Struct Assembly Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + "ihm_3dem_restraint_struct_assembly_id_fkey" ] }, - "entity_id" + "RID" ] }, + "fitting_method", + "number_of_gaussians", + [ + "PDB", + "ihm_3dem_restraint_map_segment_flag_fkey" + ], + "cross_correlation_coefficient", { - "comment": "A reference to table struct_asym.id.", - "markdown_name": "Asym Id 1", + "comment": "A reference to table citation.id.", + "markdown_name": "Fitting Method Citation Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_asym_id_1_fkey" + "ihm_3dem_restraint_fitting_method_citation_id_fkey" ] }, "RID" ] }, + "details", { - "comment": "A reference to table entity_poly_seq.mon_id", - "markdown_name": "Component Id 1", + "comment": "A reference to table ihm_dataset_list.id.", + "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + "ihm_3dem_restraint_dataset_list_id_fkey" ] }, - "mon_id" + "RID" ] - }, + } + ], + "detailed": [ + "RID", { - "comment": "A reference to table entity_poly_seq.num", - "markdown_name": "Sequence Id 1", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + "ihm_3dem_restraint_structure_id_fkey" ] }, - "num" + "RID" ] }, - [ - "PDB", - "ihm_predicted_contact_restraint_rep_atom_1_fkey" - ], - "entity_description_2", + "id", { - "comment": "A reference to table entity_poly_seq.entity_id", - "markdown_name": "Entity Id 2", + "comment": "A reference to table ihm_model_list.model_id.", + "markdown_name": "Model Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" + "ihm_3dem_restraint_model_id_fkey" ] }, - "entity_id" + "RID" ] }, { - "comment": "A reference to table struct_asym.id.", - "markdown_name": "Asym Id 2", + "comment": "A reference to table ihm_struct_assembly.id.", + "markdown_name": "Struct Assembly Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_asym_id_2_fkey" + "ihm_3dem_restraint_struct_assembly_id_fkey" ] }, "RID" ] }, + "fitting_method", + "number_of_gaussians", + [ + "PDB", + "ihm_3dem_restraint_map_segment_flag_fkey" + ], + "cross_correlation_coefficient", { - "comment": "A reference to table entity_poly_seq.mon_id", - "markdown_name": "Component Id 2", + "comment": "A reference to table citation.id.", + "markdown_name": "Fitting Method Citation Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" + "ihm_3dem_restraint_fitting_method_citation_id_fkey" ] }, - "mon_id" + "RID" ] }, + "details", { - "comment": "A reference to table entity_poly_seq.num", - "markdown_name": "Sequence Id 2", + "comment": "A reference to table ihm_dataset_list.id.", + "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" + "ihm_3dem_restraint_dataset_list_id_fkey" ] }, - "mon_id" + "RID" ] }, [ "PDB", - "ihm_predicted_contact_restraint_rep_atom_2_fkey" + "ihm_3dem_restraint_RCB_fkey" ], [ "PDB", - "ihm_predicted_contact_restraint_restraint_type_fkey" + "ihm_3dem_restraint_RMB_fkey" ], - "distance_lower_limit", - "distance_upper_limit", - "probability", + "RCT", + "RMT", [ "PDB", - "ihm_predicted_contact_restraint_model_granularity_fkey" + "ihm_3dem_restraint_Owner_fkey" + ] + ], + "entry": [ + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_3dem_restraint_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment": "A reference to table ihm_model_list.model_id.", + "markdown_name": "Model Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_3dem_restraint_model_id_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to table ihm_struct_assembly.id.", + "markdown_name": "Struct Assembly Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_3dem_restraint_struct_assembly_id_fkey" + ] + }, + "RID" + ] + }, + "fitting_method", + "number_of_gaussians", + [ + "PDB", + "ihm_3dem_restraint_map_segment_flag_fkey" ], + "cross_correlation_coefficient", { - "comment": "A reference to table software.pdbx_ordinal.", - "markdown_name": "Software Id", + "comment": "A reference to table citation.id.", + "markdown_name": "Fitting Method Citation Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_software_id_fkey" + "ihm_3dem_restraint_fitting_method_citation_id_fkey" ] }, "RID" ] }, + "details", { "comment": "A reference to table ihm_dataset_list.id.", "markdown_name": "Dataset List Id", @@ -8491,46 +9713,71 @@ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_dataset_list_id_fkey" + "ihm_3dem_restraint_dataset_list_id_fkey" ] }, "RID" ] - }, + } + ] + } + }, + { + "schema": "PDB", + "table": "ihm_derived_distance_restraint", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Distance Restraints Between Molecular Features", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_derived_distance_restraint", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", { - "comment": "Refers to a combination of Entity Id, Sequence Id and Component Id in the entity_poly_seq table.", - "markdown_name": "Polymeric Residue 1", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + "ihm_derived_distance_restraint_structure_id_fkey" ] }, "RID" ] }, + "id", + "group_id", { - "comment": "Refers to a combination of Entity Id, Sequence Id and Component Id in the entity_poly_seq table.", - "markdown_name": "Polymeric Residue 2", + "comment": "A reference to table ihm_feature_list.feature_id.", + "markdown_name": "Feature Id 1", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" + "ihm_derived_distance_restraint_feature_id_1_fkey" ] }, "RID" ] }, { - "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", - "markdown_name": "Uploaded Restraint File", + "comment": "A reference to table ihm_feature_list.feature_id.", + "markdown_name": "Feature Id 2", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_Entry_Related_File_fkey" + "ihm_derived_distance_restraint_feature_id_2_fkey" ] }, "RID" @@ -8538,207 +9785,216 @@ }, [ "PDB", - "ihm_predicted_contact_restraint_RCB_fkey" + "ihm_derived_distance_restraint_group_conditionality_fkey" ], [ "PDB", - "ihm_predicted_contact_restraint_RMB_fkey" + "ihm_derived_distance_restraint_restraint_type_fkey" ], - "RCT", - "RMT", - [ - "PDB", - "ihm_predicted_contact_restraint_Owner_fkey" - ] - ], - "entry": [ + "distance_lower_limit", + "distance_upper_limit", + "distance_lower_limit_esd", + "distance_upper_limit_esd", + "distance_threshold_mean", + "distance_threshold_esd", + "probability", + "random_exclusion_fraction", + "mic_value", { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "A reference to table ihm_dataset_list.id.", + "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_structure_id_fkey" + "ihm_derived_distance_restraint_dataset_list_id_fkey" ] }, "RID" ] }, - "id", - "group_id", - "entity_description_1", { - "comment": "A reference to table entity_poly_seq.entity_id.", - "markdown_name": "Entity Id 1", + "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", + "markdown_name": "Uploaded Restraint File", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + "ihm_derived_distance_restraint_Entry_Related_File_fkey" ] }, - "entity_id" + "RID" ] - }, + } + ], + "detailed": [ + "RID", { - "comment": "A reference to table struct_asym.id.", - "markdown_name": "Asym Id 1", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_asym_id_1_fkey" + "ihm_derived_distance_restraint_structure_id_fkey" ] }, "RID" ] }, + "id", + "group_id", { - "comment": "A reference to table entity_poly_seq.mon_id", - "markdown_name": "Component Id 1", + "comment": "A reference to table ihm_feature_list.feature_id.", + "markdown_name": "Feature Id 1", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + "ihm_derived_distance_restraint_feature_id_1_fkey" ] }, - "mon_id" + "RID" ] }, { - "comment": "A reference to table entity_poly_seq.num", - "markdown_name": "Sequence Id 1", + "comment": "A reference to table ihm_feature_list.feature_id.", + "markdown_name": "Feature Id 2", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + "ihm_derived_distance_restraint_feature_id_2_fkey" ] }, - "num" + "RID" ] }, [ "PDB", - "ihm_predicted_contact_restraint_rep_atom_1_fkey" + "ihm_derived_distance_restraint_group_conditionality_fkey" ], - "entity_description_2", - { - "comment": "A reference to table entity_poly_seq.entity_id", - "markdown_name": "Entity Id 2", - "source": [ - { - "outbound": [ - "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" - ] - }, - "entity_id" - ] - }, + [ + "PDB", + "ihm_derived_distance_restraint_restraint_type_fkey" + ], + "distance_lower_limit", + "distance_upper_limit", + "distance_lower_limit_esd", + "distance_upper_limit_esd", + "distance_threshold_mean", + "distance_threshold_esd", + "probability", + "random_exclusion_fraction", + "mic_value", { - "comment": "A reference to table struct_asym.id.", - "markdown_name": "Asym Id 2", + "comment": "A reference to table ihm_dataset_list.id.", + "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_asym_id_2_fkey" + "ihm_derived_distance_restraint_dataset_list_id_fkey" ] }, "RID" ] }, { - "comment": "A reference to table entity_poly_seq.mon_id", - "markdown_name": "Component Id 2", - "source": [ - { - "outbound": [ - "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" - ] - }, - "mon_id" - ] - }, - { - "comment": "A reference to table entity_poly_seq.num", - "markdown_name": "Sequence Id 2", + "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", + "markdown_name": "Uploaded Restraint File", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" + "ihm_derived_distance_restraint_Entry_Related_File_fkey" ] }, - "mon_id" + "RID" ] }, [ "PDB", - "ihm_predicted_contact_restraint_rep_atom_2_fkey" + "ihm_derived_distance_restraint_RCB_fkey" ], [ "PDB", - "ihm_predicted_contact_restraint_restraint_type_fkey" + "ihm_derived_distance_restraint_RMB_fkey" ], - "distance_lower_limit", - "distance_upper_limit", - "probability", + "RCT", + "RMT", [ "PDB", - "ihm_predicted_contact_restraint_model_granularity_fkey" - ], + "ihm_derived_distance_restraint_Owner_fkey" + ] + ], + "entry": [ { - "comment": "A reference to table software.pdbx_ordinal.", - "markdown_name": "Software Id", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_software_id_fkey" + "ihm_derived_distance_restraint_structure_id_fkey" ] }, "RID" ] }, + "id", + "group_id", { - "comment": "A reference to table ihm_dataset_list.id.", - "markdown_name": "Dataset List Id", + "comment": "A reference to table ihm_feature_list.feature_id.", + "markdown_name": "Feature Id 1", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_dataset_list_id_fkey" + "ihm_derived_distance_restraint_feature_id_1_fkey" ] }, "RID" ] }, { - "comment": "Refers to a combination of Entity Id, Sequence Id and Component Id in the entity_poly_seq table.", - "markdown_name": "Polymeric Residue 1", + "comment": "A reference to table ihm_feature_list.feature_id.", + "markdown_name": "Feature Id 2", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_1_fkey" + "ihm_derived_distance_restraint_feature_id_2_fkey" ] }, "RID" ] }, + [ + "PDB", + "ihm_derived_distance_restraint_group_conditionality_fkey" + ], + [ + "PDB", + "ihm_derived_distance_restraint_restraint_type_fkey" + ], + "distance_lower_limit", + "distance_upper_limit", + "distance_lower_limit_esd", + "distance_upper_limit_esd", + "distance_threshold_mean", + "distance_threshold_esd", + "probability", + "random_exclusion_fraction", + "mic_value", { - "comment": "Refers to a combination of Entity Id, Sequence Id and Component Id in the entity_poly_seq table.", - "markdown_name": "Polymeric Residue 2", + "comment": "A reference to table ihm_dataset_list.id.", + "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_predicted_contact_restraint_mm_poly_res_label_2_fkey" + "ihm_derived_distance_restraint_dataset_list_id_fkey" ] }, "RID" @@ -8747,12 +10003,13 @@ ] } }, +#if 1 { "schema": "PDB", - "table": "ihm_3dem_restraint", + "table": "ihm_derived_angle_restraint", "uri": "tag:misd.isi.edu,2015:display", "value": { - "name": "3DEM Restraints", + "name": "Angle Restraints Between Molecular Features", "comment_display": { "*": { "table_comment_display" : "inline" @@ -8762,7 +10019,7 @@ }, { "schema": "PDB", - "table": "ihm_3dem_restraint", + "table": "ihm_derived_angle_restraint", "uri": "tag:isrd.isi.edu,2016:visible-columns", "value": { "*": [ @@ -8774,68 +10031,89 @@ { "outbound": [ "PDB", - "ihm_3dem_restraint_structure_id_fkey" + "ihm_derived_angle_restraint_structure_id_fkey" ] }, "RID" ] }, "id", + "group_id", { - "comment": "A reference to table ihm_model_list.model_id.", - "markdown_name": "Model Id", + "comment": "The feature identifier for the first partner in the angle restraint", + "markdown_name": "Feature Id 1", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_model_id_fkey" + "ihm_derived_angle_restraint_ihm_feature_list_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "The feature identifier for the second partner in the angle restraint", + "markdown_name": "Feature Id 2", + "source": [ + { + "outbound": [ + "PDB", + "ihm_derived_angle_restraint_ihm_feature_list_2_combo1_fkey" ] }, "RID" ] }, { - "comment": "A reference to table ihm_struct_assembly.id.", - "markdown_name": "Struct Assembly Id", + "comment": "The feature identifier for the third partner in the angle restraint", + "markdown_name": "Feature Id 3", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_struct_assembly_id_fkey" + "ihm_derived_angle_restraint_ihm_feature_list_3_combo1_fkey" ] }, "RID" ] }, - "fitting_method", - "number_of_gaussians", [ "PDB", - "ihm_3dem_restraint_map_segment_flag_fkey" + "ihm_derived_angle_restraint_group_conditionality_fkey" ], - "cross_correlation_coefficient", + "angle_lower_limit", + "angle_upper_limit", + "angle_lower_limit_esd", + "angle_upper_limit_esd", + "probability", + [ + "PDB", + "ihm_derived_angle_restraint_restraint_type_fkey" + ], + "angle_threshold_mean", + "angle_threshold_mean_esd", { - "comment": "A reference to table citation.id.", - "markdown_name": "Fitting Method Citation Id", + "comment": "Identifier to the input data from which the angle restraint is derived", + "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_fitting_method_citation_id_fkey" + "ihm_derived_angle_restraint_ihm_dataset_list_combo1_fkey" ] }, "RID" ] }, - "details", { - "comment": "A reference to table ihm_dataset_list.id.", - "markdown_name": "Dataset List Id", + "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", + "markdown_name": "Uploaded Restraint File", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_dataset_list_id_fkey" + "ihm_derived_angle_restraint_Entry_Related_File_fkey" ] }, "RID" @@ -8851,68 +10129,89 @@ { "outbound": [ "PDB", - "ihm_3dem_restraint_structure_id_fkey" + "ihm_derived_angle_restraint_structure_id_fkey" ] }, "RID" ] }, "id", + "group_id", { - "comment": "A reference to table ihm_model_list.model_id.", - "markdown_name": "Model Id", + "comment": "The feature identifier for the first partner in the angle restraint", + "markdown_name": "Feature Id 1", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_model_id_fkey" + "ihm_derived_angle_restraint_ihm_feature_list_1_combo1_fkey" ] }, "RID" ] }, { - "comment": "A reference to table ihm_struct_assembly.id.", - "markdown_name": "Struct Assembly Id", + "comment": "The feature identifier for the second partner in the angle restraint", + "markdown_name": "Feature Id 2", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_struct_assembly_id_fkey" + "ihm_derived_angle_restraint_ihm_feature_list_2_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "The feature identifier for the third partner in the angle restraint", + "markdown_name": "Feature Id 3", + "source": [ + { + "outbound": [ + "PDB", + "ihm_derived_angle_restraint_ihm_feature_list_3_combo1_fkey" ] }, "RID" ] }, - "fitting_method", - "number_of_gaussians", [ "PDB", - "ihm_3dem_restraint_map_segment_flag_fkey" + "ihm_derived_angle_restraint_group_conditionality_fkey" ], - "cross_correlation_coefficient", + "angle_lower_limit", + "angle_upper_limit", + "angle_lower_limit_esd", + "angle_upper_limit_esd", + "probability", + [ + "PDB", + "ihm_derived_angle_restraint_restraint_type_fkey" + ], + "angle_threshold_mean", + "angle_threshold_mean_esd", { - "comment": "A reference to table citation.id.", - "markdown_name": "Fitting Method Citation Id", + "comment": "Identifier to the input data from which the angle restraint is derived", + "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_fitting_method_citation_id_fkey" + "ihm_derived_angle_restraint_ihm_dataset_list_combo1_fkey" ] }, "RID" ] }, - "details", { - "comment": "A reference to table ihm_dataset_list.id.", - "markdown_name": "Dataset List Id", + "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", + "markdown_name": "Uploaded Restraint File", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_dataset_list_id_fkey" + "ihm_derived_angle_restraint_Entry_Related_File_fkey" ] }, "RID" @@ -8920,17 +10219,17 @@ }, [ "PDB", - "ihm_3dem_restraint_RCB_fkey" + "ihm_derived_angle_restraint_RCB_fkey" ], [ "PDB", - "ihm_3dem_restraint_RMB_fkey" + "ihm_derived_angle_restraint_RMB_fkey" ], "RCT", "RMT", [ "PDB", - "ihm_3dem_restraint_Owner_fkey" + "ihm_derived_angle_restraint_Owner_fkey" ] ], "entry": [ @@ -8941,68 +10240,89 @@ { "outbound": [ "PDB", - "ihm_3dem_restraint_structure_id_fkey" + "ihm_derived_angle_restraint_structure_id_fkey" ] }, "RID" ] }, "id", + "group_id", { - "comment": "A reference to table ihm_model_list.model_id.", - "markdown_name": "Model Id", + "comment": "The feature identifier for the first partner in the angle restraint", + "markdown_name": "Feature Id 1", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_model_id_fkey" + "ihm_derived_angle_restraint_ihm_feature_list_1_combo1_fkey" ] }, "RID" ] }, { - "comment": "A reference to table ihm_struct_assembly.id.", - "markdown_name": "Struct Assembly Id", + "comment": "The feature identifier for the second partner in the angle restraint", + "markdown_name": "Feature Id 2", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_struct_assembly_id_fkey" + "ihm_derived_angle_restraint_ihm_feature_list_2_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "The feature identifier for the third partner in the angle restraint", + "markdown_name": "Feature Id 3", + "source": [ + { + "outbound": [ + "PDB", + "ihm_derived_angle_restraint_ihm_feature_list_3_combo1_fkey" ] }, "RID" ] }, - "fitting_method", - "number_of_gaussians", [ "PDB", - "ihm_3dem_restraint_map_segment_flag_fkey" + "ihm_derived_angle_restraint_group_conditionality_fkey" ], - "cross_correlation_coefficient", + "angle_lower_limit", + "angle_upper_limit", + "angle_lower_limit_esd", + "angle_upper_limit_esd", + "probability", + [ + "PDB", + "ihm_derived_angle_restraint_restraint_type_fkey" + ], + "angle_threshold_mean", + "angle_threshold_mean_esd", { - "comment": "A reference to table citation.id.", - "markdown_name": "Fitting Method Citation Id", + "comment": "Identifier to the input data from which the angle restraint is derived", + "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_fitting_method_citation_id_fkey" + "ihm_derived_angle_restraint_ihm_dataset_list_combo1_fkey" ] }, "RID" ] }, - "details", { - "comment": "A reference to table ihm_dataset_list.id.", - "markdown_name": "Dataset List Id", + "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", + "markdown_name": "Uploaded Restraint File", "source": [ { "outbound": [ "PDB", - "ihm_3dem_restraint_dataset_list_id_fkey" + "ihm_derived_angle_restraint_Entry_Related_File_fkey" ] }, "RID" @@ -9013,10 +10333,10 @@ }, { "schema": "PDB", - "table": "ihm_derived_distance_restraint", + "table": "ihm_derived_dihedral_restraint", "uri": "tag:misd.isi.edu,2015:display", "value": { - "name": "Distance Restraints Between Molecular Features", + "name": "Dihedral Restraints Between Molecular Features", "comment_display": { "*": { "table_comment_display" : "inline" @@ -9026,7 +10346,7 @@ }, { "schema": "PDB", - "table": "ihm_derived_distance_restraint", + "table": "ihm_derived_dihedral_restraint", "uri": "tag:isrd.isi.edu,2016:visible-columns", "value": { "*": [ @@ -9038,7 +10358,7 @@ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_structure_id_fkey" + "ihm_derived_dihedral_restraint_structure_id_fkey" ] }, "RID" @@ -9047,26 +10367,52 @@ "id", "group_id", { - "comment": "A reference to table ihm_feature_list.feature_id.", + "comment": "The feature identifier for the first partner in the dihedral restraint", "markdown_name": "Feature Id 1", "source": [ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_feature_id_1_fkey" + "ihm_derived_dihedral_restraint_ihm_feature_list_1_combo1_fkey" ] }, "RID" ] }, { - "comment": "A reference to table ihm_feature_list.feature_id.", + "comment": "The feature identifier for the second partner in the dihedral restraint", "markdown_name": "Feature Id 2", "source": [ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_feature_id_2_fkey" + "ihm_derived_dihedral_restraint_ihm_feature_list_2_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "The feature identifier for the third partner in the dihedral restraint", + "markdown_name": "Feature Id 3", + "source": [ + { + "outbound": [ + "PDB", + "ihm_derived_dihedral_restraint_ihm_feature_list_3_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "The feature identifier for the fourth partner in the dihedral restraint", + "markdown_name": "Feature Id 4", + "source": [ + { + "outbound": [ + "PDB", + "ihm_derived_dihedral_restraint_ihm_feature_list_4_combo1_fkey" ] }, "RID" @@ -9074,29 +10420,27 @@ }, [ "PDB", - "ihm_derived_distance_restraint_group_conditionality_fkey" + "ihm_derived_dihedral_restraint_group_conditionality_fkey" ], + "dihedral_lower_limit", + "dihedral_upper_limit", + "dihedral_lower_limit_esd", + "dihedral_upper_limit_esd", + "probability", [ "PDB", - "ihm_derived_distance_restraint_restraint_type_fkey" + "ihm_derived_dihedral_restraint_restraint_type_fkey" ], - "distance_lower_limit", - "distance_upper_limit", - "distance_lower_limit_esd", - "distance_upper_limit_esd", - "distance_threshold_mean", - "distance_threshold_esd", - "probability", - "random_exclusion_fraction", - "mic_value", + "dihedral_threshold_mean", + "dihedral_threshold_mean_esd", { - "comment": "A reference to table ihm_dataset_list.id.", + "comment": "Identifier to the input data from which the dihedral restraint is derived", "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_dataset_list_id_fkey" + "ihm_derived_dihedral_restraint_ihm_dataset_list_combo1_fkey" ] }, "RID" @@ -9109,7 +10453,7 @@ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_Entry_Related_File_fkey" + "ihm_derived_dihedral_restraint_Entry_Related_File_fkey" ] }, "RID" @@ -9125,7 +10469,7 @@ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_structure_id_fkey" + "ihm_derived_dihedral_restraint_structure_id_fkey" ] }, "RID" @@ -9134,26 +10478,52 @@ "id", "group_id", { - "comment": "A reference to table ihm_feature_list.feature_id.", + "comment": "The feature identifier for the first partner in the dihedral restraint", "markdown_name": "Feature Id 1", "source": [ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_feature_id_1_fkey" + "ihm_derived_dihedral_restraint_ihm_feature_list_1_combo1_fkey" ] }, "RID" ] }, { - "comment": "A reference to table ihm_feature_list.feature_id.", + "comment": "The feature identifier for the second partner in the dihedral restraint", "markdown_name": "Feature Id 2", "source": [ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_feature_id_2_fkey" + "ihm_derived_dihedral_restraint_ihm_feature_list_2_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "The feature identifier for the third partner in the dihedral restraint", + "markdown_name": "Feature Id 3", + "source": [ + { + "outbound": [ + "PDB", + "ihm_derived_dihedral_restraint_ihm_feature_list_3_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "The feature identifier for the fourth partner in the dihedral restraint", + "markdown_name": "Feature Id 4", + "source": [ + { + "outbound": [ + "PDB", + "ihm_derived_dihedral_restraint_ihm_feature_list_4_combo1_fkey" ] }, "RID" @@ -9161,29 +10531,27 @@ }, [ "PDB", - "ihm_derived_distance_restraint_group_conditionality_fkey" + "ihm_derived_dihedral_restraint_group_conditionality_fkey" ], + "dihedral_lower_limit", + "dihedral_upper_limit", + "dihedral_lower_limit_esd", + "dihedral_upper_limit_esd", + "probability", [ "PDB", - "ihm_derived_distance_restraint_restraint_type_fkey" + "ihm_derived_dihedral_restraint_restraint_type_fkey" ], - "distance_lower_limit", - "distance_upper_limit", - "distance_lower_limit_esd", - "distance_upper_limit_esd", - "distance_threshold_mean", - "distance_threshold_esd", - "probability", - "random_exclusion_fraction", - "mic_value", + "dihedral_threshold_mean", + "dihedral_threshold_mean_esd", { - "comment": "A reference to table ihm_dataset_list.id.", + "comment": "Identifier to the input data from which the dihedral restraint is derived", "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_dataset_list_id_fkey" + "ihm_derived_dihedral_restraint_ihm_dataset_list_combo1_fkey" ] }, "RID" @@ -9196,7 +10564,7 @@ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_Entry_Related_File_fkey" + "ihm_derived_dihedral_restraint_Entry_Related_File_fkey" ] }, "RID" @@ -9204,17 +10572,17 @@ }, [ "PDB", - "ihm_derived_distance_restraint_RCB_fkey" + "ihm_derived_dihedral_restraint_RCB_fkey" ], [ "PDB", - "ihm_derived_distance_restraint_RMB_fkey" + "ihm_derived_dihedral_restraint_RMB_fkey" ], "RCT", "RMT", [ "PDB", - "ihm_derived_distance_restraint_Owner_fkey" + "ihm_derived_dihedral_restraint_Owner_fkey" ] ], "entry": [ @@ -9225,7 +10593,7 @@ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_structure_id_fkey" + "ihm_derived_dihedral_restraint_structure_id_fkey" ] }, "RID" @@ -9234,26 +10602,52 @@ "id", "group_id", { - "comment": "A reference to table ihm_feature_list.feature_id.", + "comment": "The feature identifier for the first partner in the dihedral restraint", "markdown_name": "Feature Id 1", "source": [ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_feature_id_1_fkey" + "ihm_derived_dihedral_restraint_ihm_feature_list_1_combo1_fkey" ] }, "RID" ] }, { - "comment": "A reference to table ihm_feature_list.feature_id.", + "comment": "The feature identifier for the second partner in the dihedral restraint", "markdown_name": "Feature Id 2", "source": [ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_feature_id_2_fkey" + "ihm_derived_dihedral_restraint_ihm_feature_list_2_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "The feature identifier for the third partner in the dihedral restraint", + "markdown_name": "Feature Id 3", + "source": [ + { + "outbound": [ + "PDB", + "ihm_derived_dihedral_restraint_ihm_feature_list_3_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "The feature identifier for the fourth partner in the dihedral restraint", + "markdown_name": "Feature Id 4", + "source": [ + { + "outbound": [ + "PDB", + "ihm_derived_dihedral_restraint_ihm_feature_list_4_combo1_fkey" ] }, "RID" @@ -9261,29 +10655,40 @@ }, [ "PDB", - "ihm_derived_distance_restraint_group_conditionality_fkey" + "ihm_derived_dihedral_restraint_group_conditionality_fkey" ], + "dihedral_lower_limit", + "dihedral_upper_limit", + "dihedral_lower_limit_esd", + "dihedral_upper_limit_esd", + "probability", [ "PDB", - "ihm_derived_distance_restraint_restraint_type_fkey" + "ihm_derived_dihedral_restraint_restraint_type_fkey" ], - "distance_lower_limit", - "distance_upper_limit", - "distance_lower_limit_esd", - "distance_upper_limit_esd", - "distance_threshold_mean", - "distance_threshold_esd", - "probability", - "random_exclusion_fraction", - "mic_value", + "dihedral_threshold_mean", + "dihedral_threshold_mean_esd", { - "comment": "A reference to table ihm_dataset_list.id.", + "comment": "Identifier to the input data from which the dihedral restraint is derived", "markdown_name": "Dataset List Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_distance_restraint_dataset_list_id_fkey" + "ihm_derived_dihedral_restraint_ihm_dataset_list_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", + "markdown_name": "Uploaded Restraint File", + "source": [ + { + "outbound": [ + "PDB", + "ihm_derived_dihedral_restraint_Entry_Related_File_fkey" ] }, "RID" @@ -9295,10 +10700,10 @@ #if 1 { "schema": "PDB", - "table": "ihm_derived_angle_restraint", + "table": "ihm_entry_collection", "uri": "tag:misd.isi.edu,2015:display", "value": { - "name": "Angle Restraints Between Molecular Features", + "name": "Entry Collections", "comment_display": { "*": { "table_comment_display" : "inline" @@ -9308,108 +10713,238 @@ }, { "schema": "PDB", - "table": "ihm_derived_angle_restraint", + "table": "ihm_entry_collection", "uri": "tag:isrd.isi.edu,2016:visible-columns", "value": { "*": [ "RID", + "id", + "name", + "details" + ], + "detailed": [ + "RID", + "id", + "name", + "details", + [ + "PDB", + "ihm_entry_collection_RCB_fkey" + ], + [ + "PDB", + "ihm_entry_collection_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_entry_collection_Owner_fkey" + ] + ], + "entry": [ + "id", + "name", + "details" + ] + } + }, + { + "schema": "PDB", + "table": "ihm_entry_collection", + "uri": "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value": { + "detailed": [ { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "Entries in this collection", + "markdown_name": "Entry", "source": [ + { + "inbound": [ + "PDB", + "ihm_entry_collection_mapping_collection_id_fkey" + ] + }, { "outbound": [ "PDB", - "ihm_derived_angle_restraint_structure_id_fkey" + "ihm_entry_collection_mapping_entry_id_fkey" ] }, "RID" ] + } + ], + "filter": "detailed" + } + }, + { + "schema": "PDB", + "table": "ihm_entry_collection_mapping", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Entry Collection Mappings", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_entry_collection_mapping", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "compact": [ + "RID", + { + "comment": "Entry Collection Id", + "markdown_name": "Entry Collection Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_entry_collection_mapping_collection_id_fkey" + ] + }, + "id" + ] }, - "id", - "group_id", { - "comment": "The feature identifier for the first partner in the angle restraint", - "markdown_name": "Feature Id 1", + "comment": "Entry Id", + "markdown_name": "Entry Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_feature_list_1_combo1_fkey" + "ihm_entry_collection_mapping_entry_id_fkey" ] }, - "RID" + "id" ] }, + { + "comment": "Entry Accession Code", + "markdown_name": "Accession Code", + "source": [ + { + "outbound": [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "Accession_Code" + ] + } + ], + "detailed": [ + "RID", { - "comment": "The feature identifier for the second partner in the angle restraint", - "markdown_name": "Feature Id 2", + "comment": "Entry Collection Id", + "markdown_name": "Entry Collection Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_feature_list_2_combo1_fkey" + "ihm_entry_collection_mapping_collection_id_fkey" ] }, - "RID" + "id" ] }, { - "comment": "The feature identifier for the third partner in the angle restraint", - "markdown_name": "Feature Id 3", + "comment": "Entry Id", + "markdown_name": "Entry Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_feature_list_3_combo1_fkey" + "ihm_entry_collection_mapping_entry_id_fkey" ] }, - "RID" + "id" ] }, + { + "comment": "Entry Accession Code", + "markdown_name": "Accession Code", + "source": [ + { + "outbound": [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "Accession_Code" + ] + }, [ "PDB", - "ihm_derived_angle_restraint_group_conditionality_fkey" + "ihm_entry_collection_mapping_RCB_fkey" ], - "angle_lower_limit", - "angle_upper_limit", - "angle_lower_limit_esd", - "angle_upper_limit_esd", - "probability", [ "PDB", - "ihm_derived_angle_restraint_restraint_type_fkey" + "ihm_entry_collection_mapping_RMB_fkey" ], - "angle_threshold_mean", - "angle_threshold_mean_esd", + "RCT", + "RMT", + [ + "PDB", + "ihm_entry_collection_mapping_Owner_fkey" + ] + ], + "entry": [ { - "comment": "Identifier to the input data from which the angle restraint is derived", - "markdown_name": "Dataset List Id", + "comment": "Entry Collection Id", + "markdown_name": "Entry Collection Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_dataset_list_combo1_fkey" + "ihm_entry_collection_mapping_collection_id_fkey" ] }, - "RID" + "id" ] }, { - "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", - "markdown_name": "Uploaded Restraint File", + "comment": "Entry Id", + "markdown_name": "Entry Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_Entry_Related_File_fkey" + "ihm_entry_collection_mapping_entry_id_fkey" ] }, - "RID" + "id" ] } - ], - "detailed": [ + ] + } + }, +#endif +#if 1 + { + "schema": "PDB", + "table": "ihm_multi_state_scheme", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Multi-State Schemes", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_multi_state_scheme", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ "RID", { "comment": "A reference to table entry.id.", @@ -9418,338 +10953,367 @@ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_structure_id_fkey" + "ihm_multi_state_scheme_structure_id_fkey" ] }, "RID" ] }, "id", - "group_id", - { - "comment": "The feature identifier for the first partner in the angle restraint", - "markdown_name": "Feature Id 1", - "source": [ - { - "outbound": [ - "PDB", - "ihm_derived_angle_restraint_ihm_feature_list_1_combo1_fkey" - ] - }, - "RID" - ] - }, + "name", + "details" + ], + "detailed": [ + "RID", { - "comment": "The feature identifier for the second partner in the angle restraint", - "markdown_name": "Feature Id 2", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_feature_list_2_combo1_fkey" + "ihm_multi_state_scheme_structure_id_fkey" ] }, "RID" ] }, + "id", + "name", + "details", + [ + "PDB", + "ihm_multi_state_scheme_RCB_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_multi_state_scheme_Owner_fkey" + ] + ], + "entry": [ + "id", { - "comment": "The feature identifier for the third partner in the angle restraint", - "markdown_name": "Feature Id 3", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_feature_list_3_combo1_fkey" + "ihm_multi_state_scheme_structure_id_fkey" ] }, "RID" ] }, + "name", + "details" + ] + } + }, + { + "schema": "PDB", + "table": "ihm_multi_state_scheme", + "uri": "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value": { + "detailed": [ [ "PDB", - "ihm_derived_angle_restraint_group_conditionality_fkey" + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" ], - "angle_lower_limit", - "angle_upper_limit", - "angle_lower_limit_esd", - "angle_upper_limit_esd", - "probability", [ "PDB", - "ihm_derived_angle_restraint_restraint_type_fkey" - ], - "angle_threshold_mean", - "angle_threshold_mean_esd", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + ], + "filter": "detailed" + } + }, + { + "schema": "PDB", + "table": "ihm_multi_state_scheme_connectivity", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Multi-State Scheme Connectivities", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_multi_state_scheme_connectivity", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", { - "comment": "Identifier to the input data from which the angle restraint is derived", - "markdown_name": "Dataset List Id", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_dataset_list_combo1_fkey" + "ihm_multi_state_scheme_connectivity_structure_id_fkey" ] }, "RID" ] }, + "id", { - "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", - "markdown_name": "Uploaded Restraint File", + "comment": "Identifier for the multi-state scheme", + "markdown_name": "Scheme Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_Entry_Related_File_fkey" + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" ] }, "RID" ] }, - [ - "PDB", - "ihm_derived_angle_restraint_RCB_fkey" - ], - [ - "PDB", - "ihm_derived_angle_restraint_RMB_fkey" - ], - "RCT", - "RMT", - [ - "PDB", - "ihm_derived_angle_restraint_Owner_fkey" - ] - ], - "entry": [ { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "Identifier for the starting state in the multi-state scheme", + "markdown_name": "Begin State Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_structure_id_fkey" + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" ] }, "RID" ] }, - "id", - "group_id", { - "comment": "The feature identifier for the first partner in the angle restraint", - "markdown_name": "Feature Id 1", + "comment": "Identifier for the ending state in the multi-state scheme", + "markdown_name": "End State Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_feature_list_1_combo1_fkey" + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" ] }, "RID" ] }, { - "comment": "The feature identifier for the second partner in the angle restraint", - "markdown_name": "Feature Id 2", + "comment": "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name": "Dataset Group Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_feature_list_2_combo1_fkey" + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" ] }, "RID" ] }, + "details" + ], + "detailed": [ + "RID", { - "comment": "The feature identifier for the third partner in the angle restraint", - "markdown_name": "Feature Id 3", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_feature_list_3_combo1_fkey" + "ihm_multi_state_scheme_connectivity_structure_id_fkey" ] }, "RID" ] }, - [ - "PDB", - "ihm_derived_angle_restraint_group_conditionality_fkey" - ], - "angle_lower_limit", - "angle_upper_limit", - "angle_lower_limit_esd", - "angle_upper_limit_esd", - "probability", - [ - "PDB", - "ihm_derived_angle_restraint_restraint_type_fkey" - ], - "angle_threshold_mean", - "angle_threshold_mean_esd", + "id", { - "comment": "Identifier to the input data from which the angle restraint is derived", - "markdown_name": "Dataset List Id", + "comment": "Identifier for the multi-state scheme", + "markdown_name": "Scheme Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_ihm_dataset_list_combo1_fkey" + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" ] }, "RID" ] }, { - "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", - "markdown_name": "Uploaded Restraint File", + "comment": "Identifier for the starting state in the multi-state scheme", + "markdown_name": "Begin State Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_angle_restraint_Entry_Related_File_fkey" + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" ] }, "RID" ] - } - ] - } - }, - { - "schema": "PDB", - "table": "ihm_derived_dihedral_restraint", - "uri": "tag:misd.isi.edu,2015:display", - "value": { - "name": "Dihedral Restraints Between Molecular Features", - "comment_display": { - "*": { - "table_comment_display" : "inline" - } - } - } - }, - { - "schema": "PDB", - "table": "ihm_derived_dihedral_restraint", - "uri": "tag:isrd.isi.edu,2016:visible-columns", - "value": { - "*": [ - "RID", + }, { - "comment": "A reference to table entry.id.", - "markdown_name": "Structure Id", + "comment": "Identifier for the ending state in the multi-state scheme", + "markdown_name": "End State Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_structure_id_fkey" + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" ] }, "RID" ] }, - "id", - "group_id", { - "comment": "The feature identifier for the first partner in the dihedral restraint", - "markdown_name": "Feature Id 1", + "comment": "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name": "Dataset Group Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_1_combo1_fkey" + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" ] }, "RID" ] }, + "details", + [ + "PDB", + "ihm_multi_state_scheme_connectivity_RCB_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_multi_state_scheme_connectivity_Owner_fkey" + ] + ], + "entry": [ { - "comment": "The feature identifier for the second partner in the dihedral restraint", - "markdown_name": "Feature Id 2", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_2_combo1_fkey" + "ihm_multi_state_scheme_connectivity_structure_id_fkey" ] }, "RID" ] }, + "id", { - "comment": "The feature identifier for the third partner in the dihedral restraint", - "markdown_name": "Feature Id 3", + "comment": "Identifier for the multi-state scheme", + "markdown_name": "Scheme Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_3_combo1_fkey" + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" ] }, "RID" ] }, { - "comment": "The feature identifier for the fourth partner in the dihedral restraint", - "markdown_name": "Feature Id 4", + "comment": "Identifier for the starting state in the multi-state scheme", + "markdown_name": "Begin State Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_4_combo1_fkey" + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" ] }, "RID" ] }, - [ - "PDB", - "ihm_derived_dihedral_restraint_group_conditionality_fkey" - ], - "dihedral_lower_limit", - "dihedral_upper_limit", - "dihedral_lower_limit_esd", - "dihedral_upper_limit_esd", - "probability", - [ - "PDB", - "ihm_derived_dihedral_restraint_restraint_type_fkey" - ], - "dihedral_threshold_mean", - "dihedral_threshold_mean_esd", { - "comment": "Identifier to the input data from which the dihedral restraint is derived", - "markdown_name": "Dataset List Id", + "comment": "Identifier for the ending state in the multi-state scheme", + "markdown_name": "End State Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_dataset_list_combo1_fkey" + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" ] }, "RID" ] }, { - "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", - "markdown_name": "Uploaded Restraint File", + "comment": "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name": "Dataset Group Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_Entry_Related_File_fkey" + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" ] }, "RID" ] - } - ], + }, + "details" + ] + } + }, + { + "schema": "PDB", + "table": "ihm_multi_state_scheme_connectivity", + "uri": "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value": { "detailed": [ + [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ], + [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + ], + "filter": "detailed" + } + }, + { + "schema": "PDB", + "table": "ihm_kinetic_rate", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Kinetic Rates from Biophysical Experiments", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_kinetic_rate", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ "RID", { "comment": "A reference to table entry.id.", @@ -9758,120 +11322,137 @@ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_structure_id_fkey" + "ihm_kinetic_rate_structure_id_fkey" ] }, "RID" ] }, "id", - "group_id", - { - "comment": "The feature identifier for the first partner in the dihedral restraint", - "markdown_name": "Feature Id 1", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", + { + "comment": "Identifier for the multi-state scheme connectivity", + "markdown_name": "Scheme Connectivity Id", "source": [ - { + { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_1_combo1_fkey" - ] - }, + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ] + }, "RID" - ] + ] }, - { - "comment": "The feature identifier for the second partner in the dihedral restraint", - "markdown_name": "Feature Id 2", + { + "comment": "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name": "External File Id", "source": [ - { + { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_2_combo1_fkey" - ] - }, + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ] + }, "RID" - ] + ] + }, + { + "comment": "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name": "Dataset Group Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] }, + "details" + ], + "detailed": [ + "RID", { - "comment": "The feature identifier for the third partner in the dihedral restraint", - "markdown_name": "Feature Id 3", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_3_combo1_fkey" + "ihm_kinetic_rate_structure_id_fkey" ] }, "RID" ] }, + "id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", { - "comment": "The feature identifier for the fourth partner in the dihedral restraint", - "markdown_name": "Feature Id 4", + "comment": "Identifier for the multi-state scheme connectivity", + "markdown_name": "Scheme Connectivity Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_4_combo1_fkey" + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" ] }, "RID" ] }, - [ - "PDB", - "ihm_derived_dihedral_restraint_group_conditionality_fkey" - ], - "dihedral_lower_limit", - "dihedral_upper_limit", - "dihedral_lower_limit_esd", - "dihedral_upper_limit_esd", - "probability", - [ - "PDB", - "ihm_derived_dihedral_restraint_restraint_type_fkey" - ], - "dihedral_threshold_mean", - "dihedral_threshold_mean_esd", { - "comment": "Identifier to the input data from which the dihedral restraint is derived", - "markdown_name": "Dataset List Id", + "comment": "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name": "External File Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_dataset_list_combo1_fkey" + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" ] }, "RID" ] }, { - "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", - "markdown_name": "Uploaded Restraint File", + "comment": "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name": "Dataset Group Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_Entry_Related_File_fkey" + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" ] }, "RID" ] }, + "details", [ "PDB", - "ihm_derived_dihedral_restraint_RCB_fkey" + "ihm_kinetic_rate_RCB_fkey" ], [ "PDB", - "ihm_derived_dihedral_restraint_RMB_fkey" + "ihm_kinetic_rate_RMB_fkey" ], "RCT", "RMT", [ "PDB", - "ihm_derived_dihedral_restraint_Owner_fkey" + "ihm_kinetic_rate_Owner_fkey" ] ], "entry": [ @@ -9882,197 +11463,266 @@ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_structure_id_fkey" + "ihm_kinetic_rate_structure_id_fkey" ] }, "RID" ] }, "id", - "group_id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", { - "comment": "The feature identifier for the first partner in the dihedral restraint", - "markdown_name": "Feature Id 1", + "comment": "Identifier for the multi-state scheme connectivity", + "markdown_name": "Scheme Connectivity Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_1_combo1_fkey" + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" ] }, "RID" ] }, { - "comment": "The feature identifier for the second partner in the dihedral restraint", - "markdown_name": "Feature Id 2", + "comment": "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name": "External File Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_2_combo1_fkey" + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" ] }, "RID" ] }, { - "comment": "The feature identifier for the third partner in the dihedral restraint", - "markdown_name": "Feature Id 3", + "comment": "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name": "Dataset Group Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_3_combo1_fkey" + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" ] }, "RID" ] }, + "details" + ] + } + }, + { + "schema": "PDB", + "table": "ihm_relaxation_time", + "uri": "tag:misd.isi.edu,2015:display", + "value": { + "name": "Relaxation times from Biophysical Experiments", + "comment_display": { + "*": { + "table_comment_display" : "inline" + } + } + } + }, + { + "schema": "PDB", + "table": "ihm_relaxation_time", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", { - "comment": "The feature identifier for the fourth partner in the dihedral restraint", - "markdown_name": "Feature Id 4", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_feature_list_4_combo1_fkey" + "ihm_relaxation_time_structure_id_fkey" ] }, "RID" ] }, - [ - "PDB", - "ihm_derived_dihedral_restraint_group_conditionality_fkey" - ], - "dihedral_lower_limit", - "dihedral_upper_limit", - "dihedral_lower_limit_esd", - "dihedral_upper_limit_esd", - "probability", - [ + "id", + "value", + [ "PDB", - "ihm_derived_dihedral_restraint_restraint_type_fkey" + "ihm_relaxation_time_unit_fkey" ], - "dihedral_threshold_mean", - "dihedral_threshold_mean_esd", + "amplitude", { - "comment": "Identifier to the input data from which the dihedral restraint is derived", - "markdown_name": "Dataset List Id", + "comment": "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name": "External File Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_ihm_dataset_list_combo1_fkey" + "ihm_relaxation_time_ihm_external_files_combo2_fkey" ] }, "RID" ] }, { - "comment": "A reference to the uploaded restraint file in the table Entry_Related_File.id.", - "markdown_name": "Uploaded Restraint File", + "comment": "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name": "Dataset Group Id", "source": [ { "outbound": [ "PDB", - "ihm_derived_dihedral_restraint_Entry_Related_File_fkey" + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" ] }, "RID" ] - } - ] - } - }, -#if 1 - { - "schema": "PDB", - "table": "ihm_entry_collection", - "uri": "tag:misd.isi.edu,2015:display", - "value": { - "name": "Entry Collections", - "comment_display": { - "*": { - "table_comment_display" : "inline" - } - } - } - }, - { - "schema": "PDB", - "table": "ihm_entry_collection", - "uri": "tag:isrd.isi.edu,2016:visible-columns", - "value": { - "*": [ - "RID", - "id", - "name", + }, "details" ], "detailed": [ "RID", + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, "id", - "name", - "details", + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", + { + "comment": "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name": "External File Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name": "Dataset Group Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", [ "PDB", - "ihm_entry_collection_RCB_fkey" + "ihm_relaxation_time_RCB_fkey" ], [ "PDB", - "ihm_entry_collection_RMB_fkey" + "ihm_relaxation_time_RMB_fkey" ], "RCT", "RMT", [ "PDB", - "ihm_entry_collection_Owner_fkey" + "ihm_relaxation_time_Owner_fkey" ] ], "entry": [ + { + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, "id", - "name", - "details" - ] - } - }, - { - "schema": "PDB", - "table": "ihm_entry_collection", - "uri": "tag:isrd.isi.edu,2016:visible-foreign-keys", - "value": { - "detailed": [ + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", { - "comment": "Entries in this collection", - "markdown_name": "Entry", + "comment": "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name": "External File Id", "source": [ { - "inbound": [ + "outbound": [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "ihm_relaxation_time_ihm_external_files_combo2_fkey" ] }, + "RID" + ] + }, + { + "comment": "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name": "Dataset Group Id", + "source": [ { "outbound": [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" ] }, "RID" ] - } - ], - "filter": "detailed" + }, + "details" + ] } }, { "schema": "PDB", - "table": "ihm_entry_collection_mapping", + "table": "ihm_relaxation_time", + "uri": "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value": { + "detailed": [ + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + ], + "filter": "detailed" + } + }, + { + "schema": "PDB", + "table": "ihm_relaxation_time_multi_state_scheme", "uri": "tag:misd.isi.edu,2015:display", "value": { - "name": "Entry Collection Mappings", + "name": "Mapping experimentally measured relaxation times with multi-state schemes", "comment_display": { "*": { "table_comment_display" : "inline" @@ -10082,134 +11732,192 @@ }, { "schema": "PDB", - "table": "ihm_entry_collection_mapping", + "table": "ihm_relaxation_time_multi_state_scheme", "uri": "tag:isrd.isi.edu,2016:visible-columns", "value": { - "compact": [ + "*": [ "RID", { - "comment": "Entry Collection Id", - "markdown_name": "Entry Collection Id", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" ] }, - "id" + "RID" ] }, + "id", { - "comment": "Entry Id", - "markdown_name": "Entry Id", + "comment": "Identifier for the multi-state scheme", + "markdown_name": "Scheme Id", "source": [ { "outbound": [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" ] }, - "id" + "RID" ] }, - { - "comment": "Entry Accession Code", - "markdown_name": "Accession Code", + { + "comment": "Identifier for the multi-state scheme connectivity", + "markdown_name": "Scheme Connectivity Id", "source": [ - { + { "outbound": [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" - ] - }, - "Accession_Code" - ] - } + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "Identifier for the relaxation time", + "markdown_name": "Relaxation Time Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" ], "detailed": [ "RID", { - "comment": "Entry Collection Id", - "markdown_name": "Entry Collection Id", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" ] }, - "id" + "RID" ] }, + "id", { - "comment": "Entry Id", - "markdown_name": "Entry Id", + "comment": "Identifier for the multi-state scheme", + "markdown_name": "Scheme Id", "source": [ { "outbound": [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" ] }, - "id" + "RID" ] }, - { - "comment": "Entry Accession Code", - "markdown_name": "Accession Code", + { + "comment": "Identifier for the multi-state scheme connectivity", + "markdown_name": "Scheme Connectivity Id", "source": [ - { + { "outbound": [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "Identifier for the relaxation time", + "markdown_name": "Relaxation Time Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" ] }, - "Accession_Code" - ] + "RID" + ] }, + "details", [ "PDB", - "ihm_entry_collection_mapping_RCB_fkey" + "ihm_relaxation_time_multi_state_scheme_RCB_fkey" ], [ "PDB", - "ihm_entry_collection_mapping_RMB_fkey" + "ihm_relaxation_time_multi_state_scheme_RMB_fkey" ], "RCT", "RMT", [ "PDB", - "ihm_entry_collection_mapping_Owner_fkey" + "ihm_relaxation_time_multi_state_scheme_Owner_fkey" ] ], "entry": [ { - "comment": "Entry Collection Id", - "markdown_name": "Entry Collection Id", + "comment": "A reference to table entry.id.", + "markdown_name": "Structure Id", "source": [ { "outbound": [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" ] }, - "id" + "RID" ] }, + "id", { - "comment": "Entry Id", - "markdown_name": "Entry Id", + "comment": "Identifier for the multi-state scheme", + "markdown_name": "Scheme Id", "source": [ { "outbound": [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" ] }, - "id" + "RID" ] - } + }, + { + "comment": "Identifier for the multi-state scheme connectivity", + "markdown_name": "Scheme Connectivity Id", + "source": [ + { + "outbound": [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment": "Identifier for the relaxation time", + "markdown_name": "Relaxation Time Id", + "source": [ + { + "outbound": [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" ] } }, @@ -12432,6 +14140,14 @@ [ "PDB", "ihm_localization_density_files_file_id_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" ] ], "filter": "detailed" @@ -15297,6 +17013,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -15322,6 +17042,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -15360,6 +17084,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -15579,6 +17307,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -15656,6 +17388,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -15746,6 +17482,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -19883,11 +21623,11 @@ ], [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ], [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_ensemble_model_group_id_begin_fkey" ], [ "PDB", @@ -25956,6 +27696,20 @@ "*": [ "RID", "Name", +#if defined(dev) + { + "markdown_name" : "Archive Category", + "source" : [ + { + "outbound" : [ + "Vocab", + "System_Generated_File_Type_Archive_Category_Name_fkey" + ] + }, + "Name" + ] + }, +#endif "Description", "ID", "URI", @@ -25987,11 +27741,58 @@ "RMT", [ "Vocab", - "System_Generated_File_Type_Owner_fkey" + "System_Generated_File_Type_Owner_fkey" + ] + ] + } + }, +#if defined(dev) + { + "schema": "Vocab", + "table": "Archive_Category", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", + "Name", + "Directory_Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "Archive_Category_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "Archive_Category_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "Archive_Category_Owner_fkey" ] ] } }, +#endif { "schema": "Vocab", "table": "ihm_dataset_list_data_type", @@ -26568,6 +28369,50 @@ ] } }, + { + "schema": "Vocab", + "table": "struct_pdbx_structure_determination_methodology", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_Owner_fkey" + ] + ] + } + }, { "schema": "Vocab", "table": "software_type", @@ -26624,6 +28469,94 @@ ] } }, + { + "schema": "Vocab", + "table": "ihm_relaxation_time_unit", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_relaxation_time_unit_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_relaxation_time_unit_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "ihm_relaxation_time_unit_term_Owner_fkey" + ] + ] + } + }, + { + "schema": "Vocab", + "table": "ihm_equilibrium_constant_determination_method", + "uri": "tag:isrd.isi.edu,2016:visible-columns", + "value": { + "*": [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_Owner_fkey" + ] + ] + } + }, { "schema": "Vocab", "table": "ihm_geometric_object_half_torus_section", @@ -27626,36 +29559,36 @@ "url": "/chaise/recordset/catalog_number/PDB:ihm_multi_state_modeling" }, { - "name": "Ihm Ordered Ensemble", - "url": "/chaise/recordset/catalog_number/PDB:ihm_ordered_ensemble" + "name": "Ihm Ordered Model", + "url": "/chaise/recordset/catalog_number/PDB:ihm_ordered_model" } ], - "name": "Multi-state Modeling and Ordered Ensembles" + "name": "Multi-state Modeling, Ordered Models, and Ensembles" }, { "children": [ { - "name": "PDBX Entity Poly Na Type", - "url": "/chaise/recordset/catalog_number/PDB:pdbx_entity_poly_na_type" + "name": "ihm Multi-State Scheme", + "url": "/chaise/recordset/catalog_number/PDB:ihm_multi_state_scheme" }, { - "name": "PDBX Entry Details", - "url": "/chaise/recordset/catalog_number/PDB:pdbx_entry_details" + "name": "ihm Multi-State Scheme Connectivity", + "url": "/chaise/recordset/catalog_number/PDB:ihm_multi_state_scheme_connectivity" }, { - "name": "PDBX Inhibitor Info", - "url": "/chaise/recordset/catalog_number/PDB:pdbx_inhibitor_info" + "name": "ihm Kinetic Rate", + "url": "/chaise/recordset/catalog_number/PDB:ihm_kinetic_rate" }, { - "name": "PDBX Ion Info", - "url": "/chaise/recordset/catalog_number/PDB:pdbx_ion_info" + "name": "ihm Relaxation Time", + "url": "/chaise/recordset/catalog_number/PDB:ihm_relaxation_time" }, { - "name": "PDBX Protein Info", - "url": "/chaise/recordset/catalog_number/PDB:pdbx_protein_info" + "name": "ihm Relaxation Time Multi-State Scheme", + "url": "/chaise/recordset/catalog_number/PDB:ihm_relaxation_time_multi_state_scheme" } ], - "name": "PDBX Related" + "name": "Multi-State Schemes" }, { "children": [ @@ -27779,6 +29712,19 @@ } ], "name": "Entry Collection" + }, + { + "children": [ + { + "name": "PDB Archive", + "url": "/chaise/recordset/catalog_number/PDB:PDB_Archive" + }, + { + "name": "Entry Latest Archive", + "url": "/chaise/recordset/catalog_number/PDB:Entry_Latest_Archive" + } + ], + "name": "Archive" } ], "name": "Data Categories" @@ -27925,6 +29871,10 @@ "name": "Database Hosted", "url": "/chaise/recordset/catalog_number/Vocab:ihm_dataset_list_database_hosted" }, + { + "name": "Related DB Reference DB Name", + "url": "/chaise/recordset/catalog_number/Vocab:ihm_dataset_related_db_reference_db_name" + }, { "name": "Group Conditionality", "url": "/chaise/recordset/catalog_number/Vocab:ihm_derived_distance_restraint_group_conditionality" @@ -28084,6 +30034,14 @@ { "name": "Experiment Type", "url": "/chaise/recordset/catalog_number/Vocab:ihm_multi_state_modeling_experiment_type" + }, + { + "name": "Relaxation Time Unit", + "url": "/chaise/recordset/catalog_number/Vocab:ihm_relaxation_time_unit" + }, + { + "name": "Equilibrium Constant Determination Methods", + "url": "/chaise/recordset/catalog_number/Vocab:ihm_equilibrium_constant_determination_method" } ], "name": "Ihm Multi State Modeling" @@ -28219,6 +30177,10 @@ }, { "children": [ + { + "name": "PDBX Structure Determination Methodology", + "url": "/chaise/recordset/catalog_number/Vocab:struct_pdbx_structure_determination_methodology" + }, { "name": "PDBX CASP Flag", "url": "/chaise/recordset/catalog_number/Vocab:struct_pdbx_CASP_flag" @@ -28236,6 +30198,12 @@ }, { "children": [ +#if defined(dev) + { + "name": "Archive Category", + "url": "/chaise/recordset/catalog_number/Vocab:Archive_Category" + }, +#endif { "name": "File Format", "url": "/chaise/recordset/catalog_number/Vocab:File_Format" @@ -28698,6 +30666,30 @@ "domain_filter_pattern": "structure_id={{structure_id}}" } }, + { + "foreign_key": "ihm_ordered_model_ihm_model_group_1_combo1_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_ordered_model", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + //"from_name": "Ihm Model Group Id Begin", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "ihm_ordered_model_ihm_model_group_2_combo1_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_ordered_model", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + //"from_name": "Ihm Model Group Id End", + "template_engine": "handlebars" + } + }, { "foreign_key": "ihm_ordered_ensemble_model_group_id_begin_fkey", "foreign_key_schema": "PDB", @@ -30638,6 +32630,140 @@ "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", "template_engine": "handlebars" } + }, + { + "foreign_key": "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_multi_state_scheme_connectivity", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_multi_state_scheme_connectivity", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + //"from_name": "Ihm Multi State Modeling Begin State", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_multi_state_scheme_connectivity", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + //"from_name": "Ihm Multi State Modeling End State", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "multi_state_scheme_connectivity_dataset_group_combo1_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_multi_state_scheme_connectivity", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_kinetic_rate", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "ihm_kinetic_rate_ihm_external_files_combo2_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_kinetic_rate", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_kinetic_rate", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "ihm_relaxation_time_ihm_external_files_combo2_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_relaxation_time", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "ihm_relaxation_time_ihm_dataset_group_combo1_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_relaxation_time", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "relaxation_time_multi_state_scheme_connectivity_combo2_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_relaxation_time_multi_state_scheme", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_relaxation_time_multi_state_scheme", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine": "handlebars" + } + }, + { + "foreign_key": "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey", + "foreign_key_schema": "PDB", + "schema": "PDB", + "table": "ihm_relaxation_time_multi_state_scheme", + "uri": "tag:isrd.isi.edu,2016:foreign-key", + "value": { + "domain_filter_pattern": "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine": "handlebars" + } } #endif ] diff --git a/config-scripts/annotations/dev_annotation_config.json b/config-scripts/annotations/dev_annotation_config.json index b9be81c..f2dd5a5 100644 --- a/config-scripts/annotations/dev_annotation_config.json +++ b/config-scripts/annotations/dev_annotation_config.json @@ -498,36 +498,36 @@ "url" : "/chaise/recordset/#99/PDB:ihm_multi_state_modeling" }, { - "name" : "Ihm Ordered Ensemble", - "url" : "/chaise/recordset/#99/PDB:ihm_ordered_ensemble" + "name" : "Ihm Ordered Model", + "url" : "/chaise/recordset/#99/PDB:ihm_ordered_model" } ], - "name" : "Multi-state Modeling and Ordered Ensembles" + "name" : "Multi-state Modeling, Ordered Models, and Ensembles" }, { "children" : [ { - "name" : "PDBX Entity Poly Na Type", - "url" : "/chaise/recordset/#99/PDB:pdbx_entity_poly_na_type" + "name" : "ihm Multi-State Scheme", + "url" : "/chaise/recordset/#99/PDB:ihm_multi_state_scheme" }, { - "name" : "PDBX Entry Details", - "url" : "/chaise/recordset/#99/PDB:pdbx_entry_details" + "name" : "ihm Multi-State Scheme Connectivity", + "url" : "/chaise/recordset/#99/PDB:ihm_multi_state_scheme_connectivity" }, { - "name" : "PDBX Inhibitor Info", - "url" : "/chaise/recordset/#99/PDB:pdbx_inhibitor_info" + "name" : "ihm Kinetic Rate", + "url" : "/chaise/recordset/#99/PDB:ihm_kinetic_rate" }, { - "name" : "PDBX Ion Info", - "url" : "/chaise/recordset/#99/PDB:pdbx_ion_info" + "name" : "ihm Relaxation Time", + "url" : "/chaise/recordset/#99/PDB:ihm_relaxation_time" }, { - "name" : "PDBX Protein Info", - "url" : "/chaise/recordset/#99/PDB:pdbx_protein_info" + "name" : "ihm Relaxation Time Multi-State Scheme", + "url" : "/chaise/recordset/#99/PDB:ihm_relaxation_time_multi_state_scheme" } ], - "name" : "PDBX Related" + "name" : "Multi-State Schemes" }, { "children" : [ @@ -651,6 +651,19 @@ } ], "name" : "Entry Collection" + }, + { + "children" : [ + { + "name" : "PDB Archive", + "url" : "/chaise/recordset/#99/PDB:PDB_Archive" + }, + { + "name" : "Entry Latest Archive", + "url" : "/chaise/recordset/#99/PDB:Entry_Latest_Archive" + } + ], + "name" : "Archive" } ], "name" : "Data Categories" @@ -807,6 +820,10 @@ "name" : "Database Hosted", "url" : "/chaise/recordset/#99/Vocab:ihm_dataset_list_database_hosted" }, + { + "name" : "Related DB Reference DB Name", + "url" : "/chaise/recordset/#99/Vocab:ihm_dataset_related_db_reference_db_name" + }, { "name" : "Group Conditionality", "url" : "/chaise/recordset/#99/Vocab:ihm_derived_distance_restraint_group_conditionality" @@ -966,6 +983,14 @@ { "name" : "Experiment Type", "url" : "/chaise/recordset/#99/Vocab:ihm_multi_state_modeling_experiment_type" + }, + { + "name" : "Relaxation Time Unit", + "url" : "/chaise/recordset/#99/Vocab:ihm_relaxation_time_unit" + }, + { + "name" : "Equilibrium Constant Determination Methods", + "url" : "/chaise/recordset/#99/Vocab:ihm_equilibrium_constant_determination_method" } ], "name" : "Ihm Multi State Modeling" @@ -1101,6 +1126,10 @@ }, { "children" : [ + { + "name" : "PDBX Structure Determination Methodology", + "url" : "/chaise/recordset/#99/Vocab:struct_pdbx_structure_determination_methodology" + }, { "name" : "PDBX CASP Flag", "url" : "/chaise/recordset/#99/Vocab:struct_pdbx_CASP_flag" @@ -1118,6 +1147,10 @@ }, { "children" : [ + { + "name" : "Archive Category", + "url" : "/chaise/recordset/#99/Vocab:Archive_Category" + }, { "name" : "File Format", "url" : "/chaise/recordset/#99/Vocab:File_Format" @@ -1261,6 +1294,42 @@ "url_pattern" : "/hatrac/dev/WWW/Page_Asset/{{{MD5}}}.{{#encode}}{{{Filename}}}{{/encode}}" } }, + { + "column" : "Current_File_Holdings_URL", + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:isrd.isi.edu,2017:asset", + "value" : { + "byte_count_column" : "Current_File_Holdings_Bytes", + "filename_column" : "Current_File_Holdings_Name", + "md5" : "Current_File_Holdings_MD5", + "url_pattern" : "/hatrac/dev/pdb/archive/holdings/{{{Current_File_Holdings_Name}}}" + } + }, + { + "column" : "Released_Structures_LMD_URL", + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:isrd.isi.edu,2017:asset", + "value" : { + "byte_count_column" : "Released_Structures_LMD_Bytes", + "filename_column" : "Released_Structures_LMD_Name", + "md5" : "Released_Structures_LMD_MD5", + "url_pattern" : "/hatrac/dev/pdb/archive/holdings/{{{Released_Structures_LMD_Name}}}" + } + }, + { + "column" : "Unreleased_Entries_URL", + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:isrd.isi.edu,2017:asset", + "value" : { + "byte_count_column" : "Unreleased_Entries_Bytes", + "filename_column" : "Unreleased_Entries_Name", + "md5" : "Unreleased_Entries_MD5", + "url_pattern" : "/hatrac/dev/pdb/archive/holdings/{{{Unreleased_Entries_Name}}}" + } + }, { "column" : "Image_File_URL", "schema" : "PDB", @@ -1392,7 +1461,7 @@ "filename_column" : "File_Name", "md5" : "File_MD5", "template_engine" : "handlebars", - "url_pattern" : "/hatrac/dev/pdb/generated/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/id/{{{Structure_Id}}}/final_mmCIF/{{{File_Name}}}" + "url_pattern" : "/hatrac/dev/pdb/generated/uid/{{#if _Entry_RCB}}{{#regexFindFirst _Entry_RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/id/{{{Structure_Id}}}/final_mmCIF/{{{File_Name}}}" } }, { @@ -1496,6 +1565,98 @@ "uri" : "tag:isrd.isi.edu,2018:required", "value" : {} }, + { + "column" : "Archive_Category", + "schema" : "Vocab", + "table" : "System_Generated_File_Type", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "Archive Category" + } + }, + { + "column" : "Current_File_Holdings_URL", + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "Current File Holdings" + } + }, + { + "column" : "Released_Structures_LMD_URL", + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "Released Structures LMD" + } + }, + { + "column" : "Unreleased_Entries_URL", + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "Unreleased Entries" + } + }, + { + "column" : "Current_File_Holdings_MD5", + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "Current File Holdings MD5" + } + }, + { + "column" : "Unreleased_Entries_MD5", + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "Unreleased Entries MD5" + } + }, + { + "column" : "Released_Structures_LMD_MD5", + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "Released Structures LMD MD5" + } + }, + { + "column" : "mmCIF_URL", + "schema" : "PDB", + "table" : "Entry_Latest_Archive", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "mmCIF" + } + }, + { + "column" : "mmCIF_URL", + "schema" : "PDB", + "table" : "Entry_Latest_Archive", + "uri" : "tag:isrd.isi.edu,2016:column-display", + "value" : { + "*" : { + "markdown_pattern" : "[{{Entry}}]({{#encode}}{{{mmCIF_URL}}}{{/encode}})" + } + } + }, + { + "column" : "Released_Structures_LMD_Name", + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "Released Structures LMD Name" + } + }, { "column" : "pdbx_descriptor", "schema" : "PDB", @@ -3026,6 +3187,28 @@ "domain_filter_pattern" : "structure_id={{structure_id}}" } }, + { + "foreign_key" : "ihm_ordered_model_ihm_model_group_1_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_ordered_model", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_ordered_model_ihm_model_group_2_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_ordered_model", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, { "foreign_key" : "ihm_ordered_ensemble_model_group_id_begin_fkey", "foreign_key_schema" : "PDB", @@ -4965,6 +5148,138 @@ "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", "template_engine" : "handlebars" } + }, + { + "foreign_key" : "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "multi_state_scheme_connectivity_dataset_group_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_kinetic_rate_ihm_external_files_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_ihm_external_files_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_ihm_dataset_group_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "relaxation_time_multi_state_scheme_connectivity_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } } ], "known_attributes" : { @@ -5040,6 +5355,19 @@ } } }, + { + "schema" : "PDB", + "table" : "PDB_Archive", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "PDB Archive" + } + }, { "schema" : "PDB", "table" : "ihm_localization_density_files", @@ -7984,7 +8312,7 @@ }, { "schema" : "PDB", - "table" : "ihm_ordered_ensemble", + "table" : "ihm_ordered_model", "uri" : "tag:misd.isi.edu,2015:display", "value" : { "comment_display" : { @@ -7992,12 +8320,12 @@ "table_comment_display" : "inline" } }, - "name" : "Ordered States" + "name" : "Ordered Models" } }, { "schema" : "PDB", - "table" : "ihm_ordered_ensemble", + "table" : "ihm_ordered_model", "uri" : "tag:isrd.isi.edu,2016:visible-columns", "value" : { "*" : [ @@ -8009,7 +8337,7 @@ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_structure_id_fkey" + "ihm_ordered_model_structure_id_fkey" ] }, "RID" @@ -8023,26 +8351,26 @@ "step_description", "ordered_by", { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the origin of the directed edge", "markdown_name" : "Model Group Id Begin", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ] }, "RID" ] }, { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the end of the directed edge", "markdown_name" : "Model Group Id End", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" ] }, "RID" @@ -8058,7 +8386,7 @@ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_structure_id_fkey" + "ihm_ordered_model_structure_id_fkey" ] }, "RID" @@ -8072,26 +8400,26 @@ "step_description", "ordered_by", { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the origin of the directed edge", "markdown_name" : "Model Group Id Begin", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ] }, "RID" ] }, { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the end of the directed edge", "markdown_name" : "Model Group Id End", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" ] }, "RID" @@ -8099,17 +8427,17 @@ }, [ "PDB", - "ihm_ordered_ensemble_RCB_fkey" + "ihm_ordered_model_RCB_fkey" ], [ "PDB", - "ihm_ordered_ensemble_RMB_fkey" + "ihm_ordered_model_RMB_fkey" ], "RCT", "RMT", [ "PDB", - "ihm_ordered_ensemble_Owner_fkey" + "ihm_ordered_model_Owner_fkey" ] ], "entry" : [ @@ -8120,7 +8448,7 @@ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_structure_id_fkey" + "ihm_ordered_model_structure_id_fkey" ] }, "RID" @@ -8134,26 +8462,206 @@ "step_description", "ordered_by", { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the origin of the directed edge", "markdown_name" : "Model Group Id Begin", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ] }, "RID" ] }, { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the end of the directed edge", "markdown_name" : "Model Group Id End", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" + ] + }, + "RID" + ] + } + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_ordered_ensemble", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Ordered Ensembles (to be deprecated and superseded by Ordered Models)" + } + }, + { + "schema" : "PDB", + "table" : "ihm_ordered_ensemble", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id Begin", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_begin_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id End", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_end_fkey" + ] + }, + "RID" + ] + } + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id Begin", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_begin_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id End", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_end_fkey" + ] + }, + "RID" + ] + }, + [ + "PDB", + "ihm_ordered_ensemble_RCB_fkey" + ], + [ + "PDB", + "ihm_ordered_ensemble_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_ordered_ensemble_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id Begin", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_begin_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id End", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_end_fkey" ] }, "RID" @@ -9578,6 +10086,10 @@ [ "PDB", "ihm_multi_state_model_group_link_state_id_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" ] ], "filter" : "detailed" @@ -9712,6 +10224,18 @@ [ "PDB", "ihm_modeling_post_process_dataset_group_id_fkey" + ], + [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" ] ], "filter" : "detailed" @@ -9830,6 +10354,22 @@ "RID", "Accession_Serial", "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, { "markdown_name" : "Entry", "source" : [ @@ -9842,6 +10382,25 @@ "RID" ] }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + { + "outbound" : [ + "PDB", + "entry_Workflow_Status_fkey" + ] + }, + "Name" + ] + }, + "Notes", { "markdown_name" : "RCB", "source" : [ @@ -9901,6 +10460,23 @@ }, "Accession_Serial", "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + "Notes", { "markdown_name" : "Entry", "source" : [ @@ -9912,6 +10488,24 @@ }, "RID" ] + }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + { + "outbound" : [ + "PDB", + "entry_Workflow_Status_fkey" + ] + }, + "Name" + ] } ], "entry" : [ @@ -9926,20 +10520,103 @@ }, "RID" ] - } + }, + "Accession_Serial", + "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + "Notes" ], "entry/edit" : [ - "Accession_Code" - ], - "filter" : { - "and" : [ - { + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + "RID" + ] + }, + "Accession_Serial", + "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + "Notes" + ], + "filter" : { + "and" : [ + { "markdown_name" : "Accession Serial", "source" : "Accession_Serial" }, { "markdown_name" : "Accession Code", "source" : "Accession_Code" + }, + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + { + "outbound" : [ + "PDB", + "entry_Workflow_Status_fkey" + ] + }, + "Name" + ] } ] } @@ -10004,6 +10681,7 @@ "Deposit_Date", "Release_Date", "Method_Details", + "Manual_Processing", { "markdown_name" : "RCB", "source" : [ @@ -10101,6 +10779,7 @@ "Method_Details", "Submitter_Flag", "Submitter_Flag_Date", + "Manual_Processing", "Notes", [ "PDB", @@ -10115,6 +10794,7 @@ "entry_Workflow_Status_fkey" ], "Method_Details", + "Manual_Processing", "Notes" ], "entry/edit" : [ @@ -10129,6 +10809,7 @@ "Release_Date", "Submitter_Flag", "Submitter_Flag_Date", + "Manual_Processing", "Notes" ], "export/compact" : [ @@ -10238,6 +10919,10 @@ }, "RID" ] + }, + { + "markdown_name" : "Manual Processing", + "source" : "Manual_Processing" } ] } @@ -10245,36 +10930,110 @@ }, { "schema" : "PDB", - "table" : "entry", - "uri" : "tag:isrd.isi.edu,2019:export", + "table" : "PDB_Archive", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", "value" : { - "compact" : { - "templates" : [ + "*" : [ + "RID", + "Submission_Time", + "Submitted_Entries", + "Current_File_Holdings_URL", + "Released_Structures_LMD_URL", + "Unreleased_Entries_URL", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "PDB", + "PDB_Archive_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "PDB", + "PDB_Archive_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT" + ], + "detailed" : [ + "RID", + "Submission_Time", + "Submitted_Entries", + "Current_File_Holdings_URL", + { + "markdown_name" : "Current File Holdings Size (Bytes)", + "source" : "Current_File_Holdings_Bytes" + }, + "Released_Structures_LMD_URL", + { + "markdown_name" : "Released Structures LMD Size (Bytes)", + "source" : "Released_Structures_LMD_Bytes" + }, + "Unreleased_Entries_URL", + { + "markdown_name" : "Unreleased Entries Bytes Size (Bytes)", + "source" : "Unreleased_Entries_Bytes" + }, + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "PDB", + "PDB_Archive_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "PDB", + "PDB_Archive_RMB_fkey" + ] + }, + "Full_Name" + ] + } + ], + "entry" : [ + "Submission_Time", + "Submitted_Entries", + "Current_File_Holdings_URL", + "Released_Structures_LMD_URL", + "Unreleased_Entries_URL" + ], + "entry/edit" : [ + "Submission_Time", + "Submitted_Entries", + "Current_File_Holdings_URL", + "Released_Structures_LMD_URL", + "Unreleased_Entries_URL" + ], + "filter" : { + "and" : [ { - "displayname" : "BDBag", - "outputs" : [ - { - "destination" : { - "name" : "entry", - "type" : "csv" - }, - "source" : { - "api" : "entity", - "table" : "PDB:entry" - } - }, - { - "destination" : { - "name" : "Entry_Generated_File", - "type" : "download" - }, - "source" : { - "api" : "attribute", - "path" : "PDB:Entry_Generated_File/url:=File_URL" - } - } - ], - "type" : "BAG" + "markdown_name" : "Submission Date", + "source" : "Submission_Time" + }, + { + "markdown_name" : "Submitted Entries", + "source" : "Submitted_Entries" } ] } @@ -10282,47 +11041,311 @@ }, { "schema" : "PDB", - "table" : "entry", - "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "table" : "Entry_Latest_Archive", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", "value" : { + "*" : [ + "RID", + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "RID" + ] + }, + { + "markdown_name" : "Archive", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Archive_Submission_Time_fkey" + ] + }, + "RID" + ] + }, + "mmCIF_URL", + { + "markdown_name" : "Accession Code", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "Accession_Code" + ] + }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "Workflow_Status" + ] + }, + "Submitted_Files", + "Submission_Time", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT" + ], "detailed" : [ - [ - "PDB", - "Entry_Generated_File_Structure_Id_fkey" - ], - [ - "PDB", - "struct_entry_id_fkey" - ], - [ - "PDB", - "audit_author_structure_id_fkey" - ], - [ - "PDB", - "citation_structure_id_fkey" - ], - [ - "PDB", - "citation_author_structure_id_fkey" - ], - [ - "PDB", - "software_structure_id_fkey" - ], - [ - "PDB", - "chem_comp_structure_id_fkey" - ], - [ - "PDB", - "entity_structure_id_fkey" - ], - [ - "PDB", - "entity_name_com_structure_id_fkey" - ], - [ + "RID", + "Submission_Time", + { + "markdown_name" : "Accession Code", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "Accession_Code" + ] + }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "Workflow_Status" + ] + }, + "Submitted_Files", + "mmCIF_URL", + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "RID" + ] + }, + { + "markdown_name" : "Archive", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Archive_Submission_Time_fkey" + ] + }, + "RID" + ] + }, + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_RMB_fkey" + ] + }, + "Full_Name" + ] + } + ], + "entry" : [ + "Submission_Time", + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "RID" + ] + }, + { + "markdown_name" : "Archive", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Archive_Submission_Time_fkey" + ] + }, + "RID" + ] + } + ], + "entry/edit" : [ + "Submission_Time", + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Entry_fkey" + ] + }, + "RID" + ] + }, + { + "markdown_name" : "Archive", + "source" : [ + { + "outbound" : [ + "PDB", + "Entry_Latest_Archive_Archive_Submission_Time_fkey" + ] + }, + "RID" + ] + } + ], + "filter" : { + "and" : [ + { + "markdown_name" : "Submission Date", + "source" : "Submission_Time" + } + ] + } + } + }, + { + "schema" : "PDB", + "table" : "entry", + "uri" : "tag:isrd.isi.edu,2019:export", + "value" : { + "compact" : { + "templates" : [ + { + "displayname" : "BDBag", + "outputs" : [ + { + "destination" : { + "name" : "entry", + "type" : "csv" + }, + "source" : { + "api" : "entity", + "table" : "PDB:entry" + } + }, + { + "destination" : { + "name" : "Entry_Generated_File", + "type" : "download" + }, + "source" : { + "api" : "attribute", + "path" : "PDB:Entry_Generated_File/url:=File_URL" + } + } + ], + "type" : "BAG" + } + ] + } + } + }, + { + "schema" : "PDB", + "table" : "entry", + "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value" : { + "detailed" : [ + [ + "PDB", + "Entry_Generated_File_Structure_Id_fkey" + ], + [ + "PDB", + "struct_entry_id_fkey" + ], + [ + "PDB", + "audit_author_structure_id_fkey" + ], + [ + "PDB", + "citation_structure_id_fkey" + ], + [ + "PDB", + "citation_author_structure_id_fkey" + ], + [ + "PDB", + "software_structure_id_fkey" + ], + [ + "PDB", + "chem_comp_structure_id_fkey" + ], + [ + "PDB", + "entity_structure_id_fkey" + ], + [ + "PDB", + "entity_name_com_structure_id_fkey" + ], + [ "PDB", "entity_name_sys_structure_id_fkey" ], @@ -10482,6 +11505,10 @@ "PDB", "ihm_multi_state_model_group_link_structure_id_fkey" ], + [ + "PDB", + "ihm_ordered_model_structure_id_fkey" + ], [ "PDB", "ihm_ordered_ensemble_structure_id_fkey" @@ -10650,6 +11677,26 @@ "PDB", "ihm_geometric_object_distance_restraint_structure_id_fkey" ], + [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ], { "comment" : "Collections to which the entry belongs", "markdown_name" : "Entry Collections", @@ -13483,67 +14530,1062 @@ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Accession Code", + "markdown_name" : "Accession Code", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "Accession_Code" + ] + }, + [ + "PDB", + "ihm_entry_collection_mapping_RCB_fkey" + ], + [ + "PDB", + "ihm_entry_collection_mapping_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_entry_collection_mapping_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "Entry Collection Id", + "markdown_name" : "Entry Collection Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_collection_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Id", + "markdown_name" : "Entry Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "id" + ] + } + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Multi-State Schemes" + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "name", + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "name", + "details", + [ + "PDB", + "ihm_multi_state_scheme_RCB_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_multi_state_scheme_Owner_fkey" + ] + ], + "entry" : [ + "id", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "name", + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value" : { + "detailed" : [ + [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + ], + "filter" : "detailed" + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Multi-State Scheme Connectivities" + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the starting state in the multi-state scheme", + "markdown_name" : "Begin State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the ending state in the multi-state scheme", + "markdown_name" : "End State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the starting state in the multi-state scheme", + "markdown_name" : "Begin State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the ending state in the multi-state scheme", + "markdown_name" : "End State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_multi_state_scheme_connectivity_RCB_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_multi_state_scheme_connectivity_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the starting state in the multi-state scheme", + "markdown_name" : "Begin State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the ending state in the multi-state scheme", + "markdown_name" : "End State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value" : { + "detailed" : [ + [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ], + [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + ], + "filter" : "detailed" + } + }, + { + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Kinetic Rates from Biophysical Experiments" + } + }, + { + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_kinetic_rate_RCB_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_kinetic_rate_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Relaxation times from Biophysical Experiments" + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", + { + "comment" : "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", + { + "comment" : "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_relaxation_time_RCB_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_relaxation_time_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", + { + "comment" : "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value" : { + "detailed" : [ + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + ], + "filter" : "detailed" + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Mapping experimentally measured relaxation times with multi-state schemes" + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the relaxation time", + "markdown_name" : "Relaxation Time Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" ] }, - "id" + "RID" ] }, { - "comment" : "Entry Accession Code", - "markdown_name" : "Accession Code", + "comment" : "Identifier for the relaxation time", + "markdown_name" : "Relaxation Time Id", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" ] }, - "Accession_Code" + "RID" ] }, + "details", [ "PDB", - "ihm_entry_collection_mapping_RCB_fkey" + "ihm_relaxation_time_multi_state_scheme_RCB_fkey" ], [ "PDB", - "ihm_entry_collection_mapping_RMB_fkey" + "ihm_relaxation_time_multi_state_scheme_RMB_fkey" ], "RCT", "RMT", [ "PDB", - "ihm_entry_collection_mapping_Owner_fkey" + "ihm_relaxation_time_multi_state_scheme_Owner_fkey" ] ], "entry" : [ { - "comment" : "Entry Collection Id", - "markdown_name" : "Entry Collection Id", + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" ] }, - "id" + "RID" ] }, + "id", { - "comment" : "Entry Id", - "markdown_name" : "Entry Id", + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" ] }, - "id" + "RID" ] - } + }, + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the relaxation time", + "markdown_name" : "Relaxation Time Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" ] } }, @@ -15764,6 +17806,14 @@ [ "PDB", "ihm_localization_density_files_file_id_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" ] ], "filter" : "detailed" @@ -18627,6 +20677,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -18652,6 +20706,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -18690,6 +20748,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -18909,6 +20971,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -18986,6 +21052,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -19076,6 +21146,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -22874,12 +24948,26 @@ "File_Bytes", "File_MD5" ], - "entry" : [], + "entry" : [ + "File_URL", + [ + "PDB", + "Entry_Generated_File_System_Generated_File_Type_fkey" + ], + [ + "PDB", + "Entry_Generated_File_Structure_Id_Entry_RCB_fkey" + ] + ], "entry/edit" : [ "File_URL", [ "PDB", "Entry_Generated_File_System_Generated_File_Type_fkey" + ], + [ + "PDB", + "Entry_Generated_File_Structure_Id_Entry_RCB_fkey" ] ] } @@ -23232,11 +25320,11 @@ ], [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ], [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_ensemble_model_group_id_begin_fkey" ], [ "PDB", @@ -29305,6 +31393,18 @@ "*" : [ "RID", "Name", + { + "markdown_name" : "Archive Category", + "source" : [ + { + "outbound" : [ + "Vocab", + "System_Generated_File_Type_Archive_Category_Name_fkey" + ] + }, + "Name" + ] + }, "Description", "ID", "URI", @@ -29341,6 +31441,51 @@ ] } }, + { + "schema" : "Vocab", + "table" : "Archive_Category", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + "Name", + "Directory_Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "Archive_Category_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "Archive_Category_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "Archive_Category_Owner_fkey" + ] + ] + } + }, { "schema" : "Vocab", "table" : "ihm_dataset_list_data_type", @@ -29917,6 +32062,50 @@ ] } }, + { + "schema" : "Vocab", + "table" : "struct_pdbx_structure_determination_methodology", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_Owner_fkey" + ] + ] + } + }, { "schema" : "Vocab", "table" : "software_type", @@ -29973,6 +32162,94 @@ ] } }, + { + "schema" : "Vocab", + "table" : "ihm_relaxation_time_unit", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_relaxation_time_unit_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_relaxation_time_unit_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "ihm_relaxation_time_unit_term_Owner_fkey" + ] + ] + } + }, + { + "schema" : "Vocab", + "table" : "ihm_equilibrium_constant_determination_method", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_Owner_fkey" + ] + ] + } + }, { "schema" : "Vocab", "table" : "ihm_geometric_object_half_torus_section", diff --git a/config-scripts/annotations/production_annotation_config.json b/config-scripts/annotations/production_annotation_config.json index 96f5a79..5b202ec 100644 --- a/config-scripts/annotations/production_annotation_config.json +++ b/config-scripts/annotations/production_annotation_config.json @@ -48,15 +48,78 @@ "WWW", "Page_Asset" ] + }, + { + "checksum_types" : [ + "sha256", + "md5" + ], + "column_map" : { + "Method_Details" : "Integrative modeling", + "Workflow_Status" : "DEPO", + "mmCIF_File_Bytes" : "{file_size}", + "mmCIF_File_MD5" : "{md5}", + "mmCIF_File_Name" : "{file_name}", + "mmCIF_File_URL" : "{URI}" + }, + "create_record_before_upload" : false, + "file_pattern" : "(?i)^.*/deriva/(?P[^/]*)/entry/.*[.](?Pcif)$", + "hatrac_options" : { + "versioned_urls" : true + }, + "hatrac_templates" : { + "content-disposition" : "filename*=UTF-8''{file_name}", + "hatrac_uri" : "/hatrac/pdb/submitted/uid/{globus_ID}/entry/mmcif/{file_name}" + }, + "metadata_query_templates" : [], + "record_query_template" : "/entity/{target_table}/mmCIF_File_MD5={md5}&RCB=https%3A%2F%2Fauth.globus.org%2F{globus_ID}", + "record_update_template" : "/attributegroup/{target_table}/RID;mmCIF_File_MD5,mmCIF_File_URL,mmCIF_File_Name,mmCIF_File_Bytes", + "require_record_update_template" : true, + "target_table" : [ + "PDB", + "entry" + ] + }, + { + "checksum_types" : [ + "sha256", + "md5" + ], + "column_map" : { + "Image_File_Bytes" : "{file_size}", + "Image_File_MD5" : "{md5}", + "Image_File_Name" : "{file_name}", + "Image_File_URL" : "{URI}", + "RID" : "{entry_rid}" + }, + "create_record_before_upload" : false, + "dir_pattern" : "(?i)^.*/deriva/(?P[^/]*)/entry/(?P[^/]*)[.](?Ppng|jpg|jpeg)", + "hatrac_options" : { + "versioned_urls" : true + }, + "hatrac_templates" : { + "content-disposition" : "filename*=UTF-8''{file_name}", + "hatrac_uri" : "/hatrac/pdb/submitted/uid/{globus_ID}/entry/image/{file_name}" + }, + "metadata_query_templates" : [ + "/attribute/{target_table}/mmCIF_File_Name={base_name}.cif&RCB=https%3A%2F%2Fauth.globus.org%2F{globus_ID}/entry_rid:=RID" + ], + "record_query_template" : "/entity/{target_table}/RID={entry_rid}", + "record_update_template" : "/attributegroup/{target_table}/RID;Image_File_MD5,Image_File_URL,Image_File_Name,Image_File_Bytes", + "require_record_update_template" : true, + "target_table" : [ + "PDB", + "entry" + ] } ], "version_compatibility" : [ [ - ">=0.4.3", - "<1.0.0" + ">=1.4.0", + "<2.0.0" ] ], - "version_update_url" : "https://github.com/informatics-isi-edu/deriva-qt/releases" + "version_update_url" : "https://github.com/informatics-isi-edu/deriva-client" } }, { @@ -435,36 +498,36 @@ "url" : "/chaise/recordset/#1/PDB:ihm_multi_state_modeling" }, { - "name" : "Ihm Ordered Ensemble", - "url" : "/chaise/recordset/#1/PDB:ihm_ordered_ensemble" + "name" : "Ihm Ordered Model", + "url" : "/chaise/recordset/#1/PDB:ihm_ordered_model" } ], - "name" : "Multi-state Modeling and Ordered Ensembles" + "name" : "Multi-state Modeling, Ordered Models, and Ensembles" }, { "children" : [ { - "name" : "PDBX Entity Poly Na Type", - "url" : "/chaise/recordset/#1/PDB:pdbx_entity_poly_na_type" + "name" : "ihm Multi-State Scheme", + "url" : "/chaise/recordset/#1/PDB:ihm_multi_state_scheme" }, { - "name" : "PDBX Entry Details", - "url" : "/chaise/recordset/#1/PDB:pdbx_entry_details" + "name" : "ihm Multi-State Scheme Connectivity", + "url" : "/chaise/recordset/#1/PDB:ihm_multi_state_scheme_connectivity" }, { - "name" : "PDBX Inhibitor Info", - "url" : "/chaise/recordset/#1/PDB:pdbx_inhibitor_info" + "name" : "ihm Kinetic Rate", + "url" : "/chaise/recordset/#1/PDB:ihm_kinetic_rate" }, { - "name" : "PDBX Ion Info", - "url" : "/chaise/recordset/#1/PDB:pdbx_ion_info" + "name" : "ihm Relaxation Time", + "url" : "/chaise/recordset/#1/PDB:ihm_relaxation_time" }, { - "name" : "PDBX Protein Info", - "url" : "/chaise/recordset/#1/PDB:pdbx_protein_info" + "name" : "ihm Relaxation Time Multi-State Scheme", + "url" : "/chaise/recordset/#1/PDB:ihm_relaxation_time_multi_state_scheme" } ], - "name" : "PDBX Related" + "name" : "Multi-State Schemes" }, { "children" : [ @@ -557,13 +620,17 @@ "name" : "Accession Code", "url" : "/chaise/recordset/#1/PDB:Accession_Code" }, + { + "name" : "Curation Log", + "url" : "/chaise/recordset/#1/PDB:Curation_Log" + }, { "name" : "Entry Error File", "url" : "/chaise/recordset/#1/PDB:Entry_Error_File" }, { - "name" : "Entry mmCIF File", - "url" : "/chaise/recordset/#1/PDB:Entry_mmCIF_File" + "name" : "Entry Generated File", + "url" : "/chaise/recordset/#1/PDB:Entry_Generated_File" }, { "name" : "Entry Related File", @@ -584,6 +651,19 @@ } ], "name" : "Entry Collection" + }, + { + "children" : [ + { + "name" : "PDB Archive", + "url" : "/chaise/recordset/#1/PDB:PDB_Archive" + }, + { + "name" : "Entry Latest Archive", + "url" : "/chaise/recordset/#1/PDB:Entry_Latest_Archive" + } + ], + "name" : "Archive" } ], "name" : "Data Categories" @@ -740,6 +820,10 @@ "name" : "Database Hosted", "url" : "/chaise/recordset/#1/Vocab:ihm_dataset_list_database_hosted" }, + { + "name" : "Related DB Reference DB Name", + "url" : "/chaise/recordset/#1/Vocab:ihm_dataset_related_db_reference_db_name" + }, { "name" : "Group Conditionality", "url" : "/chaise/recordset/#1/Vocab:ihm_derived_distance_restraint_group_conditionality" @@ -899,6 +983,14 @@ { "name" : "Experiment Type", "url" : "/chaise/recordset/#1/Vocab:ihm_multi_state_modeling_experiment_type" + }, + { + "name" : "Relaxation Time Unit", + "url" : "/chaise/recordset/#1/Vocab:ihm_relaxation_time_unit" + }, + { + "name" : "Equilibrium Constant Determination Methods", + "url" : "/chaise/recordset/#1/Vocab:ihm_equilibrium_constant_determination_method" } ], "name" : "Ihm Multi State Modeling" @@ -1034,6 +1126,10 @@ }, { "children" : [ + { + "name" : "PDBX Structure Determination Methodology", + "url" : "/chaise/recordset/#1/Vocab:struct_pdbx_structure_determination_methodology" + }, { "name" : "PDBX CASP Flag", "url" : "/chaise/recordset/#1/Vocab:struct_pdbx_CASP_flag" @@ -1064,8 +1160,8 @@ "url" : "/chaise/recordset/#1/Vocab:Process_Status" }, { - "name" : "Validation File Type", - "url" : "/chaise/recordset/#1/Vocab:Validation_File_Type" + "name" : "System Generated File Type", + "url" : "/chaise/recordset/#1/Vocab:System_Generated_File_Type" }, { "name" : "Workflow Status", @@ -1146,38 +1242,6 @@ } } }, - { - "column" : "id", - "schema_pattern" : "Vocab", - "table_pattern" : ".*", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, - { - "column" : "uri", - "schema_pattern" : "Vocab", - "table_pattern" : ".*", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, - { - "column" : "description", - "schema_pattern" : "Vocab", - "table_pattern" : ".*", - "uri" : "tag:misd.isi.edu,2015:display", - "value" : { - "name" : "Description" - } - }, - { - "column" : "name", - "schema_pattern" : "Vocab", - "table_pattern" : ".*", - "uri" : "tag:misd.isi.edu,2015:display", - "value" : { - "name" : "Name" - } - }, { "column" : "synonyms", "schema_pattern" : "Vocab", @@ -1226,13 +1290,6 @@ "url_pattern" : "/hatrac/WWW/Page_Asset/{{{MD5}}}.{{#encode}}{{{Filename}}}{{/encode}}" } }, - { - "column" : "id", - "schema" : "PDB", - "table" : "entry", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, { "column" : "Image_File_URL", "schema" : "PDB", @@ -1242,7 +1299,8 @@ "byte_count_column" : "Image_File_Bytes", "filename_column" : "Image_File_Name", "md5" : "Image_File_MD5", - "url_pattern" : "/hatrac/pdb/entry/submitted/image/{{$moment.year}}/{{{Image_File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/submitted/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/image/{{{Image_File_MD5}}}{{{_Image_File_URL.filename_ext}}}" } }, { @@ -1252,7 +1310,7 @@ "uri" : "tag:isrd.isi.edu,2016:column-display", "value" : { "compact" : { - "markdown_pattern" : "{{#if Image_File_URL }}[![{{Image_File_Name}}]({{{Image_File_URL}}}){width=auto height=200}]({{{Image_File_URL}}}){target=_blank}{{/if}}", + "markdown_pattern" : "{{#if Image_File_URL }}[![{{Image_File_Name}}]({{{Image_File_URL}}}){width=auto height=100}]({{{Image_File_URL}}}){target=_blank}{{/if}}", "template_engine" : "handlebars" }, "detailed" : { @@ -1269,8 +1327,13 @@ "value" : { "byte_count_column" : "mmCIF_File_Bytes", "filename_column" : "mmCIF_File_Name", + "filename_ext_filter" : [ + ".cif", + ".CIF" + ], "md5" : "mmCIF_File_MD5", - "url_pattern" : "/hatrac/pdb/entry/submitted/mmCIF/{{$moment.year}}/{{{mmCIF_File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/submitted/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/mmCIF/{{{mmCIF_File_MD5}}}{{{_mmCIF_File_URL.filename_ext}}}" } }, { @@ -1351,19 +1414,20 @@ { "column" : "File_URL", "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:isrd.isi.edu,2017:asset", "value" : { "byte_count_column" : "File_Bytes", "filename_column" : "File_Name", "md5" : "File_MD5", - "url_pattern" : "/hatrac/pdb/entry/{{$moment.year}}/{{{Structure_Id}}}/final_mmCIF/{{{File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/generated/uid/{{#if _Entry_RCB}}{{#regexFindFirst _Entry_RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/id/{{{Structure_Id}}}/final_mmCIF/{{{File_Name}}}" } }, { "column" : "File_URL", "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:isrd.isi.edu,2016:column-display", "value" : { "*" : { @@ -1374,7 +1438,7 @@ { "column" : "File_URL", "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:isrd.isi.edu,2018:required", "value" : {} }, @@ -1387,7 +1451,8 @@ "byte_count_column" : "File_Bytes", "filename_column" : "File_Name", "md5" : "File_MD5", - "url_pattern" : "/hatrac/pdb/entry/{{$moment.year}}/{{{Entry_RID}}}/validation_error/{{{File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/generated/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/rid/{{{Entry_RID}}}/validation_error/{{{File_Name}}}" } }, { @@ -1417,7 +1482,8 @@ "byte_count_column" : "mmCIF_File_Bytes", "filename_column" : "mmCIF_File_Name", "md5" : "mmCIF_File_MD5", - "url_pattern" : "/hatrac/pdb/entry/{{$moment.year}}/{{{structure_id}}}/submitted_starting_model/{{{mmCIF_File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/submitted/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/id/{{{structure_id}}}/starting_model/{{{mmCIF_File_MD5}}}{{{_mmCIF_File_URL.filename_ext}}}" } }, { @@ -1429,7 +1495,8 @@ "byte_count_column" : "File_Bytes", "filename_column" : "File_Name", "md5" : "File_MD5", - "url_pattern" : "/hatrac/pdb/entry/{{$moment.year}}/{{{structure_id}}}/submitted_related_file/{{{File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/submitted/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/id/{{{structure_id}}}/related_file/{{{File_MD5}}}{{{_File_URL.filename_ext}}}" } }, { @@ -1521,13 +1588,31 @@ "name" : "User Provided Image File" } }, + { + "column" : "Submitter_Flag_Date", + "schema" : "PDB", + "table" : "entry", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "Last Communicated" + } + }, + { + "column" : "Method_Details", + "schema" : "PDB", + "table" : "entry", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "User Provided Method Details" + } + }, { "column" : "File_URL", "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:misd.isi.edu,2015:display", "value" : { - "name" : "System Generated mmCIF File" + "name" : "System Generated File" } }, { @@ -2970,6 +3055,28 @@ "domain_filter_pattern" : "structure_id={{structure_id}}" } }, + { + "foreign_key" : "ihm_ordered_model_ihm_model_group_1_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_ordered_model", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_ordered_model_ihm_model_group_2_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_ordered_model", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, { "foreign_key" : "ihm_ordered_ensemble_model_group_id_begin_fkey", "foreign_key_schema" : "PDB", @@ -4909,6 +5016,138 @@ "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", "template_engine" : "handlebars" } + }, + { + "foreign_key" : "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "multi_state_scheme_connectivity_dataset_group_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_kinetic_rate_ihm_external_files_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_ihm_external_files_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_ihm_dataset_group_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "relaxation_time_multi_state_scheme_connectivity_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } } ], "known_attributes" : { @@ -7346,24 +7585,6 @@ "markdown_name" : "Models Submitted^*^" } }, - { - "schema" : "PDB", - "table" : "Accession_Code", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, - { - "schema" : "PDB", - "table" : "audit_conform", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, - { - "schema" : "PDB", - "table" : "Conform_Dictionary", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, { "schema" : "PDB", "table" : "ihm_model_list", @@ -7946,7 +8167,7 @@ }, { "schema" : "PDB", - "table" : "ihm_ordered_ensemble", + "table" : "ihm_ordered_model", "uri" : "tag:misd.isi.edu,2015:display", "value" : { "comment_display" : { @@ -7954,12 +8175,12 @@ "table_comment_display" : "inline" } }, - "name" : "Ordered States" + "name" : "Ordered Models" } }, { "schema" : "PDB", - "table" : "ihm_ordered_ensemble", + "table" : "ihm_ordered_model", "uri" : "tag:isrd.isi.edu,2016:visible-columns", "value" : { "*" : [ @@ -7971,7 +8192,7 @@ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_structure_id_fkey" + "ihm_ordered_model_structure_id_fkey" ] }, "RID" @@ -7985,26 +8206,26 @@ "step_description", "ordered_by", { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the origin of the directed edge", "markdown_name" : "Model Group Id Begin", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ] }, "RID" ] }, { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the end of the directed edge", "markdown_name" : "Model Group Id End", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" ] }, "RID" @@ -8020,7 +8241,7 @@ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_structure_id_fkey" + "ihm_ordered_model_structure_id_fkey" ] }, "RID" @@ -8034,26 +8255,26 @@ "step_description", "ordered_by", { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the origin of the directed edge", "markdown_name" : "Model Group Id Begin", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ] }, "RID" ] }, { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the end of the directed edge", "markdown_name" : "Model Group Id End", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" ] }, "RID" @@ -8061,17 +8282,17 @@ }, [ "PDB", - "ihm_ordered_ensemble_RCB_fkey" + "ihm_ordered_model_RCB_fkey" ], [ "PDB", - "ihm_ordered_ensemble_RMB_fkey" + "ihm_ordered_model_RMB_fkey" ], "RCT", "RMT", [ "PDB", - "ihm_ordered_ensemble_Owner_fkey" + "ihm_ordered_model_Owner_fkey" ] ], "entry" : [ @@ -8082,7 +8303,7 @@ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_structure_id_fkey" + "ihm_ordered_model_structure_id_fkey" ] }, "RID" @@ -8096,26 +8317,26 @@ "step_description", "ordered_by", { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the origin of the directed edge", "markdown_name" : "Model Group Id Begin", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ] }, "RID" ] }, { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the end of the directed edge", "markdown_name" : "Model Group Id End", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" ] }, "RID" @@ -8126,7 +8347,7 @@ }, { "schema" : "PDB", - "table" : "ihm_geometric_object_list", + "table" : "ihm_ordered_ensemble", "uri" : "tag:misd.isi.edu,2015:display", "value" : { "comment_display" : { @@ -8134,13 +8355,193 @@ "table_comment_display" : "inline" } }, - "name" : "Geometric Objects used as Restraints" + "name" : "Ordered Ensembles (to be deprecated and superseded by Ordered Models)" } }, { "schema" : "PDB", - "table" : "ihm_geometric_object_list", - "uri" : "tag:isrd.isi.edu,2016:table-display", + "table" : "ihm_ordered_ensemble", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id Begin", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_begin_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id End", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_end_fkey" + ] + }, + "RID" + ] + } + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id Begin", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_begin_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id End", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_end_fkey" + ] + }, + "RID" + ] + }, + [ + "PDB", + "ihm_ordered_ensemble_RCB_fkey" + ], + [ + "PDB", + "ihm_ordered_ensemble_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_ordered_ensemble_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id Begin", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_begin_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id End", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_end_fkey" + ] + }, + "RID" + ] + } + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_geometric_object_list", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Geometric Objects used as Restraints" + } + }, + { + "schema" : "PDB", + "table" : "ihm_geometric_object_list", + "uri" : "tag:isrd.isi.edu,2016:table-display", "value" : { "row_name" : { "row_markdown_pattern" : "{{{object_id}}}" @@ -9540,6 +9941,10 @@ [ "PDB", "ihm_multi_state_model_group_link_state_id_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" ] ], "filter" : "detailed" @@ -9674,6 +10079,18 @@ [ "PDB", "ihm_modeling_post_process_dataset_group_id_fkey" + ], + [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" ] ], "filter" : "detailed" @@ -9752,9 +10169,13 @@ { "inbound" : [ "PDB", - "Entry_mmCIF_File_Structure_Id_fkey" + "Entry_Generated_File_Structure_Id_fkey" ] }, + { + "filter" : "File_Type", + "operand_pattern" : "mmCIF" + }, "RID" ] } @@ -9788,6 +10209,22 @@ "RID", "Accession_Serial", "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, { "markdown_name" : "Entry", "source" : [ @@ -9800,6 +10237,25 @@ "RID" ] }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + { + "outbound" : [ + "PDB", + "entry_Workflow_Status_fkey" + ] + }, + "Name" + ] + }, + "Notes", { "markdown_name" : "RCB", "source" : [ @@ -9859,6 +10315,23 @@ }, "Accession_Serial", "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + "Notes", { "markdown_name" : "Entry", "source" : [ @@ -9870,6 +10343,24 @@ }, "RID" ] + }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + { + "outbound" : [ + "PDB", + "entry_Workflow_Status_fkey" + ] + }, + "Name" + ] } ], "entry" : [ @@ -9884,11 +10375,60 @@ }, "RID" ] - } + }, + "Accession_Serial", + "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + "Notes" ], "entry/edit" : [ - "Accession_Code" - ], + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + "RID" + ] + }, + "Accession_Serial", + "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + "Notes" + ], "filter" : { "and" : [ { @@ -9898,6 +10438,40 @@ { "markdown_name" : "Accession Code", "source" : "Accession_Code" + }, + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + { + "outbound" : [ + "PDB", + "entry_Workflow_Status_fkey" + ] + }, + "Name" + ] } ] } @@ -9912,6 +10486,7 @@ "RID", "id", "mmCIF_File_URL", + "Submitter_Flag_Date", "Image_File_URL", [ "PDB", @@ -9947,12 +10522,12 @@ "template_engine" : "handlebars" }, "entity" : true, - "markdown_name" : "System Generated mmCIF File", + "markdown_name" : "System Generated Files", "source" : [ { "inbound" : [ "PDB", - "Entry_mmCIF_File_Structure_Id_fkey" + "Entry_Generated_File_Structure_Id_fkey" ] }, "RID" @@ -9960,6 +10535,8 @@ }, "Deposit_Date", "Release_Date", + "Method_Details", + "Manual_Processing", { "markdown_name" : "RCB", "source" : [ @@ -9985,11 +10562,7 @@ ] }, "RCT", - "RMT", - [ - "PDB", - "entry_Owner_fkey" - ] + "RMT" ], "detailed" : [ "RID", @@ -10058,6 +10631,10 @@ }, "Deposit_Date", "Release_Date", + "Method_Details", + "Submitter_Flag", + "Submitter_Flag_Date", + "Manual_Processing", "Notes", [ "PDB", @@ -10071,6 +10648,8 @@ "PDB", "entry_Workflow_Status_fkey" ], + "Method_Details", + "Manual_Processing", "Notes" ], "entry/edit" : [ @@ -10080,8 +10659,12 @@ "PDB", "entry_Workflow_Status_fkey" ], + "Method_Details", "Deposit_Date", "Release_Date", + "Submitter_Flag", + "Submitter_Flag_Date", + "Manual_Processing", "Notes" ], "export/compact" : [ @@ -10095,6 +10678,9 @@ "Accession_Code", "Deposit_Date", "Release_Date", + "Method_Details", + "Submitter_Flag", + "Submitter_Flag_Date", "Record_Status_Detail" ], "filter" : { @@ -10135,6 +10721,10 @@ "markdown_name" : "Release Date", "source" : "Release_Date" }, + { + "markdown_name" : "Last Communicated", + "source" : "Submitter_Flag_Date" + }, { "hide_not_null_choice" : true, "hide_null_choice" : true, @@ -10184,6 +10774,10 @@ }, "RID" ] + }, + { + "markdown_name" : "Manual Processing", + "source" : "Manual_Processing" } ] } @@ -10211,12 +10805,12 @@ }, { "destination" : { - "name" : "Entry_mmCIF_File", + "name" : "Entry_Generated_File", "type" : "download" }, "source" : { "api" : "attribute", - "path" : "PDB:Entry_mmCIF_File/url:=File_URL" + "path" : "PDB:Entry_Generated_File/url:=File_URL" } } ], @@ -10234,7 +10828,7 @@ "detailed" : [ [ "PDB", - "Entry_mmCIF_File_Structure_Id_fkey" + "Entry_Generated_File_Structure_Id_fkey" ], [ "PDB", @@ -10428,6 +11022,10 @@ "PDB", "ihm_multi_state_model_group_link_structure_id_fkey" ], + [ + "PDB", + "ihm_ordered_model_structure_id_fkey" + ], [ "PDB", "ihm_ordered_ensemble_structure_id_fkey" @@ -10596,6 +11194,26 @@ "PDB", "ihm_geometric_object_distance_restraint_structure_id_fkey" ], + [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ], { "comment" : "Collections to which the entry belongs", "markdown_name" : "Entry Collections", @@ -10615,6 +11233,18 @@ "RID" ] }, + { + "markdown_name" : "Curation Log", + "source" : [ + { + "inbound" : [ + "PDB", + "Curation_Log_Entry_fkey" + ] + }, + "RID" + ] + }, [ "PDB", "audit_conform_structure_id_fkey" @@ -13356,60 +13986,1204 @@ "compact" : [ "RID", { - "comment" : "Entry Collection Id", - "markdown_name" : "Entry Collection Id", + "comment" : "Entry Collection Id", + "markdown_name" : "Entry Collection Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_collection_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Id", + "markdown_name" : "Entry Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Accession Code", + "markdown_name" : "Accession Code", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "Accession_Code" + ] + } + ], + "detailed" : [ + "RID", + { + "comment" : "Entry Collection Id", + "markdown_name" : "Entry Collection Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_collection_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Id", + "markdown_name" : "Entry Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Accession Code", + "markdown_name" : "Accession Code", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "Accession_Code" + ] + }, + [ + "PDB", + "ihm_entry_collection_mapping_RCB_fkey" + ], + [ + "PDB", + "ihm_entry_collection_mapping_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_entry_collection_mapping_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "Entry Collection Id", + "markdown_name" : "Entry Collection Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_collection_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Id", + "markdown_name" : "Entry Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "id" + ] + } + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Multi-State Schemes" + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "name", + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "name", + "details", + [ + "PDB", + "ihm_multi_state_scheme_RCB_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_multi_state_scheme_Owner_fkey" + ] + ], + "entry" : [ + "id", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "name", + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value" : { + "detailed" : [ + [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + ], + "filter" : "detailed" + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Multi-State Scheme Connectivities" + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the starting state in the multi-state scheme", + "markdown_name" : "Begin State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the ending state in the multi-state scheme", + "markdown_name" : "End State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the starting state in the multi-state scheme", + "markdown_name" : "Begin State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the ending state in the multi-state scheme", + "markdown_name" : "End State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_multi_state_scheme_connectivity_RCB_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_multi_state_scheme_connectivity_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the starting state in the multi-state scheme", + "markdown_name" : "Begin State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the ending state in the multi-state scheme", + "markdown_name" : "End State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value" : { + "detailed" : [ + [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ], + [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + ], + "filter" : "detailed" + } + }, + { + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Kinetic Rates from Biophysical Experiments" + } + }, + { + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_kinetic_rate_RCB_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_kinetic_rate_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Relaxation times from Biophysical Experiments" + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", + { + "comment" : "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", + { + "comment" : "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_relaxation_time_RCB_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_relaxation_time_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", + { + "comment" : "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value" : { + "detailed" : [ + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + ], + "filter" : "detailed" + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Mapping experimentally measured relaxation times with multi-state schemes" + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the relaxation time", + "markdown_name" : "Relaxation Time Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the relaxation time", + "markdown_name" : "Relaxation Time Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_RCB_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the relaxation time", + "markdown_name" : "Relaxation Time Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "Curation_Log", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Curation Log" + } + }, + { + "schema" : "PDB", + "table" : "Curation_Log", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "Entry Id", + "markdown_name" : "Entry Id", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "Curation_Log_Entry_fkey" ] }, "id" ] }, { - "comment" : "Entry Id", - "markdown_name" : "Entry Id", + "comment" : "Entry Accession Code", + "markdown_name" : "Accession Code", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "Curation_Log_Entry_fkey" ] }, - "id" + "Accession_Code" ] }, + "Log_Date", + "Details", + "Submitter_Allow", { - "comment" : "Entry Accession Code", - "markdown_name" : "Accession Code", + "markdown_name" : "RCB", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "Curation_Log_RCB_fkey" ] }, - "Accession_Code" + "Full_Name" ] - } - ], - "detailed" : [ - "RID", + }, { - "comment" : "Entry Collection Id", - "markdown_name" : "Entry Collection Id", + "markdown_name" : "RMB", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "Curation_Log_RMB_fkey" ] }, - "id" + "Full_Name" ] }, + "RCT", + "RMT" + ], + "detailed" : [ + "RID", { "comment" : "Entry Id", "markdown_name" : "Entry Id", @@ -13417,7 +15191,7 @@ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "Curation_Log_Entry_fkey" ] }, "id" @@ -13430,41 +15204,43 @@ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "Curation_Log_Entry_fkey" ] }, "Accession_Code" ] }, - [ - "PDB", - "ihm_entry_collection_mapping_RCB_fkey" - ], - [ - "PDB", - "ihm_entry_collection_mapping_RMB_fkey" - ], - "RCT", - "RMT", - [ - "PDB", - "ihm_entry_collection_mapping_Owner_fkey" - ] - ], - "entry" : [ + "Log_Date", + "Details", + "Submitter_Allow", { - "comment" : "Entry Collection Id", - "markdown_name" : "Entry Collection Id", + "markdown_name" : "RCB", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "Curation_Log_RCB_fkey" ] }, - "id" + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "PDB", + "Curation_Log_RMB_fkey" + ] + }, + "Full_Name" ] }, + "RCT", + "RMT" + ], + "entry" : [ { "comment" : "Entry Id", "markdown_name" : "Entry Id", @@ -13472,12 +15248,15 @@ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "Curation_Log_Entry_fkey" ] }, "id" ] - } + }, + "Log_Date", + "Details", + "Submitter_Allow" ] } }, @@ -15544,6 +17323,14 @@ [ "PDB", "ihm_localization_density_files_file_id_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" ] ], "filter" : "detailed" @@ -18407,6 +20194,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -18432,6 +20223,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -18470,6 +20265,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -18689,6 +20488,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -18766,6 +20569,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -18856,6 +20663,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -19990,12 +21801,6 @@ "markdown_name" : "Sequences of Polymeric Entities^*^" } }, - { - "schema" : "PDB", - "table" : "entity_poly_seq", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, { "schema" : "PDB", "table" : "entity_poly_seq", @@ -20835,12 +22640,6 @@ "markdown_name" : "Instances of Molecular Entities^*^" } }, - { - "schema" : "PDB", - "table" : "struct_asym", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, { "schema" : "PDB", "table" : "struct_asym", @@ -22544,7 +24343,7 @@ }, { "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:misd.isi.edu,2015:display", "value" : { "comment_display" : { @@ -22552,12 +24351,12 @@ "table_comment_display" : "inline" } }, - "name" : "System Generated mmCIF File" + "name" : "System Generated Files" } }, { "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:isrd.isi.edu,2016:table-display", "value" : { "row_name" : { @@ -22567,12 +24366,16 @@ }, { "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:isrd.isi.edu,2016:visible-columns", "value" : { "*" : [ "RID", "File_URL", + [ + "PDB", + "Entry_Generated_File_System_Generated_File_Type_fkey" + ], { "aggregate" : "array_d", "array_options" : { @@ -22596,7 +24399,7 @@ { "inbound" : [ "PDB", - "Conform_Dictionary_Entry_mmCIF_File_fkey" + "Conform_Dictionary_Entry_Generated_File_fkey" ] }, { @@ -22610,12 +24413,16 @@ }, [ "PDB", - "Entry_mmCIF_File_Structure_Id_fkey" + "Entry_Generated_File_Structure_Id_fkey" ] ], "detailed" : [ "RID", "File_URL", + [ + "PDB", + "Entry_Generated_File_System_Generated_File_Type_fkey" + ], { "aggregate" : "array_d", "array_options" : { @@ -22639,7 +24446,7 @@ { "inbound" : [ "PDB", - "Conform_Dictionary_Entry_mmCIF_File_fkey" + "Conform_Dictionary_Entry_Generated_File_fkey" ] }, { @@ -22653,14 +24460,32 @@ }, [ "PDB", - "Entry_mmCIF_File_Structure_Id_fkey" + "Entry_Generated_File_Structure_Id_fkey" ], "File_Bytes", "File_MD5" ], - "entry" : [], + "entry" : [ + "File_URL", + [ + "PDB", + "Entry_Generated_File_System_Generated_File_Type_fkey" + ], + [ + "PDB", + "Entry_Generated_File_Structure_Id_Entry_RCB_fkey" + ] + ], "entry/edit" : [ - "File_URL" + "File_URL", + [ + "PDB", + "Entry_Generated_File_System_Generated_File_Type_fkey" + ], + [ + "PDB", + "Entry_Generated_File_Structure_Id_Entry_RCB_fkey" + ] ] } }, @@ -22687,12 +24512,6 @@ } } }, - { - "schema" : "PDB", - "table" : "Entry_Error_File", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, { "schema" : "PDB", "table" : "Entry_Error_File", @@ -22708,7 +24527,7 @@ "File_URL", [ "PDB", - "Entry_Error_File_File_Type_fkey" + "Entry_Error_File_System_Generated_File_Type_fkey" ] ], "detailed" : [ @@ -22723,7 +24542,7 @@ "File_URL", [ "PDB", - "Entry_Error_File_File_Type_fkey" + "Entry_Error_File_System_Generated_File_Type_fkey" ] ], "entry" : [ @@ -22734,7 +24553,7 @@ ], [ "PDB", - "Entry_Error_File_File_Type_fkey" + "Entry_Error_File_System_Generated_File_Type_fkey" ] ] } @@ -23018,11 +24837,11 @@ ], [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ], [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_ensemble_model_group_id_begin_fkey" ], [ "PDB", @@ -29085,7 +30904,7 @@ }, { "schema" : "Vocab", - "table" : "Validation_File_Type", + "table" : "System_Generated_File_Type", "uri" : "tag:isrd.isi.edu,2016:visible-columns", "value" : { "*" : [ @@ -29100,7 +30919,7 @@ { "outbound" : [ "Vocab", - "Validation_File_Type_RCB_fkey" + "System_Generated_File_Type_RCB_fkey" ] }, "Full_Name" @@ -29112,7 +30931,7 @@ { "outbound" : [ "Vocab", - "Validation_File_Type_RMB_fkey" + "System_Generated_File_Type_RMB_fkey" ] }, "Full_Name" @@ -29122,7 +30941,7 @@ "RMT", [ "Vocab", - "Validation_File_Type_Owner_fkey" + "System_Generated_File_Type_Owner_fkey" ] ] } @@ -29703,6 +31522,50 @@ ] } }, + { + "schema" : "Vocab", + "table" : "struct_pdbx_structure_determination_methodology", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_Owner_fkey" + ] + ] + } + }, { "schema" : "Vocab", "table" : "software_type", @@ -29759,6 +31622,94 @@ ] } }, + { + "schema" : "Vocab", + "table" : "ihm_relaxation_time_unit", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_relaxation_time_unit_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_relaxation_time_unit_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "ihm_relaxation_time_unit_term_Owner_fkey" + ] + ] + } + }, + { + "schema" : "Vocab", + "table" : "ihm_equilibrium_constant_determination_method", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_Owner_fkey" + ] + ] + } + }, { "schema" : "Vocab", "table" : "ihm_geometric_object_half_torus_section", diff --git a/config-scripts/annotations/staging_annotation_config.json b/config-scripts/annotations/staging_annotation_config.json index deeaaef..e2a8750 100644 --- a/config-scripts/annotations/staging_annotation_config.json +++ b/config-scripts/annotations/staging_annotation_config.json @@ -48,15 +48,78 @@ "WWW", "Page_Asset" ] + }, + { + "checksum_types" : [ + "sha256", + "md5" + ], + "column_map" : { + "Method_Details" : "Integrative modeling", + "Workflow_Status" : "DEPO", + "mmCIF_File_Bytes" : "{file_size}", + "mmCIF_File_MD5" : "{md5}", + "mmCIF_File_Name" : "{file_name}", + "mmCIF_File_URL" : "{URI}" + }, + "create_record_before_upload" : false, + "file_pattern" : "(?i)^.*/deriva/(?P[^/]*)/entry/.*[.](?Pcif)$", + "hatrac_options" : { + "versioned_urls" : true + }, + "hatrac_templates" : { + "content-disposition" : "filename*=UTF-8''{file_name}", + "hatrac_uri" : "/hatrac/pdb/submitted/uid/{globus_ID}/entry/mmcif/{file_name}" + }, + "metadata_query_templates" : [], + "record_query_template" : "/entity/{target_table}/mmCIF_File_MD5={md5}&RCB=https%3A%2F%2Fauth.globus.org%2F{globus_ID}", + "record_update_template" : "/attributegroup/{target_table}/RID;mmCIF_File_MD5,mmCIF_File_URL,mmCIF_File_Name,mmCIF_File_Bytes", + "require_record_update_template" : true, + "target_table" : [ + "PDB", + "entry" + ] + }, + { + "checksum_types" : [ + "sha256", + "md5" + ], + "column_map" : { + "Image_File_Bytes" : "{file_size}", + "Image_File_MD5" : "{md5}", + "Image_File_Name" : "{file_name}", + "Image_File_URL" : "{URI}", + "RID" : "{entry_rid}" + }, + "create_record_before_upload" : false, + "dir_pattern" : "(?i)^.*/deriva/(?P[^/]*)/entry/(?P[^/]*)[.](?Ppng|jpg|jpeg)", + "hatrac_options" : { + "versioned_urls" : true + }, + "hatrac_templates" : { + "content-disposition" : "filename*=UTF-8''{file_name}", + "hatrac_uri" : "/hatrac/pdb/submitted/uid/{globus_ID}/entry/image/{file_name}" + }, + "metadata_query_templates" : [ + "/attribute/{target_table}/mmCIF_File_Name={base_name}.cif&RCB=https%3A%2F%2Fauth.globus.org%2F{globus_ID}/entry_rid:=RID" + ], + "record_query_template" : "/entity/{target_table}/RID={entry_rid}", + "record_update_template" : "/attributegroup/{target_table}/RID;Image_File_MD5,Image_File_URL,Image_File_Name,Image_File_Bytes", + "require_record_update_template" : true, + "target_table" : [ + "PDB", + "entry" + ] } ], "version_compatibility" : [ [ - ">=0.4.3", - "<1.0.0" + ">=1.4.0", + "<2.0.0" ] ], - "version_update_url" : "https://github.com/informatics-isi-edu/deriva-qt/releases" + "version_update_url" : "https://github.com/informatics-isi-edu/deriva-client" } }, { @@ -435,36 +498,36 @@ "url" : "/chaise/recordset/#50/PDB:ihm_multi_state_modeling" }, { - "name" : "Ihm Ordered Ensemble", - "url" : "/chaise/recordset/#50/PDB:ihm_ordered_ensemble" + "name" : "Ihm Ordered Model", + "url" : "/chaise/recordset/#50/PDB:ihm_ordered_model" } ], - "name" : "Multi-state Modeling and Ordered Ensembles" + "name" : "Multi-state Modeling, Ordered Models, and Ensembles" }, { "children" : [ { - "name" : "PDBX Entity Poly Na Type", - "url" : "/chaise/recordset/#50/PDB:pdbx_entity_poly_na_type" + "name" : "ihm Multi-State Scheme", + "url" : "/chaise/recordset/#50/PDB:ihm_multi_state_scheme" }, { - "name" : "PDBX Entry Details", - "url" : "/chaise/recordset/#50/PDB:pdbx_entry_details" + "name" : "ihm Multi-State Scheme Connectivity", + "url" : "/chaise/recordset/#50/PDB:ihm_multi_state_scheme_connectivity" }, { - "name" : "PDBX Inhibitor Info", - "url" : "/chaise/recordset/#50/PDB:pdbx_inhibitor_info" + "name" : "ihm Kinetic Rate", + "url" : "/chaise/recordset/#50/PDB:ihm_kinetic_rate" }, { - "name" : "PDBX Ion Info", - "url" : "/chaise/recordset/#50/PDB:pdbx_ion_info" + "name" : "ihm Relaxation Time", + "url" : "/chaise/recordset/#50/PDB:ihm_relaxation_time" }, { - "name" : "PDBX Protein Info", - "url" : "/chaise/recordset/#50/PDB:pdbx_protein_info" + "name" : "ihm Relaxation Time Multi-State Scheme", + "url" : "/chaise/recordset/#50/PDB:ihm_relaxation_time_multi_state_scheme" } ], - "name" : "PDBX Related" + "name" : "Multi-State Schemes" }, { "children" : [ @@ -557,13 +620,17 @@ "name" : "Accession Code", "url" : "/chaise/recordset/#50/PDB:Accession_Code" }, + { + "name" : "Curation Log", + "url" : "/chaise/recordset/#50/PDB:Curation_Log" + }, { "name" : "Entry Error File", "url" : "/chaise/recordset/#50/PDB:Entry_Error_File" }, { - "name" : "Entry mmCIF File", - "url" : "/chaise/recordset/#50/PDB:Entry_mmCIF_File" + "name" : "Entry Generated File", + "url" : "/chaise/recordset/#50/PDB:Entry_Generated_File" }, { "name" : "Entry Related File", @@ -584,6 +651,19 @@ } ], "name" : "Entry Collection" + }, + { + "children" : [ + { + "name" : "PDB Archive", + "url" : "/chaise/recordset/#50/PDB:PDB_Archive" + }, + { + "name" : "Entry Latest Archive", + "url" : "/chaise/recordset/#50/PDB:Entry_Latest_Archive" + } + ], + "name" : "Archive" } ], "name" : "Data Categories" @@ -740,6 +820,10 @@ "name" : "Database Hosted", "url" : "/chaise/recordset/#50/Vocab:ihm_dataset_list_database_hosted" }, + { + "name" : "Related DB Reference DB Name", + "url" : "/chaise/recordset/#50/Vocab:ihm_dataset_related_db_reference_db_name" + }, { "name" : "Group Conditionality", "url" : "/chaise/recordset/#50/Vocab:ihm_derived_distance_restraint_group_conditionality" @@ -899,6 +983,14 @@ { "name" : "Experiment Type", "url" : "/chaise/recordset/#50/Vocab:ihm_multi_state_modeling_experiment_type" + }, + { + "name" : "Relaxation Time Unit", + "url" : "/chaise/recordset/#50/Vocab:ihm_relaxation_time_unit" + }, + { + "name" : "Equilibrium Constant Determination Methods", + "url" : "/chaise/recordset/#50/Vocab:ihm_equilibrium_constant_determination_method" } ], "name" : "Ihm Multi State Modeling" @@ -1034,6 +1126,10 @@ }, { "children" : [ + { + "name" : "PDBX Structure Determination Methodology", + "url" : "/chaise/recordset/#50/Vocab:struct_pdbx_structure_determination_methodology" + }, { "name" : "PDBX CASP Flag", "url" : "/chaise/recordset/#50/Vocab:struct_pdbx_CASP_flag" @@ -1064,8 +1160,8 @@ "url" : "/chaise/recordset/#50/Vocab:Process_Status" }, { - "name" : "Validation File Type", - "url" : "/chaise/recordset/#50/Vocab:Validation_File_Type" + "name" : "System Generated File Type", + "url" : "/chaise/recordset/#50/Vocab:System_Generated_File_Type" }, { "name" : "Workflow Status", @@ -1146,38 +1242,6 @@ } } }, - { - "column" : "id", - "schema_pattern" : "Vocab", - "table_pattern" : ".*", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, - { - "column" : "uri", - "schema_pattern" : "Vocab", - "table_pattern" : ".*", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, - { - "column" : "description", - "schema_pattern" : "Vocab", - "table_pattern" : ".*", - "uri" : "tag:misd.isi.edu,2015:display", - "value" : { - "name" : "Description" - } - }, - { - "column" : "name", - "schema_pattern" : "Vocab", - "table_pattern" : ".*", - "uri" : "tag:misd.isi.edu,2015:display", - "value" : { - "name" : "Name" - } - }, { "column" : "synonyms", "schema_pattern" : "Vocab", @@ -1226,13 +1290,6 @@ "url_pattern" : "/hatrac/WWW/Page_Asset/{{{MD5}}}.{{#encode}}{{{Filename}}}{{/encode}}" } }, - { - "column" : "id", - "schema" : "PDB", - "table" : "entry", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, { "column" : "Image_File_URL", "schema" : "PDB", @@ -1242,7 +1299,8 @@ "byte_count_column" : "Image_File_Bytes", "filename_column" : "Image_File_Name", "md5" : "Image_File_MD5", - "url_pattern" : "/hatrac/pdb/entry/submitted/image/{{$moment.year}}/{{{Image_File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/submitted/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/image/{{{Image_File_MD5}}}{{{_Image_File_URL.filename_ext}}}" } }, { @@ -1252,7 +1310,7 @@ "uri" : "tag:isrd.isi.edu,2016:column-display", "value" : { "compact" : { - "markdown_pattern" : "{{#if Image_File_URL }}[![{{Image_File_Name}}]({{{Image_File_URL}}}){width=auto height=200}]({{{Image_File_URL}}}){target=_blank}{{/if}}", + "markdown_pattern" : "{{#if Image_File_URL }}[![{{Image_File_Name}}]({{{Image_File_URL}}}){width=auto height=100}]({{{Image_File_URL}}}){target=_blank}{{/if}}", "template_engine" : "handlebars" }, "detailed" : { @@ -1269,8 +1327,13 @@ "value" : { "byte_count_column" : "mmCIF_File_Bytes", "filename_column" : "mmCIF_File_Name", + "filename_ext_filter" : [ + ".cif", + ".CIF" + ], "md5" : "mmCIF_File_MD5", - "url_pattern" : "/hatrac/pdb/entry/submitted/mmCIF/{{$moment.year}}/{{{mmCIF_File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/submitted/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/mmCIF/{{{mmCIF_File_MD5}}}{{{_mmCIF_File_URL.filename_ext}}}" } }, { @@ -1351,19 +1414,20 @@ { "column" : "File_URL", "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:isrd.isi.edu,2017:asset", "value" : { "byte_count_column" : "File_Bytes", "filename_column" : "File_Name", "md5" : "File_MD5", - "url_pattern" : "/hatrac/pdb/entry/{{$moment.year}}/{{{Structure_Id}}}/final_mmCIF/{{{File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/generated/uid/{{#if _Entry_RCB}}{{#regexFindFirst _Entry_RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/id/{{{Structure_Id}}}/final_mmCIF/{{{File_Name}}}" } }, { "column" : "File_URL", "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:isrd.isi.edu,2016:column-display", "value" : { "*" : { @@ -1374,7 +1438,7 @@ { "column" : "File_URL", "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:isrd.isi.edu,2018:required", "value" : {} }, @@ -1387,7 +1451,8 @@ "byte_count_column" : "File_Bytes", "filename_column" : "File_Name", "md5" : "File_MD5", - "url_pattern" : "/hatrac/pdb/entry/{{$moment.year}}/{{{Entry_RID}}}/validation_error/{{{File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/generated/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/rid/{{{Entry_RID}}}/validation_error/{{{File_Name}}}" } }, { @@ -1417,7 +1482,8 @@ "byte_count_column" : "mmCIF_File_Bytes", "filename_column" : "mmCIF_File_Name", "md5" : "mmCIF_File_MD5", - "url_pattern" : "/hatrac/pdb/entry/{{$moment.year}}/{{{structure_id}}}/submitted_starting_model/{{{mmCIF_File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/submitted/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/id/{{{structure_id}}}/starting_model/{{{mmCIF_File_MD5}}}{{{_mmCIF_File_URL.filename_ext}}}" } }, { @@ -1429,7 +1495,8 @@ "byte_count_column" : "File_Bytes", "filename_column" : "File_Name", "md5" : "File_MD5", - "url_pattern" : "/hatrac/pdb/entry/{{$moment.year}}/{{{structure_id}}}/submitted_related_file/{{{File_Name}}}" + "template_engine" : "handlebars", + "url_pattern" : "/hatrac/pdb/submitted/uid/{{#if _RCB}}{{#regexFindFirst _RCB \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{else}}{{#regexFindFirst $session.client.id \"[^/]+$\"}}{{this}}{{/regexFindFirst}}{{/if}}/entry/id/{{{structure_id}}}/related_file/{{{File_MD5}}}{{{_File_URL.filename_ext}}}" } }, { @@ -1521,13 +1588,31 @@ "name" : "User Provided Image File" } }, + { + "column" : "Submitter_Flag_Date", + "schema" : "PDB", + "table" : "entry", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "Last Communicated" + } + }, + { + "column" : "Method_Details", + "schema" : "PDB", + "table" : "entry", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "name" : "User Provided Method Details" + } + }, { "column" : "File_URL", "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:misd.isi.edu,2015:display", "value" : { - "name" : "System Generated mmCIF File" + "name" : "System Generated File" } }, { @@ -2970,6 +3055,28 @@ "domain_filter_pattern" : "structure_id={{structure_id}}" } }, + { + "foreign_key" : "ihm_ordered_model_ihm_model_group_1_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_ordered_model", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_ordered_model_ihm_model_group_2_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_ordered_model", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, { "foreign_key" : "ihm_ordered_ensemble_model_group_id_begin_fkey", "foreign_key_schema" : "PDB", @@ -4909,6 +5016,138 @@ "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", "template_engine" : "handlebars" } + }, + { + "foreign_key" : "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "multi_state_scheme_connectivity_dataset_group_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_kinetic_rate_ihm_external_files_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_ihm_external_files_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_ihm_dataset_group_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "relaxation_time_multi_state_scheme_connectivity_combo2_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } + }, + { + "foreign_key" : "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey", + "foreign_key_schema" : "PDB", + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:foreign-key", + "value" : { + "domain_filter_pattern" : "{{#if _structure_id}}structure_id={{{_structure_id}}}{{/if}}", + "template_engine" : "handlebars" + } } ], "known_attributes" : { @@ -7346,24 +7585,6 @@ "markdown_name" : "Models Submitted^*^" } }, - { - "schema" : "PDB", - "table" : "Accession_Code", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, - { - "schema" : "PDB", - "table" : "audit_conform", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, - { - "schema" : "PDB", - "table" : "Conform_Dictionary", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, { "schema" : "PDB", "table" : "ihm_model_list", @@ -7946,7 +8167,7 @@ }, { "schema" : "PDB", - "table" : "ihm_ordered_ensemble", + "table" : "ihm_ordered_model", "uri" : "tag:misd.isi.edu,2015:display", "value" : { "comment_display" : { @@ -7954,12 +8175,12 @@ "table_comment_display" : "inline" } }, - "name" : "Ordered States" + "name" : "Ordered Models" } }, { "schema" : "PDB", - "table" : "ihm_ordered_ensemble", + "table" : "ihm_ordered_model", "uri" : "tag:isrd.isi.edu,2016:visible-columns", "value" : { "*" : [ @@ -7971,7 +8192,7 @@ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_structure_id_fkey" + "ihm_ordered_model_structure_id_fkey" ] }, "RID" @@ -7985,26 +8206,26 @@ "step_description", "ordered_by", { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the origin of the directed edge", "markdown_name" : "Model Group Id Begin", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ] }, "RID" ] }, { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the end of the directed edge", "markdown_name" : "Model Group Id End", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" ] }, "RID" @@ -8020,7 +8241,7 @@ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_structure_id_fkey" + "ihm_ordered_model_structure_id_fkey" ] }, "RID" @@ -8034,26 +8255,26 @@ "step_description", "ordered_by", { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the origin of the directed edge", "markdown_name" : "Model Group Id Begin", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ] }, "RID" ] }, { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the end of the directed edge", "markdown_name" : "Model Group Id End", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" ] }, "RID" @@ -8061,17 +8282,17 @@ }, [ "PDB", - "ihm_ordered_ensemble_RCB_fkey" + "ihm_ordered_model_RCB_fkey" ], [ "PDB", - "ihm_ordered_ensemble_RMB_fkey" + "ihm_ordered_model_RMB_fkey" ], "RCT", "RMT", [ "PDB", - "ihm_ordered_ensemble_Owner_fkey" + "ihm_ordered_model_Owner_fkey" ] ], "entry" : [ @@ -8082,7 +8303,7 @@ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_structure_id_fkey" + "ihm_ordered_model_structure_id_fkey" ] }, "RID" @@ -8096,26 +8317,26 @@ "step_description", "ordered_by", { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the origin of the directed edge", "markdown_name" : "Model Group Id Begin", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ] }, "RID" ] }, { - "comment" : "A reference to table ihm_model_group.id.", + "comment" : "Model group id corresponding to the node at the end of the directed edge", "markdown_name" : "Model Group Id End", "source" : [ { "outbound" : [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_model_ihm_model_group_2_combo1_fkey" ] }, "RID" @@ -8126,7 +8347,7 @@ }, { "schema" : "PDB", - "table" : "ihm_geometric_object_list", + "table" : "ihm_ordered_ensemble", "uri" : "tag:misd.isi.edu,2015:display", "value" : { "comment_display" : { @@ -8134,13 +8355,193 @@ "table_comment_display" : "inline" } }, - "name" : "Geometric Objects used as Restraints" + "name" : "Ordered Ensembles (to be deprecated and superseded by Ordered Models)" } }, { "schema" : "PDB", - "table" : "ihm_geometric_object_list", - "uri" : "tag:isrd.isi.edu,2016:table-display", + "table" : "ihm_ordered_ensemble", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id Begin", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_begin_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id End", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_end_fkey" + ] + }, + "RID" + ] + } + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id Begin", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_begin_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id End", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_end_fkey" + ] + }, + "RID" + ] + }, + [ + "PDB", + "ihm_ordered_ensemble_RCB_fkey" + ], + [ + "PDB", + "ihm_ordered_ensemble_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_ordered_ensemble_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_structure_id_fkey" + ] + }, + "RID" + ] + }, + "process_id", + "process_description", + "edge_id", + "edge_description", + "step_id", + "step_description", + "ordered_by", + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id Begin", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_begin_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "A reference to table ihm_model_group.id.", + "markdown_name" : "Model Group Id End", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_ordered_ensemble_model_group_id_end_fkey" + ] + }, + "RID" + ] + } + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_geometric_object_list", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Geometric Objects used as Restraints" + } + }, + { + "schema" : "PDB", + "table" : "ihm_geometric_object_list", + "uri" : "tag:isrd.isi.edu,2016:table-display", "value" : { "row_name" : { "row_markdown_pattern" : "{{{object_id}}}" @@ -9540,6 +9941,10 @@ [ "PDB", "ihm_multi_state_model_group_link_state_id_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" ] ], "filter" : "detailed" @@ -9674,6 +10079,18 @@ [ "PDB", "ihm_modeling_post_process_dataset_group_id_fkey" + ], + [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" ] ], "filter" : "detailed" @@ -9752,9 +10169,13 @@ { "inbound" : [ "PDB", - "Entry_mmCIF_File_Structure_Id_fkey" + "Entry_Generated_File_Structure_Id_fkey" ] }, + { + "filter" : "File_Type", + "operand_pattern" : "mmCIF" + }, "RID" ] } @@ -9788,6 +10209,22 @@ "RID", "Accession_Serial", "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, { "markdown_name" : "Entry", "source" : [ @@ -9800,6 +10237,25 @@ "RID" ] }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + { + "outbound" : [ + "PDB", + "entry_Workflow_Status_fkey" + ] + }, + "Name" + ] + }, + "Notes", { "markdown_name" : "RCB", "source" : [ @@ -9859,6 +10315,23 @@ }, "Accession_Serial", "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + "Notes", { "markdown_name" : "Entry", "source" : [ @@ -9870,6 +10343,24 @@ }, "RID" ] + }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + { + "outbound" : [ + "PDB", + "entry_Workflow_Status_fkey" + ] + }, + "Name" + ] } ], "entry" : [ @@ -9884,11 +10375,60 @@ }, "RID" ] - } + }, + "Accession_Serial", + "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + "Notes" ], "entry/edit" : [ - "Accession_Code" - ], + { + "markdown_name" : "Entry", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + "RID" + ] + }, + "Accession_Serial", + "Accession_Code", + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + "Notes" + ], "filter" : { "and" : [ { @@ -9898,6 +10438,40 @@ { "markdown_name" : "Accession Code", "source" : "Accession_Code" + }, + { + "markdown_name" : "PDBDEV Accession Code", + "source" : "PDBDEV_Accession_Code" + }, + { + "markdown_name" : "PDB Extended Code", + "source" : "PDB_Extended_Code" + }, + { + "markdown_name" : "PDB Code", + "source" : "PDB_Code" + }, + { + "markdown_name" : "PDB Accession Code", + "source" : "PDB_Accession_Code" + }, + { + "markdown_name" : "Workflow Status", + "source" : [ + { + "outbound" : [ + "PDB", + "Accession_Code_Entry_fkey" + ] + }, + { + "outbound" : [ + "PDB", + "entry_Workflow_Status_fkey" + ] + }, + "Name" + ] } ] } @@ -9912,6 +10486,7 @@ "RID", "id", "mmCIF_File_URL", + "Submitter_Flag_Date", "Image_File_URL", [ "PDB", @@ -9947,12 +10522,12 @@ "template_engine" : "handlebars" }, "entity" : true, - "markdown_name" : "System Generated mmCIF File", + "markdown_name" : "System Generated Files", "source" : [ { "inbound" : [ "PDB", - "Entry_mmCIF_File_Structure_Id_fkey" + "Entry_Generated_File_Structure_Id_fkey" ] }, "RID" @@ -9960,6 +10535,8 @@ }, "Deposit_Date", "Release_Date", + "Method_Details", + "Manual_Processing", { "markdown_name" : "RCB", "source" : [ @@ -9985,11 +10562,7 @@ ] }, "RCT", - "RMT", - [ - "PDB", - "entry_Owner_fkey" - ] + "RMT" ], "detailed" : [ "RID", @@ -10058,6 +10631,10 @@ }, "Deposit_Date", "Release_Date", + "Method_Details", + "Submitter_Flag", + "Submitter_Flag_Date", + "Manual_Processing", "Notes", [ "PDB", @@ -10071,6 +10648,8 @@ "PDB", "entry_Workflow_Status_fkey" ], + "Method_Details", + "Manual_Processing", "Notes" ], "entry/edit" : [ @@ -10080,8 +10659,12 @@ "PDB", "entry_Workflow_Status_fkey" ], + "Method_Details", "Deposit_Date", "Release_Date", + "Submitter_Flag", + "Submitter_Flag_Date", + "Manual_Processing", "Notes" ], "export/compact" : [ @@ -10095,6 +10678,9 @@ "Accession_Code", "Deposit_Date", "Release_Date", + "Method_Details", + "Submitter_Flag", + "Submitter_Flag_Date", "Record_Status_Detail" ], "filter" : { @@ -10135,6 +10721,10 @@ "markdown_name" : "Release Date", "source" : "Release_Date" }, + { + "markdown_name" : "Last Communicated", + "source" : "Submitter_Flag_Date" + }, { "hide_not_null_choice" : true, "hide_null_choice" : true, @@ -10184,6 +10774,10 @@ }, "RID" ] + }, + { + "markdown_name" : "Manual Processing", + "source" : "Manual_Processing" } ] } @@ -10211,12 +10805,12 @@ }, { "destination" : { - "name" : "Entry_mmCIF_File", + "name" : "Entry_Generated_File", "type" : "download" }, "source" : { "api" : "attribute", - "path" : "PDB:Entry_mmCIF_File/url:=File_URL" + "path" : "PDB:Entry_Generated_File/url:=File_URL" } } ], @@ -10234,7 +10828,7 @@ "detailed" : [ [ "PDB", - "Entry_mmCIF_File_Structure_Id_fkey" + "Entry_Generated_File_Structure_Id_fkey" ], [ "PDB", @@ -10428,6 +11022,10 @@ "PDB", "ihm_multi_state_model_group_link_structure_id_fkey" ], + [ + "PDB", + "ihm_ordered_model_structure_id_fkey" + ], [ "PDB", "ihm_ordered_ensemble_structure_id_fkey" @@ -10596,6 +11194,26 @@ "PDB", "ihm_geometric_object_distance_restraint_structure_id_fkey" ], + [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ], { "comment" : "Collections to which the entry belongs", "markdown_name" : "Entry Collections", @@ -10615,6 +11233,18 @@ "RID" ] }, + { + "markdown_name" : "Curation Log", + "source" : [ + { + "inbound" : [ + "PDB", + "Curation_Log_Entry_fkey" + ] + }, + "RID" + ] + }, [ "PDB", "audit_conform_structure_id_fkey" @@ -13356,60 +13986,1204 @@ "compact" : [ "RID", { - "comment" : "Entry Collection Id", - "markdown_name" : "Entry Collection Id", + "comment" : "Entry Collection Id", + "markdown_name" : "Entry Collection Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_collection_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Id", + "markdown_name" : "Entry Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Accession Code", + "markdown_name" : "Accession Code", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "Accession_Code" + ] + } + ], + "detailed" : [ + "RID", + { + "comment" : "Entry Collection Id", + "markdown_name" : "Entry Collection Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_collection_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Id", + "markdown_name" : "Entry Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Accession Code", + "markdown_name" : "Accession Code", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "Accession_Code" + ] + }, + [ + "PDB", + "ihm_entry_collection_mapping_RCB_fkey" + ], + [ + "PDB", + "ihm_entry_collection_mapping_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_entry_collection_mapping_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "Entry Collection Id", + "markdown_name" : "Entry Collection Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_collection_id_fkey" + ] + }, + "id" + ] + }, + { + "comment" : "Entry Id", + "markdown_name" : "Entry Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_entry_collection_mapping_entry_id_fkey" + ] + }, + "id" + ] + } + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Multi-State Schemes" + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "name", + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "name", + "details", + [ + "PDB", + "ihm_multi_state_scheme_RCB_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_multi_state_scheme_Owner_fkey" + ] + ], + "entry" : [ + "id", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "name", + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value" : { + "detailed" : [ + [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + ], + "filter" : "detailed" + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Multi-State Scheme Connectivities" + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the starting state in the multi-state scheme", + "markdown_name" : "Begin State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the ending state in the multi-state scheme", + "markdown_name" : "End State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the starting state in the multi-state scheme", + "markdown_name" : "Begin State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the ending state in the multi-state scheme", + "markdown_name" : "End State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_multi_state_scheme_connectivity_RCB_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_multi_state_scheme_connectivity_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the starting state in the multi-state scheme", + "markdown_name" : "Begin State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the ending state in the multi-state scheme", + "markdown_name" : "End State Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "multi_state_scheme_connectivity_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_multi_state_scheme_connectivity", + "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value" : { + "detailed" : [ + [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ], + [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + ], + "filter" : "detailed" + } + }, + { + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Kinetic Rates from Biophysical Experiments" + } + }, + { + "schema" : "PDB", + "table" : "ihm_kinetic_rate", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_kinetic_rate_RCB_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_kinetic_rate_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "transition_rate_constant", + "equilibrium_constant", + [ + "PDB", + "ihm_equilibrium_constant_determination_method_fkey" + ], + "equilibrium_constant_unit", + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the external file corresponding to the kinetic rate measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the kinetic rate is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Relaxation times from Biophysical Experiments" + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", + { + "comment" : "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", + { + "comment" : "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_relaxation_time_RCB_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_relaxation_time_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + "value", + [ + "PDB", + "ihm_relaxation_time_unit_fkey" + ], + "amplitude", + { + "comment" : "Identifier for the external file corresponding to the relaxation time measurement", + "markdown_name" : "External File Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the dataset group from which the multi-state scheme is obtained", + "markdown_name" : "Dataset Group Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_ihm_dataset_group_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time", + "uri" : "tag:isrd.isi.edu,2016:visible-foreign-keys", + "value" : { + "detailed" : [ + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + ], + "filter" : "detailed" + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Mapping experimentally measured relaxation times with multi-state schemes" + } + }, + { + "schema" : "PDB", + "table" : "ihm_relaxation_time_multi_state_scheme", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the relaxation time", + "markdown_name" : "Relaxation Time Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ], + "detailed" : [ + "RID", + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the relaxation time", + "markdown_name" : "Relaxation Time Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + }, + "RID" + ] + }, + "details", + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_RCB_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_RMB_fkey" + ], + "RCT", + "RMT", + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_Owner_fkey" + ] + ], + "entry" : [ + { + "comment" : "A reference to table entry.id.", + "markdown_name" : "Structure Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ] + }, + "RID" + ] + }, + "id", + { + "comment" : "Identifier for the multi-state scheme", + "markdown_name" : "Scheme Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the multi-state scheme connectivity", + "markdown_name" : "Scheme Connectivity Id", + "source" : [ + { + "outbound" : [ + "PDB", + "relaxation_time_multi_state_scheme_connectivity_combo2_fkey" + ] + }, + "RID" + ] + }, + { + "comment" : "Identifier for the relaxation time", + "markdown_name" : "Relaxation Time Id", + "source" : [ + { + "outbound" : [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey" + ] + }, + "RID" + ] + }, + "details" + ] + } + }, + { + "schema" : "PDB", + "table" : "Curation_Log", + "uri" : "tag:misd.isi.edu,2015:display", + "value" : { + "comment_display" : { + "*" : { + "table_comment_display" : "inline" + } + }, + "name" : "Curation Log" + } + }, + { + "schema" : "PDB", + "table" : "Curation_Log", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + { + "comment" : "Entry Id", + "markdown_name" : "Entry Id", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "Curation_Log_Entry_fkey" ] }, "id" ] }, { - "comment" : "Entry Id", - "markdown_name" : "Entry Id", + "comment" : "Entry Accession Code", + "markdown_name" : "Accession Code", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "Curation_Log_Entry_fkey" ] }, - "id" + "Accession_Code" ] }, + "Log_Date", + "Details", + "Submitter_Allow", { - "comment" : "Entry Accession Code", - "markdown_name" : "Accession Code", + "markdown_name" : "RCB", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "Curation_Log_RCB_fkey" ] }, - "Accession_Code" + "Full_Name" ] - } - ], - "detailed" : [ - "RID", + }, { - "comment" : "Entry Collection Id", - "markdown_name" : "Entry Collection Id", + "markdown_name" : "RMB", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "Curation_Log_RMB_fkey" ] }, - "id" + "Full_Name" ] }, + "RCT", + "RMT" + ], + "detailed" : [ + "RID", { "comment" : "Entry Id", "markdown_name" : "Entry Id", @@ -13417,7 +15191,7 @@ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "Curation_Log_Entry_fkey" ] }, "id" @@ -13430,41 +15204,43 @@ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "Curation_Log_Entry_fkey" ] }, "Accession_Code" ] }, - [ - "PDB", - "ihm_entry_collection_mapping_RCB_fkey" - ], - [ - "PDB", - "ihm_entry_collection_mapping_RMB_fkey" - ], - "RCT", - "RMT", - [ - "PDB", - "ihm_entry_collection_mapping_Owner_fkey" - ] - ], - "entry" : [ + "Log_Date", + "Details", + "Submitter_Allow", { - "comment" : "Entry Collection Id", - "markdown_name" : "Entry Collection Id", + "markdown_name" : "RCB", "source" : [ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_collection_id_fkey" + "Curation_Log_RCB_fkey" ] }, - "id" + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "PDB", + "Curation_Log_RMB_fkey" + ] + }, + "Full_Name" ] }, + "RCT", + "RMT" + ], + "entry" : [ { "comment" : "Entry Id", "markdown_name" : "Entry Id", @@ -13472,12 +15248,15 @@ { "outbound" : [ "PDB", - "ihm_entry_collection_mapping_entry_id_fkey" + "Curation_Log_Entry_fkey" ] }, "id" ] - } + }, + "Log_Date", + "Details", + "Submitter_Allow" ] } }, @@ -15544,6 +17323,14 @@ [ "PDB", "ihm_localization_density_files_file_id_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_ihm_external_files_combo2_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_ihm_external_files_combo2_fkey" ] ], "filter" : "detailed" @@ -18407,6 +20194,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -18432,6 +20223,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -18470,6 +20265,10 @@ ] }, "title", + [ + "PDB", + "struct_pdbx_structure_determination_methodology_fkey" + ], "pdbx_descriptor", "pdbx_details", "pdbx_model_details", @@ -18689,6 +20488,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -18766,6 +20569,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -18856,6 +20663,10 @@ "PDB", "ihm_ensemble_info_sub_sampling_type_fkey" ], + [ + "PDB", + "ihm_ensemble_info_model_group_superimposed_flag_fkey" + ], "num_ensemble_models", "num_ensemble_models_deposited", "ensemble_precision_value", @@ -19990,12 +21801,6 @@ "markdown_name" : "Sequences of Polymeric Entities^*^" } }, - { - "schema" : "PDB", - "table" : "entity_poly_seq", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, { "schema" : "PDB", "table" : "entity_poly_seq", @@ -20835,12 +22640,6 @@ "markdown_name" : "Instances of Molecular Entities^*^" } }, - { - "schema" : "PDB", - "table" : "struct_asym", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, { "schema" : "PDB", "table" : "struct_asym", @@ -22544,7 +24343,7 @@ }, { "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:misd.isi.edu,2015:display", "value" : { "comment_display" : { @@ -22552,12 +24351,12 @@ "table_comment_display" : "inline" } }, - "name" : "System Generated mmCIF File" + "name" : "System Generated Files" } }, { "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:isrd.isi.edu,2016:table-display", "value" : { "row_name" : { @@ -22567,12 +24366,16 @@ }, { "schema" : "PDB", - "table" : "Entry_mmCIF_File", + "table" : "Entry_Generated_File", "uri" : "tag:isrd.isi.edu,2016:visible-columns", "value" : { "*" : [ "RID", "File_URL", + [ + "PDB", + "Entry_Generated_File_System_Generated_File_Type_fkey" + ], { "aggregate" : "array_d", "array_options" : { @@ -22596,7 +24399,7 @@ { "inbound" : [ "PDB", - "Conform_Dictionary_Entry_mmCIF_File_fkey" + "Conform_Dictionary_Entry_Generated_File_fkey" ] }, { @@ -22610,12 +24413,16 @@ }, [ "PDB", - "Entry_mmCIF_File_Structure_Id_fkey" + "Entry_Generated_File_Structure_Id_fkey" ] ], "detailed" : [ "RID", "File_URL", + [ + "PDB", + "Entry_Generated_File_System_Generated_File_Type_fkey" + ], { "aggregate" : "array_d", "array_options" : { @@ -22639,7 +24446,7 @@ { "inbound" : [ "PDB", - "Conform_Dictionary_Entry_mmCIF_File_fkey" + "Conform_Dictionary_Entry_Generated_File_fkey" ] }, { @@ -22653,14 +24460,32 @@ }, [ "PDB", - "Entry_mmCIF_File_Structure_Id_fkey" + "Entry_Generated_File_Structure_Id_fkey" ], "File_Bytes", "File_MD5" ], - "entry" : [], + "entry" : [ + "File_URL", + [ + "PDB", + "Entry_Generated_File_System_Generated_File_Type_fkey" + ], + [ + "PDB", + "Entry_Generated_File_Structure_Id_Entry_RCB_fkey" + ] + ], "entry/edit" : [ - "File_URL" + "File_URL", + [ + "PDB", + "Entry_Generated_File_System_Generated_File_Type_fkey" + ], + [ + "PDB", + "Entry_Generated_File_Structure_Id_Entry_RCB_fkey" + ] ] } }, @@ -22687,12 +24512,6 @@ } } }, - { - "schema" : "PDB", - "table" : "Entry_Error_File", - "uri" : "tag:isrd.isi.edu,2016:generated", - "value" : null - }, { "schema" : "PDB", "table" : "Entry_Error_File", @@ -22708,7 +24527,7 @@ "File_URL", [ "PDB", - "Entry_Error_File_File_Type_fkey" + "Entry_Error_File_System_Generated_File_Type_fkey" ] ], "detailed" : [ @@ -22723,7 +24542,7 @@ "File_URL", [ "PDB", - "Entry_Error_File_File_Type_fkey" + "Entry_Error_File_System_Generated_File_Type_fkey" ] ], "entry" : [ @@ -22734,7 +24553,7 @@ ], [ "PDB", - "Entry_Error_File_File_Type_fkey" + "Entry_Error_File_System_Generated_File_Type_fkey" ] ] } @@ -23018,11 +24837,11 @@ ], [ "PDB", - "ihm_ordered_ensemble_model_group_id_begin_fkey" + "ihm_ordered_model_ihm_model_group_1_combo1_fkey" ], [ "PDB", - "ihm_ordered_ensemble_model_group_id_end_fkey" + "ihm_ordered_ensemble_model_group_id_begin_fkey" ], [ "PDB", @@ -29085,7 +30904,7 @@ }, { "schema" : "Vocab", - "table" : "Validation_File_Type", + "table" : "System_Generated_File_Type", "uri" : "tag:isrd.isi.edu,2016:visible-columns", "value" : { "*" : [ @@ -29100,7 +30919,7 @@ { "outbound" : [ "Vocab", - "Validation_File_Type_RCB_fkey" + "System_Generated_File_Type_RCB_fkey" ] }, "Full_Name" @@ -29112,7 +30931,7 @@ { "outbound" : [ "Vocab", - "Validation_File_Type_RMB_fkey" + "System_Generated_File_Type_RMB_fkey" ] }, "Full_Name" @@ -29122,7 +30941,7 @@ "RMT", [ "Vocab", - "Validation_File_Type_Owner_fkey" + "System_Generated_File_Type_Owner_fkey" ] ] } @@ -29703,6 +31522,50 @@ ] } }, + { + "schema" : "Vocab", + "table" : "struct_pdbx_structure_determination_methodology", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "struct_pdbx_structure_determination_methodology_term_Owner_fkey" + ] + ] + } + }, { "schema" : "Vocab", "table" : "software_type", @@ -29759,6 +31622,94 @@ ] } }, + { + "schema" : "Vocab", + "table" : "ihm_relaxation_time_unit", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_relaxation_time_unit_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_relaxation_time_unit_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "ihm_relaxation_time_unit_term_Owner_fkey" + ] + ] + } + }, + { + "schema" : "Vocab", + "table" : "ihm_equilibrium_constant_determination_method", + "uri" : "tag:isrd.isi.edu,2016:visible-columns", + "value" : { + "*" : [ + "RID", + "Name", + "Description", + "ID", + "URI", + { + "markdown_name" : "RCB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_RCB_fkey" + ] + }, + "Full_Name" + ] + }, + { + "markdown_name" : "RMB", + "source" : [ + { + "outbound" : [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_RMB_fkey" + ] + }, + "Full_Name" + ] + }, + "RCT", + "RMT", + [ + "Vocab", + "ihm_equilibrium_constant_determination_method_term_Owner_fkey" + ] + ] + } + }, { "schema" : "Vocab", "table" : "ihm_geometric_object_half_torus_section", diff --git a/config-scripts/pdb/order_by.json b/config-scripts/pdb/order_by.json index 6b2a2fe..da67491 100644 --- a/config-scripts/pdb/order_by.json +++ b/config-scripts/pdb/order_by.json @@ -8,6 +8,7 @@ "ihm_ordered_ensemble": ["process_id", "edge_id"], "ihm_related_datasets": ["dataset_list_id_derived", "dataset_list_id_primary"], "ihm_struct_assembly_class_link": ["assembly_id", "class_id"], - "pdbx_entity_poly_na_type": ["entity_id", "type"] + "pdbx_entity_poly_na_type": ["entity_id", "type"], + "ihm_ordered_model": ["process_id", "edge_id"] } diff --git a/config-scripts/schema-updates/ciff_extension/2024_16_update_vocab.py b/config-scripts/schema-updates/ciff_extension/2024_16_update_vocab.py new file mode 100644 index 0000000..2b7a0b2 --- /dev/null +++ b/config-scripts/schema-updates/ciff_extension/2024_16_update_vocab.py @@ -0,0 +1,78 @@ +import sys +import json +from deriva.core import get_credential, DerivaServer, BaseCLI +from deriva.core.ermrest_model import Key, Column, builtin_types +import utils + +ihm_cross_link_list_linker_type_rows = [ + {'Name': 'PDH', 'Description': 'PDH'}, + {'Name': 'DMTMM', 'Description': 'DMTMM'} + ] + +ihm_dataset_list_data_type_rows = [ + {'Name': 'Crosslinking-MS data', 'Description': 'Crosslinking-MS data'} + ] + +ihm_dataset_group_application_rows = [ + {'Name': 'modeling', 'Description': 'modeling'} + ] + +ihm_dataset_related_db_reference_db_name_rows = [ + {'Name': 'ProteomeXchange', 'Description': 'ProteomeXchange'} + ] + +struct_pdbx_structure_determination_methodology_rows = [ + {'Name': 'computational', 'Description': 'computational'}, + {'Name': 'experimental', 'Description': 'experimental'}, + {'Name': 'integrative', 'Description': 'integrative'} + ] + +ihm_relaxation_time_unit_rows = [ + {'Name': 'seconds', 'Description': 'seconds'}, + {'Name': 'milliseconds', 'Description': 'milliseconds'}, + {'Name': 'microseconds', 'Description': 'microseconds'} + ] + +ihm_equilibrium_constant_determination_method_rows = [ + {'Name': 'from population', 'Description': 'from population'}, + {'Name': 'from kinetic rates', 'Description': 'from kinetic rates'}, + {'Name': 'other', 'Description': 'other'} + ] + +ihm_ensemble_info_model_group_superimposed_flag_rows = [ + {'Name': 'YES', 'Description': 'YES'}, + {'Name': 'NO', 'Description': 'NO'} + ] + +def main(server_name, catalog_id, credentials): + server = DerivaServer('https', server_name, credentials) + catalog = server.connect_ermrest(catalog_id) + catalog.dcctx['cid'] = "oneoff/model" + model = catalog.getCatalogModel() + + """ + Create new Vocab tables + """ + utils.create_table_if_not_exist(model, 'Vocab', utils.define_Vocab_table('struct_pdbx_structure_determination_methodology', 'Structure determination methodology')) + utils.create_table_if_not_exist(model, 'Vocab', utils.define_Vocab_table('ihm_relaxation_time_unit', 'Relaxation time unit')) + utils.create_table_if_not_exist(model, 'Vocab', utils.define_Vocab_table('ihm_equilibrium_constant_determination_method', 'Method used to determine the equilibrium constant')) + utils.create_table_if_not_exist(model, 'Vocab', utils.define_Vocab_table('ihm_ensemble_info_model_group_superimposed_flag', 'Model group superimposed flag')) + + """ + Load data into new and existing vocabulary tables + """ + utils.add_rows_to_vocab_table(catalog, 'ihm_cross_link_list_linker_type', ihm_cross_link_list_linker_type_rows) + utils.add_rows_to_vocab_table(catalog, 'ihm_dataset_list_data_type', ihm_dataset_list_data_type_rows) + utils.add_rows_to_vocab_table(catalog, 'ihm_dataset_group_application', ihm_dataset_group_application_rows) + utils.add_rows_to_vocab_table(catalog, 'ihm_dataset_related_db_reference_db_name', ihm_dataset_related_db_reference_db_name_rows) + utils.add_rows_to_vocab_table(catalog, 'struct_pdbx_structure_determination_methodology', struct_pdbx_structure_determination_methodology_rows) + utils.add_rows_to_vocab_table(catalog, 'ihm_relaxation_time_unit', ihm_relaxation_time_unit_rows) + utils.add_rows_to_vocab_table(catalog, 'ihm_equilibrium_constant_determination_method', ihm_equilibrium_constant_determination_method_rows) + utils.add_rows_to_vocab_table(catalog, 'ihm_ensemble_info_model_group_superimposed_flag', ihm_ensemble_info_model_group_superimposed_flag_rows) + +if __name__ == '__main__': + args = BaseCLI("ad-hoc table creation tool", None, 1).parse_cli() + credentials = get_credential(args.host, args.credential_file) + + main(args.host, 1, credentials) + diff --git a/config-scripts/schema-updates/ciff_extension/2024_17_kinetic_schemes.py b/config-scripts/schema-updates/ciff_extension/2024_17_kinetic_schemes.py new file mode 100644 index 0000000..2ca7de1 --- /dev/null +++ b/config-scripts/schema-updates/ciff_extension/2024_17_kinetic_schemes.py @@ -0,0 +1,573 @@ +import sys +import json +from deriva.core import ErmrestCatalog, AttrDict, get_credential, DEFAULT_CREDENTIAL_FILE, tag, urlquote, DerivaServer, get_credential, BaseCLI +from deriva.core.ermrest_model import builtin_types, Schema, Table, Column, Key, ForeignKey, DomainType, ArrayType +import utils + +""" +This script will be run after: + - +""" + +# ======================================================== +# -- create a table that is not a Vocab structure +def define_tdoc_ihm_multi_state_scheme(): + table_name='ihm_multi_state_scheme' + comment='Details about multiple states that can form a connected/ordered scheme; mmCIF category: ihm_multi_state_scheme' + + column_defs = [ + Column.define( + 'id', + builtin_types.int8, + comment='A unique identifier for the multi-state scheme', + nullok=False + ), + Column.define( + 'name', + builtin_types.text, + comment='Name for the multi-state scheme', + nullok=True + ), + Column.define( + 'details', + builtin_types.text, + comment='Details about the multi-state scheme', + nullok=True + ), + Column.define( + "structure_id", + builtin_types.text, + comment='Structure identifier', + nullok=False + ) + ] + key_defs = [ + Key.define(["structure_id", "id"], constraint_names=[["PDB", "ihm_multi_state_scheme_primary_key"]] ), + Key.define(["RID"], constraint_names=[["PDB", "ihm_multi_state_scheme_RID_key"]] ), + Key.define(["RID", "structure_id", "id"], constraint_names=[["PDB", "ihm_multi_state_scheme_combo1_key"]] ) + ] + + fkey_defs = [ + ForeignKey.define(["structure_id"], "PDB", "entry", ["id"], + constraint_names=[["PDB", "ihm_multi_state_scheme_structure_id_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ) + ] + + table_def = Table.define( + table_name, + column_defs, + key_defs=key_defs, + fkey_defs=fkey_defs, + comment=comment, + provide_system=True + ) + + return table_def + +# -------------------------------------------------------------- +def define_tdoc_ihm_multi_state_scheme_connectivity(): + table_name='ihm_multi_state_scheme_connectivity' + comment='Details about the ordered connectivities among states in a multi-state scheme; mmCIF category: ihm_multi_state_scheme_connectivity' + + column_defs = [ + Column.define( + 'id', + builtin_types.int8, + comment='A unique identifier for the multi-state scheme connectivity', + nullok=False + ), + Column.define( + 'scheme_id', + builtin_types.int8, + comment='Identifier for the multi-state scheme', + nullok=False + ), + Column.define( + 'begin_state_id', + builtin_types.int8, + comment='Identifier for the starting state in the multi-state scheme', + nullok=False + ), + Column.define( + 'end_state_id', + builtin_types.int8, + comment='Identifier for the ending state in the multi-state scheme', + nullok=True + ), + Column.define( + 'dataset_group_id', + builtin_types.int8, + comment='Identifier for the dataset group from which the multi-state scheme is obtained', + nullok=False + ), + Column.define( + "details", + builtin_types.text, + comment='Details about the multi-state scheme connectivity', + nullok=True + ), + Column.define( + "structure_id", + builtin_types.text, + comment='Structure identifier', + nullok=False + ), + Column.define( + "Scheme_RID", + builtin_types.text, + comment='Identifier to the multi-state scheme RID', + nullok=False + ), + Column.define( + "State_RID", + builtin_types.text, + comment='Identifier to the multi-state modeling state RID', + nullok=False + ), + Column.define( + "Dataset_Group_RID", + builtin_types.text, + comment='Identifier to the dataset group RID', + nullok=False + ) + ] + key_defs = [ + Key.define(["structure_id", "id"], constraint_names=[["PDB", "ihm_multi_state_scheme_connectivity_primary_key"]] ), + Key.define(["RID"], constraint_names=[["PDB", "ihm_multi_state_scheme_connectivity_RID_key"]] ), + Key.define(["RID", "structure_id", "id"], constraint_names=[["PDB", "ihm_multi_state_scheme_connectivity_combo1_key"]] ), + Key.define(["RID", "id"], constraint_names=[["PDB", "ihm_multi_state_scheme_connectivity_combo2_key"]] ) + ] + + fkey_defs = [ + ForeignKey.define(["structure_id"], "PDB", "entry", ["id"], + constraint_names=[["PDB", "ihm_multi_state_scheme_connectivity_structure_id_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["Scheme_RID", "structure_id", "scheme_id"], "PDB", "ihm_multi_state_scheme", ["RID", "structure_id", "id"], + constraint_names=[["PDB", "ihm_multi_state_scheme_connectivity_scheme_combo1_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["State_RID", "structure_id", "begin_state_id"], "PDB", "ihm_multi_state_modeling", ["RID", "structure_id", "state_id"], + constraint_names=[["PDB", "ihm_multi_state_scheme_connectivity_modeling_1_combo1_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["State_RID", "end_state_id"], "PDB", "ihm_multi_state_modeling", ["RID", "state_id"], + constraint_names=[["PDB", "ihm_multi_state_scheme_connectivity_modeling_2_combo2_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["Dataset_Group_RID", "structure_id", "dataset_group_id"], "PDB", "ihm_dataset_group", ["RID", "structure_id", "id"], + constraint_names=[["PDB", "multi_state_scheme_connectivity_dataset_group_combo1_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ) + ] + + table_def = Table.define( + table_name, + column_defs, + key_defs=key_defs, + fkey_defs=fkey_defs, + comment=comment, + provide_system=True + ) + + return table_def + +# -------------------------------------------------------------- +def define_tdoc_ihm_kinetic_rate(): + table_name='ihm_kinetic_rate' + comment='Details about the kinetic rates obtained from biophysical experiments; mmCIF category: ihm_kinetic_rate' + + column_defs = [ + Column.define( + 'id', + builtin_types.int8, + comment='A unique identifier for the kinetic rate', + nullok=False + ), + Column.define( + 'transition_rate_constant', + builtin_types.float8, + comment='The transition rate constant per second; unit = reciprocal seconds', + nullok=True + ), + Column.define( + 'equilibrium_constant', + builtin_types.float8, + comment='The equilibrium constant', + nullok=True + ), + Column.define( + 'equilibrium_constant_determination_method', + builtin_types.text, + comment='Method used to determine the equilibrium constant', + nullok=True + ), + Column.define( + 'equilibrium_constant_unit', + builtin_types.text, + comment='Unit of the equilibrium constant, if applicable', + nullok=True + ), + Column.define( + 'scheme_connectivity_id', + builtin_types.int8, + comment='Identifier for the multi-state scheme connectivity', + nullok=False + ), + Column.define( + 'external_file_id', + builtin_types.int8, + comment='Identifier for the external file corresponding to the kinetic rate measurement', + nullok=True + ), + Column.define( + 'dataset_group_id', + builtin_types.int8, + comment='Identifier for the dataset group from which the kinetic rate is obtained', + nullok=False + ), + Column.define( + "details", + builtin_types.text, + comment='Details about the kinetic rate', + nullok=True + ), + Column.define( + "structure_id", + builtin_types.text, + comment='Structure identifier', + nullok=False + ), + Column.define( + "Scheme_Connectivity_RID", + builtin_types.text, + comment='Identifier to the multi-state scheme connectivity RID', + nullok=False + ), + Column.define( + "External_File_RID", + builtin_types.text, + comment='Identifier to the external file RID', + nullok=True + ), + Column.define( + "Dataset_Group_RID", + builtin_types.text, + comment='Identifier to the dataset group RID', + nullok=False + ) + ] + key_defs = [ + Key.define(["structure_id", "id"], constraint_names=[["PDB", "ihm_kinetic_rate_primary_key"]] ), + Key.define(["RID"], constraint_names=[["PDB", "ihm_kinetic_rate_RID_key"]] ) + ] + + fkey_defs = [ + ForeignKey.define(["structure_id"], "PDB", "entry", ["id"], + constraint_names=[["PDB", "ihm_kinetic_rate_structure_id_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["Scheme_Connectivity_RID", "structure_id", "scheme_connectivity_id"], "PDB", "ihm_multi_state_scheme_connectivity", ["RID", "structure_id", "id"], + constraint_names=[["PDB", "ihm_kinetic_rate_multi_state_scheme_connectivity_combo1_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["External_File_RID", "external_file_id"], "PDB", "ihm_external_files", ["RID", "id"], + constraint_names=[["PDB", "ihm_kinetic_rate_ihm_external_files_combo2_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["Dataset_Group_RID", "structure_id", "dataset_group_id"], "PDB", "ihm_dataset_group", ["RID", "structure_id", "id"], + constraint_names=[["PDB", "ihm_kinetic_rate_ihm_dataset_group_combo1_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(['equilibrium_constant_determination_method'], 'Vocab', 'ihm_equilibrium_constant_determination_method', ['Name'], + constraint_names=[ ['Vocab', 'ihm_equilibrium_constant_determination_method_fkey'] ], + on_update='CASCADE', + on_delete='NO ACTION' + ) + ] + + table_def = Table.define( + table_name, + column_defs, + key_defs=key_defs, + fkey_defs=fkey_defs, + comment=comment, + provide_system=True + ) + + return table_def + +# -------------------------------------------------------------- +def define_tdoc_ihm_relaxation_time(): + table_name='ihm_relaxation_time' + comment='Details about the relaxation_times obtained from biophysical experiments; mmCIF category: ihm_relaxation_time' + + column_defs = [ + Column.define( + 'id', + builtin_types.int8, + comment='A unique identifier for the relaxation time', + nullok=False + ), + Column.define( + 'value', + builtin_types.float8, + comment='The relaxation time value', + nullok=False + ), + Column.define( + 'unit', + builtin_types.text, + comment='The relaxation time unit', + nullok=False + ), + Column.define( + 'amplitude', + builtin_types.float8, + comment='The relaxation time amplitude', + nullok=True + ), + Column.define( + 'external_file_id', + builtin_types.int8, + comment='Identifier for the external file corresponding to the relaxation time measurement', + nullok=True + ), + Column.define( + 'dataset_group_id', + builtin_types.int8, + comment='Identifier for the dataset group from which the relaxation time is obtained', + nullok=False + ), + Column.define( + "details", + builtin_types.text, + comment='Details about the relaxation time', + nullok=True + ), + Column.define( + "structure_id", + builtin_types.text, + comment='Structure identifier', + nullok=False + ), + Column.define( + "External_File_RID", + builtin_types.text, + comment='Identifier to the external file RID', + nullok=True + ), + Column.define( + "Dataset_Group_RID", + builtin_types.text, + comment='Identifier to the dataset group RID', + nullok=False + ) + ] + key_defs = [ + Key.define(["structure_id", "id"], constraint_names=[["PDB", "ihm_relaxation_time_primary_key"]] ), + Key.define(["RID"], constraint_names=[["PDB", "ihm_relaxation_time_RID_key"]] ), + Key.define(["RID", "structure_id", "id"], constraint_names=[["PDB", "ihm_relaxation_time_combo1_key"]] ) + ] + + fkey_defs = [ + ForeignKey.define(["structure_id"], "PDB", "entry", ["id"], + constraint_names=[["PDB", "ihm_relaxation_time_structure_id_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["External_File_RID", "external_file_id"], "PDB", "ihm_external_files", ["RID", "id"], + constraint_names=[["PDB", "ihm_relaxation_time_ihm_external_files_combo2_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["Dataset_Group_RID", "structure_id", "dataset_group_id"], "PDB", "ihm_dataset_group", ["RID", "structure_id", "id"], + constraint_names=[["PDB", "ihm_relaxation_time_ihm_dataset_group_combo1_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(['unit'], 'Vocab', 'ihm_relaxation_time_unit', ['Name'], + constraint_names=[ ['Vocab', 'ihm_relaxation_time_unit_fkey'] ], + on_update='CASCADE', + on_delete='NO ACTION' + ) + ] + + table_def = Table.define( + table_name, + column_defs, + key_defs=key_defs, + fkey_defs=fkey_defs, + comment=comment, + provide_system=True + ) + + return table_def + +# -------------------------------------------------------------- +def define_tdoc_ihm_relaxation_time_multi_state_scheme(): + table_name='ihm_relaxation_time_multi_state_scheme' + comment='Details about mapping the experimentally measured relaxation times with the multi-state schemes; mmCIF category: ihm_relaxation_time_multi_state_scheme' + + column_defs = [ + Column.define( + 'id', + builtin_types.int8, + comment='A unique identifier for mapping the relaxation time with the multi-state scheme', + nullok=False + ), + Column.define( + 'relaxation_time_id', + builtin_types.int8, + comment='Identifier for the relaxation time', + nullok=False + ), + Column.define( + 'scheme_id', + builtin_types.int8, + comment='Identifier for the multi-state scheme', + nullok=False + ), + Column.define( + 'scheme_connectivity_id', + builtin_types.int8, + comment='Identifier for the multi-state scheme connectivity', + nullok=True + ), + Column.define( + "details", + builtin_types.text, + comment='Details about the relaxation time measurement', + nullok=True + ), + Column.define( + "structure_id", + builtin_types.text, + comment='Structure identifier', + nullok=False + ), + Column.define( + "Scheme_Connectivity_RID", + builtin_types.text, + comment='Identifier to the multi-state scheme connectivity RID', + nullok=True + ), + Column.define( + "Scheme_RID", + builtin_types.text, + comment='Identifier to the multi-state scheme RID', + nullok=False + ), + Column.define( + "Relaxation_Time_RID", + builtin_types.text, + comment='Identifier to the relaxation time RID', + nullok=False + ) + ] + key_defs = [ + Key.define(["structure_id", "id"], constraint_names=[["PDB", "ihm_relaxation_time_multi_state_scheme_primary_key"]] ), + Key.define(["RID"], constraint_names=[["PDB", "ihm_relaxation_time_multi_state_scheme_RID_key"]] ) + ] + + fkey_defs = [ + ForeignKey.define(["structure_id"], "PDB", "entry", ["id"], + constraint_names=[["PDB", "ihm_relaxation_time_multi_state_scheme_structure_id_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["Scheme_Connectivity_RID", "scheme_connectivity_id"], "PDB", "ihm_multi_state_scheme_connectivity", ["RID", "id"], + constraint_names=[["PDB", "relaxation_time_multi_state_scheme_connectivity_combo2_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["Scheme_RID", "structure_id", "scheme_id"], "PDB", "ihm_multi_state_scheme", ["RID", "structure_id", "id"], + constraint_names=[["PDB", "ihm_relaxation_time_multi_state_scheme_scheme_combo1_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["Relaxation_Time_RID", "structure_id", "relaxation_time_id"], "PDB", "ihm_relaxation_time", ["RID", "structure_id", "id"], + constraint_names=[["PDB", "ihm_relaxation_time_multi_state_scheme_time_combo1_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ) + ] + + table_def = Table.define( + table_name, + column_defs, + key_defs=key_defs, + fkey_defs=fkey_defs, + comment=comment, + provide_system=True + ) + + return table_def + +# -------------------------------------------------------------- +def update_PDB_existing_tables(model): + + #Create new columns in existing tables + utils.create_column_if_not_exist(model, 'PDB', 'struct', + Column.define( + 'pdbx_structure_determination_methodology', + builtin_types.text, + comment='Indicates if the structure was determined using experimental, computational, or integrative methods', + nullok=True, + default="integrative" + )) + + # Create fkeys to Vocab tables + utils.create_foreign_key_if_not_exists(model, 'PDB', 'struct', 'struct_pdbx_structure_determination_methodology_fkey', + ForeignKey.define(['pdbx_structure_determination_methodology'], 'Vocab', 'struct_pdbx_structure_determination_methodology', ['Name'], + constraint_names=[ ['Vocab', 'struct_pdbx_structure_determination_methodology_fkey'] ], + on_update='CASCADE', + on_delete='NO ACTION') + ) + + # Create/rename combo1 and combo2 keys in existing tables + utils.create_key_if_not_exists(model, 'PDB', 'ihm_multi_state_modeling', ['RID', 'structure_id', 'state_id'], 'ihm_multi_state_modeling_combo1_key') + utils.create_key_if_not_exists(model, 'PDB', 'ihm_multi_state_modeling', ['RID', 'state_id'], 'ihm_multi_state_modeling_combo2_key') + utils.create_key_if_not_exists(model, 'PDB', 'ihm_dataset_group', ['RID', 'structure_id', 'id'], 'ihm_dataset_group_combo1_key') + utils.rename_key_if_exist(model, 'PDB', 'ihm_dataset_group', 'ihm_dataset_group_RID_id_key', 'ihm_dataset_group_combo2_key') + +# ============================================================ +def main(server_name, catalog_id, credentials): + server = DerivaServer('https', server_name, credentials) + catalog = server.connect_ermrest(catalog_id) + catalog.dcctx['cid'] = 'oneoff/model' + model = catalog.getCatalogModel() + + """ + Update existing model + """ + update_PDB_existing_tables(model) + + """ + Create table + """ + utils.create_table_if_not_exist(model, 'PDB', define_tdoc_ihm_multi_state_scheme()) + utils.create_table_if_not_exist(model, 'PDB', define_tdoc_ihm_multi_state_scheme_connectivity()) + utils.create_table_if_not_exist(model, 'PDB', define_tdoc_ihm_kinetic_rate()) + utils.create_table_if_not_exist(model, 'PDB', define_tdoc_ihm_relaxation_time()) + utils.create_table_if_not_exist(model, 'PDB', define_tdoc_ihm_relaxation_time_multi_state_scheme()) + +# =================================================== + +if __name__ == '__main__': + args = BaseCLI('ad-hoc table creation tool', None, 1).parse_cli() + credentials = get_credential(args.host, args.credential_file) + + main(args.host, 1, credentials) + diff --git a/config-scripts/schema-updates/ciff_extension/2024_18_ordered_model.py b/config-scripts/schema-updates/ciff_extension/2024_18_ordered_model.py new file mode 100644 index 0000000..ac1ec13 --- /dev/null +++ b/config-scripts/schema-updates/ciff_extension/2024_18_ordered_model.py @@ -0,0 +1,154 @@ +import sys +import json +from deriva.core import ErmrestCatalog, AttrDict, get_credential, DEFAULT_CREDENTIAL_FILE, tag, urlquote, DerivaServer, get_credential, BaseCLI +from deriva.core.ermrest_model import builtin_types, Schema, Table, Column, Key, ForeignKey, DomainType, ArrayType +import utils + +""" +This script will be run after: + - +""" + +# ======================================================== +# -- create a table that is not a Vocab structure +def define_tdoc_ihm_ordered_model(): + table_name='ihm_ordered_model' + comment='Details of model groups related by time or other order; model groups are represented as nodes with directed edges between them indicating the ordering; mmCIF category: ihm_ordered_model' + + column_defs = [ + Column.define( + 'process_id', + builtin_types.int8, + comment='Identifier for the ordered process', + nullok=False + ), + Column.define( + 'process_description', + builtin_types.text, + comment='Description of the ordered process', + nullok=True + ), + Column.define( + 'edge_id', + builtin_types.int8, + comment='Identifier for the edge in a directed graph', + nullok=False + ), + Column.define( + 'edge_description', + builtin_types.text, + comment='Description of the edge in a directed graph', + nullok=True + ), + Column.define( + 'step_id', + builtin_types.int8, + comment='Identifier for a step in the ordered process', + nullok=False + ), + Column.define( + 'step_description', + builtin_types.text, + comment='Description of the step in the ordered process', + nullok=True + ), + Column.define( + 'ordered_by', + builtin_types.text, + comment='Parameter based on which the ordering is carried out, e.g., time steps, steps in an assembly process, steps in a metabolic pathway, steps in an interaction pathway', + nullok=False + ), + Column.define( + 'model_group_id_begin', + builtin_types.int8, + comment='Model group id corresponding to the node at the origin of the directed edge', + nullok=False + ), + Column.define( + 'model_group_id_end', + builtin_types.int8, + comment='Model group id corresponding to the node at the end of the directed edge', + nullok=False + ), + Column.define( + "structure_id", + builtin_types.text, + comment='Structure identifier', + nullok=False + ), + Column.define( + "Model_Group_RID", + builtin_types.text, + comment='Identifier to the model group RID', + nullok=False + ) + ] + key_defs = [ + Key.define(["structure_id", "edge_id", "process_id"], constraint_names=[["PDB", "ihm_ordered_model_primary_key"]] ), + Key.define(["RID"], constraint_names=[["PDB", "ihm_ordered_model_RID_key"]] ) + ] + + fkey_defs = [ + ForeignKey.define(["structure_id"], "PDB", "entry", ["id"], + constraint_names=[["PDB", "ihm_ordered_model_structure_id_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["Model_Group_RID", "structure_id", "model_group_id_begin"], "PDB", "ihm_model_group", ["RID", "structure_id", "id"], + constraint_names=[["PDB", "ihm_ordered_model_ihm_model_group_1_combo1_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ), + ForeignKey.define(["Model_Group_RID", "structure_id", "model_group_id_end"], "PDB", "ihm_model_group", ["RID", "structure_id", "id"], + constraint_names=[["PDB", "ihm_ordered_model_ihm_model_group_2_combo1_fkey"]], + on_update="CASCADE", + on_delete="NO ACTION" + ) + ] + + table_def = Table.define( + table_name, + column_defs, + key_defs=key_defs, + fkey_defs=fkey_defs, + comment=comment, + provide_system=True + ) + + return table_def + +# -------------------------------------------------------------- +def table_comments(model): + + model.table("PDB", "ihm_ordered_ensemble").comment = "Details of model groups related by time or other order; model groups are represented as nodes with directed edges between them indicating the ordering; mmCIF category: ihm_ordered_ensemble (to be deprecated and superseded by ihm_ordered_model)" + +# ============================================================ +def main(server_name, catalog_id, credentials): + server = DerivaServer('https', server_name, credentials) + catalog = server.connect_ermrest(catalog_id) + catalog.dcctx['cid'] = 'oneoff/model' + model = catalog.getCatalogModel() + + """ + Update table comments + """ + table_comments(model) + + """ + Create keys for existing tables + """ + utils.create_key_if_not_exists(model, 'PDB', 'ihm_model_group', ['RID', 'structure_id', 'id'], 'ihm_model_group_combo1_key') + + """ + Create table + """ + utils.create_table_if_not_exist(model, 'PDB', define_tdoc_ihm_ordered_model()) + +# =================================================== + +if __name__ == '__main__': + args = BaseCLI('ad-hoc table creation tool', None, 1).parse_cli() + credentials = get_credential(args.host, args.credential_file) + + main(args.host, 1, credentials) + diff --git a/config-scripts/schema-updates/ciff_extension/2024_19_update_data_dictionary.py b/config-scripts/schema-updates/ciff_extension/2024_19_update_data_dictionary.py new file mode 100644 index 0000000..d9c86d3 --- /dev/null +++ b/config-scripts/schema-updates/ciff_extension/2024_19_update_data_dictionary.py @@ -0,0 +1,29 @@ +import sys +import json +from deriva.core import get_credential, DerivaServer, BaseCLI +from deriva.core.ermrest_model import Key, Column, builtin_types +import utils + +Data_Dictionary_rows = [ + {'Name': 'mmcif_ihm_ext.dic', 'Category': 'IHMCIF dictionary', 'Version': '1.26', 'Location': 'https://raw.githubusercontent.com/ihmwg/IHMCIF/master/archive/mmcif_ihm_ext-v1.26.dic'}, + {'Name': 'mmcif_pdbx.dic', 'Category': 'PDBx/mmCIF', 'Version': '5.395', 'Location': 'https://raw.githubusercontent.com/wwpdb-dictionaries/mmcif_pdbx/8d720719217bbeb36093992956e346448876c458/archive/mmcif_pdbx_v50-v5.395.dic'}, + {'Name': 'mmcif_ihm_flr_ext.dic', 'Category': 'FLRCIF dictionary', 'Version': '0.01', 'Location': 'https://raw.githubusercontent.com/ihmwg/flrCIF/master/archive/mmcif_ihm_flr_ext-v0.01.dic'} + ] + +def main(server_name, catalog_id, credentials): + server = DerivaServer('https', server_name, credentials) + catalog = server.connect_ermrest(catalog_id) + catalog.dcctx['cid'] = "oneoff/model" + model = catalog.getCatalogModel() + + """ + Create new rows in Data_Dictionary table + """ + utils.insert_rows(catalog, 'PDB', 'Data_Dictionary', Data_Dictionary_rows) + +if __name__ == '__main__': + args = BaseCLI("ad-hoc table creation tool", None, 1).parse_cli() + credentials = get_credential(args.host, args.credential_file) + + main(args.host, 1, credentials) + diff --git a/config-scripts/schema-updates/ciff_extension/2024_20_update_supported_dictionary.py b/config-scripts/schema-updates/ciff_extension/2024_20_update_supported_dictionary.py new file mode 100644 index 0000000..781c290 --- /dev/null +++ b/config-scripts/schema-updates/ciff_extension/2024_20_update_supported_dictionary.py @@ -0,0 +1,30 @@ +import sys +import json +from deriva.core import get_credential, DerivaServer, BaseCLI +from deriva.core.ermrest_model import Key, Column, builtin_types +import utils + +Supported_Dictionary_columns = ['Data_Dictionary_RID', 'Data_Dictionary_Category'] + +Supported_Dictionary_rows = [ + {'RID': '1-RE2T', 'Data_Dictionary_RID': '3-XP44', 'Data_Dictionary_Category': 'IHMCIF dictionary'}, + {'RID': '1-RE2W', 'Data_Dictionary_RID': '3-XP46', 'Data_Dictionary_Category': 'PDBx/mmCIF'} + ] + +def main(server_name, catalog_id, credentials): + server = DerivaServer('https', server_name, credentials) + catalog = server.connect_ermrest(catalog_id) + catalog.dcctx['cid'] = "oneoff/model" + model = catalog.getCatalogModel() + + """ + Update rows in Supported_Dictionary table + """ + utils.update_rows(catalog, 'PDB', 'Supported_Dictionary', Supported_Dictionary_columns, Supported_Dictionary_rows, column_key='RID') + +if __name__ == '__main__': + args = BaseCLI("ad-hoc table creation tool", None, 1).parse_cli() + credentials = get_credential(args.host, args.credential_file) + + main(args.host, 1, credentials) + diff --git a/config-scripts/schema-updates/ciff_extension/2024_21_ihm_ensemble_info.py b/config-scripts/schema-updates/ciff_extension/2024_21_ihm_ensemble_info.py new file mode 100644 index 0000000..f0e8458 --- /dev/null +++ b/config-scripts/schema-updates/ciff_extension/2024_21_ihm_ensemble_info.py @@ -0,0 +1,46 @@ +import sys +import json +from deriva.core import ErmrestCatalog, AttrDict, get_credential, DEFAULT_CREDENTIAL_FILE, tag, urlquote, DerivaServer, get_credential, BaseCLI +from deriva.core.ermrest_model import builtin_types, Schema, Table, Column, Key, ForeignKey, DomainType, ArrayType +import utils + +def update_PDB_ihm_ensemble_info(model): + # Add the PDB.ihm_ensemble_info.model_group_superimposed_flag + utils.create_column_if_not_exist(model, 'PDB', 'ihm_ensemble_info', + Column.define( + 'model_group_superimposed_flag', + builtin_types.text, + comment='Flag to identify if the models in a group or cluster are structurally aligned', + nullok=True + )) + + # Create the foreign keys + utils.create_foreign_key_if_not_exists(model, 'PDB', 'ihm_ensemble_info', 'ihm_ensemble_info_model_group_superimposed_flag_fkey', + ForeignKey.define(['model_group_superimposed_flag'], 'Vocab', 'ihm_ensemble_info_model_group_superimposed_flag', ['Name'], + constraint_names=[ ['Vocab', 'ihm_ensemble_info_model_group_superimposed_flag_fkey'] ], + on_update='CASCADE', + on_delete='NO ACTION') + ) + +# ============================================================ +def main(server_name, catalog_id, credentials): + server = DerivaServer('https', server_name, credentials) + catalog = server.connect_ermrest(catalog_id) + catalog.dcctx['cid'] = 'oneoff/model' + model = catalog.getCatalogModel() + + """ + Update existing model + """ + update_PDB_ihm_ensemble_info(model) + +# =================================================== + +if __name__ == '__main__': + args = BaseCLI('ad-hoc table creation tool', None, 1).parse_cli() + credentials = get_credential(args.host, args.credential_file) +# if args.catalog is None: +# catalog_id = 99 + + main(args.host, 1, credentials) + diff --git a/config-scripts/schema-updates/ciff_extension/utils.py b/config-scripts/schema-updates/ciff_extension/utils.py index d13892d..fa6f750 100644 --- a/config-scripts/schema-updates/ciff_extension/utils.py +++ b/config-scripts/schema-updates/ciff_extension/utils.py @@ -357,3 +357,28 @@ def set_foreign_key_acls(catalog, schema_name, table_name, constraint_name, acls model.apply() print('Set acls for the foreign key {} of the table {}:{}'.format(constraint_name, schema_name, table_name)) +""" +add rows to a table +rows is a list of JSON objects having as keys columns names +""" +def insert_rows(catalog, schema_name, table_name, rows): + url = f'/entity/{urlquote(schema_name)}:{urlquote(table_name)}' + resp = catalog.post( + url, + json=rows + ) + resp.raise_for_status() + print(f'Added rows to the {schema_name}:{table_name} table.') + +""" +update rows of a table +rows is a list of JSON objects having as keys columns names inclusive the column_key. +columns is a list of columns to be updated. It does not contain the column_key. +""" +def update_rows(catalog, schema_name, table_name, columns, rows, column_key='RID'): + columns = ','.join([urlquote(col) for col in columns]) + url = f'/attributegroup/{urlquote(schema_name)}:{urlquote(table_name)}/{urlquote(column_key)};{columns}' + resp = catalog.put(url,json=rows) + resp.raise_for_status() + print(f'Updated rows of the {schema_name}:{table_name} table.') + diff --git a/pdb_dev/README.md b/pdb_dev/README.md index 96922af..4fa261e 100644 --- a/pdb_dev/README.md +++ b/pdb_dev/README.md @@ -31,7 +31,7 @@ The **`catalog_1_display_PDB_constraints.json`** file contains for each table th 4. Generating the optional foreign keys to the **`RID`** column ``` -python -m pdb_dev.config.app.get_optional_fk 1 catalog_1_display_PDB_constraints.json optional_fk.json +python -m pdb_dev.config.app.get_optional_fk data.pdb-dev.org 1 catalog_1_display_PDB_constraints.json optional_fk.json ``` The tool uses as input the **`catalog_1_display_PDB_constraints.json`** file generated at step **`3`**. The output **`optional_fk.json`** file contains the foreign key names together with foreign keys and references by columns. @@ -58,7 +58,6 @@ The output is the **`combo1_columns.json`** file. python -m pdb_dev.config.app.get_ucode_all data.pdb-dev.org 1 ``` The script needs to have the [testGetUcode.py](https://github.com/informatics-isi-edu/protein-database/blob/master/scripts/dictionary-api/testGetUcode.py), -[ihm-extension.dic](https://github.com/informatics-isi-edu/protein-database/blob/master/scripts/make-json/py-rcsb_db/CACHE/dictionaries/ihm-extension.dic) and -[mmcif_v5.342_ihm_v1.17.dic](https://github.com/informatics-isi-edu/protein-database/blob/master/scripts/make-json/py-rcsb_db/CACHE/dictionaries/mmcif_v5.342_ihm_v1.17.dic) files. +and from the `py-rcsb_db` package, the `py-rcsb_db/CACHE/dictionaries/mmcif_ihm_ext.dic` and `py-rcsb_db/CACHE/dictionaries/mmcif_ihm.dic` files. The output **`vocab_ucode.json`** file contains the vocabulary columns whose values will be converted to upper case. diff --git a/pdb_dev/config/app/get_ucode_all.py b/pdb_dev/config/app/get_ucode_all.py index fff6376..e6b0499 100644 --- a/pdb_dev/config/app/get_ucode_all.py +++ b/pdb_dev/config/app/get_ucode_all.py @@ -30,7 +30,7 @@ def column_is_fk(fkeys, table_name, column_name, model_root, indent, vocab_table if debug == True: print('{}PDB.{}.{} is not a Foreign Key'.format(indent, table_name, column_name)) -args = ['/usr/bin/python3', 'testGetUcode.py', 'ihm-extension.dic'] +args = ['/usr/bin/python3', 'testGetUcode.py', 'mmcif_ihm_ext.dic'] if debug == True: print('Running "{}"'.format(' '.join(args))) p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) @@ -43,7 +43,7 @@ def column_is_fk(fkeys, table_name, column_name, model_root, indent, vocab_table fw.write(stdoutdata.decode('utf-8')) fw.close() -args = ['/usr/bin/python3', 'testGetUcode.py', 'mmcif_v5.342_ihm_v1.17.dic'] +args = ['/usr/bin/python3', 'testGetUcode.py', 'mmcif_ihm.dic'] if debug == True: print('Running "{}"'.format(' '.join(args))) p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) @@ -71,6 +71,7 @@ def column_is_fk(fkeys, table_name, column_name, model_root, indent, vocab_table vocab_tables = [] +missing_columns = {} missing_tables = [] for input in ['ucode_ihm.log', 'ucode_mmCIF.log']: @@ -101,11 +102,18 @@ def column_is_fk(fkeys, table_name, column_name, model_root, indent, vocab_table table = model_root.schemas[schema_name].tables[table_name] fkeys = table.foreign_keys for column_name in columns: - column = table.column_definitions.__getitem__(column_name) - column_is_fk(fkeys, table_name, column_name, model_root, '', vocab_tables) + try: + column = table.column_definitions.__getitem__(column_name) + column_is_fk(fkeys, table_name, column_name, model_root, '', vocab_tables) + except: + if table_name not in missing_columns.keys(): + missing_columns[table_name] = [] + missing_columns[table_name].append(column_name) except: missing_tables.append(table_name) +print(json.dumps(missing_tables, indent=4)) +print(json.dumps(missing_columns, indent=4)) if False: for vocab_table in vocab_tables: print('select count(*) as {} from "Vocab".{};'.format(vocab_table, vocab_table)) diff --git a/scripts/pdb_processing/config/catalog_99_display_entry.json b/scripts/pdb_processing/config/catalog_99_display_entry.json index 0c338fc..211d57a 100644 --- a/scripts/pdb_processing/config/catalog_99_display_entry.json +++ b/scripts/pdb_processing/config/catalog_99_display_entry.json @@ -48,6 +48,48 @@ } }, "referenced_by": { + "Entry_Latest_Archive_Entry_fkey": { + "schema": "PDB", + "table": "Entry_Latest_Archive", + "columns": "(Entry)", + "referenced_columns": "(RID)" + }, + "ihm_multi_state_scheme_structure_id_fkey": { + "schema": "PDB", + "table": "ihm_multi_state_scheme", + "columns": "(structure_id)", + "referenced_columns": "(id)" + }, + "ihm_multi_state_scheme_connectivity_structure_id_fkey": { + "schema": "PDB", + "table": "ihm_multi_state_scheme_connectivity", + "columns": "(structure_id)", + "referenced_columns": "(id)" + }, + "ihm_kinetic_rate_structure_id_fkey": { + "schema": "PDB", + "table": "ihm_kinetic_rate", + "columns": "(structure_id)", + "referenced_columns": "(id)" + }, + "ihm_relaxation_time_structure_id_fkey": { + "schema": "PDB", + "table": "ihm_relaxation_time", + "columns": "(structure_id)", + "referenced_columns": "(id)" + }, + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey": { + "schema": "PDB", + "table": "ihm_relaxation_time_multi_state_scheme", + "columns": "(structure_id)", + "referenced_columns": "(id)" + }, + "ihm_ordered_model_structure_id_fkey": { + "schema": "PDB", + "table": "ihm_ordered_model", + "columns": "(structure_id)", + "referenced_columns": "(id)" + }, "ihm_starting_model_seq_dif_structure_id_fkey": { "schema": "PDB", "table": "ihm_starting_model_seq_dif", @@ -603,8 +645,8 @@ "Entry_Generated_File_Structure_Id_Entry_RCB_fkey": { "schema": "PDB", "table": "Entry_Generated_File", - "columns": "(Structure_Id,Entry_RCB)", - "referenced_columns": "(id,RCB)" + "columns": "(Entry_RCB,Structure_Id)", + "referenced_columns": "(RCB,id)" }, "Entry_Generated_File_Structure_Id_fkey": { "schema": "PDB", @@ -1289,6 +1331,10 @@ "PDB", "ihm_multi_state_model_group_link_structure_id_fkey" ], + [ + "PDB", + "ihm_ordered_model_structure_id_fkey" + ], [ "PDB", "ihm_ordered_ensemble_structure_id_fkey" @@ -1457,6 +1503,26 @@ "PDB", "ihm_geometric_object_distance_restraint_structure_id_fkey" ], + [ + "PDB", + "ihm_multi_state_scheme_structure_id_fkey" + ], + [ + "PDB", + "ihm_multi_state_scheme_connectivity_structure_id_fkey" + ], + [ + "PDB", + "ihm_kinetic_rate_structure_id_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_structure_id_fkey" + ], + [ + "PDB", + "ihm_relaxation_time_multi_state_scheme_structure_id_fkey" + ], { "source": [ { diff --git a/scripts/pdb_processing/config/combo1_columns.json b/scripts/pdb_processing/config/combo1_columns.json index eb25f5b..033a4cb 100644 --- a/scripts/pdb_processing/config/combo1_columns.json +++ b/scripts/pdb_processing/config/combo1_columns.json @@ -1,4 +1,59 @@ { + "ihm_multi_state_scheme_connectivity": { + "Scheme_RID": { + "ihm_multi_state_scheme": { + "scheme_id": "id" + } + }, + "State_RID": { + "ihm_multi_state_modeling": { + "end_state_id": "state_id" + } + }, + "Dataset_Group_RID": { + "ihm_dataset_group": { + "dataset_group_id": "id" + } + } + }, + "ihm_kinetic_rate": { + "Scheme_Connectivity_RID": { + "ihm_multi_state_scheme_connectivity": { + "scheme_connectivity_id": "id" + } + }, + "Dataset_Group_RID": { + "ihm_dataset_group": { + "dataset_group_id": "id" + } + } + }, + "ihm_relaxation_time": { + "Dataset_Group_RID": { + "ihm_dataset_group": { + "dataset_group_id": "id" + } + } + }, + "ihm_relaxation_time_multi_state_scheme": { + "Scheme_RID": { + "ihm_multi_state_scheme": { + "scheme_id": "id" + } + }, + "Relaxation_Time_RID": { + "ihm_relaxation_time": { + "relaxation_time_id": "id" + } + } + }, + "ihm_ordered_model": { + "Model_Group_RID": { + "ihm_model_group": { + "model_group_id_end": "id" + } + } + }, "Conform_Dictionary": { "Exported_mmCIF_RID": { "Entry_Generated_File": {} diff --git a/scripts/pdb_processing/config/ermrest_table_defs.json b/scripts/pdb_processing/config/ermrest_table_defs.json index 6585619..f5487a3 100644 --- a/scripts/pdb_processing/config/ermrest_table_defs.json +++ b/scripts/pdb_processing/config/ermrest_table_defs.json @@ -3732,6 +3732,85 @@ "ordinal_id" ] }, + "ihm_kinetic_rate": { + "name": "ihm_kinetic_rate", + "columns": [ + { + "name": "structure_id", + "type": "text", + "nullok": false, + "comment": "A reference to table entry.id." + }, + { + "name": "dataset_group_id", + "type": "int4", + "nullok": false, + "comment": "A reference to table ihm_dataset_group.id." + }, + { + "name": "details", + "type": "text", + "nullok": true, + "comment": "type:text\nAdditional details about the kinetic rate." + }, + { + "name": "equilibrium_constant", + "type": "float4", + "nullok": true, + "comment": "type:float4\nThe equilibrium constant." + }, + { + "name": "equilibrium_constant_determination_method", + "type": "text", + "nullok": true, + "comment": "type:text\nMethod used to determine the equilibrium constant." + }, + { + "name": "equilibrium_constant_unit", + "type": "text", + "nullok": true, + "comment": "type:text\nUnit of the equilibrium constant, if applicable.\n If the kinetics describes a conformational change, then the equilibrium constant will not have a unit. \n If however a complex is involved, then a unit may be necessary." + }, + { + "name": "external_file_id", + "type": "int4", + "nullok": true, + "comment": "A reference to table ihm_external_files.id." + }, + { + "name": "id", + "type": "int4", + "nullok": false, + "comment": "type:int4\nAn identifier for the kinetic rate." + }, + { + "name": "scheme_connectivity_id", + "type": "int4", + "nullok": false, + "comment": "A reference to table ihm_multi_state_scheme_connectivity.id." + }, + { + "name": "transition_rate_constant", + "type": "float4", + "nullok": true, + "comment": "type:float4\nThe transition rate constant per second." + } + ], + "vocab": { + "ihm_kinetic_rate": "equilibrium_constant_determination_method" + }, + "fkeys": [ + { + "column": "equilibrium_constant_determination_method", + "reftable": "ate_equilibrium_constant_determination_method_term", + "refcolumn": "ID" + } + ], + "pkey_columns": [ + "structure_id", + "id" + ] + }, "ihm_ligand_probe": { "name": "ihm_ligand_probe", "columns": [ @@ -4528,6 +4607,94 @@ "state_id" ] }, + "ihm_multi_state_scheme": { + "name": "ihm_multi_state_scheme", + "columns": [ + { + "name": "structure_id", + "type": "text", + "nullok": false, + "comment": "A reference to table entry.id." + }, + { + "name": "details", + "type": "text", + "nullok": true, + "comment": "type:text\nDetails about the multi-state scheme." + }, + { + "name": "id", + "type": "int4", + "nullok": false, + "comment": "type:int4\nA unique identifier for the category." + }, + { + "name": "name", + "type": "text", + "nullok": true, + "comment": "type:text\nName for the multi-state scheme." + } + ], + "vocab": {}, + "fkeys": [], + "pkey_columns": [ + "structure_id", + "id" + ] + }, + "ihm_multi_state_scheme_connectivity": { + "name": "ihm_multi_state_scheme_connectivity", + "columns": [ + { + "name": "structure_id", + "type": "text", + "nullok": false, + "comment": "A reference to table entry.id." + }, + { + "name": "begin_state_id", + "type": "int4", + "nullok": false, + "comment": "A reference to table ihm_multi_state_modeling.state_id." + }, + { + "name": "dataset_group_id", + "type": "int4", + "nullok": false, + "comment": "A reference to table ihm_dataset_group.id." + }, + { + "name": "details", + "type": "text", + "nullok": true, + "comment": "type:text\nDetails about the multi-state scheme connectivity." + }, + { + "name": "end_state_id", + "type": "int4", + "nullok": true, + "comment": "A reference to table ihm_multi_state_modeling.state_id." + }, + { + "name": "id", + "type": "int4", + "nullok": false, + "comment": "type:int4\nA unique identifier for the category." + }, + { + "name": "scheme_id", + "type": "int4", + "nullok": false, + "comment": "A reference to table ihm_multi_state_scheme.id." + } + ], + "vocab": {}, + "fkeys": [], + "pkey_columns": [ + "structure_id", + "id" + ] + }, "ihm_non_poly_feature": { "name": "ihm_non_poly_feature", "columns": [ @@ -4653,6 +4820,78 @@ "process_id" ] }, + "ihm_ordered_model": { + "name": "ihm_ordered_model", + "columns": [ + { + "name": "structure_id", + "type": "text", + "nullok": false, + "comment": "A reference to table entry.id." + }, + { + "name": "edge_description", + "type": "text", + "nullok": true, + "comment": "type:text\nDescription of the edge." + }, + { + "name": "edge_id", + "type": "int4", + "nullok": false, + "comment": "type:int4\nAn identifier that describes an edge in a directed graph, which\n represents the ordered model. \n Forms the category key together with _ihm_ordered_model.process_id." + }, + { + "name": "model_group_id_begin", + "type": "int4", + "nullok": false, + "comment": "A reference to table ihm_model_group.id." + }, + { + "name": "model_group_id_end", + "type": "int4", + "nullok": false, + "comment": "A reference to table ihm_model_group.id." + }, + { + "name": "ordered_by", + "type": "text", + "nullok": true, + "comment": "type:text\nThe parameter based on which the ordering is carried out.\nexamples:time steps,steps in an assembly process,steps in a metabolic pathway,steps in an interaction pathway" + }, + { + "name": "process_description", + "type": "text", + "nullok": true, + "comment": "type:text\nDescription of the ordered process." + }, + { + "name": "process_id", + "type": "int4", + "nullok": false, + "comment": "type:int4\nAn identifier for the ordered process. \n Forms the category key together with _ihm_ordered_model.edge_id." + }, + { + "name": "step_description", + "type": "text", + "nullok": true, + "comment": "type:text\nDescription of the step." + }, + { + "name": "step_id", + "type": "int4", + "nullok": false, + "comment": "type:int4\nIdentifier for a particular step in the ordered process." + } + ], + "vocab": {}, + "fkeys": [], + "pkey_columns": [ + "structure_id", + "edge_id", + "process_id" + ] + }, "ihm_poly_atom_feature": { "name": "ihm_poly_atom_feature", "columns": [ @@ -5337,6 +5576,120 @@ "dataset_list_id_primary" ] }, + "ihm_relaxation_time": { + "name": "ihm_relaxation_time", + "columns": [ + { + "name": "structure_id", + "type": "text", + "nullok": false, + "comment": "A reference to table entry.id." + }, + { + "name": "amplitude", + "type": "float4", + "nullok": true, + "comment": "type:float4\nRelaxation time amplitude." + }, + { + "name": "dataset_group_id", + "type": "int4", + "nullok": false, + "comment": "A reference to table ihm_dataset_group.id." + }, + { + "name": "details", + "type": "text", + "nullok": true, + "comment": "type:text\nAdditional details regarding the relaxation time." + }, + { + "name": "external_file_id", + "type": "int4", + "nullok": true, + "comment": "A reference to table ihm_external_files.id." + }, + { + "name": "id", + "type": "int4", + "nullok": false, + "comment": "type:int4\nA unique identifier for the relaxation time." + }, + { + "name": "unit", + "type": "text", + "nullok": false, + "comment": "type:text\nRelaxation time unit." + }, + { + "name": "value", + "type": "float4", + "nullok": false, + "comment": "type:float4\nRelaxation time value." + } + ], + "vocab": { + "ihm_relaxation_time": "unit" + }, + "fkeys": [ + { + "column": "unit", + "reftable": "ihm_relaxation_time_unit_term", + "refcolumn": "ID" + } + ], + "pkey_columns": [ + "structure_id", + "id" + ] + }, + "ihm_relaxation_time_multi_state_scheme": { + "name": "ihm_relaxation_time_multi_state_scheme", + "columns": [ + { + "name": "structure_id", + "type": "text", + "nullok": false, + "comment": "A reference to table entry.id." + }, + { + "name": "details", + "type": "text", + "nullok": true, + "comment": "type:text\nAdditional details about the relaxation time measurement." + }, + { + "name": "id", + "type": "int4", + "nullok": false, + "comment": "type:int4\nA unique identifier for the category." + }, + { + "name": "relaxation_time_id", + "type": "int4", + "nullok": false, + "comment": "A reference to table ihm_relaxation_time.id." + }, + { + "name": "scheme_connectivity_id", + "type": "int4", + "nullok": true, + "comment": "A reference to table ihm_multi_state_scheme_connectivity.id." + }, + { + "name": "scheme_id", + "type": "int4", + "nullok": false, + "comment": "A reference to table ihm_multi_state_scheme.id." + } + ], + "vocab": {}, + "fkeys": [], + "pkey_columns": [ + "structure_id", + "id" + ] + }, "ihm_residues_not_modeled": { "name": "ihm_residues_not_modeled", "columns": [ diff --git a/scripts/pdb_processing/config/exported_vocab.pickle b/scripts/pdb_processing/config/exported_vocab.pickle index 7ca2d49..7e2456f 100644 Binary files a/scripts/pdb_processing/config/exported_vocab.pickle and b/scripts/pdb_processing/config/exported_vocab.pickle differ diff --git a/scripts/pdb_processing/config/json-full-db-ihm_dev_full-col-ihm_dev_full.json b/scripts/pdb_processing/config/json-full-db-ihm_dev_full-col-ihm_dev_full.json index 396d2f4..79123cd 100644 --- a/scripts/pdb_processing/config/json-full-db-ihm_dev_full-col-ihm_dev_full.json +++ b/scripts/pdb_processing/config/json-full-db-ihm_dev_full-col-ihm_dev_full.json @@ -2865,6 +2865,7 @@ "CDI", "CYS", "DHSO", + "DMTMM", "DSA", "DSBU", "DSG", @@ -2878,6 +2879,7 @@ "L-Photo-Leucine", "LCSDA", "Other", + "PDH", "SDA", "TBDSPP", "sulfo-SDA", @@ -2925,6 +2927,10 @@ "value": "DHSO", "detail": "dihydrazide sulfoxide crosslinker" }, + { + "value": "DMTMM", + "detail": "4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride crosslinker" + }, { "value": "DSA", "detail": "DiSuccinimidyl Adipate" @@ -2977,6 +2983,10 @@ "value": "Other", "detail": "Other type of crosslinker" }, + { + "value": "PDH", + "detail": "pimelic acid dihydrazide crosslinker" + }, { "value": "SDA", "detail": "succinimidyl 4,4'-azipentanoate" @@ -3788,6 +3798,7 @@ "type": "string", "enum": [ "filter", + "modeling", "other", "representation", "restraint", @@ -3800,6 +3811,10 @@ "value": "filter", "detail": "dataset used for filtering sampled models" }, + { + "value": "modeling", + "detail": "dataset used in modeling" + }, { "value": "other", "detail": "dataset used in other ways" @@ -3915,6 +3930,7 @@ "3DEM volume", "CX-MS data", "Comparative model", + "Crosslinking-MS data", "DNA footprinting data", "De Novo model", "EM raw micrographs", @@ -4037,6 +4053,7 @@ "PDB-Dev", "PRIDE", "ProXL", + "ProteomeXchange", "SASBDB", "iProX", "jPOSTrepo" @@ -6467,6 +6484,118 @@ "uniqueItems": true, "rcsb_nested_indexing": false }, + "ihm_kinetic_rate": { + "type": "array", + "items": { + "type": "object", + "properties": { + "structure_id": { + "$ref": "#entry/id", + "_primary_key": true + }, + "dataset_group_id": { + "$ref": "#ihm_dataset_group/id" + }, + "details": { + "type": "string", + "description": "Additional details about the kinetic rate.", + "rcsb_description": [ + { + "text": "Additional details about the kinetic rate.", + "context": "dictionary" + } + ] + }, + "equilibrium_constant": { + "type": "number", + "description": "The equilibrium constant.", + "rcsb_description": [ + { + "text": "The equilibrium constant.", + "context": "dictionary" + } + ] + }, + "equilibrium_constant_determination_method": { + "type": "string", + "enum": [ + "from kinetic rates", + "from population", + "other" + ], + "description": "Method used to determine the equilibrium constant.", + "rcsb_enum_annotated": [ + { + "value": "from kinetic rates", + "detail": "equilibrium constant is determined from kinetic rates, kAB/kBA" + }, + { + "value": "from population", + "detail": "equilibrium constant is determined from population" + }, + { + "value": "other", + "detail": "equilibrium constant is determined from another method not listed" + } + ], + "rcsb_description": [ + { + "text": "Method used to determine the equilibrium constant.", + "context": "dictionary" + } + ] + }, + "equilibrium_constant_unit": { + "type": "string", + "description": "Unit of the equilibrium constant, if applicable.\n If the kinetics describes a conformational change, then the equilibrium constant will not have a unit. \n If however a complex is involved, then a unit may be necessary.", + "rcsb_description": [ + { + "text": "Unit of the equilibrium constant, if applicable.\n If the kinetics describes a conformational change, then the equilibrium constant will not have a unit. \n If however a complex is involved, then a unit may be necessary.", + "context": "dictionary" + } + ] + }, + "external_file_id": { + "$ref": "#ihm_external_files/id" + }, + "id": { + "type": "integer", + "description": "An identifier for the kinetic rate.", + "_primary_key": true, + "rcsb_description": [ + { + "text": "An identifier for the kinetic rate.", + "context": "dictionary" + } + ] + }, + "scheme_connectivity_id": { + "$ref": "#ihm_multi_state_scheme_connectivity/id" + }, + "transition_rate_constant": { + "type": "number", + "description": "The transition rate constant per second.", + "rcsb_units": "reciprocal_seconds", + "rcsb_description": [ + { + "text": "The transition rate constant per second.", + "context": "dictionary" + } + ] + } + }, + "additionalProperties": false, + "required": [ + "structure_id", + "dataset_group_id", + "id", + "scheme_connectivity_id" + ] + }, + "minItems": 1, + "uniqueItems": true, + "rcsb_nested_indexing": false + }, "ihm_ligand_probe": { "type": "array", "items": { @@ -7583,6 +7712,113 @@ "uniqueItems": true, "rcsb_nested_indexing": false }, + "ihm_multi_state_scheme": { + "type": "array", + "items": { + "type": "object", + "properties": { + "structure_id": { + "$ref": "#entry/id", + "_primary_key": true + }, + "details": { + "type": "string", + "description": "Details about the multi-state scheme.", + "rcsb_description": [ + { + "text": "Details about the multi-state scheme.", + "context": "dictionary" + } + ] + }, + "id": { + "type": "integer", + "description": "A unique identifier for the category.", + "_primary_key": true, + "rcsb_description": [ + { + "text": "A unique identifier for the category.", + "context": "dictionary" + } + ] + }, + "name": { + "type": "string", + "description": "Name for the multi-state scheme.", + "rcsb_description": [ + { + "text": "Name for the multi-state scheme.", + "context": "dictionary" + } + ] + } + }, + "additionalProperties": false, + "required": [ + "structure_id", + "id" + ] + }, + "minItems": 1, + "uniqueItems": true, + "rcsb_nested_indexing": false + }, + "ihm_multi_state_scheme_connectivity": { + "type": "array", + "items": { + "type": "object", + "properties": { + "structure_id": { + "$ref": "#entry/id", + "_primary_key": true + }, + "begin_state_id": { + "$ref": "#ihm_multi_state_modeling/state_id" + }, + "dataset_group_id": { + "$ref": "#ihm_dataset_group/id" + }, + "details": { + "type": "string", + "description": "Details about the multi-state scheme connectivity.", + "rcsb_description": [ + { + "text": "Details about the multi-state scheme connectivity.", + "context": "dictionary" + } + ] + }, + "end_state_id": { + "$ref": "#ihm_multi_state_modeling/state_id" + }, + "id": { + "type": "integer", + "description": "A unique identifier for the category.", + "_primary_key": true, + "rcsb_description": [ + { + "text": "A unique identifier for the category.", + "context": "dictionary" + } + ] + }, + "scheme_id": { + "$ref": "#ihm_multi_state_scheme/id" + } + }, + "additionalProperties": false, + "required": [ + "structure_id", + "begin_state_id", + "dataset_group_id", + "id", + "scheme_id" + ] + }, + "minItems": 1, + "uniqueItems": true, + "rcsb_nested_indexing": false + }, "ihm_non_poly_feature": { "type": "array", "items": { @@ -7747,6 +7983,114 @@ "uniqueItems": true, "rcsb_nested_indexing": false }, + "ihm_ordered_model": { + "type": "array", + "items": { + "type": "object", + "properties": { + "structure_id": { + "$ref": "#entry/id", + "_primary_key": true + }, + "edge_description": { + "type": "string", + "description": "Description of the edge.", + "rcsb_description": [ + { + "text": "Description of the edge.", + "context": "dictionary" + } + ] + }, + "edge_id": { + "type": "integer", + "description": "An identifier that describes an edge in a directed graph, which\n represents the ordered model. \n Forms the category key together with _ihm_ordered_model.process_id.", + "_primary_key": true, + "rcsb_description": [ + { + "text": "An identifier that describes an edge in a directed graph, which\n represents the ordered model. \n Forms the category key together with _ihm_ordered_model.process_id.", + "context": "dictionary" + } + ] + }, + "model_group_id_begin": { + "$ref": "#ihm_model_group/id" + }, + "model_group_id_end": { + "$ref": "#ihm_model_group/id" + }, + "ordered_by": { + "type": "string", + "examples": [ + "time steps", + "steps in an assembly process", + "steps in a metabolic pathway", + "steps in an interaction pathway" + ], + "description": "The parameter based on which the ordering is carried out.", + "rcsb_description": [ + { + "text": "The parameter based on which the ordering is carried out.", + "context": "dictionary" + } + ] + }, + "process_description": { + "type": "string", + "description": "Description of the ordered process.", + "rcsb_description": [ + { + "text": "Description of the ordered process.", + "context": "dictionary" + } + ] + }, + "process_id": { + "type": "integer", + "description": "An identifier for the ordered process. \n Forms the category key together with _ihm_ordered_model.edge_id.", + "_primary_key": true, + "rcsb_description": [ + { + "text": "An identifier for the ordered process. \n Forms the category key together with _ihm_ordered_model.edge_id.", + "context": "dictionary" + } + ] + }, + "step_description": { + "type": "string", + "description": "Description of the step.", + "rcsb_description": [ + { + "text": "Description of the step.", + "context": "dictionary" + } + ] + }, + "step_id": { + "type": "integer", + "description": "Identifier for a particular step in the ordered process.", + "rcsb_description": [ + { + "text": "Identifier for a particular step in the ordered process.", + "context": "dictionary" + } + ] + } + }, + "additionalProperties": false, + "required": [ + "structure_id", + "edge_id", + "model_group_id_begin", + "model_group_id_end", + "process_id", + "step_id" + ] + }, + "minItems": 1, + "uniqueItems": true, + "rcsb_nested_indexing": false + }, "ihm_poly_atom_feature": { "type": "array", "items": { @@ -8689,6 +9033,143 @@ "uniqueItems": true, "rcsb_nested_indexing": false }, + "ihm_relaxation_time": { + "type": "array", + "items": { + "type": "object", + "properties": { + "structure_id": { + "$ref": "#entry/id", + "_primary_key": true + }, + "amplitude": { + "type": "number", + "description": "Relaxation time amplitude.", + "rcsb_description": [ + { + "text": "Relaxation time amplitude.", + "context": "dictionary" + } + ] + }, + "dataset_group_id": { + "$ref": "#ihm_dataset_group/id" + }, + "details": { + "type": "string", + "description": "Additional details regarding the relaxation time.", + "rcsb_description": [ + { + "text": "Additional details regarding the relaxation time.", + "context": "dictionary" + } + ] + }, + "external_file_id": { + "$ref": "#ihm_external_files/id" + }, + "id": { + "type": "integer", + "description": "A unique identifier for the relaxation time.", + "_primary_key": true, + "rcsb_description": [ + { + "text": "A unique identifier for the relaxation time.", + "context": "dictionary" + } + ] + }, + "unit": { + "type": "string", + "enum": [ + "microseconds", + "milliseconds", + "seconds" + ], + "description": "Relaxation time unit.", + "rcsb_description": [ + { + "text": "Relaxation time unit.", + "context": "dictionary" + } + ] + }, + "value": { + "type": "number", + "description": "Relaxation time value.", + "rcsb_description": [ + { + "text": "Relaxation time value.", + "context": "dictionary" + } + ] + } + }, + "additionalProperties": false, + "required": [ + "structure_id", + "dataset_group_id", + "id", + "unit", + "value" + ] + }, + "minItems": 1, + "uniqueItems": true, + "rcsb_nested_indexing": false + }, + "ihm_relaxation_time_multi_state_scheme": { + "type": "array", + "items": { + "type": "object", + "properties": { + "structure_id": { + "$ref": "#entry/id", + "_primary_key": true + }, + "details": { + "type": "string", + "description": "Additional details about the relaxation time measurement.", + "rcsb_description": [ + { + "text": "Additional details about the relaxation time measurement.", + "context": "dictionary" + } + ] + }, + "id": { + "type": "integer", + "description": "A unique identifier for the category.", + "_primary_key": true, + "rcsb_description": [ + { + "text": "A unique identifier for the category.", + "context": "dictionary" + } + ] + }, + "relaxation_time_id": { + "$ref": "#ihm_relaxation_time/id" + }, + "scheme_connectivity_id": { + "$ref": "#ihm_multi_state_scheme_connectivity/id" + }, + "scheme_id": { + "$ref": "#ihm_multi_state_scheme/id" + } + }, + "additionalProperties": false, + "required": [ + "structure_id", + "id", + "relaxation_time_id", + "scheme_id" + ] + }, + "minItems": 1, + "uniqueItems": true, + "rcsb_nested_indexing": false + }, "ihm_residues_not_modeled": { "type": "array", "items": { diff --git a/scripts/pdb_processing/config/mmCIF_defaults.json b/scripts/pdb_processing/config/mmCIF_defaults.json index 55f9227..33a56b9 100644 --- a/scripts/pdb_processing/config/mmCIF_defaults.json +++ b/scripts/pdb_processing/config/mmCIF_defaults.json @@ -1,4 +1,10 @@ { + "Entry_Latest_Archive": [ + "mmCIF_URL" + ], + "ihm_ordered_model": [ + "ordered_by" + ], "ihm_starting_model_seq_dif": [ "db_asym_id", "db_comp_id" diff --git a/scripts/pdb_processing/config/optional_fk.json b/scripts/pdb_processing/config/optional_fk.json index 70e8552..b83a2df 100644 --- a/scripts/pdb_processing/config/optional_fk.json +++ b/scripts/pdb_processing/config/optional_fk.json @@ -2,12 +2,12 @@ "ihm_non_poly_feature": [ { "fk_columns": [ - "Asym_RID", - "asym_id" + "asym_id", + "Asym_RID" ], "ref_columns": [ - "RID", - "id" + "id", + "RID" ], "ref_table": "struct_asym", "fk_name": "ihm_non_poly_feature_asym_id_fkey", @@ -22,12 +22,12 @@ "software": [ { "fk_columns": [ - "citation_id", - "Citation_RID" + "Citation_RID", + "citation_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "citation", "fk_name": "software_citation_id_fkey", @@ -42,12 +42,12 @@ "ihm_geometric_object_plane": [ { "fk_columns": [ - "transformation_id", - "Transformation_RID" + "Transformation_RID", + "transformation_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "ihm_geometric_object_transformation", "fk_name": "ihm_geometric_object_plane_transformation_id_fkey", @@ -80,12 +80,12 @@ }, { "fk_columns": [ - "External_Files_RID", - "script_file_id" + "script_file_id", + "External_Files_RID" ], "ref_columns": [ - "RID", - "id" + "id", + "RID" ], "ref_table": "ihm_external_files", "fk_name": "ihm_starting_computational_models_script_file_id_fkey", @@ -100,12 +100,12 @@ "ihm_probe_list": [ { "fk_columns": [ - "probe_chem_comp_descriptor_id", - "Probe_chem_comp_descriptor_RID" + "Probe_chem_comp_descriptor_RID", + "probe_chem_comp_descriptor_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "ihm_chemical_component_descriptor", "fk_name": "ihm_probe_list_probe_chem_comp_descriptor_id_fkey", @@ -118,12 +118,12 @@ }, { "fk_columns": [ - "Reactive_probe_chem_comp_descriptor_RID", - "reactive_probe_chem_comp_descriptor_id" + "reactive_probe_chem_comp_descriptor_id", + "Reactive_probe_chem_comp_descriptor_RID" ], "ref_columns": [ - "RID", - "id" + "id", + "RID" ], "ref_table": "ihm_chemical_component_descriptor", "fk_name": "ihm_probe_list_reactive_probe_chem_comp_descriptor_id_fkey", @@ -138,12 +138,12 @@ "ihm_poly_atom_feature": [ { "fk_columns": [ - "asym_id", - "Asym_RID" + "Asym_RID", + "asym_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "struct_asym", "fk_name": "ihm_poly_atom_feature_asym_id_fkey", @@ -198,12 +198,12 @@ "ihm_interface_residue_feature": [ { "fk_columns": [ - "dataset_list_id", - "Dataset_List_RID" + "Dataset_List_RID", + "dataset_list_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "ihm_dataset_list", "fk_name": "ihm_interface_residue_feature_dataset_list_id_fkey", @@ -236,12 +236,12 @@ "ihm_geometric_object_axis": [ { "fk_columns": [ - "Transformation_RID", - "transformation_id" + "transformation_id", + "Transformation_RID" ], "ref_columns": [ - "RID", - "id" + "id", + "RID" ], "ref_table": "ihm_geometric_object_transformation", "fk_name": "ihm_geometric_object_axis_transformation_id_fkey", @@ -276,12 +276,12 @@ "ihm_modeling_protocol_details": [ { "fk_columns": [ - "software_id", - "Software_RID" + "Software_RID", + "software_id" ], "ref_columns": [ - "pdbx_ordinal", - "RID" + "RID", + "pdbx_ordinal" ], "ref_table": "software", "fk_name": "ihm_modeling_protocol_details_software_id_fkey", @@ -330,12 +330,12 @@ }, { "fk_columns": [ - "dataset_group_id", - "Dataset_group_RID" + "Dataset_group_RID", + "dataset_group_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "ihm_dataset_group", "fk_name": "ihm_modeling_protocol_details_dataset_group_id_fkey", @@ -370,12 +370,12 @@ "ihm_epr_restraint": [ { "fk_columns": [ - "fitting_method_citation_id", - "Fitting_method_citation_RID" + "Fitting_method_citation_RID", + "fitting_method_citation_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "citation", "fk_name": "ihm_epr_restraint_fitting_method_citation_id_fkey", @@ -390,12 +390,12 @@ "ihm_localization_density_files": [ { "fk_columns": [ - "entity_poly_segment_id", - "Entity_poly_segment_RID" + "Entity_poly_segment_RID", + "entity_poly_segment_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "ihm_entity_poly_segment", "fk_name": "ihm_localization_density_files_entity_poly_segment_id_fkey", @@ -408,12 +408,12 @@ }, { "fk_columns": [ - "Asym_RID", - "asym_id" + "asym_id", + "Asym_RID" ], "ref_columns": [ - "RID", - "id" + "id", + "RID" ], "ref_table": "struct_asym", "fk_name": "ihm_localization_density_files_asym_id_fkey", @@ -426,12 +426,12 @@ }, { "fk_columns": [ - "entity_id", - "Entity_RID" + "Entity_RID", + "entity_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "entity", "fk_name": "ihm_localization_density_files_entity_id_fkey", @@ -466,12 +466,12 @@ "ihm_poly_probe_position": [ { "fk_columns": [ - "mut_res_chem_comp_id", - "Mut_res_chem_comp_RID" + "Mut_res_chem_comp_RID", + "mut_res_chem_comp_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "chem_comp", "fk_name": "ihm_poly_probe_position_mut_res_chem_comp_id_fkey", @@ -484,12 +484,12 @@ }, { "fk_columns": [ - "mod_res_chem_comp_descriptor_id", - "Mod_res_chem_comp_descriptor_RID" + "Mod_res_chem_comp_descriptor_RID", + "mod_res_chem_comp_descriptor_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "ihm_chemical_component_descriptor", "fk_name": "ihm_poly_probe_position_mod_res_chem_comp_descriptor_id_fkey", @@ -504,12 +504,12 @@ "ihm_predicted_contact_restraint": [ { "fk_columns": [ - "software_id", - "Software_RID" + "Software_RID", + "software_id" ], "ref_columns": [ - "pdbx_ordinal", - "RID" + "RID", + "pdbx_ordinal" ], "ref_table": "software", "fk_name": "ihm_predicted_contact_restraint_software_id_fkey", @@ -600,12 +600,12 @@ }, { "fk_columns": [ - "Ensemble_file_RID", - "ensemble_file_id" + "ensemble_file_id", + "Ensemble_file_RID" ], "ref_columns": [ - "RID", - "id" + "id", + "RID" ], "ref_table": "ihm_external_files", "fk_name": "ihm_ensemble_info_ensemble_file_id_fkey", @@ -618,12 +618,12 @@ }, { "fk_columns": [ - "Post_process_RID", - "post_process_id" + "post_process_id", + "Post_process_RID" ], "ref_columns": [ - "RID", - "id" + "id", + "RID" ], "ref_table": "ihm_modeling_post_process", "fk_name": "ihm_ensemble_info_post_process_id_fkey", @@ -658,12 +658,12 @@ "ihm_poly_probe_conjugate": [ { "fk_columns": [ - "Chem_comp_descriptor_RID", - "chem_comp_descriptor_id" + "chem_comp_descriptor_id", + "Chem_comp_descriptor_RID" ], "ref_columns": [ - "RID", - "id" + "id", + "RID" ], "ref_table": "ihm_chemical_component_descriptor", "fk_name": "ihm_poly_probe_conjugate_chem_comp_descriptor_id_fkey", @@ -696,12 +696,12 @@ }, { "fk_columns": [ - "dataset_group_id", - "Dataset_group_RID" + "Dataset_group_RID", + "dataset_group_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "ihm_dataset_group", "fk_name": "ihm_modeling_post_process_dataset_group_id_fkey", @@ -714,12 +714,12 @@ }, { "fk_columns": [ - "Software_RID", - "software_id" + "software_id", + "Software_RID" ], "ref_columns": [ - "RID", - "pdbx_ordinal" + "pdbx_ordinal", + "RID" ], "ref_table": "software", "fk_name": "ihm_modeling_post_process_software_id_fkey", @@ -732,12 +732,12 @@ }, { "fk_columns": [ - "struct_assembly_id", - "Struct_assembly_RID" + "Struct_assembly_RID", + "struct_assembly_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "ihm_struct_assembly", "fk_name": "ihm_modeling_post_process_struct_assembly_id_fkey", @@ -752,12 +752,12 @@ "ihm_starting_comparative_models": [ { "fk_columns": [ - "alignment_file_id", - "Alignment_file_RID" + "Alignment_file_RID", + "alignment_file_id" ], "ref_columns": [ - "id", - "RID" + "RID", + "id" ], "ref_table": "ihm_external_files", "fk_name": "ihm_starting_comparative_models_alignment_file_id_fkey", diff --git a/scripts/pdb_processing/config/order_by.json b/scripts/pdb_processing/config/order_by.json index 6b2a2fe..da67491 100644 --- a/scripts/pdb_processing/config/order_by.json +++ b/scripts/pdb_processing/config/order_by.json @@ -8,6 +8,7 @@ "ihm_ordered_ensemble": ["process_id", "edge_id"], "ihm_related_datasets": ["dataset_list_id_derived", "dataset_list_id_primary"], "ihm_struct_assembly_class_link": ["assembly_id", "class_id"], - "pdbx_entity_poly_na_type": ["entity_id", "type"] + "pdbx_entity_poly_na_type": ["entity_id", "type"], + "ihm_ordered_model": ["process_id", "edge_id"] } diff --git a/scripts/pdb_processing/config/tables_groups.json b/scripts/pdb_processing/config/tables_groups.json index c0cecb4..6a55fb4 100644 --- a/scripts/pdb_processing/config/tables_groups.json +++ b/scripts/pdb_processing/config/tables_groups.json @@ -3,6 +3,7 @@ "Accession_Code", "Data_Dictionary", "Entry_Related_File_Templates", + "PDB_Archive", "entry", "ihm_entry_collection" ], @@ -10,6 +11,7 @@ "Curation_Log", "Entry_Error_File", "Entry_Generated_File", + "Entry_Latest_Archive", "Entry_Related_File", "Supported_Dictionary", "atom_type", @@ -31,6 +33,7 @@ "ihm_model_representation", "ihm_modeling_protocol", "ihm_multi_state_modeling", + "ihm_multi_state_scheme", "ihm_struct_assembly", "ihm_struct_assembly_class", "pdbx_entry_details", @@ -58,7 +61,9 @@ "ihm_geometric_object_torus", "ihm_model_list", "ihm_multi_state_model_group_link", + "ihm_multi_state_scheme_connectivity", "ihm_ordered_ensemble", + "ihm_ordered_model", "ihm_probe_list", "ihm_pseudo_site", "ihm_related_datasets", @@ -82,6 +87,7 @@ "ihm_geometric_object_half_torus", "ihm_hdx_restraint", "ihm_interface_residue_feature", + "ihm_kinetic_rate", "ihm_ligand_probe", "ihm_model_group_link", "ihm_model_representative", @@ -89,6 +95,7 @@ "ihm_modeling_protocol_details", "ihm_non_poly_feature", "ihm_pseudo_site_feature", + "ihm_relaxation_time", "ihm_sas_restraint", "struct_ref_seq" ], @@ -101,6 +108,7 @@ "ihm_poly_probe_position", "ihm_poly_residue_feature", "ihm_predicted_contact_restraint", + "ihm_relaxation_time_multi_state_scheme", "ihm_residues_not_modeled", "struct_ref_seq_dif" ], diff --git a/scripts/ubuntu/pdb/pdb-software-lib.sh b/scripts/ubuntu/pdb/pdb-software-lib.sh index 5819894..35c7dd2 100755 --- a/scripts/ubuntu/pdb/pdb-software-lib.sh +++ b/scripts/ubuntu/pdb/pdb-software-lib.sh @@ -162,7 +162,7 @@ python_ihm_pull_checkout() python_ihm_install() { - pip3 install ihm==1.2 + pip3 install ihm==1.3 } python_ihm_validation()