From 86cd5a01a726812a01ede97ed89b9cdc07a3a652 Mon Sep 17 00:00:00 2001 From: Brinda Vallat Date: Thu, 7 Sep 2023 10:49:03 -0400 Subject: [PATCH 1/2] Frontend related schema updates to support search of sequence coverage data --- config/exdb-config-schema.yml | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/config/exdb-config-schema.yml b/config/exdb-config-schema.yml index f5324b94..8d18318f 100644 --- a/config/exdb-config-schema.yml +++ b/config/exdb-config-schema.yml @@ -144,6 +144,7 @@ # RO-4002: Improve indexing for pdbx_initial_refinement_model # 26-Jul-2023 bv RO-3979: Add support for reference sequence and entity sequence coverage information for polymer entities # 08-Aug-2023 dwp RO-4015: Remove GO and InterPro context values from rcsb_nested_indexing_context.context_attributes in pdbx_core_polymer_entity +# 07-Sep-2023 bv RO-3979: Frontend related schema updates to support search of sequence coverage data # --- database_catalog_configuration: @@ -5520,9 +5521,8 @@ document_helper_configuration: - rcsb_polymer_entity_feature_summary.count - rcsb_polymer_entity_feature_summary.coverage # - # BV: To be uncommented when data is populated in the documents for reference sequence and entity sequence coverage - #- rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers_reference_sequence_coverage - #- rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers_entity_sequence_coverage + - rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers_reference_sequence_coverage + - rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers_entity_sequence_coverage # #- rcsb_entity_source_organism.ncbi_scientific_name #- rcsb_entity_source_organism.ncbi_common_names @@ -5985,13 +5985,12 @@ document_helper_configuration: - ATTRIBUTE_NAME: rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers_database_name TYPE: brief TEXT: Database Name - # BV: To be uncommented when the data is populated in the documents for reference sequence and entity sequence coverage - #- ATTRIBUTE_NAME: rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers_reference_sequence_coverage - # TYPE: brief - # TEXT: Reference Sequence Coverage - #- ATTRIBUTE_NAME: rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers_entity_sequence_coverage - # TYPE: brief - # TEXT: Entity Sequence Coverage + - ATTRIBUTE_NAME: rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers_reference_sequence_coverage + TYPE: brief + TEXT: Reference Sequence Coverage + - ATTRIBUTE_NAME: rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers_entity_sequence_coverage + TYPE: brief + TEXT: Entity Sequence Coverage - ATTRIBUTE_NAME: struct_keywords.pdbx_keywords TYPE: brief TEXT: Structure Keywords From 471f100198566094167cb174449be4a1ff3941da Mon Sep 17 00:00:00 2001 From: Brinda Vallat Date: Thu, 7 Sep 2023 11:46:17 -0400 Subject: [PATCH 2/2] Update schema --- ...l-pdbx_comp_model_core_polymer_entity.json | 20 +++++++++++++++++++ ...dbx_core-col-pdbx_core_polymer_entity.json | 20 +++++++++++++++++++ ...l-pdbx_comp_model_core_polymer_entity.json | 20 +++++++++++++++++++ ...dbx_core-col-pdbx_core_polymer_entity.json | 20 +++++++++++++++++++ 4 files changed, 80 insertions(+) diff --git a/json_schema_definitions/json-full-db-pdbx_comp_model_core-col-pdbx_comp_model_core_polymer_entity.json b/json_schema_definitions/json-full-db-pdbx_comp_model_core-col-pdbx_comp_model_core_polymer_entity.json index 8da25309..23d01cf1 100644 --- a/json_schema_definitions/json-full-db-pdbx_comp_model_core-col-pdbx_comp_model_core_polymer_entity.json +++ b/json_schema_definitions/json-full-db-pdbx_comp_model_core-col-pdbx_comp_model_core_polymer_entity.json @@ -3398,6 +3398,16 @@ { "text": "Indicates what fraction of this polymer entity sequence is covered by the reference sequence.", "context": "dictionary" + }, + { + "text": "Entity Sequence Coverage", + "context": "brief" + } + ], + "rcsb_search_group": [ + { + "group_name": "Polymer Molecular Features", + "priority_order": 135 } ] }, @@ -3435,6 +3445,16 @@ { "text": "Indicates what fraction of the reference sequence is covered by this polymer entity sequence.", "context": "dictionary" + }, + { + "text": "Reference Sequence Coverage", + "context": "brief" + } + ], + "rcsb_search_group": [ + { + "group_name": "Polymer Molecular Features", + "priority_order": 130 } ] } diff --git a/json_schema_definitions/json-full-db-pdbx_core-col-pdbx_core_polymer_entity.json b/json_schema_definitions/json-full-db-pdbx_core-col-pdbx_core_polymer_entity.json index e2dba8f0..f9bc24c3 100644 --- a/json_schema_definitions/json-full-db-pdbx_core-col-pdbx_core_polymer_entity.json +++ b/json_schema_definitions/json-full-db-pdbx_core-col-pdbx_core_polymer_entity.json @@ -3398,6 +3398,16 @@ { "text": "Indicates what fraction of this polymer entity sequence is covered by the reference sequence.", "context": "dictionary" + }, + { + "text": "Entity Sequence Coverage", + "context": "brief" + } + ], + "rcsb_search_group": [ + { + "group_name": "Polymer Molecular Features", + "priority_order": 135 } ] }, @@ -3435,6 +3445,16 @@ { "text": "Indicates what fraction of the reference sequence is covered by this polymer entity sequence.", "context": "dictionary" + }, + { + "text": "Reference Sequence Coverage", + "context": "brief" + } + ], + "rcsb_search_group": [ + { + "group_name": "Polymer Molecular Features", + "priority_order": 130 } ] } diff --git a/json_schema_definitions/json-min-db-pdbx_comp_model_core-col-pdbx_comp_model_core_polymer_entity.json b/json_schema_definitions/json-min-db-pdbx_comp_model_core-col-pdbx_comp_model_core_polymer_entity.json index 07c08091..974a273b 100644 --- a/json_schema_definitions/json-min-db-pdbx_comp_model_core-col-pdbx_comp_model_core_polymer_entity.json +++ b/json_schema_definitions/json-min-db-pdbx_comp_model_core-col-pdbx_comp_model_core_polymer_entity.json @@ -3386,6 +3386,16 @@ { "text": "Indicates what fraction of this polymer entity sequence is covered by the reference sequence.", "context": "dictionary" + }, + { + "text": "Entity Sequence Coverage", + "context": "brief" + } + ], + "rcsb_search_group": [ + { + "group_name": "Polymer Molecular Features", + "priority_order": 135 } ] }, @@ -3423,6 +3433,16 @@ { "text": "Indicates what fraction of the reference sequence is covered by this polymer entity sequence.", "context": "dictionary" + }, + { + "text": "Reference Sequence Coverage", + "context": "brief" + } + ], + "rcsb_search_group": [ + { + "group_name": "Polymer Molecular Features", + "priority_order": 130 } ] } diff --git a/json_schema_definitions/json-min-db-pdbx_core-col-pdbx_core_polymer_entity.json b/json_schema_definitions/json-min-db-pdbx_core-col-pdbx_core_polymer_entity.json index 78b165a7..cd58887b 100644 --- a/json_schema_definitions/json-min-db-pdbx_core-col-pdbx_core_polymer_entity.json +++ b/json_schema_definitions/json-min-db-pdbx_core-col-pdbx_core_polymer_entity.json @@ -3386,6 +3386,16 @@ { "text": "Indicates what fraction of this polymer entity sequence is covered by the reference sequence.", "context": "dictionary" + }, + { + "text": "Entity Sequence Coverage", + "context": "brief" + } + ], + "rcsb_search_group": [ + { + "group_name": "Polymer Molecular Features", + "priority_order": 135 } ] }, @@ -3423,6 +3433,16 @@ { "text": "Indicates what fraction of the reference sequence is covered by this polymer entity sequence.", "context": "dictionary" + }, + { + "text": "Reference Sequence Coverage", + "context": "brief" + } + ], + "rcsb_search_group": [ + { + "group_name": "Polymer Molecular Features", + "priority_order": 130 } ] }