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Dictionary Index mmcif_investigation.dic

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General

Dictionary title
InvestigationCIF
Dictionary description
The InvestigationCIF dictionary is an extension of the PDBx/mmCIF dictionary. This dictionary is actively developed and maintained in a github repository available at https://github.com/PDBeurope/InvestigationCIF. It captures the relationship between related structures that are part of the same project.
Original developers
wwPDB members: Genevieve L. Evans, Ahsan, James Tolchard, Ezra Peisach, and Sameer Velankar
Dictionary maintainers
wwPDB members: Genevieve L. Evans, Ahsan, Ezra Peisach
Dictionary name
mmcif_investigation.dic
Dictionary version
1.0.6
Last update
2025-08-30

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Dictionary Revision History

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Version Revision Date Revision Description
1.0.6 2025-08-30
Changes (ge):
+ Changed (fraghub to ligscreen changes):
_pdbx_fraghub_investigation_lib_component_mix --> _pdbx_ligscreen_investigation_lib_component_mix
_pdbx_fraghub_investigation_lib_component_mix.frag_component_mix_id --> _pdbx_ligscreen_investigation_lib_component_mix.lib_component_mix_id
_pdbx_fraghub_investigation_lib_component --> _pdbx_ligscreen_investigation_lib_component
_pdbx_fraghub_investigation_campaign --> _pdbx_ligscreen_investigation_campaign
_pdbx_fraghub_investigation_series --> _pdbx_ligscreen_investigation_series
_pdbx_fraghub_investigation_screening_exp --> _pdbx_ligscreen_investigation_screening_exp
_pdbx_fraghub_investigation_screening_exp.frag_component_mix_id --> _pdbx_fraghub_investigation_screening_exp.lib_component_mix_id
+ Changed to "Ligand Screening" from "Fragment Screening" in the enumerated options listed under _pdbx_investigation.type
+ Changed to "ligscreen" from "fraghub" in the enumerated options listed under _pdbx_investigation.db
+ Updated _category_examples section appropriately in _pdbx_investigation.
+ Updated category and item descriptions section appropriately to address the dictionary being relevant to all ligand screens (not just fragment screens).
+ Various small fixes:
- _pdbx_investigation.project --> _pdbx_investigation.project_id
- _pdbx_investigation_focus.component_id --> _pdbx_investigation_focus.key_component_id
- _pdbx_ligscreen_investigation_campaign.pipeline-version --> _pdbx_ligscreen_investigation_campaign.pipeline_version
- in _pdbx_investigation_archived_data.archive_db_name enumeration list changed PDB-DEV to PDB-IHM
+ Admin-type fixes:
- removed, or replaced with mmcif_investigation.dic, instances of mmcif_pdbx_audit_support-extension.dic (old name for dictionary)
- added _item_enumeration.name in all enumeration lists for items
+ To capture history of ligand screening and time-resolved seperately in future --> changed PDBX_DICTIONARY_COMPONENT and PDBX_DICTIONARY_COMPONENT_HISTORY categories
For PDBX_DICTIONARY_COMPONENT_HISTORY category added placeholder info for dictionary_component_id:
- mmcif_investigation_timeresolved.dic
- mmcif_investigation_ligscreen.dic (replacing mmcif_investigation_fraghub.dic)
+ Updated to mmcif_investigation.dic
- _datablock.id
- _dictionary.title
- _dictionary.datablock_id
+ Reclassify the category_group appropriately, with the following groups:
- investigation_group
- investigation_sample_group (new category group)
- ligscreen_group (changed from "fraghub_group" as id in CATEGORY_GROUP_LIST category)
+ Removed the following categories (and associated items)
- _citation
- _citation_author
- _pdbx_audit
- _pdbx_audit_support
- _pdbx_investigation_status
- _contact_author
+ Added category: PDBX_LIGSCREEN_INVESTIGATION_AUTHOR, including the following items:
- campaign_id
- investigation_id
- ordinal
- name
- identifier_orcid
+ Added items to ITEM_TYPE_LIST category, with the following new _item_type_list.code:
- inchi
- inchikey
- yyyy
+ Updated items in PDBX_INVESTIGATION_ENTITY_POLY
- item changed: seq_one_letter_code --> seq_one_letter_code_with_nstd
- item added: seq_one_letter_code_sample
- item removed: src_method
+ Additions were made to enable capture of biological entity information when protein / DNA / RNA sequence is unknown.
- In PDBX_INVESTIGATION_SAMPLE category:
= Changed _pdbx_investigation_sample.poly_descript_id so it is not a manditory item
= Added New item _pdbx_investigation_sample.descript_id as a non-manditory item
- New category called PDBX_INVESTIGATION_ENTITY, with items:
= entity_id
= poly_entity_id
= src_method
= src_organism_scientific
= src_ncbi_taxonomy_id
- New category called PDBX_INVESTIGATION_DESCRIPT, with items:
= id
= entity_id		 mmcif_investigation.dic
1.0.5 2025-04-11
Changes (ge):
+ Updated description for _pdbx_fraghub_investigation_series category.
+ Added / changed enumerated list of libraries in _pdbx_fraghub_investigation_series.fragment_lib
+ Added new items to _pdbx_fraghub_investigation_series to capture providence of fragment library identification:
- fragment_lib_purchase_year
- fragment_lib_identification_method
+ Added new items to _pdbx_fraghub_investigation_fraglib_component to better capture chemical descriptors providence:
- isomeric_smiles
- isomeric_smiles_program
- isomeric_smiles_program_version
- inchi_descriptor_program
- inchi_descriptor_program_version
- inchikey_descriptor_program
- inchikey_descriptor_program_version
+ Added new item to _pdbx_investigation_entity_nonpoly for:
- isomeric_smiles
- isomeric_smiles_program
- isomeric_smiles_program_version
- inchi_descriptor_program
- inchi_descriptor_program_version
- inchikey_descriptor_program
- inchikey_descriptor_program_version
+ Updated item description in _pdbx_fraghub_investigation_fraglib_component and _pdbx_investigation_entity_nonpoly of:
- name
- cas_identifier		 mmcif_investigation.dic
1.0.4.9 2024-09-10
Minor changes (ge):
+ Added / changed enumerated list of libraries in _pdbx_fraghub_investigation_series.fragment_lib
+ Changed items to _pdbx_fraghub_investigation_fraglib_component for:
- inchi_descriptor (not required)
+ Added new item to _pdbx_investigation_entity_nonpoly for:
- inchikey_descriptor (manditory)
+ Changed items to _pdbx_investigation_entity_nonpoly for:
- inchi_descriptor (not required)		 mmcif_investigation.dic
1.0.4.8 2024-09-10
Minor changes (GE):
+ Added / changed enumerated list of libraries in _pdbx_fraghub_investigation_series.fragment_lib
+ Added new items to _pdbx_fraghub_investigation_fraglib_component for:
- inchikey_descriptor (manditory)
- authors_SMILES (this item maybe removed -- added to test usefulness of capturing authors SMILES but need to discuss as not standardized)
+ Changed items to _pdbx_fraghub_investigation_fraglib_component for:
- inchi_descriptor (not required)
+ Added new item to _pdbx_investigation_entity_nonpoly for:
- inchikey_descriptor (manditory)
+ Changed items to _pdbx_investigation_entity_nonpoly for:
- inchi_descriptor (not required)		 mmcif_investigation.dic
1.0.4.7 2024-02-08
Minor changes (GE):
+ Changed from:
_pdbx_fraghub_investigation_campaign.pipeline_verison
to:
_pdbx_fraghub_investigation_campaign.pipeline-verison
+ Enumeration list expanded for pdbx _fraghub_investigation_campaign.facility
(also: changed _item_type.code to line from code)
+ Made non-mandatory:
_pdbx_fraghub_investigation_screening_result.fraglib_component_id
_pdbx_fraghub_investigation_screening_exp.exp_acc
+ Added to category:
_pdbx_fraghub_investigation_screening_exp
to:
_pdbx_fraghub_investigation_screening_exp.archive_db_acc
+ In _pdbx_fraghub_investigation_screening_exp.exp_method:
changed from:
EM to:
"ELECTRON MICROSCOPY"
(also fixed mispelling in enumeration)		 mmcif_investigation.dic
1.0.4.6 2022-12-12
Changes (GE)
+ Multiple corrections
+ Corrections made to parent:child links, key items and mandatory items
+ Added to _item_type_list and added _item_units_list, etc (from mmcif_pdbx_v50)		 mmcif_investigation.dic
1.0.4.5 2022-02-14
Minor changes (GE)
+ Corrections made to parent:child links, key items and mandatory items
+ Url examples include either https or http		 mmcif_investigation.dic
1.0.4 2022-01-12
Changes (GE)
+ Added "instance_id" to pdbx_investigation_exp so for one experimemt_id can have a BMRB / EMDB code and PDB code.
+ Corrections made to parent:child links, key items and mandatory items
+ Added: _category_group.id to further clarify "investigation_group" vs "fraghub group" categories
+ Changed data items in _pdbx_investigation category
+ The _pdbx_investigation categories have been more standardized and now all included term the "pdbx_investigation"
e.g. pdbi has been replaced with pdbx_investigation
+ Changed:
_pdbx_entity_poly --> _pdbx_investigation_entity_poly
_pdbx_entity_poly_link --> _pdbx_investigation_poly_descript
_pdbx_entity_nonpoly --> _pdbx_investigation_entity_nonpoly
_pdbx_entity_nonpoly_link --> _pdbx_investigation_nonpoly_descript
+ _pdbx_investigation_exp.exp_method is now "line" instead of "text"
+ The _fraghub_investigation cateories have been more standardized and now all included term the "fraghub_investigation".
+ Changed:
_fraghub_investigation_frag_screening_exp --> _fraghub_investigation_screening_exp
_fraghub_entity_frag_library_link --> _fraghub_investigation_screen_descript
_fraghub_entity_frag_library --> _fraghub_investigation_entity_screen
_pdbx_investigation_series --> _fraghub_investigation_series
_pdbx_investigation_campaign --> _fraghub_investigation_campaign		 mmcif_investigation.dic
1.0.3 2022-07-15
Changes (JT)
+ Added references to in silico methods and DBs		 mmcif_investigation.dic
1.0.2 2022-07-12
Changes (JT)
+ Namespace changes for investigation files.		 mmcif_investigation.dic
1.0.1 2022-06-31
Changes (JT)
+ Corrections made to parent:child links and mandatory items		 mmcif_investigation.dic
1.0.0 2022-06-30
Changes (JT)
+ Initial collation of mmcif_pdbx and mmcif_ma categories		 mmcif_investigation.dic
0.4 2022-10-18
Changes (EP):
+ Version separated from core dictonary. Many intermediate versions took place.		 mmcif_investigation.dic
0.3 2012-09-01
Changes (JW):
+ Adjust data types		 mmcif_investigation.dic
0.2 2012-05-02
Changes (JW):
+ Remove author relationship		 mmcif_investigation.dic
0.1 2012-04-11
Changes (JW):
+ Initial version		 mmcif_investigation.dic
1.0.6 2025-08-30
Changes (ge):
+ Changed (fraghub to ligscreen changes):
_pdbx_fraghub_investigation_lib_component_mix --> _pdbx_ligscreen_investigation_lib_component_mix
_pdbx_fraghub_investigation_lib_component_mix.frag_component_mix_id --> _pdbx_ligscreen_investigation_lib_component_mix.lib_component_mix_id
_pdbx_fraghub_investigation_lib_component --> _pdbx_ligscreen_investigation_lib_component
_pdbx_fraghub_investigation_campaign --> _pdbx_ligscreen_investigation_campaign
_pdbx_fraghub_investigation_series --> _pdbx_ligscreen_investigation_series
_pdbx_fraghub_investigation_screening_exp --> _pdbx_ligscreen_investigation_screening_exp
_pdbx_fraghub_investigation_screening_exp.frag_component_mix_id --> _pdbx_fraghub_investigation_screening_exp.lib_component_mix_id
+ Changed to "Ligand Screening" from "Fragment Screening" in the enumerated options listed under _pdbx_investigation.type
+ Changed to "ligscreen" from "fraghub" in the enumerated options listed under _pdbx_investigation.db
+ Updated _category_examples section appropriately in _pdbx_investigation.
+ Updated category and item descriptions section appropriately to address the dictionary being relevant to all ligand screens (not just fragment screens).
+ Various small fixes:
- _pdbx_investigation.project --> _pdbx_investigation.project_id
- _pdbx_investigation_focus.component_id --> _pdbx_investigation_focus.key_component_id
- _pdbx_ligscreen_investigation_campaign.pipeline-version --> _pdbx_ligscreen_investigation_campaign.pipeline_version
- in _pdbx_investigation_archived_data.archive_db_name enumeration list changed PDB-DEV to PDB-IHM
+ Admin-type fixes:
- removed, or replaced with mmcif_investigation.dic, instances of mmcif_pdbx_audit_support-extension.dic (old name for dictionary)
- added _item_enumeration.name in all enumeration lists for items
+ To capture history of ligand screening and time-resolved seperately in future --> changed PDBX_DICTIONARY_COMPONENT and PDBX_DICTIONARY_COMPONENT_HISTORY categories
For PDBX_DICTIONARY_COMPONENT_HISTORY category added placeholder info for dictionary_component_id:
- mmcif_investigation_timeresolved.dic
- mmcif_investigation_ligscreen.dic (replacing mmcif_investigation_fraghub.dic)
+ Updated to mmcif_investigation.dic
- _datablock.id
- _dictionary.title
- _dictionary.datablock_id
+ Reclassify the category_group appropriately, with the following groups:
- investigation_group
- investigation_sample_group (new category group)
- ligscreen_group (changed from "fraghub_group" as id in CATEGORY_GROUP_LIST category)
+ Removed the following categories (and associated items)
- _citation
- _citation_author
- _pdbx_audit
- _pdbx_audit_support
- _pdbx_investigation_status
- _contact_author
+ Added category: PDBX_LIGSCREEN_INVESTIGATION_AUTHOR, including the following items:
- campaign_id
- investigation_id
- ordinal
- name
- identifier_orcid
+ Added items to ITEM_TYPE_LIST category, with the following new _item_type_list.code:
- inchi
- inchikey
- yyyy
+ Updated items in PDBX_INVESTIGATION_ENTITY_POLY
- item changed: seq_one_letter_code --> seq_one_letter_code_with_nstd
- item added: seq_one_letter_code_sample
- item removed: src_method
+ Additions were made to enable capture of biological entity information when protein / DNA / RNA sequence is unknown.
- In PDBX_INVESTIGATION_SAMPLE category:
= Changed _pdbx_investigation_sample.poly_descript_id so it is not a manditory item
= Added New item _pdbx_investigation_sample.descript_id as a non-manditory item
- New category called PDBX_INVESTIGATION_ENTITY, with items:
= entity_id
= poly_entity_id
= src_method
= src_organism_scientific
= src_ncbi_taxonomy_id
- New category called PDBX_INVESTIGATION_DESCRIPT, with items:
= id
= entity_id		 mmcif_investigation.dic
1.0.5 2025-04-11
Changes (ge):
+ Updated description for _pdbx_fraghub_investigation_series category.
+ Added / changed enumerated list of libraries in _pdbx_fraghub_investigation_series.fragment_lib
+ Added new items to _pdbx_fraghub_investigation_series to capture providence of fragment library identification:
- fragment_lib_purchase_year
- fragment_lib_identification_method
+ Added new items to _pdbx_fraghub_investigation_fraglib_component to better capture chemical descriptors providence:
- isomeric_smiles
- isomeric_smiles_program
- isomeric_smiles_program_version
- inchi_descriptor_program
- inchi_descriptor_program_version
- inchikey_descriptor_program
- inchikey_descriptor_program_version
+ Added new item to _pdbx_investigation_entity_nonpoly for:
- isomeric_smiles
- isomeric_smiles_program
- isomeric_smiles_program_version
- inchi_descriptor_program
- inchi_descriptor_program_version
- inchikey_descriptor_program
- inchikey_descriptor_program_version
+ Updated item description in _pdbx_fraghub_investigation_fraglib_component and _pdbx_investigation_entity_nonpoly of:
- name
- cas_identifier		 mmcif_investigation.dic
1.0.4.9 2024-09-10
Minor changes (ge):
+ Added / changed enumerated list of libraries in _pdbx_fraghub_investigation_series.fragment_lib
+ Changed items to _pdbx_fraghub_investigation_fraglib_component for:
- inchi_descriptor (not required)
+ Added new item to _pdbx_investigation_entity_nonpoly for:
- inchikey_descriptor (manditory)
+ Changed items to _pdbx_investigation_entity_nonpoly for:
- inchi_descriptor (not required)		 mmcif_investigation.dic
1.0.4.8 2024-09-10
Minor changes (GE):
+ Added / changed enumerated list of libraries in _pdbx_fraghub_investigation_series.fragment_lib
+ Added new items to _pdbx_fraghub_investigation_fraglib_component for:
- inchikey_descriptor (manditory)
- authors_SMILES (this item maybe removed -- added to test usefulness of capturing authors SMILES but need to discuss as not standardized)
+ Changed items to _pdbx_fraghub_investigation_fraglib_component for:
- inchi_descriptor (not required)
+ Added new item to _pdbx_investigation_entity_nonpoly for:
- inchikey_descriptor (manditory)
+ Changed items to _pdbx_investigation_entity_nonpoly for:
- inchi_descriptor (not required)		 mmcif_investigation.dic
1.0.4.7 2024-02-08
Minor changes (GE):
+ Changed from:
_pdbx_fraghub_investigation_campaign.pipeline_verison
to:
_pdbx_fraghub_investigation_campaign.pipeline-verison
+ Enumeration list expanded for pdbx _fraghub_investigation_campaign.facility
(also: changed _item_type.code to line from code)
+ Made non-mandatory:
_pdbx_fraghub_investigation_screening_result.fraglib_component_id
_pdbx_fraghub_investigation_screening_exp.exp_acc
+ Added to category:
_pdbx_fraghub_investigation_screening_exp
to:
_pdbx_fraghub_investigation_screening_exp.archive_db_acc
+ In _pdbx_fraghub_investigation_screening_exp.exp_method:
changed from:
EM to:
"ELECTRON MICROSCOPY"
(also fixed mispelling in enumeration)		 mmcif_investigation.dic
1.0.4.6 2022-12-12
Changes (GE)
+ Multiple corrections
+ Corrections made to parent:child links, key items and mandatory items
+ Added to _item_type_list and added _item_units_list, etc (from mmcif_pdbx_v50)		 mmcif_investigation.dic
1.0.4.5 2022-02-14
Minor changes (GE)
+ Corrections made to parent:child links, key items and mandatory items
+ Url examples include either https or http		 mmcif_investigation.dic
1.0.4 2022-01-12
Changes (GE)
+ Added "instance_id" to pdbx_investigation_exp so for one experimemt_id can have a BMRB / EMDB code and PDB code.
+ Corrections made to parent:child links, key items and mandatory items
+ Added: _category_group.id to further clarify "investigation_group" vs "fraghub group" categories
+ Changed data items in _pdbx_investigation category
+ The _pdbx_investigation categories have been more standardized and now all included term the "pdbx_investigation"
e.g. pdbi has been replaced with pdbx_investigation
+ Changed:
_pdbx_entity_poly --> _pdbx_investigation_entity_poly
_pdbx_entity_poly_link --> _pdbx_investigation_poly_descript
_pdbx_entity_nonpoly --> _pdbx_investigation_entity_nonpoly
_pdbx_entity_nonpoly_link --> _pdbx_investigation_nonpoly_descript
+ _pdbx_investigation_exp.exp_method is now "line" instead of "text"
+ The _fraghub_investigation cateories have been more standardized and now all included term the "fraghub_investigation".
+ Changed:
_fraghub_investigation_frag_screening_exp --> _fraghub_investigation_screening_exp
_fraghub_entity_frag_library_link --> _fraghub_investigation_screen_descript
_fraghub_entity_frag_library --> _fraghub_investigation_entity_screen
_pdbx_investigation_series --> _fraghub_investigation_series
_pdbx_investigation_campaign --> _fraghub_investigation_campaign		 mmcif_investigation.dic
1.0.3 2022-07-15
Changes (JT)
+ Added references to in silico methods and DBs		 mmcif_investigation.dic
1.0.2 2022-07-12
Changes (JT)
+ Namespace changes for investigation files.		 mmcif_investigation.dic
1.0.1 2022-06-31
Changes (JT)
+ Corrections made to parent:child links and mandatory items		 mmcif_investigation.dic
1.0.0 2022-06-30
Changes (JT)
+ Initial collation of mmcif_pdbx and mmcif_ma categories		 mmcif_investigation.dic
0.4 2022-10-18
Changes (EP):
+ Version separated from core dictonary. Many intermediate versions took place.		 mmcif_investigation.dic
0.3 2012-09-01
Changes (JW):
+ Adjust data types		 mmcif_investigation.dic
0.2 2012-05-02
Changes (JW):
+ Remove author relationship		 mmcif_investigation.dic
0.1 2012-04-11
Changes (JW):
+ Initial version		 mmcif_investigation.dic