CIF_COD

Version: 0.3.1 (2020-07-15)

COD_DATA_SOURCE

The CATEGORY of data items used to record and trace sources of the information deposited into the COD.

_cod_data_source.file

Specifies the name of the file that served as the source of the data for the given COD entry. The file name should be recorded without the path or other URL components since these components usually have no sense on the recipient's system. In Unix parlance, the recorded value should consists of the basename of the original file. If case the full persistent URI is known, the _cod_data_source.URI or _cod_data_source.URL data items should be used to record it instead.

For many data sources, however, the basename contains enough information to locate the original source of information. For example, CIFs published in IUCr journals have a Coeditor Code as a CIF file name that can be used to identify the original paper where the structure is discussed.

_cod_data_source.block

Specifies the name of the data block within the file that served as a source of data for the given COD entry (see _cod_data_source.file). Only the data block code following the 'data_' header keyword should be recorded. For example, if the data block starts with the 'data_I' header, only the 'I' should be recorder as the data value.

_cod_data_source.URI

Specifies the uniform resource identifier (URI) of the file that served as a source of data for the given COD entry (see _cod_data_source.file).

_cod_data_source.URN

Specifies the uniform resource name (URN) of the file that served as a source of data for the given COD entry (see _cod_data_source.file).

_cod_data_source.URL

Specifies the uniform resource locator (URL) of the file that served as a source of data for the given COD entry (see _cod_data_source.file).

_cod_data_source.MD5_sum

Specifies the MD5 cryptographic checksum of the file that served as a source of data for the given COD entry. The checksum should be computed from the same file that is referenced using the _cod_data_source.file data item.

_cod_data_source.SHA1_sum

Specifies the SHA1 cryptographic checksum of the file that served as a source of data for the given COD entry. The checksum should be computed from the same file that is referenced using the _cod_data_source.file data item.

_cod_data_source.SHA256_sum

Specifies the SHA256 cryptographic checksum of the file that served as a source of data for the given COD entry. The checksum should be computed from the same file that is referenced using the _cod_data_source.file data item.

COD_DATABASE_CODE

Data items in the COD_DATABASE_CODE category record various persistent unique identifiers used in the COD.

Examples:

data_2011000
_cod_database_code 2011000

_cod_database_code.structure

A persistent unique identifier assigned to each crystal structure upon successful deposition to the COD. The identifier is guaranteed not to change and is the preferred way of referencing individual COD entries.

The identifier is sometimes also referred to as "COD number", however, the term "COD ID" is favoured in formal documentation.

This data item is intended to be placed exclusively in crystal structure data files curated by the COD.

Examples:

_cod_database_code.diffrn_file

A persistent unique identifier assigned to each diffraction data file upon successful deposition to the COD. The term "COD DIFFRN ID" is used in formal documentation to refer to this identifier.

Normally, the COD DIFFRN ID assigned to the structure factor (a.k.a. Fobs) file matches the one assigned to the corresponding crystal structure entry (see _cod_database_code_structure).

Data of powder diffraction experiments are handled slightly differently since a single set of diffractograms can be used in the refinement of multiple phases. In such cases, diffractograms from the same set are recorded in separate data blocks of a single file and all assigned the same COD DIFFRN ID. The COD DIFFRN ID can then be referenced by each refined phase (see _cod_related_diffrn_file_code). The phases themselves, however, are each assigned a unique COD ID. It is recommended, although not required, that the COD DIFFRN ID of the diffractogram set matches the COD ID assigned to the first phase of the experiment.

This data item is intended to be placed exclusively in diffraction data files curated by the COD.

COD_RELATED

The COD_RELATED category groups categories that are used to describe various relationships between COD entries and related entries in the COD or other databases.

COD_RELATED_DIFFRN_FILE

Data items in the COD_RELATED_DIFFRN_FILE category record references to diffraction datasets that were used to solve the given crystal structure. The category is intended to be used with diffraction datasets that have been deposited to the COD and assigned persistent unique identifiers.

_cod_related_diffrn_file.code

Records the COD DIFFRN ID of a COD diffraction file that was used to solve the given crystal structure entry, i.e. the entry containing this data item.

This data item is intended to be placed exclusively in crystal structure data files curated by the COD.

COD_RELATED_STRUCTURE_ENTRY

Data items in the COD_RELATED_STRUCTURE_ENTRY category record references to crystal structures that were solved using the given diffraction dataset. The category is intended to be used with crystal structures that have been deposited to the COD and assigned persistent unique identifiers.

_cod_related_structure_entry.code

Records the COD IDs of a crystal structure entries that were solved using the given diffraction file, i.e. the file containing this data item.

In case a diffraction data file contains more than one data block, each data block should have its own instance of this data item. A typical example of such situation would be a powder diffraction file with several diffractograms each stored in a separate data block (see _cod_database_code.diffrn_file).

This data item is intended to be placed exclusively in diffraction data files curated by the COD.

COD_RELATED_DUPLICATE_ENTRY

Data items in the COD_RELATED_DUPLICATE_ENTRY category record references to duplicate COD entries.

Entries are considered duplicates of each other if they originate from the same publication and carry exactly the same information. The COD actively safeguards against the inclusion of such entries, however, historically some duplicates have been assigned distinct COD IDs. Since COD ID assignment is permanent these entries cannot simply be removed from the database and are instead marked using appropriate data items when noticed.

The duplicate relationship is modelled as unidirectional and intransitive. As a result, the referenced entry itself must not contain any references of this kind. For example, if three entries are all duplicates of each other, one of them should be selected as the main one and the remaining two entries should both reference it. The selected main entry must contain the most complete and comprehensive structure description of all of the duplicates.

Care should be taken to exclude these duplicate entries from computations and statistics.

Examples:

data_1000000
_cod_database_code                1000000
_cod_related_duplicate_entry.code 2011331

_cod_related_duplicate_entry.code

Records the COD ID of an entry that is considered to be a duplicate of the given COD entry, i.e. the entry containing this data item.

The duplicate relationship is modelled as unidirectional and intransitive. As a result, the referenced entry itself must not contain any references of this kind. For example, if three entries are all duplicates of each other, one of them should be selected as the main one and the remaining two entries should both reference it. The selected main entry must contain the most complete and comprehensive structure description of all of the duplicates.

Care should be taken to exclude these duplicate entries from computations and statistics.

COD_RELATED_OPTIMAL_ENTRY

Data items in the COD_RELATED_OPTIMAL_ENTRY category record references to COD entries that describe structures solved in an optimal manner.

Data items in this category must only be used to record relationships between entries originating from the same publication, for instance, to relate the optimal interpretation to the suboptimal ones that were only included for comparison purposes.

Only the optimal structures should be used for computations and statistics except when purposely comparing the optimal structure with the related suboptimal ones (see COD_RELATED_SUBOPTIMAL_ENTRY).

Examples:

data_2100860
_cod_database_code               2100860
_cod_related_optimal_entry.code  2100858

_cod_related_optimal_entry.code

Records the COD ID of an entry that describes the optimally solved structure as compared to the given suboptimal COD entry, i.e. the entry containing this data item.

Entries marked as optimal must originate from the same publication as the suboptimal ones. For example, the suboptimal structures might be provided by the authors to demonstrate that an alternative space group choice or a structure solution method are indeed inferior.

It is recommended that the suboptimal entries be reciprocally referenced by the optimal entry (see COD_RELATED_SUBOPTIMAL_ENTRY).

COD_RELATED_SUBOPTIMAL_ENTRY

Data items in the COD_RELATED_SUBOPTIMAL_ENTRY category record references to COD entries that describe structures solved in a suboptimal manner.

Data items in this category must only be used to record relationships between entries originating from the same publication, for instance, to refer to interpretations of the structural data that were deliberately processed in a suboptimal way and are only provided for comparison purposes.

Care should be taken to exclude such suboptimal structures from computations and statistics except when purposely comparing them with the related optimal structure (see COD_RELATED_OPTIMAL_ENTRY).

Examples:

data_2100858
_cod_database_code               2100858
loop_
_cod_related_suboptimal_entry.code
2100860
2100862

_cod_related_suboptimal_entry.code

Records COD IDs of entries that describe suboptimally solved structures as compared to the given optimal COD entry, i.e. the entry containing this data item.

Entries marked as suboptimal must originate from the same publication as the optimal one. For example, the suboptimal structures might be provided by the authors to complement the structure solution strategy discussion.

It is recommended that the optimal entry be reciprocally referenced by the suboptimal entries (see COD_RELATED_OPTIMAL_ENTRY).

COD_RELATED_ENANTIOMER_ENTRY

Data items in the COD_RELATED_ENANTIOMER_ENTRY category record enantiomeric relationships between COD entries.

Data items in this category must only be used to record relationships between entries originating from the same publication.

Examples:

data_4105625
_cod_database_code               4105625
loop_
_cod_related_enantiomer_entry.code
4105851

data_0555010
_cod_database_code               0555010
loop_
_cod_related_enantiomer_entry_code
0555013
0555014
0555015

_cod_related_enantiomer_entry.code

Records COD IDs of entries that describe structures of enantiomers as compared to the given COD entry, i.e. the entry containing this data item.

Entries marked as having the enantiomeric relationship must all originate from the same publication.

Normally, an enantiomeric relationship is a pairwise one, however, it is possible for a single publication to yield several structures of the same enantiomer. In cases like these all of the corresponding enantiomer entries should be referenced.

Due to the symmetrical nature of the enantiomeric relationship it is recommended that the referenced entries also contain reciprocal references.

COD_RELATED_SAME_STRUCTURE_ENTRY

Data items in the COD_RELATED_SAME_STRUCTURE_ENTRY category record relationships between COD entries that describe nearly identical structures solved using the measurements of the same crystal.

It is assumed that entries related in this way contain almost exactly the same information and mainly only differ by originating from different publications. For example, it is not uncommon for authors to include previously published structures as a supplementary material of their own work to showcase a trend or for comparison purposes. Since each COD entry records the fact that a structure has been published in a peer-reviewed source such structures are intentionally included into the COD and should not be considered duplicate entries (see COD_RELATED_DUPLICATE_ENTRY).

The same structure relationship is modelled as unidirectional and intransitive. As a result, the referenced entry itself must not contain any references of this kind. For example, if three entries all describe the same structure, one of them should be selected as the main one and the remaining two entries should both reference it. The selected main entry must be published prior to all of the other related entries.

Entries related in this way all share almost exactly the same information therefore care should be taken to only include the main structure in computations and statistics.

Examples:

data_4060527
_cod_database_code                      4060527
_cod_related_same_structure_entry.code  4062828

_cod_related_same_structure_entry.code

Records the COD ID of an entry that describes a nearly identical structure solved using the measurements of the same crystal as the given COD entry, i.e. the entry containing this data item.

The same structure relationship is modelled as unidirectional and intransitive. As a result, the referenced entry itself must not contain any references of this kind. For example, if three entries all describe the same crystal structure, one of them should be selected as the main one and the remaining two entries should both reference it. The selected main entry must be published prior to all of the other related entries.

Entries related in this way all share almost exactly the same information therefore care should be taken to only include the main structure in computations and statistics.

COD_RELATED_ENTRY

The CATEGORY of data items used to describe the relationship between a COD entry and related entries in the COD or other databases.

_cod_related_entry.id

Value is a unique key to a set of COD_RELATED_ENTRY items in a looped list.

_cod_related_entry.code

The unique identifier of the related entry assigned by the related database (see _cod_related_entry.database).

Examples:

_cod_related_entry.database

The name of the database that stores the related entry.

Examples:

_cod_related_entry.description

A short description detailing the nature of the relationship between the entry in the COD and the one in the related database.

_cod_related_entry.uri

The uniform resource identifier (URI) of the related entry (see _cod_related_entry.code).

COD_STRUCTURE

Data items in the COD_STRUCTURE category record details about the crystal structure.

Examples:

data_1546034
_cod_database_code                    1546034
_cod_structure_determination_method   'powder diffraction'

_cod_structure.determination_method

Specifies the method that was used to determine the crystal structure.

Values:

COD_ORIGINAL

Data items in the COD_ORIGINAL category record the original values of certain data items that were changed during the COD data curation process.

Examples:

_cell_angle_alpha                90.
_cell_angle_beta                 90.
_cell_angle_gamma                90.
_cell_formula_units_Z            2
_cell_length_a                   3.884
_cell_length_b                   3.884
_cell_length_c                   12.6
_cell_volume                     190.077

_chemical_formula_sum            'O4 Sr2 Ti'

_cod_original_cell_volume        190.08
_cod_original_formula_sum        'O4 Sr2 Ti1'

_cod_original.cell_volume

Original crystal unit cell volume provided by the CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored using the regular _cell.volume data item).

_cod_original.formula_weight

Original chemical formula mass in daltons provided by the CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored using the regular _chemical_formula.weight data item).

_cod_original.formula_units_Z

Original number of the formula units in the unit cell provided by the CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored using the regular _cell.formula_units_Z data item).

_cod_original.formula_structural

Original value of the _chemical_formula_structural data item as reported by the CIF authors. Should be recorded if the _chemical_formula_structural data item value was changed during the COD data curation process.

_cod_original.formula_sum

Original chemical formula in which all discrete bonded residues and ions are summed over the constituent elements following the Hill system ordering provided by the CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored using the regular _chemical_formula.sum data item).

_cod_original.formula_moiety

Original chemical formula with each discrete bonded residue or ion shown as a separate moiety provided by the CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored using the regular _chemical_formula.moiety data item).

_cod_original.formula_iupac

Original chemical formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other data items from the CHEMICAL_FORMULA category provided by the CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored using the regular _chemical_formula.iupac data item).

_cod_original.sg_symbol_H-M

Original Hermann-Mauguin space group symbol provided by the CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored using the regular _space_group.name_H-M_alt data item).

_cod_original.sg_symbol_Hall

Original space group symbol as described by Hall provided by the CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored using the regular _space_group.name_Hall data item).

_cod_original.sg_number

Original space group number from International Tables for Crystallography Vol. A (2002) provided by the CIF authors. Should be provided if it is different from the value computed by the COD scripts (stored using the regular _space_group.IT_number data item).

COD_CHANGELOG_ENTRY

Data items from the COD_CHANGELOG_ENTRY are used to document changes made to the Crystallography Open Database entry.

_cod_changelog_entry.id

Value is a unique key to a set of COD_CHANGELOG_ENTRY items in a looped list.

_cod_changelog_entry.author

A string that identifies the person or software that changed the entry.

_cod_changelog_entry.date

The changelog entry creation timestamp expressed as a date-time or a full-date production of RFC3339 ABNF. Date-time production is preferred.

_cod_changelog_entry.text

A human-readable description of the change that was made.

COD_DEPOSITOR

The CATEGORY of data items used to store the information related to the depositor of the data.

Examples:

_cod_depositor.requested_release_date

Specifies the date after which the data can be released into the public domain. Prior to the public release the given data is treated as confidential prepublication material.

_cod_depositor.comments

This data item is considered deprecated and is only retained in this dictionary for compatibility purposes. Data items from the COD_CHANGELOG_ENTRY and COD_ENTRY_ISSUE categories should be used instead.

Human readable comments from COD depositors and human readable log records from CIF processing programs.

Examples:

The following automatic conversions were performed:
'_symmetry_cell_setting' value 'Monoclinic' changed
to 'monoclinic' according to
'/home/saulius/struct/CIF-dictionaries/cif_core.dic'
dictionary named 'cif_core.dic' version 2.4.1
from 2010-06-29.

Automatic conversion script
Id: cif_fix_enum 1468 2010-11-05 11:02:30Z adriana

The H-M space group name 'A 1 1 2/a' in the original CIF
seems to be wrong, it is incompatible with the 'b axis
unique' comment. The b axis unique symbol should be
'A 1 2/a 1'. Encifer shows better packing when
H-M symbol is changed to 'A 1 2/a 1'

Saulius Gražulis

COD_ENTRY_ISSUE

Data items from the COD_ENTRY_ISSUE category record issues pertaining to a specific COD entry. A proper issue record should include a human-readable description and assigned an appropriate severity level.

Examples:

loop_
_cod_entry_issue.id
_cod_entry_issue.origin
_cod_entry_issue.severity
_cod_entry_issue.description
_cod_entry_issue.author
_cod_entry_issue.date
1 original note
;
  Anisotropic parameter values were not provided in the
  original publication.
;
'John Doe' 2010-07-15
2 upstream warning
;
  The declared distance between atoms 'C1' and 'O2' does not match
  the one calculated from the atomic coordinates.
;

_cod_entry_issue.id

Value is a unique key to a set of COD_ENTRY_ISSUE items in a looped list.

_cod_entry_issue.origin

The most original source that is known to be affected by the described issue.

Values:

_cod_entry_issue.severity

The severity level of the detected issue.

Values:

_cod_entry_issue.description

A human-readable description of the issue.

Examples:

The reported bond distances/angles involving atoms 'O4' and 'O11' do not
match the ones calculated from the given coordinates.

This entry is one of the GNU Xtal software test files. It describes a
hypothetical structure in an awkward high symmetry.

_cod_entry_issue.author

A string that identifies the person who described the issue.

_cod_entry_issue.date

The issue description creation timestamp expressed as a date-time or a full-date production of RFC3339 ABNF. Date-time production is preferred.