Supporting Data ihm-extension.dic

Dictionary Revision History

Version Revision Date Revision Description
0.106 2017-07-13
Changes (bv):
+ Updated dictionary description and version history
0.105 2017-05-25
Changes (bv):
+ Added item description to _ihm_ensemble_info.ensemble_file_id
+ Added item description to _ihm_2dem_class_average_restraint.pixel_size_width
+ Added item description to _ihm_2dem_class_average_restraint.pixel_size_height
+ Added category description to ihm_2dem_class_average_fitting
+ Added enumeration 'DCD' to _ihm_external_files.file_format
+ Changed _ihm_external_files.file_size_kb to _ihm_external_files.file_size_bytes
0.104 2017-04-19
Changes (bv):
+ Updated IHM_STARTING_MODEL_DETAILS
+ Updated IHM_STARTING_COMPARATIVE_MODELS
+ Updated IHM_STARTING_MODEL_SEQ_DIF
+ Updated IHM_MODEL_REPRESENTATION
+ Updated IHM_DATASET_LIST
+ Added IHM_DATASET_GROUP
+ Updated IHM_MODELING_PROTOCOL
0.103 2017-03-30
Changes (bv):
+ Updated IHM_STARTING_MODEL_DETAILS
+ Updated IHM_STARTING_COMPARATIVE_MODELS
+ Updated IHM_DATASET_LIST, IHM_RELATED_DATASETS
+ Updated IHM_DATASET_RELATED_DB_REFERENCE
+ Updated IHM_DATASET_EXTERNAL_REFERENCE
+ Added examples to IHM_EXTERNAL_REFERENCE_INFO and IHM_EXTERNAL_FILES
0.102 2017-03-29
Changes (bv):
+ Updated examples in IHM_STARTING_COMPARATIVE_MODELS
0.101 2017-03-29
Changes (bv):
+ Updated _ihm_starting_model_seq_dif.db_entity_id as non-mandatory
0.100 2017-03-23
Changes (bv):
+ Release as provisional version 0.100
+ Added _ihm_external_files.content_type
+ Added _ihm_external_files.details
+ Removed IHM_MODELING_WORKFLOW_FILES
0.000 2017-03-20
Changes (jdw/bv)
+ Release as initial version 0.000
+ Changed _imp to _ihm
+ Changed _imp_template_details to _ihm_starting_model_details
+ Changed _imp_tempate_model_coord to _ihm_starting_model_coord
+ Changed _imp_pseudo_atom_site to _ihm_sphere_object_site
+ Added enumeration 'integrative' to _ihm_starting_model_details.starting_model_source
+ Separated ihm_cross_link_restraint and ihm_cross_link_list categories
+ Updated ambiguous crosslinks in ihm_cross_link_restraint and ihm_cross_link_list categories
+ Added ihm_dataset_list, ihm_related_database_reference and ihm_dataset_other categories
+ Added ihm_cross_link_result (yet to be completed) and ihm_entity_assembly categories
+ Updated ihm_2dem_class_average_restraint category
+ Removed ihm_cross_link_db_reference, ihm_cross_link_reference_auxiliary, ihm_2dem_class_average categories
+ Revised several data items to be non-mandatory
+ Changed category key item in ihm_model_details category to account for multiple coarse-grained representations
of the same model segment (introduced _ihm_model_details.ordinal_id)
+ Updated _ihm_sphere_obj_site.entity_instance_id, ihm_cross_link_restraint (psi and sigma parameters)
+ Added ihm_modeling_protocol, ihm_cluster_info, ihm_struct_assembly (previously ihm_entity_assembly)
+ Added _ihm_3dem_restraint category; minor changes to other categories
+ Changed ihm_model_details category name to ihm_model_representation (handles multi-scale representation)
+ Changed several data items in the ihm_modeling_protocol category
+ Added ihm_modeling_post_process, ihm_model_list, ihm_multi_state_modeling,
ihm_time_ordered_ensemble, ihm_gaussian_object_site categories
+ Linked ihm_model_list to ihm_sphere_obj_site through model_id
+ Linked ihm_starting_model_details to ihm_dataset_list through dataset_list_id
+ Added new data item _ihm_model_representation.representation_id and more changes to ihm_modeling_protocol
and ihm_gaussian_obj_site categories.
+ Added ihm_gaussian_obj_ensemble category to represent ensembles as gaussian objects - to be different from
+ ihm_gaussian_object_site category that is used in model representation and hence by visualization software.
+ Changed ihm_cluster_info category name to ihm_ensemble_info and changed relevant data item names accordingly.
+ Changed ihm_related_database_reference category name to ihm_dataset_related_db_reference to be consistent
with other similar categories
+ Minor changes in other categories: ihm_model_list, ihm_dataset_list, ihm_modeling_protocol, ihm_ensemble_info,
ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_2dem_class_average_restraint (data items are now
similar to 2D class average images in EMPIAR), ihm_model_represenation.
+ Updated parent-child relationships across several categories (ihm_modeling_protocol, ihm_ensemble_info
ihm_model_list, ihm_multi_state_modeling, ihm_time_ordered_ensemble, ihm_2dem_class_average_fitting,
ihm_cross_link_result)
+ Updated examples in ihm_dataset_list, ihm_dataset_other and ihm_dataset_related_db_reference
+ Changed ihm_modeling_experiment to ihm_modeling_protocol to be consistent with the model archive naming convention
+ Added ihm_sas_restraint category; added _ihm_3dem_restraint.map_segment_flag
+ Modified the following categories: ihm_model_list, ihm_modeling_protocol, ihm_multi_state_modeling,
ihm_time_ordered_ensemble
+ Minor updates to ihm_cross_link_list, ihm_cross_link_restraint and ihm_model_representation categories.
+ Added _ihm_sphere_obj_site.rmsf and _ihm_starting_model_details.asym_id
+ Added ihm_related_datasets and ihm_cross_link_result_parameters
+ Added _ihm_3dem_restraint.struct_assembly_id, _ihm_sas_restraint.struct_assembly_id,
_ihm_starting_model_details.notes and _ihm_starting_model_coord.group_PDB
+ Changed _ihm_3dem_restraint.id to _ihm_3dem_restraint.ordinal_id and _ihm_sas_restraint.id to
_ihm_sas_restraint.ordinal_id
+ Changed _ihm_dataset_related_db_reference.access_code to _ihm_dataset_related_db_reference.accession_code
+ Added new categories to reference externally hosted files: IHM_LOCALIZATION_DENSITY_FILES,
+ IHM_STARTING_MODEL_ALIGNMENT_FILES, IHM_MODELING_WORKFLOW_FILES
+ Added IHM_DATA_DOI_URL_INFO category to include a URL corresponding to a DOI. This enables automated
download of files.
+ Removed redundant DOI references from several categories
+ Added _ihm_starting_model_details.starting_model_sequence_offset
+ Changed _ihm_starting_model_details.starting_model_db_pdb_auth_asym_id to
_ihm_starting_model_details.starting_model_auth_asym_id
+ Changed IHM_DOI_URL_INFO to IHM_EXTERNAL_REFERENCE_INFO; modified all downstream dependencies
+ Changed IHM_DATASET_OTHER to IHM_DATASET_EXTERNAL_REFERENCE_DETAILS; modified all downstream dependencies
+ Modified definitions within IHM_EXTERNAL_REFERENCE_INFO
+ Added IHM_EXTERNAL_FILES category; Removed IHM_STARTING_MODEL_ALIGNMENT_FILES category
+ Changed IHM_MODELING_WORKFLOW_FILES, IHM_LOCALIZATION_DENSITY_FILES
+ Changed IHM_DATASET_EXTERNAL_REFERENCE_DETAILS to IHM_DATASET_EXTERNAL_REFERENCE
+ Modified IHM_STARTING_MODEL_DETAILS category
+ Added IHM_STARTING_COMPARATIVE_MODELS category
+ Added IHM_STARTING_MODEL_SEQ_DIF category; removed _ihm_starting_model_details.notes
+ Updated IHM_ENSEMBLE_INFO, IHM_EXTERNAL_FILES and IHM_EXTERNAL_REFERENCE_INFO
+ Added _ihm_multi_state_modeling.experiment_type; updated IHM_ENSEMBLE_INFO
Data Type Code Primitive Type Code Regular Expression Description
code char [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words ...
float numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? float item types are the subset of numbers that are the floating
numbers.
int numb [+-]?[0-9]+ int item types are the subset of numbers that are the negative
or positive integers.
line char [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* char item types / multi-word items ...
name uchar _[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+ name item types take the form...
text char [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* text item types / multi-line text ...
ucode uchar [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
uline uchar [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* char item types / multi-word items (case insensitive)...
SubCategory Identifier Description
Units Identifier Description
8pi2_angstroms_squared 8pi2 * Angstroms squared (metres * 10(-10))2
angstroms Angstroms (metres * 10(-10))

Units Conversion List

From Units&Identifier To Units&Identifier Operator Conversion Factor