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flr_sample.dic
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# ----------------------------------------------------------------------------------------------------------------------------
# File: fluoresence-extension.dic
# Date:20-APR-2018 CS/BV/JW
#
# Draft dictionary extension for Fluorescence repository
#
# ----------------------------------------------------------------------------------------------------------------------------
####################
## FLR_EXPERIMENT ##
####################
save_flr_experiment
_category.description
; Data items in the FLR_EXPERIMENT category records the
details of the Fluorescence experiment.
;
_category.id flr_experiment
_category.mandatory_code no
loop_
_category_key.name '_flr_experiment.id'
loop_
_category_group.id 'inclusive_group'
'flr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_flr_experiment.id
_flr_experiment.averaging_mode
_flr_experiment.experiment_type
_flr_experiment.temp_condition_id
1 single-molecule 'confocal with point detector' 1
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id flr_experiment
save_
save__flr_experiment.id
_item_description.description
; A unique identifier for the experimental setup.
;
_item.name '_flr_experiment.id'
_item.category_id flr_experiment
_item.mandatory_code yes
_item_type.code int
save_
save__flr_experiment.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_flr_experiment.entry_id'
_item.category_id flr_experiment
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_flr_experiment.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__flr_experiment.averaging_mode
_item_description.description
; The mode of averaging in the experiment.
;
_item.name '_flr_experiment.averaging_mode'
_item.category_id flr_experiment
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
'single-molecule'
'ensemble'
'sub-ensemble'
save_
save__flr_experiment.inst_id
_item_description.description
; The instrument used in the experiment.
;
_item.name '_flr_experiment.inst_id'
_item.category_id flr_experiment
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_flr_experiment.inst_id'
_item_linked.parent_name '_flr_instrument.id'
save_
save__flr_experiment.sample_id
_item_description.description
; The sample used in the experiment.
;
_item.name '_flr_experiment.sample_id'
_item.category_id flr_experiment
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_flr_experiment.sample_id'
_item_linked.parent_name '_flr_sample.id'
save_
save__flr_experiment.setting_id
_item_description.description
; The experimental settings used in the experiment.
;
_item.name '_flr_experiment.setting_id'
_item.category_id flr_experiment
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_flr_experiment.setting_id'
_item_linked.parent_name '_flr_exp_setting.id'
save_
save__flr_experiment.temp_condition_id
_item_description.description
; An id for the temperature condition.
;
_item.name '_flr_experiment.temp_condition_id'
_item.category_id flr_experiment
_item.mandatory_code yes
_item_type.code int
save_
#########################################
## FLR_SAMPLE_CONDITION_LIQUID_SOLVENT ##
#########################################
save_flr_sample_condition_liquid_solvent
_category.description
; Data items in the FLR_SAMPLE_CONDITION_LIQUID_SOLVENT category records the
details of experimental sample conditions for the liquid phase.
;
_category.id flr_sample_condition_liquid_solvent
_category.mandatory_code no
loop_
_category_key.name '_flr_sample_condition_liquid_solvent.sample_condition_id'
loop_
_category_group.id 'inclusive_group'
'flr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_flr_sample_condition_liquid_solvent.sample_condition_id
_flr_sample_condition_liquid_solvent.sample_condition_type
_flr_sample_condition_liquid_solvent.sample_condition_immobilization_sub_type
_flr_sample_condition_liquid_solvent.sample_condition_immobilization_details
1 'immobilized' 'directly tethered to the surface' 'The molecule is immobilized via biotin-streptavidin linkage'
#...abbreviated....
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id flr_sample_condition_liquid_solvent
save_
save__flr_sample_condition_liquid_solvent.sample_condition_id
_item_description.description
; An identifier for the sample condition.
;
_item.name '_flr_sample_condition_liquid_solvent.sample_condition_id'
_item.category_id flr_sample_condition_liquid_solvent
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_flr_sample_condition_liquid_solvent.sample_condition_id'
_item_linked.parent_name '_flr_sample.sample_condition_id'
save_
save__flr_sample_condition_liquid_solvent.sample_condition_type
_item_description.description
; The sample condition type.
;
_item.name '_flr_sample_condition_liquid_solvent.sample_condition_type'
_item.category_id flr_sample_condition_liquid_solvent
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
'free'
'immobilized'
'trapped'
'other'
save_
save__flr_sample_condition_liquid_solvent.sample_condition_immobilized_sub_type
_item_description.description
; The immobilized sample condition sub-type.
;
_item.name '_flr_sample_condition_liquid_solvent.sample_condition_immobilized_sub_type'
_item.category_id flr_sample_condition_liquid_solvent
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
'directly tethered to the surface'
'encapsulated in an immobilized liposome'
save_
save__flr_sample_condition_liquid_solvent.sample_condition_immobilization_details
_item_description.description
; Details of immobilization.
;
_item.name '_flr_sample_condition_liquid_solvent.sample_condition_immobilization_details'
_item.category_id flr_sample_condition_liquid_solvent
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'The molecule is immobilized via biotin-streptavidin linkage'
save_
############################################
## FLR_SAMPLE_CONDITION_VITRIFIED_SOLVENT ##
############################################
save_flr_sample_condition_vitrified_solvent
_category.description
; Data items in the FLR_SAMPLE_CONDITION_VITRIFIED_SOLVENT category records the
details of experimental sample conditions for the vitrified phase.
;
_category.id flr_sample_condition_vitrified_solvent
_category.mandatory_code no
loop_
_category_key.name '_flr_sample_condition_vitrified_solvent.sample_condition_id'
loop_
_category_group.id 'inclusive_group'
'flr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_flr_sample_condition_vitrified_solvent.sample_condition_id
1
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id flr_sample_condition_vitrified_solvent
save_
save__flr_sample_condition_vitrified_solvent.sample_condition_id
_item_description.description
; An identifier for the sample condition.
;
_item.name '_flr_sample_condition_vitrified_solvent.sample_condition_id'
_item.category_id flr_sample_condition_vitrified_solvent
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_flr_sample_condition_vitrified_solvent.sample_condition_id'
_item_linked.parent_name '_flr_sample.sample_condition_id'
save_
#################################
## FLR_EXPERIMENT_TEMP_DETAILS ##
#################################
save_flr_experiment_temp_details
_category.description
; Data items in the FLR_EXPERIMENT_TEMP_DETAILS category records the
details of the temperature details of the Fluorescence experiment.
;
_category.id flr_experiment_temp_details
_category.mandatory_code no
loop_
_category_key.name '_flr_experiment_temp_details.temp_condition_id'
loop_
_category_group.id 'inclusive_group'
'flr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_flr_experiment_temp_details.temp_condition_id
_flr_experiment_temp_details.temp_mode
_flr_experiment_temp_details.constant_temp_value
1 constant 298.0
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id flr_experiment_temperature_details
save_
save__flr_experiment_temp_details.temp_condition_id
_item_description.description
; The identifier for the temperature condition.
;
_item.name '_flr_experiment_temp_details.temp_condition_id'
_item.category_id flr_experiment_temp_details
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_flr_experiment_temp_details.temp_condition_id'
_item_linked.parent_name '_flr_experiment.temp_condition_id'
save_
save__flr_experiment_temp_details.temp_mode
_item_description.description
; The temperature mode.
;
_item.name '_flr_experiment_temp_details.temp_mode'
_item.category_id flr_experiment_temp_details
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
'constant'
'ramp'
save_
save__flr_experiment_temp_details.constant_temp_value
_item_description.description
; The temperature value in kelvin, if constant.
;
_item.name '_flr_experiment_temp_details.constant_temp_value'
_item.category_id flr_experiment_temp_details
_item.mandatory_code no
_item.units_code kelvin
_item_type.code float
loop_
_item_examples.case
'298.0'
'300.0'
save_
save__flr_experiment_temp_details.ramp_temp_lower_limit
_item_description.description
; The value of temperature lower limit in kelvin, if ramp.
;
_item.name '_flr_experiment_temp_details.ramp_temp_lower_limit'
_item.category_id flr_experiment_temp_details
_item.mandatory_code no
_item.units_code kelvin
_item_type.code float
loop_
_item_examples.case
'200.0'
'250.0'
save_
save__flr_experiment_temp_details.ramp_temp_upper_limit
_item_description.description
; The value of temperature upper limit in kelvin, if ramp.
;
_item.name '_flr_experiment_temp_details.ramp_temp_upper_limit'
_item.category_id flr_experiment_temp_details
_item.mandatory_code no
_item.units_code kelvin
_item_type.code float
loop_
_item_examples.case
'280.0'
'300.0'
save_
save__flr_experiment_temp_details.ramp_velocity
_item_description.description
; The velocity of the ramp.
;
_item.name '_flr_experiment_temp_details.ramp_velocity'
_item.category_id flr_experiment_temp_details
_item.mandatory_code no
_item.units_code degrees/minute
_item_type.code float
loop_
_item_examples.case
'1.0'
save_
############
# FLR_SAMPLE
############
save_flr_sample
_category.description
; Data items in the FLR_SAMPLE category records the
details of the sample in the Fluorescence experiment.
;
_category.id flr_sample
_category.mandatory_code no
loop_
_category_key.name '_flr_sample.id'
loop_
_category_group.id 'inclusive_group'
'flr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
#...abbreviated...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id flr_sample
save_
save__flr_sample.id
_item_description.description
; An identifier for the experimental sample.
;
_item.name '_flr_sample.id'
_item.category_id flr_sample
_item.mandatory_code yes
_item_type.code int
save_
save__flr_sample.sample_description
_item_description.description
; An author provided description for the sample.
;
_item.name '_flr_sample.sample_description'
_item.category_id flr_sample
_item.mandatory_code no
_item_type.code line
save_
save__flr_sample.sample_details
_item_description.description
; Additional details about the sample.
;
_item.name '_flr_sample.sample_details'
_item.category_id flr_sample
_item.mandatory_code no
_item_type.code text
save_
save__flr_sample.num_of_probes
_item_description.description
; Number of probes in the sample.
;
_item.name '_flr_sample.num_of_probes'
_item.category_id flr_sample
_item.mandatory_code yes
_item_type.code int
save_
save__flr_sample.solvent_phase
_item_description.description
; The phase of the solvent.
;
_item.name '_flr_sample.solvent_phase'
_item.category_id flr_sample
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'liquid' 'Freely diffusing molecules in solution'
'vitrified' 'Molecules in vitrified solution'
'other' 'Other'
save_
save__flr_sample.sample_condition_id
_item_description.description
; The id corresponding to the sample condition.
;
_item.name '_flr_sample.sample_condition_id'
_item.category_id flr_sample
_item.mandatory_code yes
_item_type.code int
save_
save__flr_sample.entity_assembly_id
_item_description.description
; This data item is a pointer to _flr_entity_assembly.assembly_id
in the FLR_ENTITY_ASSEMBLY category.
;
_item.name '_flr_sample.entity_assembly_id'
_item.category_id flr_sample
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_flr_sample.entity_assembly_id'
_item_linked.parent_name '_flr_entity_assembly.assembly_id'
save_
#########################
## FLR_ENTITY_ASSEMBLY ##
#########################
save_flr_entity_assembly
_category.description
; Data items in the FLR_ENTITY_ASSEMBLY category records the
details of the components in the entity assembly.
;
_category.id flr_entity_assembly
_category.mandatory_code no
loop_
_category_key.name '_flr_entity_assembly.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'flr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id flr_entity_assembly
save_
save__flr_entity_assembly.ordinal_id
_item_description.description
; A unique identifier for the category.
;
_item.name '_flr_entity_assembly.ordinal_id'
_item.category_id flr_entity_assembly
_item.mandatory_code yes
_item_type.code int
save_
save__flr_entity_assembly.assembly_id
_item_description.description
; An identifier for the entity assembly.
;
_item.name '_flr_entity_assembly.assembly_id'
_item.category_id flr_entity_assembly
_item.mandatory_code yes
_item_type.code int
save_
save__flr_entity_assembly.entity_id
_item_description.description
; An identifier for the entity.
;
_item.name '_flr_entity_assembly.entity_id'
_item.category_id flr_entity_assembly
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_flr_entity_assembly.entity_id'
_item_linked.parent_name '_entity.id'
save_
save__flr_entity_assembly.num_copies
_item_description.description
; The number of copies/instances of the entity in the assembly.
;
_item.name '_flr_entity_assembly.num_copies'
_item.category_id flr_entity_assembly
_item.mandatory_code yes
_item_type.code int
save_
save__flr_entity_assembly.entity_description
_item_description.description
; The description of the entity.
;
_item.name '_flr_entity_assembly.entity_description'
_item.category_id flr_entity_assembly
_item.mandatory_code no
_item_type.code line
_item_linked.child_name '_flr_entity_assembly.entity_description'
_item_linked.parent_name '_entity.pdbx_description'
save_