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Expression data in relational tables

expression_experiment (relational)

Column TypeNull allowed
id intNo
created_by varchar(30)No
created_datime datetimeNo
last_modified_by varchar(30)No
last_modified_datime datetimeNo
gerd_expt_id varchar(15)No
gerd_created_by varchar(30)Yes
gerd_created_date datetimeNo
mol_name varchar(7)No
name varchar(80)No
reference intNo
notes textNo

gerd_data (relational)

Column TypeNull allowed
id intNo
created_by varchar(30)No
created_datime datetimeNo
last_modified_by varchar(30)No
last_modified_datime datetimeNo
expression_experiment_id intNo
gerd_created_by varchar(50)Yes
gerd_created_date datetimeNo
expression_experiment_datum varchar(15)No
gerd_accession varchar(10)No
gerd_name varchar(120)No
organism varchar(120)No
developmental_stage varchar(120)Yes
cell varchar(120)Yes
cell_cycle varchar(120)Yes
tissue varchar(120)Yes
transforming_gene varchar(120)Yes
mutant_gene varchar(120)Yes
strain_or_subline varchar(120)Yes
time0 varchar(120)Yes
unit varchar(20)Yes
level_unit varchar(120)Yes
var_method varchar(120)Yes
expression_profile varchar(120)Yes
notes textYes

gerd_ext_factors (relational)

Column TypeNull allowed
gerd_data_id intNo
name varchar(150)No
dose_level realYes
dose_units varchar(50)Yes

expression_levels (relational)

Column TypeNull allowed
gerd_data_id intNo
level_type varchar(15)No
time realYes
quant_level realYes
variance realYes
qual_level varchar(50)Yes

The relational tables were normalized from the following Prolog tables

 
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
gerd_expt_id string no id in GERD none
gerd_created_by string no GERD initial annotator none
gerd_created_date string no date of GERD initial annotation  
mol_name string no RNA or protein none
epodb_unit_id table_id yes pointer to transcript unit or protein unit none
name string no experiment name from controlled vocabulary none
reference string no journal reference none
notes string yes annotators comments none
 

 
id identity no EpoDB Id none
created_by string no annotator initials none
created_datime datetime no time of parsing none
last_modified_by string no annotator initials none
last_modified_datime datetime no time of update none
expression_experiment_id table_id no pointer to row in experiment table none
gerd_created_by string no GERD initial annotator none
gerd_created_date string no date of GERD initial annotation none
mol_name string no RNA or protein none
expression_experiment_datum string no data id from GERD none
gerd_unit record yes transcript or protein unit accession, name and organism from GERD none
developmental_stage string set no stage of expression from controlled vocabulary none
cell string set no cells where expression occurs none
cell_cycle string set yes cell cycle stage when expression occurs none
tissue string set no tissue where expression is known to occur none
external_factors record set yes factors that modulate expression none
transforming_gene string yes gene used to transform cells none
mutant_gene record set yes gene name(s) and mutation(s) in genotype none
strain_or_subline record yes strains or sublines none
qual_level_of_expression record yes time0, units, level, and time_level none
quant_level_of_expression record yes time0, time_units, var_method, level_unit and time_level_var none
expression_profile record yes description and symbol none
notes string yes annotators comments none
 


next up previous
Next: About this document ... Up: Guide to the EpoDB Previous: Transcription data in table

Chris Stoeckert 10/4/98Fidel Salas 1/15/1998