Expression data in relational tables

id int No

created_by varchar(30) No

created_datime datetime No

last_modified_by varchar(30) No

last_modified_datime datetime No

gerd_expt_id varchar(15) No

gerd_created_by varchar(30) Yes

gerd_created_date datetime No

mol_name varchar(7) No

name varchar(80) No

reference int No

notes text No

id int No

created_by varchar(30) No

created_datime datetime No

last_modified_by varchar(30) No

last_modified_datime datetime No

expression_experiment_id int No

gerd_created_by varchar(50) Yes

gerd_created_date datetime No

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 text Yes

gerd_data_id int No

name varchar(150) No

dose_level real Yes

dose_units varchar(50) Yes

gerd_data_id int No

level_type varchar(15) No

time real Yes

quant_level real Yes

variance real Yes

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