11h41 : la base que j’avais défini précédemment comportait un certain nombre d’erreur et ne prenait pas en compte les appâts multiples sur une même lame (voir explication)
je l’ai reprise en partant cette fois du point de vu de l’utilisateur, ce qui a mon avis est mieux.
Comment j’ai procédé –> j’ai essayé de voir la façon dont allait procéder l’utilisateur pour rentrer des données en me basant sur la version actuelle de SganArrayL et sur ce que je sais des manip.
d’un point de vue théorique, une manip consiste à hybrider les extraits d’une souche appât et d’une souche contrôle sur une lame et cela plusieurs fois en marquant éventuellement les extraits avec différents fluorochromes.
d’un point de vue pratique, une manip consiste le meme jour a hybrider 6 lames avec plusieurs souche appat différentes et plusieurs controle. l’utilisateur va alors scanner toutes ces lames, générés les fichiers gpr correspondant et les introduire dans la base de données.
l’élément central pour l’utilisateur c’est alors la lame. je suis donc parti de ca pour organiser la base. la table hyb_slide est celle autour de laquelle gravitent toutes les autres plus ou moins directement. c’est finalement assez logique.
cette table comprend un id comme clé primaire, une reférence de lame, un champs metatdat qui ne sera jamais rempli. c juste pour me rappeler de traiter les metadonnées du fichier gpr, un champ de commentaire, un lien vers l’image de la lame, et un lien vers le fichier gpr correspondant. de plus cette table est liée a la table des_experiment par le champs exp_id.
cette table contient un champs common_ref, un champ quality et un champs description. voir MIAME
de plus cette table est liée a des_biblio (liste d’article), des_citations (liste de citation), des_authors (listes des auteurs) et aussi a des_experimental_factors.
la table hyb_slide est aussi liée a la table prep_sample
cette table rassemble les éléments d’autres tables., biomaterial_manipulation, labelling_protocol, organism, extract_preparation
cettet table est dan sla partie sample used, extract preparetion and labelling (voir MIAME). dans cette partie on trouve aussi une table prep_strain, qui va associer a un gène une mutation et une utilisation, par exemple,
orf -> YPL093W – mutation -> DAMP – utilisation -> bait
ou aussi
orf -> YFR057W – mutation -> DAMP – utilisation -> control
le type de mutation et d’utilisation sont dans 2 tables liées à celle-ci.
les orf sont dans une table bank_orf et liée aussi a celle-ci.
la table prep_strain est liée à hyb_strain, elle-meme liée à hyb_slide. hyb_strain est liée aussi a hyb_fluorophore, qui contient la liste des marqueurs fluo utilisés (a priori cy3, cy5, alexa). on peut ainsi par cette table dire pour une plaque quelles sont les bait et control et quels marqueurs ont été utilisés.
hyb_slide est aussi liée à hyb_protocol et hyb_scan_protocol et surtout a hyb_mating_date, qui listera toute les differentes date d’hybridation.
les resultats traité ou non, sont dans la partie measurment data and specification.
la table mes_sot_data est liée à hyb_slide. elle va reprednre les info général sur chaque spot, diamètre, et flag. elle est liée à array_spots de la partie array description
cette table contient les info de position et de nom de chaque spot. elle est liée à array_chip_types pour le type de puce, array_spot_type pour le type de spot (feature ou control) et a bank_orf, pour l’orf a laquelle correspond ce spot.
la table mes_raw_signal est la table contenant les valeurs brute de fluorescence des spot. elles contient 7 champs propres correspondant aux valeurs du signal moyen, median et a l’ecart-type ainsin qu’aux valeurs du background moyen et median et a l’ecart-type. il y a aussi une valeur du rapport signal/bruit (SNR). cette table est liée à spd_id pour savoir de quelle spot il s’agit et à hyb_strain pour savoir de quel marqueur (et donc de quel gène) c’est le signal. dans le cas d’une lame à 3 couleurs ont va donc avoir pour chaque spot 3 lignes de resultats soit environ 60 000 lignes par lame. –> cela représente pour les 1000 gènes du projet genogim environ 2000 lames soit 120 millions de lignes pour cette table (voir le post sur les limites de postgresql).
les données doivent ensuite etre traité et entre autre il y a des ratio a effectué entre les différents signaux d’une meme lame. les ratio a effectué seront précisé dans mes_analysed_protocol. cette table est liée a 2 petite table mes_numerator et mes_denominator qui contiennent la litse des gene utilisé comme numérateur du ratio et comme dénominateur du ratio. il y a en plus une table mes_ratio_protocol decrivant les étape de l’analyse des signaux. enfin les valeurs de ratio sont stockées dans mes_analysed_data. cette table est liée a mes_analysed_protocol et contient 3 champs pour le moment, raw_ratio, centered_ratio et norm_ratio, pour les données brute, centrée et normalisée.
voila qui est fait.
j’ai généré les fichier sql pour créer et affacer la base et aussi faire les requètes.
ils sont dans /home/gim2/vpworkspace/
ce sont les fichier llp create.ddl , llp drop.ddl , llp insert.sql , llp select.sql , llp update.sql , llp delete.sql
create table bank_orf (orf_id serial not null, orf_name varchar(255), orf_gene varchar(255), primary key (orf_id));
create table prep_mutation (mut_id serial not null, mut_type varchar(255), primary key (mut_id));
create table prep_strain (pstr_id serial not null, orf_id serial not null, mut_id serial not null, use_id serial not null, primary key (pstr_id));
create table des_authors (auth_id serial not null, auth_first_name varchar(50), auth_last_name varchar(50), loc_id serial not null, primary key (auth_id));
create table des_locations (loc_id serial not null, loc_name varchar(255), loc_address1 varchar(255), loc_address2 varchar(255), loc_zip_code int4, loc_city varchar(255), primary key (loc_id));
create table array_chip_types (ct_id serial not null, ct_name varchar(255), primary key (ct_id));
create table des_experiment_types (et_id serial not null, et_name varchar(255), et_desc varchar(255), primary key (et_id));
create table des_biblio (biblio_id serial not null, biblio_text varchar(255), primary key (biblio_id));
create table des_experiments (exp_id serial not null, exp_common_ref bool, exp_quality text, et_id serial not null, ef_id serial not null, exp_description text, primary key (exp_id));
create table des_citation (cit_id serial not null, cit_text varchar(255), primary key (cit_id));
create table prep_organism (org_id serial not null, orf_name varchar(255), primary key (org_id));
create table prep_orf_usage (use_id serial not null, use_type varchar(10), primary key (use_id));
create table prep_biomaterial_manipulation (biomat_id serial not null, biomat_growth_cond varchar(30), biomat_treatment_type varchar(25), biomat_separation_technique varchar(25), primary key (biomat_id));
create table prep_extraction_preparation (expr_id serial not null, expr_extract_type varchar(15), expr_amplification varchar(15), extp_id serial not null, primary key (expr_id));
create table prep_labeling_protocol (labp_id serial not null, labp_amount varchar(15), labp_label_used varchar(15), labp_incorporation text, primary key (labp_id));
create table hyb_protocol (hybp_id serial not null, hybp_protocol text, primary key (hybp_id));
create table hyb_mating_date (mdate_id serial not null, mdate_date date, primary key (mdate_id));
create table hyd_slide (sl_id serial not null, sl_ref varchar(10), exp_id serial not null, sl_metadata varchar(255), hybp_id serial not null, sl_comment varchar(255), mdate_id serial not null, scan_id serial not null, sl_image_path varchar(255), sl_gpr_path int4, auth_id serial not null, sa_id serial not null, ct_id serial not null, primary key (sl_id));
create table hyb_strain (hstr_id serial not null, hstr_generation_nb float4, sl_id serial not null, fluo_id serial not null, pstr_id serial not null, primary key (hstr_id));
create table hyb_fluorophore (fluo_id serial not null, "fluo name" varchar(10), fluo_lambda int2, primary key (fluo_id));
create table hyb_scan_protocol (scan_id serial not null, scan_protocol text, primary key (scan_id));
create table array_spots (sp_id serial not null, sp_block int4, sp_col int4, sp_row int4, sp_name int4, spt_id serial not null, ct_id serial not null, orf_id serial, primary key (sp_id));
create table mes_spot_data (spd_id serial not null, spd_diameter int4, spd_flag varchar(10), spd_autoflag varchar(10), sl_id serial not null, sp_id serial not null, primary key (spd_id));
create table mes_raw_signal (rsg_id serial not null, rsg_foreground_median int4, rsg_foreground_mean int4, rsg_forground_sd int4, rsg_background int4, rsg_background_median int4, rsg_background_mean int4, rsg_background_sd int4, rsg_snr float4, spd_id serial not null, hstr_id serial not null, primary key (rsg_id));
create table mes_analysed_data (anad_id serial, spd_id serial not null, anad_raw_ratio float8, anad_centered_ratio float8, anad_norm_ratio float8, anap_id serial not null);
create table mes_analysed_protocol (anap_id serial not null, num_id serial not null, den_id serial not null, ratp_id serial not null, primary key (anap_id));
create table mes_numerator (num_id serial not null, str_id serial not null, primary key (num_id));
create table mes_denominator (den_id serial not null, str_id serial not null, primary key (den_id));
create table array_spot_type (spt_id serial not null, spt_type varchar(10), constraint spt_type primary key (spt_id));
create table prep_sample (sa_id serial not null, biomat_id serial not null, labp_id serial not null, expr_id serial not null, org_id serial not null, primary key (sa_id));
create table des_authors_exp (auth_id serial not null, exp_id serial not null, primary key (auth_id, exp_id));
create table des_experimental_factors (ef_id serial not null, ef_factor varchar(30), primary key (ef_id));
create table des_biblio_exp (biblio_id serial not null, exp_id serial not null, primary key (biblio_id, exp_id));
create table des_cit_exp (cit_id serial not null, exp_id serial not null, primary key (cit_id, exp_id));
create table prep_extraction_prot (extp_id serial not null, extp_text text, primary key (extp_id));
create table mes_ratio_protocol (ratp_id serial not null, ratp_text text, primary key (ratp_id));
alter table prep_strain add constraint FKprep_strai403802 foreign key (orf_id) references bank_orf;
alter table prep_strain add constraint FKprep_strai214282 foreign key (mut_id) references prep_mutation;
alter table des_authors add constraint FKdes_author231061 foreign key (loc_id) references des_locations;
alter table des_experiments add constraint FKdes_experi225877 foreign key (et_id) references des_experiment_types;
alter table prep_sample add constraint FKprep_sampl485169 foreign key (org_id) references prep_organism;
alter table prep_strain add constraint FKprep_strai136538 foreign key (use_id) references prep_orf_usage;
alter table prep_sample add constraint FKprep_sampl452472 foreign key (labp_id) references prep_labeling_protocol;
alter table mes_spot_data add constraint FKmes_spot_d918897 foreign key (sp_id) references array_spots;
alter table mes_raw_signal add constraint FKmes_raw_si626364 foreign key (spd_id) references mes_spot_data;
alter table mes_analysed_protocol add constraint FKmes_analys951623 foreign key (num_id) references mes_numerator;
alter table mes_analysed_protocol add constraint FKmes_analys786494 foreign key (den_id) references mes_denominator;
alter table mes_analysed_data add constraint FKmes_analys587731 foreign key (anap_id) references mes_analysed_protocol;
alter table hyd_slide add constraint FKhyd_slide72580 foreign key (mdate_id) references hyb_mating_date;
alter table hyd_slide add constraint FKhyd_slide483698 foreign key (hybp_id) references hyb_protocol;
alter table array_spots add constraint FKarray_spot230773 foreign key (spt_id) references array_spot_type;
alter table array_spots add constraint FKarray_spot154343 foreign key (orf_id) references bank_orf;
alter table prep_sample add constraint FKprep_sampl459810 foreign key (expr_id) references prep_extraction_preparation;
alter table des_authors_exp add constraint FKdes_author795609 foreign key (auth_id) references des_authors;
alter table des_experiments add constraint FKdes_experi36244 foreign key (ef_id) references des_experimental_factors;
alter table des_authors_exp add constraint FKdes_author917097 foreign key (exp_id) references des_experiments;
alter table hyd_slide add constraint FKhyd_slide920516 foreign key (ct_id) references array_chip_types;
alter table des_biblio_exp add constraint FKdes_biblio481512 foreign key (biblio_id) references des_biblio;
alter table des_biblio_exp add constraint FKdes_biblio538208 foreign key (exp_id) references des_experiments;
alter table des_cit_exp add constraint FKdes_cit_ex676417 foreign key (cit_id) references des_citation;
alter table des_cit_exp add constraint FKdes_cit_ex401799 foreign key (exp_id) references des_experiments;
alter table prep_sample add constraint FKprep_sampl686540 foreign key (biomat_id) references prep_biomaterial_manipulation;
alter table prep_extraction_preparation add constraint FKprep_extra865431 foreign key (extp_id) references prep_extraction_prot;
alter table hyd_slide add constraint FKhyd_slide628246 foreign key (exp_id) references des_experiments;
alter table hyd_slide add constraint FKhyd_slide329699 foreign key (sa_id) references prep_sample;
alter table hyb_strain add constraint FKhyb_strain18944 foreign key (pstr_id) references prep_strain;
alter table hyb_strain add constraint FKhyb_strain340557 foreign key (sl_id) references hyd_slide;
alter table hyb_strain add constraint FKhyb_strain6029 foreign key (fluo_id) references hyb_fluorophore;
alter table hyd_slide add constraint FKhyd_slide946515 foreign key (scan_id) references hyb_scan_protocol;
alter table array_spots add constraint FKarray_spot991272 foreign key (ct_id) references array_chip_types;
alter table mes_spot_data add constraint FKmes_spot_d379231 foreign key (sl_id) references hyd_slide;
alter table mes_raw_signal add constraint FKmes_raw_si231276 foreign key (hstr_id) references hyb_strain;
alter table mes_denominator add constraint FKmes_denomi703686 foreign key (str_id) references hyb_strain;
alter table mes_numerator add constraint FKmes_numera792103 foreign key (str_id) references hyb_strain;
alter table mes_analysed_protocol add constraint FKmes_analys48304 foreign key (ratp_id) references mes_ratio_protocol;
alter table hyd_slide add constraint FKhyd_slide369363 foreign key (auth_id) references des_authors;
alter table mes_analysed_data add constraint FKmes_analys921582 foreign key (spd_id) references mes_spot_data;
alter table prep_strain drop constraint FKprep_strai403802;
alter table prep_strain drop constraint FKprep_strai214282;
alter table des_authors drop constraint FKdes_author231061;
alter table des_experiments drop constraint FKdes_experi225877;
alter table prep_sample drop constraint FKprep_sampl485169;
alter table prep_strain drop constraint FKprep_strai136538;
alter table prep_sample drop constraint FKprep_sampl452472;
alter table mes_spot_data drop constraint FKmes_spot_d918897;
alter table mes_raw_signal drop constraint FKmes_raw_si626364;
alter table mes_analysed_protocol drop constraint FKmes_analys951623;
alter table mes_analysed_protocol drop constraint FKmes_analys786494;
alter table mes_analysed_data drop constraint FKmes_analys587731;
alter table hyd_slide drop constraint FKhyd_slide72580;
alter table hyd_slide drop constraint FKhyd_slide483698;
alter table array_spots drop constraint FKarray_spot230773;
alter table array_spots drop constraint FKarray_spot154343;
alter table prep_sample drop constraint FKprep_sampl459810;
alter table des_authors_exp drop constraint FKdes_author795609;
alter table des_experiments drop constraint FKdes_experi36244;
alter table des_authors_exp drop constraint FKdes_author917097;
alter table hyd_slide drop constraint FKhyd_slide920516;
alter table des_biblio_exp drop constraint FKdes_biblio481512;
alter table des_biblio_exp drop constraint FKdes_biblio538208;
alter table des_cit_exp drop constraint FKdes_cit_ex676417;
alter table des_cit_exp drop constraint FKdes_cit_ex401799;
alter table prep_sample drop constraint FKprep_sampl686540;
alter table prep_extraction_preparation drop constraint FKprep_extra865431;
alter table hyd_slide drop constraint FKhyd_slide628246;
alter table hyd_slide drop constraint FKhyd_slide329699;
alter table hyb_strain drop constraint FKhyb_strain18944;
alter table hyb_strain drop constraint FKhyb_strain340557;
alter table hyb_strain drop constraint FKhyb_strain6029;
alter table hyd_slide drop constraint FKhyd_slide946515;
alter table array_spots drop constraint FKarray_spot991272;
alter table mes_spot_data drop constraint FKmes_spot_d379231;
alter table mes_raw_signal drop constraint FKmes_raw_si231276;
alter table mes_denominator drop constraint FKmes_denomi703686;
alter table mes_numerator drop constraint FKmes_numera792103;
alter table mes_analysed_protocol drop constraint FKmes_analys48304;
alter table hyd_slide drop constraint FKhyd_slide369363;
alter table mes_analysed_data drop constraint FKmes_analys921582;
drop table bank_orf;
drop table prep_mutation;
drop table prep_strain;
drop table des_authors;
drop table des_locations;
drop table array_chip_types;
drop table des_experiment_types;
drop table des_biblio;
drop table des_experiments;
drop table des_citation;
drop table prep_organism;
drop table prep_orf_usage;
drop table prep_biomaterial_manipulation;
drop table prep_extraction_preparation;
drop table prep_labeling_protocol;
drop table hyb_protocol;
drop table hyb_mating_date;
drop table hyd_slide;
drop table hyb_strain;
drop table hyb_fluorophore;
drop table hyb_scan_protocol;
drop table array_spots;
drop table mes_spot_data;
drop table mes_raw_signal;
drop table mes_analysed_data;
drop table mes_analysed_protocol;
drop table mes_numerator;
drop table mes_denominator;
drop table array_spot_type;
drop table prep_sample;
drop table des_authors_exp;
drop table des_experimental_factors;
drop table des_biblio_exp;
drop table des_cit_exp;
drop table prep_extraction_prot;
drop table mes_ratio_protocol;
insert into bank_orf(orf_id, orf_name, orf_gene) values (?, ?, ?);
insert into prep_mutation(mut_id, mut_type) values (?, ?);
insert into prep_strain(pstr_id, orf_id, mut_id, use_id) values (?, ?, ?, ?);
insert into des_authors(auth_id, auth_first_name, auth_last_name, loc_id) values (?, ?, ?, ?);
insert into des_locations(loc_id, loc_name, loc_address1, loc_address2, loc_zip_code, loc_city) values (?, ?, ?, ?, ?, ?);
insert into array_chip_types(ct_id, ct_name) values (?, ?);
insert into des_experiment_types(et_id, et_name, et_desc) values (?, ?, ?);
insert into des_biblio(biblio_id, biblio_text) values (?, ?);
insert into des_experiments(exp_id, exp_common_ref, exp_quality, et_id, ef_id, exp_description) values (?, ?, ?, ?, ?, ?);
insert into des_citation(cit_id, cit_text) values (?, ?);
insert into prep_organism(org_id, orf_name) values (?, ?);
insert into prep_orf_usage(use_id, use_type) values (?, ?);
insert into prep_biomaterial_manipulation(biomat_id, biomat_growth_cond, biomat_treatment_type, biomat_separation_technique) values (?, ?, ?, ?);
insert into prep_extraction_preparation(expr_id, expr_extract_type, expr_amplification, extp_id) values (?, ?, ?, ?);
insert into prep_labeling_protocol(labp_id, labp_amount, labp_label_used, labp_incorporation) values (?, ?, ?, ?);
insert into hyb_protocol(hybp_id, hybp_protocol) values (?, ?);
insert into hyb_mating_date(mdate_id, mdate_date) values (?, ?);
insert into hyd_slide(sl_id, sl_ref, exp_id, sl_metadata, hybp_id, sl_comment, mdate_id, scan_id, sl_image_path, sl_gpr_path, auth_id, sa_id, ct_id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?);
insert into hyb_strain(hstr_id, hstr_generation_nb, sl_id, fluo_id, pstr_id) values (?, ?, ?, ?, ?);
insert into hyb_fluorophore(fluo_id, "fluo name", fluo_lambda) values (?, ?, ?);
insert into hyb_scan_protocol(scan_id, scan_protocol) values (?, ?);
insert into array_spots(sp_id, sp_block, sp_col, sp_row, sp_name, spt_id, ct_id, orf_id) values (?, ?, ?, ?, ?, ?, ?, ?);
insert into mes_spot_data(spd_id, spd_diameter, spd_flag, spd_autoflag, sl_id, sp_id) values (?, ?, ?, ?, ?, ?);
insert into mes_raw_signal(rsg_id, rsg_foreground_median, rsg_foreground_mean, rsg_forground_sd, rsg_background, rsg_background_median, rsg_background_mean, rsg_background_sd, rsg_snr, spd_id, hstr_id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?);
insert into mes_analysed_data(anad_id, spd_id, anad_raw_ratio, anad_centered_ratio, anad_norm_ratio, anap_id) values (?, ?, ?, ?, ?, ?);
insert into mes_analysed_protocol(anap_id, num_id, den_id, ratp_id) values (?, ?, ?, ?);
insert into mes_numerator(num_id, str_id) values (?, ?);
insert into mes_denominator(den_id, str_id) values (?, ?);
insert into array_spot_type(spt_id, spt_type) values (?, ?);
insert into prep_sample(sa_id, biomat_id, labp_id, expr_id, org_id) values (?, ?, ?, ?, ?);
insert into des_authors_exp(auth_id, exp_id) values (?, ?);
insert into des_experimental_factors(ef_id, ef_factor) values (?, ?);
insert into des_biblio_exp(biblio_id, exp_id) values (?, ?);
insert into des_cit_exp(cit_id, exp_id) values (?, ?);
insert into prep_extraction_prot(extp_id, extp_text) values (?, ?);
insert into mes_ratio_protocol(ratp_id, ratp_text) values (?, ?);
- pour selectionner des données
select orf_id, orf_name, orf_gene from bank_orf;
select mut_id, mut_type from prep_mutation;
select pstr_id, orf_id, mut_id, use_id from prep_strain;
select auth_id, auth_first_name, auth_last_name, loc_id from des_authors;
select loc_id, loc_name, loc_address1, loc_address2, loc_zip_code, loc_city from des_locations;
select ct_id, ct_name from array_chip_types;
select et_id, et_name, et_desc from des_experiment_types;
select biblio_id, biblio_text from des_biblio;
select exp_id, exp_common_ref, exp_quality, et_id, ef_id, exp_description from des_experiments;
select cit_id, cit_text from des_citation;
select org_id, orf_name from prep_organism;
select use_id, use_type from prep_orf_usage;
select biomat_id, biomat_growth_cond, biomat_treatment_type, biomat_separation_technique from prep_biomaterial_manipulation;
select expr_id, expr_extract_type, expr_amplification, extp_id from prep_extraction_preparation;
select labp_id, labp_amount, labp_label_used, labp_incorporation from prep_labeling_protocol;
select hybp_id, hybp_protocol from hyb_protocol;
select mdate_id, mdate_date from hyb_mating_date;
select sl_id, sl_ref, exp_id, sl_metadata, hybp_id, sl_comment, mdate_id, scan_id, sl_image_path, sl_gpr_path, auth_id, sa_id, ct_id from hyd_slide;
select hstr_id, hstr_generation_nb, sl_id, fluo_id, pstr_id from hyb_strain;
select fluo_id, "fluo name", fluo_lambda from hyb_fluorophore;
select scan_id, scan_protocol from hyb_scan_protocol;
select sp_id, sp_block, sp_col, sp_row, sp_name, spt_id, ct_id, orf_id from array_spots;
select spd_id, spd_diameter, spd_flag, spd_autoflag, sl_id, sp_id from mes_spot_data;
select rsg_id, rsg_foreground_median, rsg_foreground_mean, rsg_forground_sd, rsg_background, rsg_background_median, rsg_background_mean, rsg_background_sd, rsg_snr, spd_id, hstr_id from mes_raw_signal;
select anad_id, spd_id, anad_raw_ratio, anad_centered_ratio, anad_norm_ratio, anap_id from mes_analysed_data;
select anap_id, num_id, den_id, ratp_id from mes_analysed_protocol;
select num_id, str_id from mes_numerator;
select den_id, str_id from mes_denominator;
select spt_id, spt_type from array_spot_type;
select sa_id, biomat_id, labp_id, expr_id, org_id from prep_sample;
select auth_id, exp_id from des_authors_exp;
select ef_id, ef_factor from des_experimental_factors;
select biblio_id, exp_id from des_biblio_exp;
select cit_id, exp_id from des_cit_exp;
select extp_id, extp_text from prep_extraction_prot;
select ratp_id, ratp_text from mes_ratio_protocol;
- pour modifier des données
update bank_orf set orf_name = ?, orf_gene = ? where orf_id = ?;
update prep_mutation set mut_type = ? where mut_id = ?;
update prep_strain set orf_id = ?, mut_id = ?, use_id = ? where pstr_id = ?;
update des_authors set auth_first_name = ?, auth_last_name = ?, loc_id = ? where auth_id = ?;
update des_locations set loc_name = ?, loc_address1 = ?, loc_address2 = ?, loc_zip_code = ?, loc_city = ? where loc_id = ?;
update array_chip_types set ct_name = ? where ct_id = ?;
update des_experiment_types set et_name = ?, et_desc = ? where et_id = ?;
update des_biblio set biblio_text = ? where biblio_id = ?;
update des_experiments set exp_common_ref = ?, exp_quality = ?, et_id = ?, ef_id = ?, exp_description = ? where exp_id = ?;
update des_citation set cit_text = ? where cit_id = ?;
update prep_organism set orf_name = ? where org_id = ?;
update prep_orf_usage set use_type = ? where use_id = ?;
update prep_biomaterial_manipulation set biomat_growth_cond = ?, biomat_treatment_type = ?, biomat_separation_technique = ? where biomat_id = ?;
update prep_extraction_preparation set expr_extract_type = ?, expr_amplification = ?, extp_id = ? where expr_id = ?;
update prep_labeling_protocol set labp_amount = ?, labp_label_used = ?, labp_incorporation = ? where labp_id = ?;
update hyb_protocol set hybp_protocol = ? where hybp_id = ?;
update hyb_mating_date set mdate_date = ? where mdate_id = ?;
update hyd_slide set sl_ref = ?, exp_id = ?, sl_metadata = ?, hybp_id = ?, sl_comment = ?, mdate_id = ?, scan_id = ?, sl_image_path = ?, sl_gpr_path = ?, auth_id = ?, sa_id = ?, ct_id = ? where sl_id = ?;
update hyb_strain set hstr_generation_nb = ?, sl_id = ?, fluo_id = ?, pstr_id = ? where hstr_id = ?;
update hyb_fluorophore set "fluo name" = ?, fluo_lambda = ? where fluo_id = ?;
update hyb_scan_protocol set scan_protocol = ? where scan_id = ?;
update array_spots set sp_block = ?, sp_col = ?, sp_row = ?, sp_name = ?, spt_id = ?, ct_id = ?, orf_id = ? where sp_id = ?;
update mes_spot_data set spd_diameter = ?, spd_flag = ?, spd_autoflag = ?, sl_id = ?, sp_id = ? where spd_id = ?;
update mes_raw_signal set rsg_foreground_median = ?, rsg_foreground_mean = ?, rsg_forground_sd = ?, rsg_background = ?, rsg_background_median = ?, rsg_background_mean = ?, rsg_background_sd = ?, rsg_snr = ?, spd_id = ?, hstr_id = ? where rsg_id = ?;
update mes_analysed_data set anad_id = ?, spd_id = ?, anad_raw_ratio = ?, anad_centered_ratio = ?, anad_norm_ratio = ?, anap_id = ? where ;
update mes_analysed_protocol set num_id = ?, den_id = ?, ratp_id = ? where anap_id = ?;
update mes_numerator set str_id = ? where num_id = ?;
update mes_denominator set str_id = ? where den_id = ?;
update array_spot_type set spt_type = ? where spt_id = ?;
update prep_sample set biomat_id = ?, labp_id = ?, expr_id = ?, org_id = ? where sa_id = ?;
update des_authors_exp set where auth_id = ? and exp_id = ?;
update des_experimental_factors set ef_factor = ? where ef_id = ?;
update des_biblio_exp set where biblio_id = ? and exp_id = ?;
update des_cit_exp set where cit_id = ? and exp_id = ?;
update prep_extraction_prot set extp_text = ? where extp_id = ?;
update mes_ratio_protocol set ratp_text = ? where ratp_id = ?;
delete from bank_orf where orf_id = ?;
delete from prep_mutation where mut_id = ?;
delete from prep_strain where pstr_id = ?;
delete from des_authors where auth_id = ?;
delete from des_locations where loc_id = ?;
delete from array_chip_types where ct_id = ?;
delete from des_experiment_types where et_id = ?;
delete from des_biblio where biblio_id = ?;
delete from des_experiments where exp_id = ?;
delete from des_citation where cit_id = ?;
delete from prep_organism where org_id = ?;
delete from prep_orf_usage where use_id = ?;
delete from prep_biomaterial_manipulation where biomat_id = ?;
delete from prep_extraction_preparation where expr_id = ?;
delete from prep_labeling_protocol where labp_id = ?;
delete from hyb_protocol where hybp_id = ?;
delete from hyb_mating_date where mdate_id = ?;
delete from hyd_slide where sl_id = ?;
delete from hyb_strain where hstr_id = ?;
delete from hyb_fluorophore where fluo_id = ?;
delete from hyb_scan_protocol where scan_id = ?;
delete from array_spots where sp_id = ?;
delete from mes_spot_data where spd_id = ?;
delete from mes_raw_signal where rsg_id = ?;
delete from mes_analysed_data where ;
delete from mes_analysed_protocol where anap_id = ?;
delete from mes_numerator where num_id = ?;
delete from mes_denominator where den_id = ?;
delete from array_spot_type where spt_id = ?;
delete from prep_sample where sa_id = ?;
delete from des_authors_exp where auth_id = ?andexp_id = ?;
delete from des_experimental_factors where ef_id = ?;
delete from des_biblio_exp where biblio_id = ?andexp_id = ?;
delete from des_cit_exp where cit_id = ?andexp_id = ?;
delete from prep_extraction_prot where extp_id = ?;
delete from mes_ratio_protocol where ratp_id = ?;
