Added the medium BMS23 to the database #16 #49

draeger-lab · Jan 23, 2024 · ad6eecc · ad6eecc
1 parent 7232cb6
commit ad6eecc
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Showing 2 changed files with 51 additions and 6 deletions.
diff --git a/src/refinegems/data/database/data.db b/src/refinegems/data/database/data.db
diff --git a/src/refinegems/data/database/media_db.sql b/src/refinegems/data/database/media_db.sql
@@ -14,6 +14,7 @@ INSERT INTO "medium" VALUES(7,'MP-AU','Multi-Purpose Artificial Urine','https://
 INSERT INTO "medium" VALUES(8,'RPMI','Roswell Park Memorial Institute 1640 Medium','https://www.thermofisher.com/de/de/home/technical-resources/media-formulation.114.html (visited on 2023-03-22)');
 INSERT INTO "medium" VALUES(9,'SNM3','Synthetic Nasal Medium Version 3','https://doi.org/10.1371/journal.ppat.1003862');
 INSERT INTO "medium" VALUES(10,'artSw','Artificial Sweat','https://doi.org/10.1128/spectrum.04180-22, Table 1');
+INSERT INTO "medium" VALUES(11,'BMS23','Basal Medium as described in Swaney et al. 2023','https://doi.org/10.1128/spectrum.04180-22, Material & Methods; M9 components from: https://www.sigmaaldrich.com/DE/de/product/sigma/m6030');
 
 
 CREATE TABLE IF NOT EXISTS "medium2substance" (
@@ -612,6 +613,25 @@ INSERT INTO "medium2substance" VALUES(10,172,NULL,'L-Citrulline');
 INSERT INTO "medium2substance" VALUES(10,194,NULL,'L-Tryptophan');
 INSERT INTO "medium2substance" VALUES(10,168,NULL,'L-Asparagine');
 INSERT INTO "medium2substance" VALUES(10,192,NULL,'L-Threonine');
+INSERT INTO "medium2substance" VALUES(11,56,NULL,'From M9: NH4Cl');
+INSERT INTO "medium2substance" VALUES(11,89,NULL,'Cobalt Chloride hexahydrate');
+INSERT INTO "medium2substance" VALUES(11,81,NULL,'Cobalt Chloride hexahydrate, Calcium Chloride anhydrous, Thiamine HCl; From M9: NaCl, NH4Cl');
+INSERT INTO "medium2substance" VALUES(11,286,NULL,'Cobalt Chloride hexahydrate, Magnesium Sulfate heptahydrate');
+INSERT INTO "medium2substance" VALUES(11,75,NULL,'Calcium Chloride anhydrous, Calcium pantothenate');
+INSERT INTO "medium2substance" VALUES(11,201,NULL,'Magnesium Sulfate heptahydrate');
+INSERT INTO "medium2substance" VALUES(11,258,NULL,'Magnesium Sulfate heptahydrate');
+INSERT INTO "medium2substance" VALUES(11,102,NULL,'Glucose');
+INSERT INTO "medium2substance" VALUES(11,120,NULL,'Oxygen');
+INSERT INTO "medium2substance" VALUES(11,150,NULL,'Thiamine HCl, From M9: KH2PO4, Na2HPO4');
+INSERT INTO "medium2substance" VALUES(11,232,NULL,'From M9: KH2PO4, Na2HPO4');
+INSERT INTO "medium2substance" VALUES(11,235,NULL,'From M9: KH2PO4');
+INSERT INTO "medium2substance" VALUES(11,251,NULL,'From M9: NaCl, Na2HPO4');
+INSERT INTO "medium2substance" VALUES(11,166,NULL,'L-Arginine');
+INSERT INTO "medium2substance" VALUES(11,189,NULL,'L-Proline');
+INSERT INTO "medium2substance" VALUES(11,270,NULL,'Thiamine HCl');
+INSERT INTO "medium2substance" VALUES(11,66,NULL,'Biotin');
+INSERT INTO "medium2substance" VALUES(11,240,NULL,'Nicotinic acid');
+INSERT INTO "medium2substance" VALUES(11,25,NULL,'Calcium pantothenate');
 
 
 CREATE TABLE IF NOT EXISTS "subset" (
@@ -774,7 +794,7 @@ INSERT INTO "substance" VALUES(62,'Arsenite','AsO3');
 INSERT INTO "substance" VALUES(63,'Behenate [Docosanoate]','C22H43O2');
 INSERT INTO "substance" VALUES(64,'Benzoate [Benzoic acid]','C7H5O2');
 INSERT INTO "substance" VALUES(65,'Billirubin','C33H36N4O6');
-INSERT INTO "substance" VALUES(66,'Biotin','C10H16N2O3S');
+INSERT INTO "substance" VALUES(66,'Biotin','C10H15N2O3S');
 INSERT INTO "substance" VALUES(67,'Butyrate','C4H7O2');
 INSERT INTO "substance" VALUES(68,'Butyryl carnitine','C11H21NO4');
 INSERT INTO "substance" VALUES(69,'CAMP [Cyclic AMP]','C10H12N5O6P');
@@ -1062,7 +1082,7 @@ INSERT INTO "substance2db" VALUES(22,'34hpp','BiGG');
 INSERT INTO "substance2db" VALUES(23,'3hexdcrn','BiGG');
 INSERT INTO "substance2db" VALUES(24,'3mob','BiGG');
 INSERT INTO "substance2db" VALUES(25,'pnto__R','BiGG');
-INSERT INTO "substance2db" VALUES(270,'thm','BiGG');
+INSERT INTO "substance2db" VALUES(270,'thm','BiGG+VMH');
 INSERT INTO "substance2db" VALUES(26,'pydxn','BiGG');
 INSERT INTO "substance2db" VALUES(27,'pydam','BiGG');
 INSERT INTO "substance2db" VALUES(28,'4abz','BiGG');
@@ -1115,7 +1135,7 @@ INSERT INTO "substance2db" VALUES(63,'docosac','BiGG');
 INSERT INTO "substance2db" VALUES(63,'MNXM162817','MetaNetX');
 INSERT INTO "substance2db" VALUES(64,'bz','BiGG');
 INSERT INTO "substance2db" VALUES(65,'bilirub','BiGG');
-INSERT INTO "substance2db" VALUES(66,'btn','BiGG');
+INSERT INTO "substance2db" VALUES(66,'btn','BiGG+VMH');
 INSERT INTO "substance2db" VALUES(67,'but','BiGG');
 INSERT INTO "substance2db" VALUES(67,'MNXM162281','MetaNetX');
 INSERT INTO "substance2db" VALUES(68,'c4crn','BiGG');
@@ -1141,7 +1161,7 @@ INSERT INTO "substance2db" VALUES(85,'cro4','BiGG');
 INSERT INTO "substance2db" VALUES(86,'chsterol','BiGG');
 INSERT INTO "substance2db" VALUES(87,'cbl1','BiGG');
 INSERT INTO "substance2db" VALUES(88,'cbl2','BiGG');
-INSERT INTO "substance2db" VALUES(89,'cobalt2','BiGG');
+INSERT INTO "substance2db" VALUES(89,'cobalt2','BiGG+VMH');
 INSERT INTO "substance2db" VALUES(90,'cu2','BiGG');
 INSERT INTO "substance2db" VALUES(91,'crtstrn','BiGG');
 INSERT INTO "substance2db" VALUES(91,'MNXM162953','MetaNetX');
@@ -1280,7 +1300,7 @@ INSERT INTO "substance2db" VALUES(198,'pb2','BiGG');
 INSERT INTO "substance2db" VALUES(198,'pb','BiGG');
 INSERT INTO "substance2db" VALUES(199,'lnlc','BiGG');
 INSERT INTO "substance2db" VALUES(200,'HC02191','BiGG');
-INSERT INTO "substance2db" VALUES(201,'mg2','BiGG');
+INSERT INTO "substance2db" VALUES(201,'mg2','BiGG+VMH');
 INSERT INTO "substance2db" VALUES(202,'male','BiGG');
 INSERT INTO "substance2db" VALUES(203,'malt','BiGG');
 INSERT INTO "substance2db" VALUES(204,'mn2','BiGG');
@@ -1328,7 +1348,7 @@ INSERT INTO "substance2db" VALUES(237,'ppa','BiGG');
 INSERT INTO "substance2db" VALUES(237,'MNXM162260','MetaNetX');
 INSERT INTO "substance2db" VALUES(238,'pheme','BiGG');
 INSERT INTO "substance2db" VALUES(239,'ptrc','BiGG');
-INSERT INTO "substance2db" VALUES(240,'nac','BiGG');
+INSERT INTO "substance2db" VALUES(240,'nac','BiGG+VMH');
 INSERT INTO "substance2db" VALUES(240,'nicnt','BiGG');
 INSERT INTO "substance2db" VALUES(241,'pydx5p','BiGG');
 INSERT INTO "substance2db" VALUES(242,'pyr','BiGG+VMH');
@@ -1615,3 +1635,28 @@ INSERT INTO "substance2db" VALUES(172,'C00327','KEGG');
 INSERT INTO "substance2db" VALUES(194,'C00078','KEGG');
 INSERT INTO "substance2db" VALUES(168,'C00152','KEGG');
 INSERT INTO "substance2db" VALUES(192,'C00188','KEGG');
+INSERT INTO "substance2db" VALUES(89,'cpd00149','SEED');
+INSERT INTO "substance2db" VALUES(201,'cpd00254','SEED');
+INSERT INTO "substance2db" VALUES(120,'cpd00007','SEED');
+INSERT INTO "substance2db" VALUES(270,'cpd00305','SEED');
+INSERT INTO "substance2db" VALUES(66,'cpd00104','SEED');
+INSERT INTO "substance2db" VALUES(240,'cpd00218','SEED');
+INSERT INTO "substance2db" VALUES(25,'cpd00644','SEED');
+INSERT INTO "substance2db" VALUES(56,'MNXM729302','MetaNetX');
+INSERT INTO "substance2db" VALUES(89,'MNXM90960','MetaNetX');
+INSERT INTO "substance2db" VALUES(201,'MNXM653','MetaNetX');
+INSERT INTO "substance2db" VALUES(120,'MNXM735438','MetaNetX');
+INSERT INTO "substance2db" VALUES(270,'MNXM730135','MetaNetX');
+INSERT INTO "substance2db" VALUES(66,'MNXM304','MetaNetX');
+INSERT INTO "substance2db" VALUES(240,'MNXM274','MetaNetX');
+INSERT INTO "substance2db" VALUES(25,'MNXM734864','MetaNetX');
+INSERT INTO "substance2db" VALUES(25,'pnto_R','VMH');
+INSERT INTO "substance2db" VALUES(56,'C00014','KEGG');
+INSERT INTO "substance2db" VALUES(56,'C01342','KEGG');
+INSERT INTO "substance2db" VALUES(89,'C00175','KEGG');
+INSERT INTO "substance2db" VALUES(201,'C00305','KEGG');
+INSERT INTO "substance2db" VALUES(120,'C00007','KEGG');
+INSERT INTO "substance2db" VALUES(270,'C00378','KEGG');
+INSERT INTO "substance2db" VALUES(66,'C00120','KEGG');
+INSERT INTO "substance2db" VALUES(240,'C00253','KEGG');
+INSERT INTO "substance2db" VALUES(25,'C00864','KEGG');