chore: merge in latest develop branch

data/deprecatedIdentifiers/deprecatedReactions.tsv

@@ -207,7 +207,15 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR01666"	""	""	""	""	"R-HSA-193399"	"HMR_1666"	"MNXR125298"	"HMR_1666"	"RCR20514"	""	0	"RHEA:72683"	"RHEA:72683"	"HMR_1666"
 "MAR01458"	""	"HSD17B4x"	""	""	""	"HSD17B4x"	"MNXR100720"	""	""	""	0	""	""	"HSD17B4x"
 "MAR01651"	"R04812"	""	"RE3250M"	""	""	"HMR_1651"	""	"HMR_1651"	"RCR12831"	""	0	""	""	"HMR_1651"
+"MAR01639"	""	""	"RE3247X;RE3247M"	"r0706"	"R-HSA-192335"	"RE3247X;r0706;HMR_1637;RE3247M"	"MNXR105369;MNXR124225"	"HMR_1639;HMR_1637"	"RCR10917;RCR13607"	""	0	""	""	"HMR_1639;HMR_1637;MAR01637"
+"MAR03301"	""	""	"RE1516X"	""	""	""	""	"HMR_3301"	"RCR12606"	""	0	""	""	"HMR_3301"
+"MAR03306"	""	""	"RE1517X"	""	""	""	""	"HMR_3306"	"RCR12610"	""	0	""	""	"HMR_3306"
+"MAR03311"	""	""	"RE1518X"	""	""	""	""	"HMR_3311"	"RCR14519"	""	0	""	""	"HMR_3311"
+"MAR04966"	""	"FAOXC101C102x"	""	""	""	"FAOXC101C102x"	""	""	""	""	0	""	""	"FAOXC101C102x"
+"MAR03364"	""	""	"RE2913X"	""	""	""	""	"HMR_3364"	"RCR12576"	""	0	""	""	"HMR_3364"
+"MAR03369"	""	""	"RE2914X"	""	""	""	""	"HMR_3369"	"RCR12580"	""	0	""	""	"HMR_3369"
 "MAR09887"	""	"GLNB0AT3tc"	""	""	""	"GLNB0AT3tc"	""	""	""	""	0	""	""	"GLNB0AT3tc"
+"MAR00059"	""	"ACOX22x"	""	""	""	"ACOX22x"	"MNXR95389"	""	""	""	0	""	""	"ACOX22x"
 "MAR00024"	""	""	""	""	""	"HMR_0024"	""	"HMR_0024"	"RCR13367"	""	0	""	""	"HMR_0024"
 "MAR00025"	""	""	""	""	""	"HMR_0025;HMR_0030"	""	"HMR_0025;HMR_0030"	"RCR20226;RCR20227"	""	0	""	""	"HMR_0025;HMR_0030;MAR00030"
 "MAR00026"	""	""	""	""	""	"HMR_0026"	""	"HMR_0026"	"RCR21051"	""	0	""	""	"HMR_0026"
@@ -224,3 +232,12 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR02006"	""	"CPS_m"	""	""	""	"r0034"	""	""	""	""	0	""	""	"r0034"
 "MAR06400"	"R07768"	""	"R07768C"	""	""	"HMR_6400"	"MNXR111356"	"HMR_6400"	"RCR11944"	""	0	""	""	"HMR_6400"
 "MAR06401"	"R07769"	""	"R07769C"	""	""	"HMR_6401"	"MNXR111357"	"HMR_6401"	"RCR11945"	""	0	""	""	"HMR_6401"
+"MAR03940"	"R01795"	"PHETHPTOX"	"R01795C"	"r0399"	""	"r0399"	"MNXR102632;MNXR107174"	"HMR_3940"	"RCR11388"	""	0	""	"RHEA:30787"	"HMR_3940"
+"MAR07785"	""	"ATPtx"	""	""	""	"ATPtx"	"MNXR96140"	"HMR_7785"	"RCR20040"	""	0	""	""	"HMR_7785"
+"MAR07775"	""	"NADHtpu"	""	""	""	"NADHtpu;NADtpu"	"MNXR101881"	"HMR_7775"	"RCR20024"	""	0	""	""	"HMR_7775"
+"MAR07788"	""	"FADH2tx"	""	""	""	"FADH2tx"	"MNXR99212"	"HMR_7788"	"RCR20202"	""	0	""	""	"HMR_7788"
+"MAR04915"	""	"COAtp"	""	"r0864"	""	"COAtp"	"MNXR96815"	"HMR_4915"	"RCR20004"	""	0	""	""	"HMR_4915"
+"MAR07771"	""	"NADtpu"	""	""	""	"NADtx"	"MNXR101881"	"HMR_7771"	"RCR20023"	""	0	""	""	"HMR_7771"
+"MAR07782"	""	"ADPtx"	""	""	""	"ADPtx"	"MNXR95484"	"HMR_7782"	"RCR20201"	""	0	""	""	"HMR_7782"
+"MAR07783"	""	"AMPtp"	""	""	""	"AMPtp"	"MNXR95830"	"HMR_7783"	"RCR20046"	""	0	""	""	"HMR_7783"
+"MAR07790"	""	"FADtx"	""	""	""	"FADtx"	"MNXR99217"	"HMR_7790"	"RCR20203"	""	0	""	""	"HMR_7790"

data/metabolicTasks/metabolicTasks_CellfieConsensus.txt

@@ -211,7 +211,7 @@
 				NAD+[m]	1	1	CO2[m]	1	1								
 							NADH[m]	1	1								
 	34	Synthesis of fructose-6-phosphate from erythrose-4-phosphate (HMP shunt)		fructose-6-phosphate[c]	1	1	erythrose-4-phosphate[c]	1	1								
-				GAP[c]	1	1	D-xylulose-5-phosphate[c]	1	1								
+				D-glyceraldehyde 3-phosphate[c]	1	1	D-xylulose-5-phosphate[c]	1	1								
 	35	Synthesis of ribose-5-phosphate		glucose[c]	1	1	ribose-5-phosphate[c]	1	1								
 				ATP[c]	1	1	ADP[c]	1	1								
 				NADP+[c]	2	2	H+[c]	3	3								
@@ -226,7 +226,7 @@
 	38	Glycogen degradation		glycogenin G4G7[c]	1	1	glucose[c]	8									
 				Pi[c]	3		NA[c]	1	1								
 				H2O[c]	8		glucose-1-phosphate[c]	3									
-	39	Fructose degradation (to glucose-3-phosphate)		fructose[c]	1	1	GAP[c]	2	2								
+	39	Fructose degradation (to glucose-3-phosphate)		fructose[c]	1	1	D-glyceraldehyde 3-phosphate[c]	2	2								
 				ATP[c]	2	2	ADP[c]	2	2								
 							H+[c]	2	2								
 	40	Fructose to glucose conversion (via fructose-6-phosphate)		fructose[c]	1	1	glucose[c]	1	1