Human 1.18

.all-contributorsrc

@@ -336,6 +336,15 @@
       "contributions": [
         "bug"
       ]
+    },
+    {
+      "login": "Christoff1993",
+      "name": "Christoff1993",
+      "avatar_url": "https://avatars.githubusercontent.com/u/95428150?v=4",
+      "profile": "https://github.com/Christoff1993",
+      "contributions": [
+        "bug"
+      ]
     }
   ],
   "repoType": "github",

.github/workflows/yaml-validation.yml

@@ -16,7 +16,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: YAML Lint
-        uses: ibiqlik/action-yamllint@v1.0.0
+        uses: metabolicatlas/action-yamllint@v3
         with:
           ## File(s) or Directory, separate by space if multiple files or folder are specified
           file_or_dir: model/

code/test/sanityCheck.py

@@ -4,6 +4,7 @@
 
 import pandas as pd
 import cobra
+from collections import Counter
 
 
 def get_column_from_tsv(tsv_file, column_id, to_list=True):
@@ -106,11 +107,28 @@ def checkUnusedEntities(model, entity_type):
     assert len(unused_entities) == 0, f"Found unused {entity_type}: {unused_entities}"
 
 
+def checkDupRxn(model):
+    """
+    Check for duplicate reactions in the model
+    """
+
+    reaction_equations = [rxn.build_reaction_string(use_metabolite_names=False) for rxn in model.reactions]
+    duplicate_reactions = [reaction for reaction, count in Counter(reaction_equations).items() if count > 1]
+    dup_list = [model.reactions[idx].id for idx, val in enumerate(reaction_equations) if val in duplicate_reactions]
+
+    if duplicate_reactions:
+        output = f"The following {len(dup_list)} reactions are duplicates, please check: " + ';'.join(dup_list)
+        print(output)
+
+    assert len(duplicate_reactions) == 0, "Found duplicated reactions!"
+
+
 if __name__ == "__main__":
     rxns, mets, genes, model = load_yml("model/Human-GEM.yml")
     checkRxnAnnotation(rxns)
     checkMetAnnotation(mets)
     checkGeneAnnotation(genes)
     checkUnusedEntities(model, "metabolites")
     checkUnusedEntities(model, "genes")
+    checkDupRxn(model)
     print("All checks have passed.")

data/deprecatedIdentifiers/deprecatedMetabolites.tsv

@@ -2237,6 +2237,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM01445m"	"MAM01445"	"cholate"	"C00695"	"HMDB0000619"	"CHEBI:16359"	"221493"	"LMST04010001"	""	"HC00502"	"cholate"	"MNXM450"	"m01445m"	"m01445m"
 "MAM01514m"	"MAM01514"	"cholcoa"	"C01794"	"HMDB0001374"	"CHEBI:15519"	"439573"	""	""	"HC00844"	"cholcoa"	"MNXM162468;MNXM431"	"m01514m"	"m01514m"
 "MAM00759c"	"MAM00759"	""	"C13712"	""	""	""	"LMST02030130"	""	""	"M00759"	"MNXM3494"	"m00759c"	"m00759c"
+"MAM02397c"	"MAM02397"	""	"C16239"	""	""	""	""	""	""	"M02397"	"MNXM19093"	"m02397c"	"m02397c"
 "MAM01268c"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268c"	"m01268c"
 "MAM01268m"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268m"	"m01268m"
 "MAM01268n"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268n"	"m01268n"
@@ -2247,3 +2248,13 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02757l"	"MAM02757"	""	""	""	""	""	""	""	""	"M02757"	""	"m02757l"	"m02757l"
 "MAM02757n"	"MAM02757"	""	""	""	""	""	""	""	""	"M02757"	""	"m02757n"	"m02757n"
 "MAM01816n"	"MAM01816"	""	""	""	""	""	"PROTEIN"	""	""	"M01816"	""	"m01816n"	"m01816n"
+"MAM00926c"	"MAM00926"	"4aphdob"	"C01252"	"HMDB0000978"	"CHEBI:17442"	"472"	""	""	""	"4aphdob"	"MNXM163204"	"m00926c"	"m00926c"
+"MAM20020r"	"MAM20020"	"C00061"	""	""	"CHEBI:58210"	""	""	""	""	""	"MNXM1105928"	""	""
+"MAM20022i"	"MAM20022"	"C01847"	""	""	"CHEBI:57618"	""	""	""	""	""	"MNXM1107623"	""	""
+"MAM20023i"	"MAM20023"	"C00061"	""	""	"CHEBI:58210"	""	""	""	""	""	"MNXM1105928"	""	""
+"MAM02398c"	"MAM02398"	""	"C16238"	""	""	"23724672"	""	"CE5656"	""	"CE5656"	"MNXM2392"	"m02398c"	"m02398c"
+"MAM01701c"	"MAM01701"	"dhlam"	"C00579"	"HMDB0000985"	"CHEBI:17694"	"663"	""	""	"HC00437"	"dhlam"	"MNXM1277"	"m01701c"	"m01701c"
+"MAM03684c"	"MAM03684"	"hxa"	""	""	"CHEBI:17120"	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_c"
+"MAM03684m"	"MAM03684"	"hxa"	""	""	""	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_m"
+"MAM03684e"	"MAM03684"	"hxa"	""	""	""	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_s"
+"MAM03684x"	"MAM03684"	"hxa"	""	""	""	""	""	""	""	"hxa"	"MNXM1653"	""	"hxa_p"

data/deprecatedIdentifiers/deprecatedReactions.tsv

@@ -230,3 +230,35 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR00096"	""	"BUP2"	""	""	""	"BUP2"	"MNXR96346"	""	""	""	0	""	""	"BUP2"
 "MAR02027"	""	"r0193"	""	""	""	"r0193"	"MNXR105313"	""	""	""	0	""	""	"r0193"
 "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"
+"MAR08564"	""	"KYNAKGAT"	""	""	""	"KYNAKGAT"	"MNXR100948"	"HMR_8564"	"RCR11356"	""	0	""	""	"HMR_8564"
+"MAR08565"	"R03445"	"KYNATESYN"	""	""	""	"KYNATESYN"	"MNXR100949"	"HMR_8565"	"RCR11357"	""	0	""	"RHEA:42452"	"HMR_8565"
+"MAR04843"	""	""	""	"r0801"	""	"r0801"	"MNXR105390"	"HMR_4843"	"RCR20168"	""	0	""	""	"HMR_4843"
+"MAR09019"	""	""	""	""	""	"HMR_9019"	""	"HMR_9019"	"RCR20242"	""	0	""	""	"HMR_9019"
+"MAR07823"	""	"DNDPt51m"	""	""	""	"DCTPtm"	"MNXR97204"	""	""	""	0	""	""	"DCTPtm"
+"MAR07926"	""	"DGTPtm"	""	""	""	"DGTPtm"	"MNXR97327"	""	""	""	0	""	""	"DGTPtm"
+"MAR01483"	""	"LIPOti"	""	""	""	"LIPOti"	"MNXR101093"	""	""	""	0	""	""	"LIPOti"
+"MAR06406"	""	"LIPOti"	"RT1089"	""	""	""	"MNXR101093"	"HMR_6406"	"RCR41534"	""	0	""	""	"HMR_6406"
+"MAR00478"	"R00844"	""	""	""	"R-HSA-75889"	"HMR_0478"	"MNXR99876"	"HMR_0478"	"RCR14575"	""	0	"RHEA:11098"	"RHEA:11096"	"HMR_0478"
+"MAR00482"	"R00848;R00849"	"G3PD2m"	"R00848C"	"r0205"	""	"HMR_0482;r0205"	"MNXR99875;MNXR106713"	"HMR_0482;HMR_0483"	"RCR14578;RCR21050"	""	0	""	"RHEA:31283;RHEA:18977"	"HMR_0482;HMR_0483;MAR00483"
+"MAR20012"	"R02123"	"HMR_6647;RADH;R_HMR_6647;R_RADH"	""	""	""	""	"MNXR146215"	""	""	""	0	"RHEA:42080"	""	""
+"MAR20089"	"R02701"	""	""	""	""	""	"MNXR151808"	""	""	""	0	"RHEA:18533"	""	""
+"MAR06398"	"R07770"	""	"R07770C"	""	""	"RE1944C"	"MNXR101081"	"HMR_6398"	"RCR14489"	""	0	""	"RHEA:12913"	"HMR_6398"
+"MAR06399"	"R07771"	""	"R07771C"	""	""	"HMR_6399"	"MNXR111358"	"HMR_6399"	"RCR14490"	""	0	""	"RHEA:20473"	"HMR_6399"
+"MAR06408"	""	""	"RT0295"	""	""	"HMR_6408"	""	"HMR_6408"	"RCR21069"	""	0	""	""	"HMR_6408"
+"MAR11292"	""	"HXAt3"	""	""	""	"HXAt3"	""	""	""	""	0	""	""	"HXAt3"
+"MAR11293"	""	"EX_hxa_e"	""	""	""	"EX_hxa[e]"	"MNXR98664"	""	""	""	0	""	""	"EX_hxa[e]"
+"MAR09949"	""	"FACOAE60"	""	""	""	"HXCOAc"	"MNXR99139"	""	""	""	0	""	""	"HXCOAc"
+"MAR04239"	"R01933"	"2OXOADOXm"	"R01933M"	"r0448"	""	"2OXOADOXm"	"MNXR94818"	"HMR_4239"	"RCR11332"	""	0	"RHEA:30796"	"RHEA:30795"	"HMR_4239"
+"MAR04940"	""	""	""	"r0885"	""	"r0885"	"MNXR105402"	"HMR_4940"	"RCR20265"	"2.A.29.2.7"	0	""	""	"HMR_4940"
+"MAR06391"	""	""	""	"r2520"	""	"r2520"	"MNXR106328"	"HMR_6391"	"RCR20063"	""	0	""	""	"HMR_6391"

data/metabolicTasks/metabolicTasks_CellfieConsensus.txt

@@ -220,12 +220,12 @@
 	36	Synthesis of lactose		glucose[g]	1	1	lactose[g]	1	1								
 				UDP-galactose[g]	1	1	UDP[g]	1	1								
 							H+[g]	1	1								
-	37	Glycogen biosynthesis		NA[c]	1	1	glycogenin G4G7[c]	1	1								
-				UDP-glucose[c]	11		H+[c]	11									
-							UDP[c]	11									
-	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									
+#	37	Glycogen biosynthesis		NA[c]	1	1	glycogenin G4G7[c]	1	1								The metabolite NA[c] in this task is conflicting with HumanGEM
+#				UDP-glucose[c]	11		H+[c]	11									
+#							UDP[c]	11									
+#	38	Glycogen degradation		glycogenin G4G7[c]	1	1	glucose[c]	8									The metabolite NA[c] in this task is conflicting with HumanGEM
+#				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	D-glyceraldehyde 3-phosphate[c]	2	2								
 				ATP[c]	2	2	ADP[c]	2	2								
 							H+[c]	2	2								
@@ -1130,14 +1130,14 @@
 	180	Pyridoxal-phosphate synthesis		pyridoxal[c]	1	1	pyridoxal-phosphate[c]	1	1								
 				ATP[c]	1	1	ADP[c]	1	1								
 							H+[c]	1	1								
-	181	Synthesis of bilirubin		heme[c]	1	1	bilirubin[c]	1	1								
-				NADPH[c]	0	4	H2O[c]	0	3								
-				H+[c]	0	6	Fe2+[c]	0	1								
-				O2[c]	0	3	Fe3+[c]	0	1								
-				FADH2[c]	0	1	NADP+[c]	0	4								
-							FAD[c]	0	1								
-							CO[c]	1	1								
-							NA[c]	0	1								
+#	181	Synthesis of bilirubin		heme[c]	1	1	bilirubin[c]	1	1								The metabolite NA[c] in this task is conflicting with HumanGEM
+#				NADPH[c]	0	4	H2O[c]	0	3								
+#				H+[c]	0	6	Fe2+[c]	0	1								
+#				O2[c]	0	3	Fe3+[c]	0	1								
+#				FADH2[c]	0	1	NADP+[c]	0	4								
+#							FAD[c]	0	1								
+#							CO[c]	1	1								
+#							NA[c]	0	1								
 	182	Heme synthesis		glycine[m]	16	16	heme[m]	2	2								
 				succinyl-CoA[m]	16	18	H2O[m]	26	26								
 				Fe2+[m]	2	2	CoA[m]	16	18