Fix duplicate metabolites identified by PubChem IDs(2)

data/deprecatedIdentifiers/deprecatedMetabolites.tsv

@@ -2212,4 +2212,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM00591c"	"MAM00591"	""	"C14748"	""	"CHEBI:34306"	""	""	""	"HC02179"	""	"MNXM6760"	"m00591c"	"m00591c"
 "MAM00591e"	"MAM00591"	""	"C14748"	""	"CHEBI:34306"	""	""	""	"HC02179"	""	"MNXM6760"	"m00591s"	"m00591s"
 "MAM03162c"	"MAM03162"	""	"C05578"	""	"CHEBI:27404"	""	""	""	""	"M03162"	"MNXM2336"	"m03162c"	"m03162c"
-"MAM03231c"	"MAM03231"	""	""	""	"CHEBI:57277"	""	""	""	""	"3hppa"	""	""	"3hppa_c"
+"MAM03231c"	"MAM03231"	""	""	""	"CHEBI:57277"	""	""	""	""	"3hppa"	""	""	"3hppa_c"
+"MAM03540c"	"MAM03540"	"ddeccrn"	""	""	""	"168381"	""	""	""	"ddeccrn"	""	""	"ddeccrn_c"
+"MAM03540e"	"MAM03540"	"ddeccrn"	""	""	""	"168381"	""	""	""	"ddeccrn"	""	""	"ddeccrn_s"

data/deprecatedIdentifiers/deprecatedReactions.tsv

@@ -173,4 +173,5 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR06252"	""	""	""	"r2346"	""	""	"MNXR106235"	"HMR_6252"	"RCR40129"	""	0	""	""	"HMR_6252"
 "MAR09733"	"R03674"	""	""	""	""	"HMR_9733"	"MNXR108330"	"HMR_9733"	"RCR14346"	""	0	""	""	"HMR_9733"
 "MAR09734"	"R04884"	""	""	""	""	"HMR_9734"	"MNXR109190"	"HMR_9734"	"RCR14347"	""	0	"RHEA:33516"	"RHEA:33515"	"HMR_9734"
-"MAR10025"	""	""	""	""	""	""	""	""	""	""	0	""	""	"HMR_10025"
+"MAR10025"	""	""	""	""	""	""	""	""	""	""	0	""	""	"HMR_10025"
+"MAR04506"	""	"C120CPT1"	""	""	""	"C120CPT1"	""	""	""	""	0	""	""	"C120CPT1"

model/Human-GEM.yml

@@ -49969,14 +49969,6 @@
       - charge: 0
       - inchis: "InChI=1/C17H33NO5/c1-5-6-7-8-9-10-14(19)13-17(22)23-15(18(2,3)4)11-12-16(20)21/h14-15,19H,5-13H2,1-4H3"
       - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03540c"
-      - name: "Lauroyl Carnitine"
-      - compartment: "c"
-      - formula: "C19H37NO4"
-      - charge: 0
-      - inchis: "InChI=1S/C19H37NO4/c1-5-6-7-8-9-10-11-12-13-14-19(23)24-17(15-18(21)22)16-20(2,3)4/h17H,5-16H2,1-4H3/t17-/m1/s1"
-      - metFrom: "Recon3D"
     - !!omap
       - id: "MAM00042c"
       - name: "(2E)-dodecenoyl-CoA"
@@ -50497,14 +50489,6 @@
       - charge: 0
       - inchis: "InChI=1/C19H37NO5/c1-5-6-7-8-9-10-11-12-16(21)13-19(24)25-17(14-18(22)23)15-20(2,3)4/h16-17,21H,5-15H2,1-4H3"
       - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03540e"
-      - name: "Lauroyl Carnitine"
-      - compartment: "e"
-      - formula: "C19H37NO4"
-      - charge: 0
-      - inchis: "InChI=1S/C19H37NO4/c1-5-6-7-8-9-10-11-12-13-14-19(23)24-17(15-18(21)22)16-20(2,3)4/h17H,5-16H2,1-4H3/t17-/m1/s1"
-      - metFrom: "Recon3D"
     - !!omap
       - id: "MAM03541e"
       - name: "Dodecenoyl Carnitine"
@@ -67935,6 +67919,13 @@
       - compartment: "m"
       - formula: "C24H39O4"
       - charge: -1
+    - !!omap
+      - id: "MAM01729e"
+      - name: "dodecanoylcarnitine"
+      - compartment: "e"
+      - formula: "C19H37NO4"
+      - charge: 0
+
       - inchis: ""
       - metFrom: "HMRdatabase"
 - reactions:
@@ -110746,9 +110737,9 @@
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
       - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
+      - rxnFrom: "HMRdatabase;Recon3D"
       - eccodes: "2.3.1.21"
-      - references: ""
+      - references: "PMID:12828998;PMID:9498103;PMID:3955080"
       - subsystem:
           - "Carnitine shuttle (cytosolic)"
       - confidence_score: 0
@@ -239483,24 +239474,6 @@
       - subsystem:
           - "Fatty acid oxidation"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR04506"
-      - name: "Production of Dodecanoylcarnitine"
-      - metabolites: !!omap
-          - MAM01597c: 1
-          - MAM02345c: -1
-          - MAM02348c: -1
-          - MAM03540c: 1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:12828998;PMID:9498103;PMID:3955080"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
     - !!omap
       - id: "MAR04508"
       - name: "Production of Dodecenoylcarnitine"
@@ -240716,7 +240689,7 @@
       - id: "MAR04923"
       - name: "Exchange of Lauroyl Carnitine"
       - metabolites: !!omap
-          - MAM03540e: -1
+          - MAM01729e: -1
       - lower_bound: -1000
       - upper_bound: 1000
       - gene_reaction_rule: ""
@@ -270716,8 +270689,8 @@
       - id: "MAR11266"
       - name: "Transport of Lauroyl Carnitine"
       - metabolites: !!omap
-          - MAM03540c: 1
-          - MAM03540e: -1
+          - MAM01729c: 1
+          - MAM01729e: -1
       - lower_bound: -1000
       - upper_bound: 1000
       - gene_reaction_rule: ""

model/metabolites.tsv

@@ -879,8 +879,8 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM00528c"	"MAM00528"	"mi34p"	"C04063"	"HMDB0006235"	"CHEBI:28858"	"440211"	""	""	""	"mi34p"	"MNXM163431;MNXM2768"	"m00528c"	"m00528c"
 "MAM00529c"	"MAM00529"	"mi3p__D"	"C04006"	""	"CHEBI:18169"	"440194"	""	""	""	"mi3p_D"	"MNXM540"	"m00529c"	"m00529c"
 "MAM00530c"	"MAM00530"	"mi4p__D"	"C03546"	""	"CHEBI:18384"	""	""	""	""	"mi4p_D"	"MNXM2063"	"m00530c"	"m00530c"
-"MAM00531c"	"MAM00531"	"ppmi1346p"	"C18058"	""	""	"890"	""	""	""	"ppmi1346p"	"MNXM34087"	"m00531c"	"m00531c"
-"MAM00531n"	"MAM00531"	"ppmi1346p"	"C18058"	""	""	"890"	""	""	""	"ppmi1346p"	"MNXM34087"	"m00531n"	"m00531n"
+"MAM00531c"	"MAM00531"	"ppmi1346p"	"C18058"	""	""	"96024277"	""	""	""	"ppmi1346p"	"MNXM34087"	"m00531c"	"m00531c"
+"MAM00531n"	"MAM00531"	"ppmi1346p"	"C18058"	""	""	"96024277"	""	""	""	"ppmi1346p"	"MNXM34087"	"m00531n"	"m00531n"
 "MAM00532c"	"MAM00532"	""	""	""	""	""	"LMGP10060005"	""	""	"M00532"	"MNXM116015"	"m00532c"	"m00532c"
 "MAM00533c"	"MAM00533"	""	""	""	""	""	""	"CE6504"	""	"CE6504"	"MNXM164037"	"m00533c"	"m00533c"
 "MAM00534c"	"MAM00534"	""	""	""	""	"53481443"	""	"CE3481"	""	"CE3481"	"MNXM32836"	"m00534c"	"m00534c"
@@ -1919,7 +1919,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM01227m"	"MAM01227"	""	""	""	""	""	""	"CE5719"	""	"CE5719"	"MNXM39477"	"m01227m"	"m01227m"
 "MAM01228m"	"MAM01228"	""	""	""	""	""	""	"CE5847"	""	"CE5847"	"MNXM39478"	"m01228m"	"m01228m"
 "MAM01229c"	"MAM01229"	""	""	""	""	""	""	"CE3136"	""	"CE3136"	"MNXM166718"	"m01229c"	"m01229c"
-"MAM01230c"	"MAM01230"	"retinal_cis_9"	""	""	""	"638015"	""	"CE5575"	""	"retinal_cis_9"	"MNXM162775;MNXM2209"	"m01230c"	"m01230c"
+"MAM01230c"	"MAM01230"	"retinal_cis_9"	""	""	""	"6436082"	""	"CE5575"	""	"retinal_cis_9"	"MNXM162775;MNXM2209"	"m01230c"	"m01230c"
 "MAM01230r"	"MAM01230"	"retinal_cis_9"	""	""	""	"638015"	""	"CE5575"	""	"retinal_cis_9"	"MNXM162775;MNXM2209"	"m01230r"	"m01230r"
 "MAM01231c"	"MAM01231"	""	""	""	""	"449171"	""	"CE1617"	""	"CE1617"	"MNXM10472"	"m01231c"	"m01231c"
 "MAM01231r"	"MAM01231"	""	""	""	""	"449171"	""	"CE1617"	""	"CE1617"	"MNXM10472"	"m01231r"	"m01231r"
@@ -2924,7 +2924,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM01727m"	"MAM01727"	""	""	""	""	""	""	""	""	"M01727"	""	"m01727m"	"m01727m"
 "MAM01727r"	"MAM01727"	""	""	""	""	""	""	""	""	"M01727"	""	"m01727r"	"m01727r"
 "MAM01728c"	"MAM01728"	"ddcaACP"	"C05223"	""	""	""	""	""	"HC01394"	"ddcaACP"	"MNXM5723;MNXM89851"	"m01728c"	"m01728c"
-"MAM01729c"	"MAM01729"	""	""	"HMDB0002250"	""	"168381"	""	""	""	"M01729"	"MNXM51468;MNXM588354"	"m01729c"	"m01729c"
+"MAM01729c"	"MAM01729"	""	""	"HMDB0002250"	""	"168381"	""	""	""	"M01729"	"MNXM51468;MNXM588354"	"m01729c"	"m01729c;MAM03540c"
 "MAM01729m"	"MAM01729"	""	""	"HMDB0002250"	""	"168381"	""	""	""	"M01729"	"MNXM51468;MNXM588354"	"m01729m"	"m01729m"
 "MAM01729r"	"MAM01729"	""	""	"HMDB0002250"	""	"168381"	""	""	""	"M01729"	"MNXM51468;MNXM588354"	"m01729r"	"m01729r"
 "MAM01730c"	"MAM01730"	"dolichol__L"	"C00381"	""	"CHEBI:16091"	""	"LMPR03070004"	""	""	"dolichol_L"	"MNXM147098"	"m01730c"	"m01730c"
@@ -4541,7 +4541,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02646e"	"MAM02646"	"ocdcea"	"C00712"	"HMDB0000207"	"CHEBI:30823"	"5460221"	"LMFA01030002"	""	"HC00510"	"ocdcea"	"MNXM306;MNXM727011"	"m02646s"	"m02646s"
 "MAM02647c"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5280355"	"LMFA07050055"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647c"	"m02647c"
 "MAM02647m"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5280355"	"LMFA07050055"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647m"	"m02647m"
-"MAM02647x"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5280355"	"LMFA07050055"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647p"	"m02647p"
+"MAM02647x"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5497111"	"LMFA07050055"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647p"	"m02647p"
 "MAM02647r"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5280355"	"LMFA07050055"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647r"	"m02647r"
 "MAM02648c"	"MAM02648"	"eicostet"	""	"HMDB0002177"	""	"11722594"	"LMFA01030176"	""	""	"eicostet"	"MNXM11474"	"m02648c"	"m02648c"
 "MAM02648l"	"MAM02648"	"eicostet"	""	"HMDB0002177"	""	"11722594"	"LMFA01030176"	""	""	"eicostet"	"MNXM11474"	"m02648l"	"m02648l"
@@ -4595,17 +4595,17 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02675l"	"MAM02675"	"hdcea"	"C08362"	"HMDB0003229"	"CHEBI:28716"	"445638"	"LMFA01030056"	""	"HC01981"	"hdcea"	"MNXM950"	"m02675l"	"m02675l"
 "MAM02675r"	"MAM02675"	"hdcea"	"C08362"	"HMDB0003229"	"CHEBI:28716"	"445638"	"LMFA01030056"	""	"HC01981"	"hdcea"	"MNXM950"	"m02675r"	"m02675r"
 "MAM02675e"	"MAM02675"	"hdcea"	"C08362"	"HMDB0003229"	"CHEBI:28716"	"445638"	"LMFA01030056"	""	"HC01981"	"hdcea"	"MNXM950"	"m02675s"	"m02675s"
-"MAM02676c"	"MAM02676"	"hdcecrn"	""	""	""	"11953816"	""	""	"HC10854"	"hdcecrn"	"MNXM8716"	"m02676c"	"m02676c"
-"MAM02676m"	"MAM02676"	"hdcecrn"	""	""	""	"11953816"	""	""	"HC10854"	"hdcecrn"	"MNXM8716"	"m02676m"	"m02676m"
-"MAM02676r"	"MAM02676"	"hdcecrn"	""	""	""	"11953816"	""	""	"HC10854"	"hdcecrn"	"MNXM8716"	"m02676r"	"m02676r"
+"MAM02676c"	"MAM02676"	"hdcecrn"	""	""	""	"129849228"	""	""	"HC10854"	"hdcecrn"	"MNXM8716"	"m02676c"	"m02676c"
+"MAM02676m"	"MAM02676"	"hdcecrn"	""	""	""	"129849228"	""	""	"HC10854"	"hdcecrn"	"MNXM8716"	"m02676m"	"m02676m"
+"MAM02676r"	"MAM02676"	"hdcecrn"	""	""	""	"129849228"	""	""	"HC10854"	"hdcecrn"	"MNXM8716"	"m02676r"	"m02676r"
 "MAM02677c"	"MAM02677"	"hdcoa"	""	"HMDB0006532"	"CHEBI:53152"	"53477852"	"LMFA07050059"	"CE0852"	"HC10852"	"hdcoa"	"MNXM781;MNXM90167"	"m02677c"	"m02677c"
 "MAM02677m"	"MAM02677"	"hdcoa"	""	"HMDB0006532"	"CHEBI:53152"	"53477852"	"LMFA07050059"	"CE0852"	"HC10852"	"hdcoa"	"MNXM781;MNXM90167"	"m02677m"	"m02677m"
 "MAM02677x"	"MAM02677"	"hdcoa"	""	"HMDB0006532"	"CHEBI:53152"	"53477852"	"LMFA07050059"	"CE0852"	"HC10852"	"hdcoa"	"MNXM781;MNXM90167"	"m02677p"	"m02677p"
 "MAM02677r"	"MAM02677"	"hdcoa"	""	"HMDB0006532"	"CHEBI:53152"	"53477852"	"LMFA07050059"	"CE0852"	"HC10852"	"hdcoa"	"MNXM781;MNXM90167"	"m02677r"	"m02677r"
-"MAM02678c"	"MAM02678"	"pmtcoa"	"C00154"	"HMDB0001338"	"CHEBI:15525"	"15667"	"LMFA07050002"	""	"HC00150"	"pmtcoa"	"MNXM88"	"m02678c"	"m02678c"
-"MAM02678m"	"MAM02678"	"pmtcoa"	"C00154"	"HMDB0001338"	"CHEBI:15525"	"15667"	"LMFA07050002"	""	"HC00150"	"pmtcoa"	"MNXM88"	"m02678m"	"m02678m"
-"MAM02678x"	"MAM02678"	"pmtcoa"	"C00154"	"HMDB0001338"	"CHEBI:15525"	"15667"	"LMFA07050002"	""	"HC00150"	"pmtcoa"	"MNXM88"	"m02678p"	"m02678p"
-"MAM02678r"	"MAM02678"	"pmtcoa"	"C00154"	"HMDB0001338"	"CHEBI:15525"	"15667"	"LMFA07050002"	""	"HC00150"	"pmtcoa"	"MNXM88"	"m02678r"	"m02678r"
+"MAM02678c"	"MAM02678"	"pmtcoa"	"C00154"	"HMDB0001338"	"CHEBI:15525"	"644109"	"LMFA07050002"	""	"HC00150"	"pmtcoa"	"MNXM88"	"m02678c"	"m02678c"
+"MAM02678m"	"MAM02678"	"pmtcoa"	"C00154"	"HMDB0001338"	"CHEBI:15525"	"644109"	"LMFA07050002"	""	"HC00150"	"pmtcoa"	"MNXM88"	"m02678m"	"m02678m"
+"MAM02678x"	"MAM02678"	"pmtcoa"	"C00154"	"HMDB0001338"	"CHEBI:15525"	"644109"	"LMFA07050002"	""	"HC00150"	"pmtcoa"	"MNXM88"	"m02678p"	"m02678p"
+"MAM02678r"	"MAM02678"	"pmtcoa"	"C00154"	"HMDB0001338"	"CHEBI:15525"	"644109"	"LMFA07050002"	""	"HC00150"	"pmtcoa"	"MNXM88"	"m02678r"	"m02678r"
 "MAM02679c"	"MAM02679"	"ptth"	"C00831"	"HMDB0003426"	"CHEBI:16753"	"439322"	""	""	"HC00554"	""	"MNXM727034"	"m02679c"	"m02679c"
 "MAM02679m"	"MAM02679"	"ptth"	"C00831"	"HMDB0003426"	"CHEBI:16753"	"439322"	""	""	"HC00554"	""	"MNXM727034"	"m02679m"	"m02679m"
 "MAM02680c"	"MAM02680"	"pnto__R"	"C00864"	"HMDB0000210"	"CHEBI:7916"	"988"	""	""	"HC00568"	"pnto_R"	"MNXM364"	"m02680c"	"m02680c"
@@ -5255,8 +5255,8 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03019x"	"MAM03019"	""	""	""	"CHEBI:87717"	""	""	""	""	"M03019"	""	"m03019p"	"m03019p"
 "MAM03020m"	"MAM03020"	""	""	""	"CHEBI:77549"	""	""	"CE2591"	"HC12591"	"CE2591"	"MNXM683714"	"m03020m"	"m03020m"
 "MAM03020x"	"MAM03020"	""	""	""	"CHEBI:77549"	""	""	"CE2591"	"HC12591"	"CE2591"	"MNXM683714"	"m03020p"	"m03020p"
-"MAM03021m"	"MAM03021"	""	"C05279"	"HMDB0011123"	"CHEBI:28387"	"53480665"	""	""	""	"C05279"	"MNXM2039"	"m03021m"	"m03021m"
-"MAM03021x"	"MAM03021"	""	"C05279"	"HMDB0011123"	"CHEBI:28387"	"53480665"	""	""	""	"C05279"	"MNXM2039"	"m03021p"	"m03021p"
+"MAM03021m"	"MAM03021"	""	"C05279"	"HMDB0011123"	"CHEBI:28387"	"5280770"	""	""	""	"C05279"	"MNXM2039"	"m03021m"	"m03021m"
+"MAM03021x"	"MAM03021"	""	"C05279"	"HMDB0011123"	"CHEBI:28387"	"5280770"	""	""	""	"C05279"	"MNXM2039"	"m03021p"	"m03021p"
 "MAM03022m"	"MAM03022"	""	""	""	"CHEBI:87701"	""	""	""	""	"M03022"	""	"m03022m"	"m03022m"
 "MAM03022x"	"MAM03022"	""	""	""	"CHEBI:87701"	""	""	""	""	"M03022"	""	"m03022p"	"m03022p"
 "MAM03023m"	"MAM03023"	""	""	""	""	""	""	"CE2594"	"HC12594"	"CE2594;HC12594"	""	"m03023m"	"m03023m"
@@ -6244,7 +6244,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03489e"	"MAM03489"	"c10dc"	""	""	""	""	""	""	""	"c10dc"	"MNXM162993"	""	"c10dc_s"
 "MAM00181c"	"MAM00181"	""	"C05264"	""	"CHEBI:28325"	"11966158"	"LMFA07050014"	""	"HC01403"	"3hdcoa"	"MNXM674"	""	"m00181c"
 "MAM03204c"	"MAM03204"	"3deccrn"	""	""	""	""	""	""	""	"3deccrn"	"MNXM150909"	""	"3deccrn_c"
-"MAM03540c"	"MAM03540"	"ddeccrn"	""	""	""	"168381"	""	""	""	"ddeccrn"	""	""	"ddeccrn_c"
 "MAM00042c"	"MAM00042"	"dd2coa"	"C03221"	""	"CHEBI:15471"	"45266564"	"LMFA07050010"	""	"HC01078"	"dd2coa"	"MNXM642"	""	"m00042c"
 "MAM03541c"	"MAM03541"	"ddece1crn"	""	""	""	""	""	""	""	"ddece1crn"	""	""	"ddece1crn_c"
 "MAM03491x"	"MAM03491"	"c12dccoa"	""	""	"CHEBI:76315"	""	""	""	""	"c12dccoa"	""	""	"c12dccoa_p"
@@ -6310,7 +6309,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03502e"	"MAM03502"	"c8dc"	""	""	""	""	""	""	""	"c8dc"	"MNXM162999"	""	"c8dc_s"
 "MAM01648r"	"MAM01648"	""	"C01571"	"HMDB0000511"	"CHEBI:30813"	"2969"	"LMFA01010010"	""	"HC02175"	"dca"	"MNXM1043;MNXM162295"	""	"m01648r"
 "MAM03202e"	"MAM03202"	"3ddcrn"	""	""	""	""	""	""	""	"3ddcrn"	"MNXM150910"	""	"3ddcrn_s"
-"MAM03540e"	"MAM03540"	"ddeccrn"	""	""	""	"168381"	""	""	""	"ddeccrn"	""	""	"ddeccrn_s"
 "MAM03541e"	"MAM03541"	"ddece1crn"	""	""	""	""	""	""	""	"ddece1crn"	""	""	"ddece1crn_s"
 "MAM03204e"	"MAM03204"	"3deccrn"	""	""	""	""	""	""	""	"3deccrn"	"MNXM150909"	""	"3deccrn_s"
 "MAM03544e"	"MAM03544"	"decdicrn"	""	""	""	"53481669"	""	""	""	"decdicrn"	""	""	"decdicrn_s"
@@ -6486,7 +6484,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02741e"	"MAM02741"	"pan4p"	"C01134"	""	"CHEBI:16858"	"987"	""	""	"HC00681"	"pan4p"	"MNXM373"	""	"m02741s"
 "MAM03933e"	"MAM03933"	"slfcys"	"C05824"	"HMDB0000731"	"CHEBI:27891"	"115015"	""	""	""	"slfcys"	"MNXM2428"	""	"slfcys_s"
 "MAM01828e"	"MAM01828"	"fmn"	"C00061"	"HMDB0001520"	"CHEBI:17621"	"643976"	""	""	"HC00064"	"fmn"	"MNXM119"	""	"m01828s"
-"MAM02679e"	"MAM02679"	"ptth"	"C00154"	"HMDB0003426"	"CHEBI:16753"	"15667"	""	""	"HC00554"	"ptth"	"MNXM1154"	""	"m02679s"
+"MAM02679e"	"MAM02679"	"ptth"	"C00154"	"HMDB0003426"	"CHEBI:16753"	"439322"	""	""	"HC00554"	"ptth"	"MNXM1154"	""	"m02679s"
 "MAM03102e"	"MAM03102"	"q10h2"	"C00390"	""	"CHEBI:17976"	"9962735"	""	""	"HC00324"	"q10h2"	"MNXM9200"	""	"m03102s"
 "MAM02439x"	"MAM02439"	"mal__L"	"C00149"	"HMDB0000156"	"CHEBI:30797"	"222656"	""	""	"HC00146"	"mal_L"	"MNXM98"	""	"m02439p"
 "MAM03933c"	"MAM03933"	"slfcys"	"C05824"	"HMDB0000731"	"CHEBI:27891"	"115015"	""	""	""	"slfcys"	"MNXM2428"	""	"slfcys_c"
@@ -6538,7 +6536,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02639e"	"MAM02639"	"odecrn"	""	"HMDB0005065"	""	""	""	""	""	"odecrn"	"MNXM65475;MNXM8956"	""	"m02639s"
 "MAM02940e"	"MAM02940"	"stcrn"	""	""	""	"6426855"	"LMFA07070008"	""	""	"stcrn"	"MNXM82716;MNXM9119"	""	"m02940s"
 "MAM02411e"	"MAM02411"	"pmtcrn"	"C02990"	"HMDB0000222"	"CHEBI:17490"	"11953816"	"LMFA07070004"	""	"HC01034"	"pmtcrn"	"MNXM162587;MNXM787"	""	"m02411s"
-"MAM02676e"	"MAM02676"	"hdcecrn"	""	""	""	"11953816"	""	""	"HC10854"	"hdcecrn"	"MNXM8716"	""	"m02676s"
+"MAM02676e"	"MAM02676"	"hdcecrn"	""	""	""	"129849228"	""	""	"HC10854"	"hdcecrn"	"MNXM8716"	""	"m02676s"
 "MAM01620e"	"MAM01620"	"pcreat"	"C02305"	""	"CHEBI:58092"	"9548602"	""	""	""	"pcreat"	"MNXM819;MNXM90130;MNXM91273"	""	"m01620s"
 "MAM01580e"	"MAM01580"	""	"C00417"	""	"CHEBI:32805"	"309"	""	""	"HC00342"	"HC00342"	"MNXM162425;MNXM813"	""	"m01580s"
 "MAM01372e"	"MAM01372"	""	"C08261"	"HMDB0000784"	"CHEBI:48131"	"2266"	"LMFA01170054"	""	""	"C08261"	"MNXM164574"	""	"m01372s"
@@ -8489,4 +8487,5 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM00995n"	"MAM00995"	""	""	""	"CHEBI:17879"	""	""	""	""	""	"MNXM164"	""	""
 "MAM01316n"	"MAM01316"	""	""	""	"CHEBI:60721"	""	""	""	""	""	"MNXM731626"	""	""
 "MAM00767n"	"MAM00767"	""	""	""	"CHEBI:84503"	""	""	""	""	""	"MNXM733937"	""	""
-"MAM01435m"	"MAM01435"	""	"C02528"	"HMDB0000518"	"CHEBI:16755"	"10133"	"LMST04010032"	""	"HC00958"	"HC00958"	"MNXM1183"	""	"MAM03318m"
+"MAM01435m"	"MAM01435"	""	"C02528"	"HMDB0000518"	"CHEBI:16755"	"10133"	"LMST04010032"	""	"HC00958"	"HC00958"	"MNXM1183"	""	"MAM03318m"
+"MAM01729e"	"MAM01729"	""	""	"HMDB0002250"	""	"168381"	""	""	""	"M01729"	"MNXM51468;MNXM588354"	""	"MAM03540e"

model/reactions.tsv

@@ -2183,7 +2183,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR02591"	"R02396"	"CSNATr"	"R02396C"	"r0534"	""	"CSNATr"	"MNXR96926"	"HMR_2591"	"RCR12360"	""	0	""	"RHEA:21136"	"HMR_2591"
 "MAR02594"	""	"C30CPT1"	""	"r1396"	""	"C30CPT1"	""	"HMR_2594"	"RCR12361"	""	0	""	""	"HMR_2594"
 "MAR02599"	"R01923"	""	"R01923X"	"r0431"	""	"r0431"	"MNXR105343;MNXR107232"	"HMR_2599"	"RCR12362"	""	0	""	"RHEA:12661"	"HMR_2599"
-"MAR02602"	""	"HMR_2602"	""	""	""	"HMR_2602"	""	"HMR_2602"	"RCR12363"	""	0	""	""	"HMR_2602"
+"MAR02602"	""	"C120CPT1;HMR_2602"	""	""	""	"C120CPT1;HMR_2602"	""	"HMR_2602"	"RCR12363"	""	0	""	""	"C120CPT1;HMR_2602;MAR04506"
 "MAR02605"	""	""	""	""	""	"HMR_2605"	""	"HMR_2605"	"RCR12364"	""	0	""	""	"HMR_2605"
 "MAR02608"	""	"HMR_2608"	""	""	""	"HMR_2608"	""	"HMR_2608"	"RCR12365"	""	0	""	""	"HMR_2608"
 "MAR02611"	""	"HMR_2611"	""	""	""	"HMR_2611"	""	"HMR_2611"	"RCR12366"	""	0	""	""	"HMR_2611"
@@ -9216,7 +9216,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04479"	""	"C10DCCACT"	""	""	""	"C10DCCACT"	"MNXR96374"	""	""	""	0	""	""	"C10DCCACT"
 "MAR04491"	""	"C10DCc"	""	""	""	"C10DCc"	"MNXR96375"	""	""	""	0	""	""	"C10DCc"
 "MAR04504"	""	"C10OHc"	""	""	""	"C10OHc"	"MNXR96376"	""	""	""	0	""	""	"C10OHc"
-"MAR04506"	""	"C120CPT1"	""	""	""	"C120CPT1"	""	""	""	""	0	""	""	"C120CPT1"
 "MAR04508"	""	"C121CPT1"	""	""	""	"C121CPT1"	""	""	""	""	0	""	""	"C121CPT1"
 "MAR04509"	""	"C12DCACOT"	""	""	""	"C12DCACOT"	""	""	""	""	0	""	""	"C12DCACOT"
 "MAR04511"	""	"C12DCACT"	""	""	""	"C12DCACT"	""	""	""	""	0	""	""	"C12DCACT"