Merge branch 'develop' into fix/CLYBL_rxns

data/deprecatedIdentifiers/deprecatedMetabolites.tsv

@@ -2200,3 +2200,5 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM01421c"	"MAM01421"	"h2co3"	"C01353"	""	"CHEBI:28976"	""	""	""	"HC02169"	"h2co3"	"MNXM60"	"m01421c"	"m01421c"
 "MAM01421m"	"MAM01421"	"h2co3"	"C01353"	""	"CHEBI:28976"	""	""	""	"HC02169"	"h2co3"	"MNXM60"	"m01421m"	"m01421m"
 "MAM01421e"	"MAM01421"	"h2co3"	"C01353"	""	"CHEBI:28976"	""	""	""	"HC02169"	"h2co3"	"MNXM60"	"m01421s"	"m01421s"
+"MAM03494c"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_c"
+"MAM03494e"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_s"

data/deprecatedIdentifiers/deprecatedReactions.tsv

@@ -105,3 +105,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR08750"	""	"H2CO3D2m"	""	""	""	"HMR_8750"	"MNXR100483"	"HMR_8750"	"RCR14129"	""	1	""	""	"HMR_8750"
 "MAR05294"	"R00362"	""	"R00362C"	"r1109"	""	"r1109"	"MNXR96731"	"HMR_5294"	"RCR11670"	""	0	"RHEA:10761"	"RHEA:10760"	"HMR_5294"
 "MAR11421"	""	"CITL"	""	""	""	"CITL"	"MNXR96731"	""	""	""	0	"RHEA:10761"	"RHEA:10760"	"CITL"
+"MAR05434"	""	"FAOXC3DC"	""	""	""	"FAOXC3DC"	""	""	""	""	0	""	""	"FAOXC3DC"

model/Human-GEM.yml

@@ -4,7 +4,7 @@
     short_name: "Human-GEM"
     full_name: "Generic genome-scale metabolic model of Homo sapiens"
     version: ""
-    date: "2023-05-22"
+    date: "2023-06-07"
     taxonomy: "9606"
     github: "https://github.com/SysBioChalmers/Human-GEM"
     description: "Genome-scale metabolic models are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. This is the latest version of Human-GEM, which is a genome-scale metabolic model of a generic human cell. The objective of Human-GEM is to serve as a community model for enabling integrative and mechanistic studies of human metabolism."
@@ -33377,33 +33377,41 @@
       - charge: -2
       - inchis: ""
       - metFrom: "HMRdatabase"
+    - !!omap
+      - id: "MAM02443e"
+      - name: "malonyl-carnitine"
+      - compartment: "e"
+      - formula: "C10H16NO6"
+      - charge: -1
+      - inchis: ""
+      - metFrom: ""
     - !!omap
       - id: "MAM02443c"
-      - name: "malonyl-carnitin"
+      - name: "malonyl-carnitine"
       - compartment: "c"
       - formula: "C10H16NO6"
       - charge: -1
       - inchis: ""
       - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM02443m"
-      - name: "malonyl-carnitin"
+      - name: "malonyl-carnitine"
       - compartment: "m"
       - formula: "C10H16NO6"
       - charge: -1
       - inchis: ""
       - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM02443x"
-      - name: "malonyl-carnitin"
+      - name: "malonyl-carnitine"
       - compartment: "x"
       - formula: "C10H16NO6"
       - charge: -1
       - inchis: ""
       - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM02443r"
-      - name: "malonyl-carnitin"
+      - name: "malonyl-carnitine"
       - compartment: "r"
       - formula: "C10H16NO6"
       - charge: -1
@@ -50377,22 +50385,6 @@
       - charge: 0
       - inchis: "InChI=1/C25H49NO5/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-22(27)19-25(30)31-23(20-24(28)29)21-26(2,3)4/h22-23,27H,5-21H2,1-4H3"
       - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03494c"
-      - name: "Malonyl Carnitine"
-      - compartment: "c"
-      - formula: "C10H16NO6"
-      - charge: -1
-      - inchis: ""
-      - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03494e"
-      - name: "Malonyl Carnitine"
-      - compartment: "e"
-      - formula: "C10H16NO6"
-      - charge: -1
-      - inchis: ""
-      - metFrom: "Recon3D"
     - !!omap
       - id: "MAM02635e"
       - name: "O-butanoylcarnitine"
@@ -86129,7 +86121,7 @@
           - MAM02871c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000101444 or ENSG00000158467 or ENSG00000168710"
+      - gene_reaction_rule: "ENSG00000101444 or ENSG00000158467"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.3.1.1"
@@ -86674,7 +86666,7 @@
           - MAM02986c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000083123 or ENSG00000091140 or ENSG00000117592 or ENSG00000121053 or ENSG00000130508 or ENSG00000142046 or ENSG00000167419 or ENSG00000248098"
+      - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000130508 or ENSG00000142046 or ENSG00000167419"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.11.1.7;1.2.4.4;1.8.1.4"
@@ -87628,7 +87620,7 @@
           - MAM02890c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000101444 or ENSG00000158467 or ENSG00000168710"
+      - gene_reaction_rule: "ENSG00000101444 or ENSG00000158467"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.3.1.1"
@@ -94227,7 +94219,7 @@
           - MAM02046e: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000074410 or ENSG00000104267 or ENSG00000107159 or ENSG00000118298 or ENSG00000131686 or ENSG00000133742 or ENSG00000159593 or ENSG00000164879 or ENSG00000167434 or ENSG00000168748 or ENSG00000169239 or ENSG00000174990 or ENSG00000185015"
+      - gene_reaction_rule: "ENSG00000074410 or ENSG00000104267 or ENSG00000107159 or ENSG00000118298 or ENSG00000131686 or ENSG00000167434"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.1"
@@ -162747,7 +162739,7 @@
           - MAM02046c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000074410 or ENSG00000104267 or ENSG00000107159 or ENSG00000118298 or ENSG00000131686 or ENSG00000133742 or ENSG00000159593 or ENSG00000164879 or ENSG00000167434 or ENSG00000168748 or ENSG00000169239 or ENSG00000174990 or ENSG00000185015"
+      - gene_reaction_rule: "ENSG00000104267 or ENSG00000133742 or ENSG00000164879 or ENSG00000168748 or ENSG00000185015"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.1"
@@ -241266,7 +241258,7 @@
       - id: "MAR04886"
       - name: "Exchange of Malonyl Carnitine"
       - metabolites: !!omap
-          - MAM03494e: -1
+          - MAM02443e: -1
       - lower_bound: -1000
       - upper_bound: 1000
       - gene_reaction_rule: ""
@@ -244109,24 +244101,6 @@
       - subsystem:
           - "Fatty acid oxidation"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR05434"
-      - name: "Malonylcoa->Malonylcarnitine"
-      - metabolites: !!omap
-          - MAM01597c: 1
-          - MAM02348c: -1
-          - MAM02444c: -1
-          - MAM03494c: 1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:12651823;PMID:18192268"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
     - !!omap
       - id: "MAR05449"
       - name: "Fatty Acid Beta Oxidation (C4->C2), Mitochondrial"
@@ -271356,8 +271330,8 @@
       - id: "MAR11256"
       - name: "Transport of Malonyl Carnitine"
       - metabolites: !!omap
-          - MAM03494c: 1
-          - MAM03494e: -1
+          - MAM02443c: 1
+          - MAM02443e: -1
       - lower_bound: -1000
       - upper_bound: 1000
       - gene_reaction_rule: ""
@@ -313807,9 +313781,6 @@
     - !!omap
       - id: "ENSG00000168679"
       - name: "SLC16A4"
-    - !!omap
-      - id: "ENSG00000168710"
-      - name: "AHCYL1"
     - !!omap
       - id: "ENSG00000168748"
       - name: "CA7"

model/genes.tsv

@@ -2139,7 +2139,6 @@ genes	geneENSTID	geneENSPID	geneUniProtID	geneSymbols	geneEntrezID	geneNames	gen
 "ENSG00000168653"	"ENST00000372967;ENST00000372969"	"ENSP00000362058;ENSP00000362060"	"O43920"	"NDUFS5"	"4725"	"NADH:ubiquinone oxidoreductase subunit S5"	"CI-15k"	"Inner mitochondria"	"SwissProt"
 "ENSG00000168671"	"ENST00000282507;ENST00000513300;ENST00000504685;ENST00000504954;ENST00000515131"	"ENSP00000282507;ENSP00000427404;ENSP00000426017;ENSP00000420865"	"Q3SY77"	"UGT3A2"	"167127"	"UDP glycosyltransferase family 3 member A2"	""	"Cytosol;Golgi apparatus;Nucleus"	"CellAtlas"
 "ENSG00000168679"	"ENST00000437429;ENST00000541986;ENST00000369779;ENST00000472422;ENST00000369781;ENST00000461647;ENST00000528649;ENST00000492412;ENST00000467986;ENST00000497687"	"ENSP00000394790;ENSP00000446087;ENSP00000358794;ENSP00000432495;ENSP00000358796;ENSP00000432190;ENSP00000434136;ENSP00000433463;ENSP00000435768"	"O15374"	"SLC16A4"	"9122"	"solute carrier family 16 member 4"	"MCT4;MCT5"	"Cytosol"	"CellAtlas"
-"ENSG00000168710"	"ENST00000369799;ENST00000475081;ENST00000359172;ENST00000481423;ENST00000469401;ENST00000393614"	"ENSP00000358814;ENSP00000352092;ENSP00000377238"	"O43865"	"AHCYL1"	"10768"	"adenosylhomocysteinase like 1"	"IRBIT;PPP1R78;XPVKONA"	"Endoplasmic reticulum;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000168748"	"ENST00000338437;ENST00000548332;ENST00000394069"	"ENSP00000345659;ENSP00000447178;ENSP00000377632"	"P43166"	"CA7"	"766"	"carbonic anhydrase 7"	""	"Cytosol"	"SwissProt"
 "ENSG00000168765"	"ENST00000369836;ENST00000464733;ENST00000461767;ENST00000479578;ENST00000326729;ENST00000495742;ENST00000369833;ENST00000485640;ENST00000336075;ENST00000638994;ENST00000478397;ENST00000493171;ENST00000493395"	"ENSP00000358851;ENSP00000316471;ENSP00000358848;ENSP00000336744;ENSP00000491134"	"Q03013"	"GSTM4"	"2948"	"glutathione S-transferase mu 4"	""	"Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000168781"	"ENST00000348806;ENST00000381885;ENST00000396923;ENST00000360135;ENST00000360301;ENST00000334933;ENST00000420765;ENST00000381879;ENST00000644537;ENST00000488490;ENST00000439195;ENST00000437065;ENST00000432870;ENST00000462136;ENST00000488768;ENST00000469229;ENST00000465123;ENST00000427877;ENST00000476294;ENST00000472547;ENST00000453080;ENST00000429176;ENST00000417085;ENST00000431962"	"ENSP00000308773;ENSP00000371309;ENSP00000380129;ENSP00000353253;ENSP00000353446;ENSP00000334779;ENSP00000400887;ENSP00000371303;ENSP00000496290;ENSP00000387999;ENSP00000410563;ENSP00000415349;ENSP00000407704;ENSP00000405106;ENSP00000390657;ENSP00000405200"	"Q6PFW1"	"PPIP5K1"	"9677"	"diphosphoinositol pentakisphosphate kinase 1"	"HISPPD2A;IPS1;KIAA0377;VIP1"	"Cytosol"	"SwissProt;CellAtlas"

model/metabolites.tsv

@@ -4170,7 +4170,8 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02440e"	"MAM02440"	""	"C00383"	"HMDB0000691"	"CHEBI:30794"	"867"	""	""	"HC00319"	"HC00319"	"MNXM163844"	"m02440s"	"m02440s"
 "MAM02441c"	"MAM02441"	""	"C19440"	"HMDB0006112"	"CHEBI:566274"	"10964"	""	"CE0737"	""	"CE0737"	"MNXM61004"	"m02441c"	"m02441c"
 "MAM02442c"	"MAM02442"	"malACP"	"C01209"	""	""	""	""	""	"HC00717"	"malACP"	"MNXM184"	"m02442c"	"m02442c"
-"MAM02443c"	"MAM02443"	""	""	"HMDB0002095"	""	"22833583"	""	""	"HC10859"	"HC10859"	"MNXM162761"	"m02443c"	"m02443c"
+"MAM02443e"	"MAM02443"	"c3dc"	""	"HMDB0002095"	""	"22833583"	""	""	"HC10859"	"HC10859;c3dc"	"MNXM162761"	""	"c3dc_s"
+"MAM02443c"	"MAM02443"	"c3dc"	""	"HMDB0002095"	""	"22833583"	""	""	"HC10859"	"HC10859;c3dc"	"MNXM162761"	"m02443c"	"m02443c;c3dc_c"
 "MAM02443m"	"MAM02443"	""	""	"HMDB0002095"	""	"22833583"	""	""	"HC10859"	"HC10859"	"MNXM162761"	"m02443m"	"m02443m"
 "MAM02443x"	"MAM02443"	""	""	"HMDB0002095"	""	"22833583"	""	""	"HC10859"	"HC10859"	"MNXM162761"	"m02443p"	"m02443p"
 "MAM02443r"	"MAM02443"	""	""	"HMDB0002095"	""	"22833583"	""	""	"HC10859"	"HC10859"	"MNXM162761"	"m02443r"	"m02443r"
@@ -6295,8 +6296,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03250c"	"MAM03250"	"3octdec2crn"	""	""	""	""	""	""	""	"3octdec2crn"	""	""	"3octdec2crn_c"
 "MAM03230c"	"MAM03230"	"3hodcoa"	""	""	""	"49859586"	""	""	""	"3hodcoa"	"MNXM31746"	""	"3hodcoa_c"
 "MAM03251c"	"MAM03251"	"3octdeccrn"	""	""	""	""	""	""	""	"3octdeccrn"	""	""	"3octdeccrn_c"
-"MAM03494c"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_c"
-"MAM03494e"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_s"
 "MAM02635e"	"MAM02635"	""	"C02862"	"HMDB0002013"	""	"439829"	"LMFA07070003"	""	"HC02150"	"c4crn"	"MNXM65151"	""	"m02635s"
 "MAM03495x"	"MAM03495"	"c4dc"	""	""	""	""	""	""	""	"c4dc"	"MNXM158939"	""	"c4dc_p"
 "MAM03495c"	"MAM03495"	"c4dc"	""	""	""	""	""	""	""	"c4dc"	"MNXM158939"	""	"c4dc_c"

model/reactions.tsv

@@ -9455,7 +9455,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR05427"	""	"FAOXC22OHC22r"	""	""	""	"FAOXC22OHC22r"	""	""	""	""	0	""	""	"FAOXC22OHC22r"
 "MAR05428"	""	"FAOXC241C221x"	""	""	""	"FAOXC241C221x"	""	""	""	""	0	""	""	"FAOXC241C221x"
 "MAR05431"	""	"FAOXC24C22x"	""	""	""	"FAOXC24C22x"	""	""	""	""	0	""	""	"FAOXC24C22x"
-"MAR05434"	""	"FAOXC3DC"	""	""	""	"FAOXC3DC"	""	""	""	""	0	""	""	"FAOXC3DC"
 "MAR05449"	""	"FAOXC4020m"	""	""	""	"FAOXC4C2m"	"MNXR99368"	""	""	""	0	""	""	"FAOXC4C2m"
 "MAR05456"	""	"FAOXC4C4DCc"	""	""	""	"FAOXC4C4DCc"	""	""	""	""	0	""	""	"FAOXC4C4DCc"
 "MAR05988"	""	"FAOXC5C3x"	""	""	""	"FAOXC5C3x"	""	""	""	""	0	""	""	"FAOXC5C3x"