Merge pull request #612 from Devlin-Moyer/develop

Fix Representation of ETF

data/deprecatedIdentifiers/deprecatedMetabolites.tsv

@@ -2200,5 +2200,7 @@ 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"
+"MAM03573m"	"MAM03573"	"etfox"	""	""	""	""	""	""	""	"etfox"	"MNXM11479"	""	"etfox_m"
+"MAM03574m"	"MAM03574"	"etfrd"	""	""	""	""	""	""	""	"etfrd"	"MNXM11480"	""	"etfrd_m"
 "MAM03494c"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_c"
-"MAM03494e"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_s"
+"MAM03494e"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_s"

data/deprecatedIdentifiers/deprecatedReactions.tsv

@@ -103,4 +103,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR04411"	""	"PIt8"	""	""	""	"PIt8"	"MNXR102875"	"HMR_4911"	"RCR40976"	""	0	""	""	"PIt8"
 "MAR08749"	""	"H2CO3D2"	""	""	""	"HMR_8749"	"MNXR100483"	"HMR_8749"	"RCR14128"	""	1	""	""	"HMR_8749"
 "MAR08750"	""	"H2CO3D2m"	""	""	""	"HMR_8750"	"MNXR100483"	"HMR_8750"	"RCR14129"	""	1	""	""	"HMR_8750"
+"MAR00562"	""	"ETF"	""	""	""	"ETF"	"MNXR97965"	""	""	""	0	""	""	"ETF"
+"MAR00563"	""	"ETFQO"	""	""	""	"ETFQO"	"MNXR97966"	""	""	""	0	""	""	"ETFQO"
 "MAR05434"	""	"FAOXC3DC"	""	""	""	"FAOXC3DC"	""	""	""	""	0	""	""	"FAOXC3DC"

model/Human-GEM.yml

@@ -44993,22 +44993,6 @@
       - charge: 0
       - inchis: ""
       - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03573m"
-      - name: "Electron Transfer Flavoprotein Oxidized"
-      - compartment: "m"
-      - formula: "R"
-      - charge: 0
-      - inchis: ""
-      - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM03574m"
-      - name: "Electron Transfer Flavoprotein Reduced"
-      - compartment: "m"
-      - formula: "RH2"
-      - charge: 0
-      - inchis: ""
-      - metFrom: "Recon3D"
     - !!omap
       - id: "MAM01893e"
       - name: "1-Acyl Phosphoglycerol"
@@ -95259,11 +95243,11 @@
           - MAM03103m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000073578 and ENSG00000117118 and ENSG00000143252 and ENSG00000204370"
+      - gene_reaction_rule: "ENSG00000140374 or ENSG00000105379 or ENSG00000171503 or ENSG00000100033 or ENSG00000250799 or ENSG00000115159 or ENSG00000102967 or ENSG00000016391"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.5.5.1"
-      - references: ""
+      - references: "PMID:34428349"
       - subsystem:
           - "Oxidative phosphorylation"
       - confidence_score: 0
@@ -222126,42 +222110,6 @@
       - subsystem:
           - "N-glycan metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR00562"
-      - name: "Electron Transfer Flavoprotein"
-      - metabolites: !!omap
-          - MAM01802m: 1
-          - MAM01803m: -1
-          - MAM03573m: -1
-          - MAM03574m: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000105379 and ENSG00000140374"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: ""
-      - references: "PMID:3170610;PMID:7601336"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
-    - !!omap
-      - id: "MAR00563"
-      - name: "Electron Transfer Flavoprotein-Ubiquinone Oxidoreductase"
-      - metabolites: !!omap
-          - MAM03102m: 1
-          - MAM03103m: -1
-          - MAM03573m: 1
-          - MAM03574m: -1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000171503"
-      - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: "1.5.5.1"
-      - references: "PMID:10444348;PMID:12049629"
-      - subsystem:
-          - "Fatty acid oxidation"
-      - confidence_score: 0
     - !!omap
       - id: "MAR00564"
       - name: "Exchange of 1 Acyl Phosphoglycerol"

model/metabolites.tsv

@@ -5622,8 +5622,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03591g"	"MAM03591"	"glc1man"	""	""	""	"440240"	""	""	""	"glc1man"	"MNXM7382"	""	"glc1man_g"
 "MAM03592g"	"MAM03592"	"glc2man"	""	""	""	""	""	""	""	"glc2man"	"MNXM13501"	""	"glc2man_g"
 "MAM03593g"	"MAM03593"	"glc3man"	""	""	""	""	""	""	""	"glc3man"	"MNXM18136"	""	"glc3man_g"
-"MAM03573m"	"MAM03573"	"etfox"	""	""	""	""	""	""	""	"etfox"	"MNXM11479"	""	"etfox_m"
-"MAM03574m"	"MAM03574"	"etfrd"	""	""	""	""	""	""	""	"etfrd"	"MNXM11480"	""	"etfrd_m"
 "MAM01893e"	"MAM01893"	"1glyc_hs"	""	""	""	""	""	""	""	"1glyc_hs"	"MNXM13807"	""	"1glyc_hs_s"
 "MAM03315e"	"MAM03315"	"9_cis_retfa"	""	""	""	""	""	""	""	"9_cis_retfa"	"MNXM146565"	""	"9_cis_retfa_s"
 "MAM03577e"	"MAM03577"	"fucfuc12gal14acglcgalgluside_hs"	""	""	""	""	""	""	""	"fucfuc12gal14acglcgalgluside_hs"	"MNXM8840"	""	"fucfuc12gal14acglcgalgluside_hs_s"

model/reactions.tsv

@@ -8255,8 +8255,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR00480"	""	"ENMAN4g"	""	""	""	"ENMAN4g"	"MNXR97929"	""	""	""	0	""	""	"ENMAN4g"
 "MAR00485"	""	"ENMAN5g"	""	""	""	"ENMAN5g"	"MNXR97930"	""	""	""	0	""	""	"ENMAN5g"
 "MAR00554"	""	"ENMAN6g"	""	""	""	"ENMAN6g"	"MNXR97931"	""	""	""	0	""	""	"ENMAN6g"
-"MAR00562"	""	"ETF"	""	""	""	"ETF"	"MNXR97965"	""	""	""	0	""	""	"ETF"
-"MAR00563"	""	"ETFQO"	""	""	""	"ETFQO"	"MNXR97966"	""	""	""	0	""	""	"ETFQO"
 "MAR00564"	""	"EX_1glyc_hs_e"	""	""	""	"EX_1glyc_hs[e]"	"MNXR97997"	""	""	""	0	""	""	"EX_1glyc_hs[e]"
 "MAR00565"	""	"EX_9_cis_retfa_e"	""	""	""	"EX_9_cis_retfa[e]"	"MNXR98098"	""	""	""	0	""	""	"EX_9_cis_retfa[e]"
 "MAR00566"	""	"EX_adrn_e"	""	""	""	"EX_adrn[e]"	"MNXR98235"	""	""	""	0	""	""	"EX_adrn[e]"