fix: removed MAR03364 and merged annotations into MAR03276

SysBioChalmers · Jun 27, 2023 · af6e183 · af6e183
1 parent c459bce
commit af6e183
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Showing 3 changed files with 5 additions and 23 deletions.
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -192,3 +192,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "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"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -117917,24 +117917,6 @@
       - subsystem:
           - "Beta oxidation of unsaturated fatty acids (n-9) (peroxisomal)"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR03364"
-      - name: ""
-      - metabolites: !!omap
-          - MAM02041x: 1
-          - MAM02630x: -1
-          - MAM02677x: -1
-          - MAM03020x: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000087008 or ENSG00000161533"
-      - rxnNotes: ""
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "1.3.3.6"
-      - references: "PMID:1047780;PMID:8973539;PMID:11135616"
-      - subsystem:
-          - "Beta oxidation of unsaturated fatty acids (n-9) (peroxisomal)"
-      - confidence_score: 0
     - !!omap
       - id: "MAR03365"
       - name: ""
@@ -233430,11 +233412,11 @@
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000087008 or ENSG00000161533"
       - rxnNotes: ""
-      - rxnFrom: "Recon3D"
-      - eccodes: "1.3.99.3"
+      - rxnFrom: "Recon3D;HMRdatabase"
+      - eccodes: "1.3.99.3;1.3.3.6"
       - references: "PMID:1047780;PMID:11135616;PMID:8973539"
       - subsystem:
-          - "Fatty acid oxidation"
+          - "Beta oxidation of unsaturated fatty acids (n-9) (peroxisomal)"
       - confidence_score: 0
     - !!omap
       - id: "MAR03289"

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -2586,7 +2586,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR03352"	""	""	""	""	""	"HMR_3352"	""	"HMR_3352"	"RCR12573"	""	0	""	""	"HMR_3352"
 "MAR03353"	""	""	""	""	""	"HMR_3353"	""	"HMR_3353"	"RCR12574"	""	0	""	""	"HMR_3353"
 "MAR03355"	"R04100"	"DCIm"	""	""	""	"FAOXC121x"	"MNXR97183"	"HMR_3355"	"RCR12575"	""	0	"RHEA:23719"	"RHEA:23716"	"HMR_3355"
-"MAR03364"	""	""	"RE2913X"	""	""	""	""	"HMR_3364"	"RCR12576"	""	0	""	""	"HMR_3364"
 "MAR03365"	""	""	"RE2919X"	""	""	"RE2919X"	""	"HMR_3365"	"RCR12577"	""	0	""	""	"HMR_3365"
 "MAR03367"	""	""	"RE2908X"	""	""	"RE2908X"	""	"HMR_3367"	"RCR12578"	""	0	""	""	"HMR_3367"
 "MAR03368"	""	""	"RE2916X"	""	""	"RE2916X"	""	"HMR_3368"	"RCR12579"	""	0	""	""	"HMR_3368"
@@ -8880,7 +8879,7 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR03271"	""	""	""	""	""	"RE2911C"	""	""	""	""	0	""	""	"RE2911C"
 "MAR03273"	""	"RE2912M"	""	""	""	"RE2912M"	""	""	""	""	0	""	""	"RE2912M"
 "MAR03274"	""	""	""	""	""	"RE2912X"	""	""	""	""	0	""	""	"RE2912X"
-"MAR03276"	""	""	""	""	""	"RE2913X"	""	""	""	""	0	""	""	"RE2913X"
+"MAR03276"	""	""	"RE2913X"	""	""	"RE2913X"	""	"HMR_3364"	"RCR12576"	""	0	""	""	"RE2913X;HMR_3364;MAR03364"
 "MAR03289"	""	""	""	""	""	"RE2914X"	""	""	""	""	0	""	""	"RE2914X"
 "MAR03291"	""	""	""	""	""	"RE2915M"	""	""	""	""	0	""	""	"RE2915M"
 "MAR03295"	""	""	""	""	""	"RE2915X"	""	""	""	""	0	""	""	"RE2915X"