From 8efc01671b15c9161c066c82e07b0f7e8f1db68d Mon Sep 17 00:00:00 2001
From: Hao Wang <haowang.bioinfo@gmail.com>
Date: Thu, 19 Oct 2023 10:33:27 +0200
Subject: [PATCH] fix: remove duplicate rxns MAR20012 and MAR20089

- MAR20012 is duplicate to MAR06646
- MAR20089 is duplicate to MAR04545
---
 .../deprecatedReactions.tsv                   |  2 +
 model/Human-GEM.yml                           | 38 -------------------
 model/reactions.tsv                           |  2 -
 3 files changed, 2 insertions(+), 40 deletions(-)

diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
index 5c0e7745..14656a44 100644
--- a/data/deprecatedIdentifiers/deprecatedReactions.tsv
+++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -247,3 +247,5 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "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"	""	""
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
index 7582d8f7..030b348b 100644
--- a/model/Human-GEM.yml
+++ b/model/Human-GEM.yml
@@ -302656,26 +302656,6 @@
       - subsystem:
           - "Retinol metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR20012"
-      - name: "MAR20012"
-      - metabolites: !!omap
-          - MAM02039c: 2
-          - MAM02040c: -1
-          - MAM02552c: -1
-          - MAM02553c: 1
-          - MAM02832c: -1
-          - MAM02833c: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000184254"
-      - rxnNotes: ""
-      - rxnFrom: ""
-      - eccodes: "1.2.1.36"
-      - references: ""
-      - subsystem:
-          - "Retinol metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR20013"
       - name: "MAR20013"
@@ -304023,24 +304003,6 @@
       - subsystem:
           - "Fatty acid metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR20089"
-      - name: "MAR20089"
-      - metabolites: !!omap
-          - MAM01107c: -1
-          - MAM01596c: 1
-          - MAM02039c: -1
-          - MAM02897c: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000132437"
-      - rxnNotes: ""
-      - rxnFrom: ""
-      - eccodes: "4.1.1.28"
-      - references: ""
-      - subsystem:
-          - "Tryptophan metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR20090"
       - name: "MAR20090"
diff --git a/model/reactions.tsv b/model/reactions.tsv
index 9e530a10..77c01bdc 100644
--- a/model/reactions.tsv
+++ b/model/reactions.tsv
@@ -12854,7 +12854,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR20009"	""	""	""	""	""	""	"MNXR133773"	""	""	""	0	"RHEA:60660"	""	""
 "MAR20010"	""	""	""	""	""	""	"MNXR133773"	""	""	""	0	"RHEA:60660"	""	""
 "MAR20011"	"R02123"	"HMR_6647;RADH;R_HMR_6647;R_RADH"	""	""	""	""	"MNXR146215"	""	""	""	0	"RHEA:42080"	""	""
-"MAR20012"	"R02123"	"HMR_6647;RADH;R_HMR_6647;R_RADH"	""	""	""	""	"MNXR146215"	""	""	""	0	"RHEA:42080"	""	""
 "MAR20013"	"R03225"	""	""	""	""	""	"MNXR108031"	""	""	""	0	"RHEA:23048"	""	""
 "MAR20016"	"R01704"	"ALDD16;R_ALDD16"	""	""	""	""	"MNXR95739"	""	""	""	0	"RHEA:33739"	""	""
 "MAR20017"	""	"ALDD8;R_ALDD8"	""	""	""	""	"MNXR95760"	""	""	""	0	"RHEA:44100"	""	""
@@ -12925,7 +12924,6 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR20086"	""	""	""	""	""	""	"MNXR168657"	""	""	""	0	"RHEA:45372"	""	""
 "MAR20087"	""	""	""	""	""	""	"MNXR168656"	""	""	""	0	"RHEA:45368"	""	""
 "MAR20088"	""	""	""	""	""	""	"MNXR168656"	""	""	""	0	"RHEA:45368"	""	""
-"MAR20089"	"R02701"	""	""	""	""	""	"MNXR151808"	""	""	""	0	"RHEA:18533"	""	""
 "MAR20090"	"R07411"	"HEMEOS;HEMEOS_1;HEMEOSm;HEMEOSm_1;R_HEMEOS;R_HEMEOS_1;R_HEMEOSm;R_HEMEOSm_1"	""	""	""	""	"MNXR115959"	""	""	""	0	"RHEA:28070"	""	""
 "MAR20091"	"R07411"	"HEMEOS;HEMEOS_1;HEMEOSm;HEMEOSm_1;R_HEMEOS;R_HEMEOS_1;R_HEMEOSm;R_HEMEOSm_1"	""	""	""	""	"MNXR115959"	""	""	""	0	"RHEA:28070"	""	""
 "MAR20092"	"R07411"	"HEMEOS;HEMEOS_1;HEMEOSm;HEMEOSm_1;R_HEMEOS;R_HEMEOS_1;R_HEMEOSm;R_HEMEOSm_1"	""	""	""	""	"MNXR115959"	""	""	""	0	"RHEA:28070"	""	""