From 086d0823cef0be12b8faee764b7d4a451c04f875 Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Thu, 3 Nov 2022 08:46:20 +0100 Subject: [PATCH 1/2] fix: make sure pmid is followed by colon --- model/Human-GEM.yml | 112 ++++++++++++++++++++++---------------------- 1 file changed, 56 insertions(+), 56 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8de84c9b..c8566eb4 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -245487,7 +245487,7 @@ - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" - - references: "PMID:12845534;PMID4652039;PMID:18195088" + - references: "PMID:12845534;PMID:4652039;PMID:18195088" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -303771,7 +303771,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID11013348;PMID6935192;PMID10557352;PMID8172618" + - references: "PMID:11013348;PMID:6935192;PMID:10557352;PMID:8172618" - subsystem: - "Steroid metabolism" - confidence_score: 0 @@ -303862,7 +303862,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID6935192" + - references: "PMID:6935192" - subsystem: - "Steroid metabolism" - confidence_score: 0 @@ -303881,7 +303881,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID6935192" + - references: "PMID:6935192" - subsystem: - "Steroid metabolism" - confidence_score: 0 @@ -303902,7 +303902,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID2018466;PMID6861760" + - references: "PMID:2018466;PMID:6861760" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -303917,7 +303917,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID2018466;PMID6861760" + - references: "PMID:2018466;PMID:6861760" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -303938,7 +303938,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID2018466;PMID6861760" + - references: "PMID:2018466;PMID:6861760" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -303953,7 +303953,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID2018466;PMID6861760" + - references: "PMID:2018466;PMID:6861760" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -303968,7 +303968,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -303983,7 +303983,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304004,7 +304004,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304024,7 +304024,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304039,7 +304039,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304060,7 +304060,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304075,7 +304075,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304090,7 +304090,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304105,7 +304105,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304120,7 +304120,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304135,7 +304135,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304150,7 +304150,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304165,7 +304165,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304180,7 +304180,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304195,7 +304195,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 @@ -304214,7 +304214,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304233,7 +304233,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304253,7 +304253,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "6.2.1.7" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304272,7 +304272,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304291,7 +304291,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304311,7 +304311,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "6.2.1.7" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304330,7 +304330,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304349,7 +304349,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304370,7 +304370,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304391,7 +304391,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304412,7 +304412,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304433,7 +304433,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304454,7 +304454,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304474,7 +304474,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "6.2.1.7" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304493,7 +304493,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304512,7 +304512,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304531,7 +304531,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304552,7 +304552,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304573,7 +304573,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304593,7 +304593,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "6.2.1.7" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304612,7 +304612,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304631,7 +304631,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304650,7 +304650,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID12810727;PMID6884990" + - references: "PMID:12810727;PMID:6884990" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -304671,7 +304671,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304689,7 +304689,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "4.1.1.97" - - references: "PMID16462750" + - references: "PMID:16462750" - subsystem: - "Purine metabolism" - confidence_score: 0 @@ -304710,7 +304710,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304728,7 +304728,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304746,7 +304746,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304764,7 +304764,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304862,7 +304862,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304883,7 +304883,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304901,7 +304901,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Transport reactions" - confidence_score: 0 @@ -304991,7 +304991,7 @@ - rxnNotes: "" - rxnFrom: "" - eccodes: "" - - references: "PMID17404808;PMID19498215" + - references: "PMID:17404808;PMID:19498215" - subsystem: - "Exchange/demand reactions" - confidence_score: 0 From 341f7b00e77d8fb375ca21edee77c0b44af9694c Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Thu, 3 Nov 2022 09:47:36 +0100 Subject: [PATCH 2/2] fix: leave reference filed blank if no PMID is available Empty reference filed for reactions MAR03259, MAR03382, MAR03824 that have no PMID --- model/Human-GEM.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index c8566eb4..f1ea8a9f 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -233792,7 +233792,7 @@ - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "3.5.1.14" - - references: "PMID:0" + - references: "" - subsystem: - "Bile acid biosynthesis" - confidence_score: 0 @@ -234434,7 +234434,7 @@ - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" - - references: "PMID:0" + - references: "" - subsystem: - "Glycerophospholipid metabolism" - confidence_score: 0 @@ -236574,7 +236574,7 @@ - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.14.14.1" - - references: "PMID:0" + - references: "" - subsystem: - "Glycerophospholipid metabolism" - confidence_score: 0