From 8525e469bb2e142bb060ec773fcf3e24fea48b93 Mon Sep 17 00:00:00 2001 From: jorgemlferreira Date: Thu, 11 Mar 2021 12:06:56 +0000 Subject: [PATCH 1/3] [FIX] changed pubchem ID for m01778c --- model/metabolites.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/metabolites.tsv b/model/metabolites.tsv index aa00c860..c101ffe0 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -3039,7 +3039,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "m01777c" "m01777" "" "" "" "" "" "" "" "" "M01777" "" "m01777c" "m01777m" "m01777" "" "" "" "" "" "" "" "" "M01777" "" "m01777m" "m01777r" "m01777" "" "" "" "" "" "" "" "" "M01777" "" "m01777r" -"m01778c" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:27997" "445639" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305" "m01778c" +"m01778c" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:27997" "5461071" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305" "m01778c" "m01778l" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:27997" "445639" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305" "m01778l" "m01778r" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:27997" "445639" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305" "m01778r" "m01778s" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:27997" "445639" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305" "m01778s" From d268ce07e716e945222db4bfd53561a69d037018 Mon Sep 17 00:00:00 2001 From: jorgemlferreira Date: Thu, 11 Mar 2021 14:26:43 +0000 Subject: [PATCH 2/3] Changelog: For elaidate: - Most of this changes are based on the fact that elaidate (CHEBI:30825) is conjugate base of elaidic acid (CHEBI:27997), so I don't know if there is need for this change or if it is necessary to introduce another metabolite into the model - CHEBI differences on the InChI which made the change in the CHEBI identifier: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on CHEBI:30825 InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9+ elaidic acid on CHEBI:27997 - Remove KEGG annotation from m01778 since there is no entry to it in the KEGG database (only its acid form) - Removed HMDB since there is no annotation for this specific metabolite and: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9+ Elaidic acid on HMDB0000573 InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on CHEBI:30825 - Removed LipidMaps entry since there is no entry to in in its database - Changed the metMetaNetXID to the correct form based on the InCHi presented on the database: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on CHEBI:30825 InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on MNXM727012 For oleate: - Most of this changes are based on the fact that oleate (CHEBI:30823) is conjugate base of oleic acid (CHEBI:16196) - CHEBI differences on the InChI which made the change in the CHEBI identifier: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate) InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9- in CHEBI:16196 (oleic acid) - Remove KEGG annotation from m02646 since there is no entry to it in the KEGG database (only its acid form) - Removed HMDB since there is no annotation for this specific metabolite and: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9- in Oleic acid on HMDB00207 InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate) - Removed LipidMaps entry since there is no entry to in in its database and InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9- on LMFA01030002 (Oleic acid) InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate) - Changed the metMetaNetXID to the correct form based on the InCHi presented on the database: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- on MNXM727011 ((9Z)-octadecenoate) InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate) --- model/metabolites.tsv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/model/metabolites.tsv b/model/metabolites.tsv index c101ffe0..5b3a4823 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -3039,10 +3039,10 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "m01777c" "m01777" "" "" "" "" "" "" "" "" "M01777" "" "m01777c" "m01777m" "m01777" "" "" "" "" "" "" "" "" "M01777" "" "m01777m" "m01777r" "m01777" "" "" "" "" "" "" "" "" "M01777" "" "m01777r" -"m01778c" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:27997" "5461071" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305" "m01778c" -"m01778l" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:27997" "445639" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305" "m01778l" -"m01778r" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:27997" "445639" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305" "m01778r" -"m01778s" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:27997" "445639" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305" "m01778s" +"m01778c" "m01778" "elaid" "" "" "CHEBI:30825" "5461071" "" "" "HC00830" "elaid" "MNXM727012" "m01778c" +"m01778l" "m01778" "elaid" "" "" "CHEBI:30825" "5461071" "" "" "HC00830" "elaid" "MNXM727012" "m01778l" +"m01778r" "m01778" "elaid" "" "" "CHEBI:30825" "5461071" "" "" "HC00830" "elaid" "MNXM727012" "m01778r" +"m01778s" "m01778" "elaid" "" "" "CHEBI:30825" "5461071" "" "" "HC00830" "elaid" "MNXM727012" "m01778s" "m01779r" "m01779" "em2emgacpail_hs" "" "" "" "" "" "" "" "em2emgacpail_hs" "MNXM5386" "m01779r" "m01780r" "m01780" "em2emgacpail_prot_hs" "" "" "" "" "" "" "" "em2emgacpail_prot_hs" "MNXM9492" "m01780r" "m01781r" "m01781" "em3gacpail_hs" "" "" "" "" "" "" "" "em3gacpail_hs" "MNXM9024" "m01781r" @@ -4544,10 +4544,10 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "m02644m" "m02644" "occoa" "C01944" "HMDB01070" "CHEBI:15533" "380" "" "" "HC00869" "occoa" "MNXM342" "m02644m" "m02644p" "m02644" "occoa" "C01944" "HMDB01070" "CHEBI:15533" "380" "" "" "HC00869" "occoa" "MNXM342" "m02644p" "m02645c" "m02645" "" "C02863" "" "" "" "" "" "" "M02645" "MNXM7606" "m02645c" -"m02646c" "m02646" "ocdcea" "C00712" "HMDB00207" "CHEBI:16196" "445639" "LMFA01030002" "" "HC00510" "ocdcea" "MNXM306" "m02646c" -"m02646l" "m02646" "ocdcea" "C00712" "HMDB00207" "CHEBI:16196" "445639" "LMFA01030002" "" "HC00510" "ocdcea" "MNXM306" "m02646l" -"m02646r" "m02646" "ocdcea" "C00712" "HMDB00207" "CHEBI:16196" "445639" "LMFA01030002" "" "HC00510" "ocdcea" "MNXM306" "m02646r" -"m02646s" "m02646" "ocdcea" "C00712" "HMDB00207" "CHEBI:16196" "445639" "LMFA01030002" "" "HC00510" "ocdcea" "MNXM306" "m02646s" +"m02646c" "m02646" "ocdcea" "" "" "CHEBI:30823" "445639" "" "" "HC00510" "ocdcea" "MNXM727011" "m02646c" +"m02646l" "m02646" "ocdcea" "" "" "CHEBI:30823" "445639" "" "" "HC00510" "ocdcea" "MNXM727011" "m02646l" +"m02646r" "m02646" "ocdcea" "" "" "CHEBI:30823" "445639" "" "" "HC00510" "ocdcea" "MNXM727011" "m02646r" +"m02646s" "m02646" "ocdcea" "" "" "CHEBI:30823" "445639" "" "" "HC00510" "ocdcea" "MNXM727011" "m02646s" "m02647c" "m02647" "odecoa" "C00510" "HMDB01322" "CHEBI:15534" "5280355" "LMFA07050055" "" "HC00400" "odecoa" "MNXM1848;MNXM686" "m02647c" "m02647m" "m02647" "odecoa" "C00510" "HMDB01322" "CHEBI:15534" "5280355" "LMFA07050055" "" "HC00400" "odecoa" "MNXM1848;MNXM686" "m02647m" "m02647p" "m02647" "odecoa" "C00510" "HMDB01322" "CHEBI:15534" "5280355" "LMFA07050055" "" "HC00400" "odecoa" "MNXM1848;MNXM686" "m02647p" From e9be6b3faef82e231cbcba229df3f4897dda3945 Mon Sep 17 00:00:00 2001 From: jorgemlferreira Date: Mon, 15 Mar 2021 10:45:23 +0000 Subject: [PATCH 3/3] Changelog: For elaidate: Reverted changes to the original information, asides from the CHEBI and PubChem identifiers. Also, added an extra identifier for the metanext ids. So after reverting to the original ids present in Human-GEM/model/metabolites.tsv in commit f8c74a5a7156ddbc8b4bed91db2c81d6a36e5176 in the master branch: - CHEBI differences on the InChI which made the change in the CHEBI identifier -> elaidic acid (CHEBI:27997) to elaidate (CHEBI:30825): InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9+ elaidic acid on CHEBI:27997 InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on CHEBI:30825 - PubChem from 445639 to 5461071 - Added metMetaNetXID MNXM727012 to the ones already present based on their InChI: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on CHEBI:30825 InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on MNXM727012 For oleate: Reverted changes to the original information, asides from the CHEBI and PubChem identifiers. Also, added an extra identifier for the metanext ids. So after reverting to the original ids present in Human-GEM/model/metabolites.tsv in commit f8c74a5a7156ddbc8b4bed91db2c81d6a36e5176 in the master branch: - CHEBI differences on the InChI which made the change in the CHEBI identifier -> oleic acid (CHEBI:16196) to oleate (CHEBI:30823): InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9- in CHEBI:16196 (oleic acid) InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate) - PubChem from 445639 to 5460221 - Added metMetaNetXID MNXM727011 to the ones already present based on their InChI: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- on MNXM727011 ((9Z)-octadecenoate) InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate) --- model/metabolites.tsv | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 5b3a4823..5611bc61 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -3039,10 +3039,10 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "m01777c" "m01777" "" "" "" "" "" "" "" "" "M01777" "" "m01777c" "m01777m" "m01777" "" "" "" "" "" "" "" "" "M01777" "" "m01777m" "m01777r" "m01777" "" "" "" "" "" "" "" "" "M01777" "" "m01777r" -"m01778c" "m01778" "elaid" "" "" "CHEBI:30825" "5461071" "" "" "HC00830" "elaid" "MNXM727012" "m01778c" -"m01778l" "m01778" "elaid" "" "" "CHEBI:30825" "5461071" "" "" "HC00830" "elaid" "MNXM727012" "m01778l" -"m01778r" "m01778" "elaid" "" "" "CHEBI:30825" "5461071" "" "" "HC00830" "elaid" "MNXM727012" "m01778r" -"m01778s" "m01778" "elaid" "" "" "CHEBI:30825" "5461071" "" "" "HC00830" "elaid" "MNXM727012" "m01778s" +"m01778c" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:30825" "5461071" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305;MNXM727012" "m01778c" +"m01778l" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:30825" "5461071" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305;MNXM727012" "m01778l" +"m01778r" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:30825" "5461071" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305;MNXM727012" "m01778r" +"m01778s" "m01778" "elaid" "C00712" "HMDB00573" "CHEBI:30825" "5461071" "LMFA01030073" "" "HC00830" "elaid" "MNXM11476;MNXM306;MNXM92305;MNXM727012" "m01778s" "m01779r" "m01779" "em2emgacpail_hs" "" "" "" "" "" "" "" "em2emgacpail_hs" "MNXM5386" "m01779r" "m01780r" "m01780" "em2emgacpail_prot_hs" "" "" "" "" "" "" "" "em2emgacpail_prot_hs" "MNXM9492" "m01780r" "m01781r" "m01781" "em3gacpail_hs" "" "" "" "" "" "" "" "em3gacpail_hs" "MNXM9024" "m01781r" @@ -4544,10 +4544,10 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "m02644m" "m02644" "occoa" "C01944" "HMDB01070" "CHEBI:15533" "380" "" "" "HC00869" "occoa" "MNXM342" "m02644m" "m02644p" "m02644" "occoa" "C01944" "HMDB01070" "CHEBI:15533" "380" "" "" "HC00869" "occoa" "MNXM342" "m02644p" "m02645c" "m02645" "" "C02863" "" "" "" "" "" "" "M02645" "MNXM7606" "m02645c" -"m02646c" "m02646" "ocdcea" "" "" "CHEBI:30823" "445639" "" "" "HC00510" "ocdcea" "MNXM727011" "m02646c" -"m02646l" "m02646" "ocdcea" "" "" "CHEBI:30823" "445639" "" "" "HC00510" "ocdcea" "MNXM727011" "m02646l" -"m02646r" "m02646" "ocdcea" "" "" "CHEBI:30823" "445639" "" "" "HC00510" "ocdcea" "MNXM727011" "m02646r" -"m02646s" "m02646" "ocdcea" "" "" "CHEBI:30823" "445639" "" "" "HC00510" "ocdcea" "MNXM727011" "m02646s" +"m02646c" "m02646" "ocdcea" "C00712" "HMDB00207" "CHEBI:30823" "5460221" "LMFA01030002" "" "HC00510" "ocdcea" "MNXM306;MNXM727011" "m02646c" +"m02646l" "m02646" "ocdcea" "C00712" "HMDB00207" "CHEBI:30823" "5460221" "LMFA01030002" "" "HC00510" "ocdcea" "MNXM306;MNXM727011" "m02646l" +"m02646r" "m02646" "ocdcea" "C00712" "HMDB00207" "CHEBI:30823" "5460221" "LMFA01030002" "" "HC00510" "ocdcea" "MNXM306;MNXM727011" "m02646r" +"m02646s" "m02646" "ocdcea" "C00712" "HMDB00207" "CHEBI:30823" "5460221" "LMFA01030002" "" "HC00510" "ocdcea" "MNXM306;MNXM727011" "m02646s" "m02647c" "m02647" "odecoa" "C00510" "HMDB01322" "CHEBI:15534" "5280355" "LMFA07050055" "" "HC00400" "odecoa" "MNXM1848;MNXM686" "m02647c" "m02647m" "m02647" "odecoa" "C00510" "HMDB01322" "CHEBI:15534" "5280355" "LMFA07050055" "" "HC00400" "odecoa" "MNXM1848;MNXM686" "m02647m" "m02647p" "m02647" "odecoa" "C00510" "HMDB01322" "CHEBI:15534" "5280355" "LMFA07050055" "" "HC00400" "odecoa" "MNXM1848;MNXM686" "m02647p" @@ -8376,4 +8376,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa "m10040c" "m10040" "" "" "" "" "" "" "" "" "" "" "" "m10041c" "m10041" "" "" "" "" "119046" "" "" "" "" "" "" "m10041s" "m10041" "" "" "" "" "119046" "" "" "" "" "" "" -"m10042c" "m10042" "" "C17689" "" "" "" "" "" "" "" "" "" +"m10042c" "m10042" "" "C17689" "" "" "" "" "" "" "" "" "" \ No newline at end of file