Skip to content

Commit

Permalink
Merge pull request #649 from JHL-452b/fix-EHMN
Browse files Browse the repository at this point in the history 
Fix duplicate metabolites identified by EHMN IDs
  • Loading branch information
@haowang-bioinfo
haowang-bioinfo authored Jun 26, 2023
2 parents dbcee94 + 4f98cd4 commit 4443e39
Show file tree
Hide file tree
Showing 5 changed files with 52 additions and 179 deletions.
10 changes: 9 additions & 1 deletion data/deprecatedIdentifiers/deprecatedMetabolites.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2219,4 +2219,12 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM03884c" "MAM03884" "phyt" "C01607" "HMDB0000801" "CHEBI:16285" "26840" "" "" "" "phyt" "MNXM91275" "" "phyt_c"
"MAM03884e" "MAM03884" "phyt" "C01607" "HMDB0000801" "CHEBI:16285" "26840" "" "" "" "phyt" "MNXM91275" "" "phyt_s"
"MAM03554c" "MAM03554" "dmnoncoa" "" "" "" "" "" "" "" "dmnoncoa" "MNXM6100" "" "dmnoncoa_c"
"MAM03884x" "MAM03884" "phyt" "C01607" "HMDB0000801" "CHEBI:16285" "26840" "" "" "" "phyt" "MNXM91275" "" "phyt_p"
"MAM03884x" "MAM03884" "phyt" "C01607" "HMDB0000801" "CHEBI:16285" "26840" "" "" "" "phyt" "MNXM91275" "" "phyt_p"
"MAM03354c" "MAM03354" "CE4837" "C16171" "HMDB0006516" "CHEBI:63548" "53477846" "" "CE4837" "" "CE4837" "MNXM165171" "" "CE4837_c"
"MAM03332c" "MAM03332" "CE2516" "C03242" "HMDB0002925" "CHEBI:53486" "5280581" "" "CE2516" "" "CE2516" "MNXM5607" "" "CE2516_c"
"MAM03332e" "MAM03332" "" "C03242" "HMDB0002925" "CHEBI:53486" "5280581" "" "CE2516" "" "CE2516" "" "" "CE2516_s"
"MAM03354r" "MAM03354" "CE4837" "C16171" "HMDB0006516" "CHEBI:63548" "53477846" "" "CE4837" "" "CE4837" "MNXM165171" "" "CE4837_r"
"MAM00029c" "MAM00029" "" "" "" "CHEBI:81563" "16061126" "LMFA03070025" "CE7090" "" "CE7090" "MNXM33782" "m00029c" "m00029c"
"MAM03368m" "MAM03368" "" "C05467" "HMDB0006891" "CHEBI:27379" "440690" "" "CE5169" "" "CE5169" "" "" "CE5169_m"
"MAM03368x" "MAM03368" "" "C05467" "HMDB0006891" "CHEBI:27379" "440690" "" "CE5169" "" "CE5169" "" "" "CE5169_p"
"MAM00902c" "MAM00902" "" "" "" "" "" "" "CE4820" "" "CE4820" "MNXM164259" "m00902c" "m00902c"
6 changes: 5 additions & 1 deletion data/deprecatedIdentifiers/deprecatedReactions.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -180,4 +180,8 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR00740" "" "FACOAL206" "" "" "" "FACOAL206" "MNXR99186" "" "" "" 0 "" "" "FACOAL206"
"MAR01617" "" "PHYTt" "" "" "" "PHYTt" "MNXR102660" "" "" "" 0 "" "" "PHYTt"
"MAR01709" "" "SCP22x" "" "" "" "SCP22x" "MNXR104294" "" "" "" 0 "" "" "SCP22x"
"MAR05323" "" "FAOXC16Brx" "" "" "" "FAOXC16BRx" "MNXR99186" "" "" "" 0 "" "" "FAOXC16BRx"
"MAR05323" "" "FAOXC16Brx" "" "" "" "FAOXC16BRx" "MNXR99186" "" "" "" 0 "" "" "FAOXC16BRx"
"MAR02588" "" "" "RE3503C" "" "" "RE3503C" "MNXR103936" "HMR_2588" "RCR12020" "" 0 "" "" "HMR_2588"
"MAR03441" "" "RE3150C" "" "" "" "RE3150C" "MNXR103806" "" "" "" 0 "" "" "RE3150C"
"MAR10164" "" "" "" "" "" "CE2516t" "" "" "" "" 0 "" "" "CE2516t"
"MAR10433" "" "" "" "" "" "EX_CE2516[e]" "" "" "" "" 0 "" "" "EX_CE2516[e]"
172 changes: 22 additions & 150 deletions model/Human-GEM.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -625,14 +625,6 @@
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00029c"
- name: "(18R)-hydroxy-(5Z,8Z,11Z,14Z,16E)-eicosapentaenoic acid"
- compartment: "c"
- formula: "C20H29O3"
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00030c"
- name: "(1aalpha,2beta,3alpha,11calpha)-1a,2,3,11c-tetrahydro-6,11-dimethylbenzo[6,7]phenanthro[3,4-b]oxirene-2,3-diol"
Expand Down Expand Up @@ -11553,14 +11545,6 @@
- charge: -4
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00902c"
- name: "3-oxo-tetracosa-9,12,15,18,21-all-cis-pentaenoyl-CoA"
- compartment: "c"
- formula: "C45H66N7O18P3S"
- charge: -4
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00903c"
- name: "3-oxo-tetracosa-9,12,15,18-all-cis-tetraenoyl-CoA"
Expand Down Expand Up @@ -48385,14 +48369,6 @@
- charge: 0
- inchis: "InChI=1S/C23H34O3/c1-15(10-12-24)20-8-9-21-17(5-4-11-23(20,21)3)6-7-18-13-19(25)14-22(26)16(18)2/h6-7,12,15,19-22,25-26H,2,4-5,8-11,13-14H2,1,3H3/b17-6+,18-7-/t15-,19+,20-,21+,22+,23?/m0/s1"
- metFrom: "Recon3D"
- !!omap
- id: "MAM03354c"
- name: "Tetracosa-9,12,15,18-All-Cis-Tetraenoyl Coenzyme A"
- compartment: "c"
- formula: "C45H70N7O17P3S"
- charge: -4
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM00681r"
- name: "2-trans-9,12,15,18-all-cis-tetracosapentaenoyl-CoA"
Expand All @@ -48401,14 +48377,6 @@
- charge: -4
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03354r"
- name: "Tetracosa-9,12,15,18-All-Cis-Tetraenoyl Coenzyme A"
- compartment: "r"
- formula: "C45H70N7O17P3S"
- charge: -4
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM00864r"
- name: "3-oxo-docosa-7,10,13,16-all-cis-tetraenoyl-CoA"
Expand Down Expand Up @@ -48777,22 +48745,6 @@
- charge: -4
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03368m"
- name: "24-Oxo-25(R)-Trihydroxycoprostanoyl Coenzyme A"
- compartment: "m"
- formula: "C48H74N7O21P3S"
- charge: -4
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03368x"
- name: "24-Oxo-25(R)-Trihydroxycoprostanoyl Coenzyme A"
- compartment: "x"
- formula: "C48H74N7O21P3S"
- charge: -4
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM01428e"
- name: "CDP-ethanolamine"
Expand Down Expand Up @@ -49297,14 +49249,6 @@
- charge: -5
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03332c"
- name: "(8Z,11Z,14Z)-Eicosatrienoic Acid"
- compartment: "c"
- formula: "C20H33O2"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM02785n"
- name: "prostaglandin E1"
Expand Down Expand Up @@ -54041,14 +53985,6 @@
- charge: 0
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM03332e"
- name: "(8Z,11Z,14Z)-Eicosatrienoic Acid"
- compartment: "e"
- formula: "C20H33O2"
- charge: -1
- inchis: ""
- metFrom: "Recon3D"
- !!omap
- id: "MAM00378e"
- name: "15(S)-HETrE"
Expand Down Expand Up @@ -67879,15 +67815,24 @@
- compartment: "m"
- formula: "C24H39O4"
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM01729e"
- name: "dodecanoylcarnitine"
- compartment: "e"
- formula: "C19H37NO4"
- charge: 0

- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00853c"
- name: "3-oxo-all-cis-6,9,12,15,18-tetracosapentaenoyl-CoA"
- compartment: "c"
- formula: "C45H66N7O18P3S"
- charge: -4
- inchis: ""
- metFrom: "Recon3D"
- reactions:
- !!omap
- id: "MAR03905"
Expand Down Expand Up @@ -101431,7 +101376,7 @@
- name: ""
- metabolites: !!omap
- MAM00121c: -1
- MAM00902c: 1
- MAM00853c: 1
- MAM01596c: 1
- MAM01597c: 1
- MAM02039c: -1
Expand All @@ -101451,7 +101396,7 @@
- name: ""
- metabolites: !!omap
- MAM00718c: 1
- MAM00902c: -1
- MAM00853c: -1
- MAM02039c: -1
- MAM02554c: 1
- MAM02555c: -1
Expand Down Expand Up @@ -102564,7 +102509,7 @@
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.13.11.34"
- references: ""
- references: "PMID:11034610"
- subsystem:
- "Omega-3 fatty acid metabolism"
- confidence_score: 0
Expand All @@ -102585,24 +102530,6 @@
- subsystem:
- "Omega-3 fatty acid metabolism"
- confidence_score: 0
- !!omap
- id: "MAR02588"
- name: ""
- metabolites: !!omap
- MAM00029c: -1
- MAM01056c: 1
- MAM02040c: 1
- MAM02630c: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000012779"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.13.11.34"
- references: "PMID:11034610"
- subsystem:
- "Omega-3 fatty acid metabolism"
- confidence_score: 0
- !!omap
- id: "MAR02368"
- name: "linoleoyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (6,7 cis-dehydrogenating)"
Expand Down Expand Up @@ -102885,9 +102812,9 @@
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000099797 or ENSG00000205678"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- rxnFrom: "HMRdatabase;Recon3D"
- eccodes: "1.3.1.93"
- references: "PMID:10970790;PMID:10970790"
- references: "PMID:10970790;PMID:10970790;PMID:10970790"
- subsystem:
- "Omega-6 fatty acid metabolism"
- confidence_score: 0
Expand Down Expand Up @@ -169370,9 +169297,9 @@
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000165029"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- rxnFrom: "HMRdatabase;Recon3D"
- eccodes: ""
- references: "PMID:16858612"
- references: "PMID:16858612;PMID:24653705;PMID:9831619;PMID:5555776;PMID:23104810"
- subsystem:
- "Transport reactions"
- confidence_score: 0
Expand Down Expand Up @@ -218731,7 +218658,7 @@
- MAM00005c: -1
- MAM00013c: -1
- MAM00014x: -1
- MAM00029c: -1
- MAM00028c: -1
- MAM00254c: -1
- MAM00254m: -1
- MAM00254x: -1
Expand Down Expand Up @@ -234646,7 +234573,7 @@
- name: ""
- metabolites: !!omap
- MAM00119c: -1
- MAM00902c: 1
- MAM00853c: 1
- MAM01596c: 1
- MAM01597c: 1
- MAM02039c: 1
Expand Down Expand Up @@ -234681,34 +234608,15 @@
- subsystem:
- "Fatty acid oxidation"
- confidence_score: 0
- !!omap
- id: "MAR03441"
- name: ""
- metabolites: !!omap
- MAM00681c: -1
- MAM02039c: -1
- MAM02554c: 1
- MAM02555c: -1
- MAM03354c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: "PMID:10970790"
- subsystem:
- "Fatty acid oxidation"
- confidence_score: 0
- !!omap
- id: "MAR03442"
- name: ""
- metabolites: !!omap
- MAM00131r: 1
- MAM00681r: -1
- MAM02039r: -1
- MAM02554r: 1
- MAM02555r: -1
- MAM03354r: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000066322"
Expand Down Expand Up @@ -235731,11 +235639,11 @@
- id: "MAR03760"
- name: "3-Hydroxyacyl Coenzyme A Dehydrogenase"
- metabolites: !!omap
- MAM00748m: 1
- MAM02039m: 1
- MAM02552m: -1
- MAM02553m: 1
- MAM03367m: -1
- MAM03368m: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000072506 or ENSG00000113790 or ENSG00000133835 or ENSG00000138796"
Expand All @@ -235750,11 +235658,11 @@
- id: "MAR03764"
- name: "3-Hydroxyacyl Coenzyme A Dehydrogenase"
- metabolites: !!omap
- MAM00748x: 1
- MAM02039x: 1
- MAM02552x: -1
- MAM02553x: 1
- MAM03367x: -1
- MAM03368x: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000113790 or ENSG00000133835"
Expand Down Expand Up @@ -252077,27 +251985,6 @@
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR10164"
- name: "Transport of (8Z, 11Z, 14Z)-Eicosatrienoic Acid, Active Transport"
- metabolites: !!omap
- MAM01285c: 1
- MAM01371c: -1
- MAM02039c: 1
- MAM02040c: -1
- MAM02751c: 1
- MAM03332c: -1
- MAM03332e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: "PMID:24653705;PMID:9831619;PMID:5555776;PMID:23104810"
- subsystem:
- "Transport reactions"
- confidence_score: 0
- !!omap
- id: "MAR10165"
- name: "Transport of 15-Hydroxy- (8Z, 11Z, 13E)-Eicosatrienoate, Active Transport"
Expand Down Expand Up @@ -256331,21 +256218,6 @@
- subsystem:
- "Exchange/demand reactions"
- confidence_score: 0
- !!omap
- id: "MAR10433"
- name: "Exchangefor (8Z, 11Z, 14Z)-Eicosatrienoic Acid"
- metabolites: !!omap
- MAM03332e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: ""
- references: ""
- subsystem:
- "Exchange/demand reactions"
- confidence_score: 0
- !!omap
- id: "MAR10434"
- name: "Exchange of Laurate"
Expand Down
Loading

0 comments on commit 4443e39

Please sign in to comment.