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fix: miscellaneous curations #325

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merged 6 commits into from
Oct 20, 2021
Merged

fix: miscellaneous curations #325

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86320d9
fix: change perxisome compartment abbreviation from "p" to "x"
haowang-bioinfo Oct 9, 2021
9897c06
fix: resolve identical mets in both sides of MAR04499
haowang-bioinfo Oct 10, 2021
a6b078d
fix: add CHEBI xref to MAM00003
haowang-bioinfo Oct 10, 2021
fb981b0
fix: add new CHEBI ids as suggested in #300
haowang-bioinfo Oct 10, 2021
082f865
fix: correct xref for MAM02679, as discussed in #297
haowang-bioinfo Oct 17, 2021
1a824e5
fix: add back BiGG id `ptth` that is correctly associated
haowang-bioinfo Oct 20, 2021
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2 changes: 1 addition & 1 deletion model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -313185,7 +313185,7 @@
- id: "ENSG00000285269"
- compartments: !!omap
- s: "Extracellular"
- p: "Peroxisome"
- x: "Peroxisome"
- m: "Mitochondria"
- c: "Cytosol"
- l: "Lysosome"
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18 changes: 9 additions & 9 deletions model/metabolites.tsv
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Expand Up @@ -3,14 +3,14 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM00001s" "MAM00001" "carveol" "C00964" "" "CHEBI:15389" "" "" "" "" "carveol" "MNXM45735" "m00001s" "m00001s"
"MAM00002c" "MAM00002" "appnn" "C09880" "HMDB06525" "CHEBI:36740" "6654" "" "" "" "appnn" "MNXM163755" "m00002c" "m00002c"
"MAM00002s" "MAM00002" "appnn" "C09880" "HMDB06525" "CHEBI:36740" "6654" "" "" "" "appnn" "MNXM163755" "m00002s" "m00002s"
"MAM00003c" "MAM00003" "" "" "" "" "" "LMFA01030283" "" "" "M00003" "MNXM150165;MNXM27815" "m00003c" "m00003c"
"MAM00003l" "MAM00003" "" "" "" "" "" "LMFA01030283" "" "" "M00003" "MNXM150165;MNXM27815" "m00003l" "m00003l"
"MAM00003r" "MAM00003" "" "" "" "" "" "LMFA01030283" "" "" "M00003" "MNXM150165;MNXM27815" "m00003r" "m00003r"
"MAM00003s" "MAM00003" "" "" "" "" "" "LMFA01030283" "" "" "M00003" "MNXM150165;MNXM27815" "m00003s" "m00003s"
"MAM00003c" "MAM00003" "" "" "" "CHEBI:78990" "" "LMFA01030283" "" "" "M00003" "MNXM150165;MNXM27815" "m00003c" "m00003c"
"MAM00003l" "MAM00003" "" "" "" "CHEBI:78990" "" "LMFA01030283" "" "" "M00003" "MNXM150165;MNXM27815" "m00003l" "m00003l"
"MAM00003r" "MAM00003" "" "" "" "CHEBI:78990" "" "LMFA01030283" "" "" "M00003" "MNXM150165;MNXM27815" "m00003r" "m00003r"
"MAM00003s" "MAM00003" "" "" "" "CHEBI:78990" "" "LMFA01030283" "" "" "M00003" "MNXM150165;MNXM27815" "m00003s" "m00003s"
"MAM00004c" "MAM00004" "" "" "" "" "" "" "" "" "M00004" "MNXM148601" "m00004c" "m00004c"
"MAM00004m" "MAM00004" "" "" "" "" "" "" "" "" "M00004" "MNXM148601" "m00004m" "m00004m"
"MAM00004r" "MAM00004" "" "" "" "" "" "" "" "" "M00004" "MNXM148601" "m00004r" "m00004r"
"MAM00005c" "MAM00005" "" "" "" "" "" "LMFA03060071" "" "" "M00005" "MNXM9658" "m00005c" "m00005c"
"MAM00005c" "MAM00005" "" "" "" "CHEBI:34127" "" "LMFA03060071" "" "" "M00005" "MNXM9658" "m00005c" "m00005c"
"MAM00006c" "MAM00006" "" "" "" "" "" "" "" "" "M00006" "" "m00006c" "m00006c"
"MAM00006m" "MAM00006" "" "" "" "" "" "" "" "" "M00006" "" "m00006m" "m00006m"
"MAM00006r" "MAM00006" "" "" "" "" "" "" "" "" "M00006" "" "m00006r" "m00006r"
Expand Down Expand Up @@ -104,7 +104,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM00044c" "MAM00044" "" "" "" "" "" "" "" "" "M00044" "" "m00044c" "m00044c"
"MAM00044m" "MAM00044" "" "" "" "" "" "" "" "" "M00044" "" "m00044m" "m00044m"
"MAM00045c" "MAM00045" "" "" "" "" "" "" "" "" "M00045" "" "m00045c" "m00045c"
"MAM00046m" "MAM00046" "" "" "" "" "" "" "" "" "M00046" "MNXM170113" "m00046m" "m00046m"
"MAM00046m" "MAM00046" "" "" "" "CHEBI:77551" "" "" "" "" "M00046" "MNXM170113" "m00046m" "m00046m"
"MAM00047c" "MAM00047" "" "" "" "" "" "" "" "" "M00047" "" "m00047c" "m00047c"
"MAM00048m" "MAM00048" "" "" "" "" "" "" "" "" "M00048" "" "m00048m" "m00048m"
"MAM00049c" "MAM00049" "" "" "" "" "" "" "" "" "M00049" "MNXM114303" "m00049c" "m00049c"
Expand Down Expand Up @@ -4259,9 +4259,9 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02482c" "MAM02482" "" "C00305" "" "CHEBI:18420" "" "" "" "" "mg2" "MNXM653" "m02482c" "m02482c"
"MAM02482s" "MAM02482" "" "C00305" "" "CHEBI:18420" "" "" "" "" "mg2" "MNXM653" "m02482s" "m02482s"
"MAM02483r" "MAM02483" "mgacpail_hs" "" "" "" "" "" "" "" "mgacpail_hs" "MNXM6329" "m02483r" "m02483r"
"MAM02484m" "MAM02484" "" "C03688" "" "" "" "PROTEIN" "" "HC02223" "HC02223" "MNXM91491" "m02484m" "m02484m"
"MAM02485c" "MAM02485" "" "C03688" "" "" "" "PROTEIN" "" "HC02222" "HC02222" "MNXM91491" "m02485c" "m02485c"
"MAM02485m" "MAM02485" "" "C03688" "" "" "" "PROTEIN" "" "HC02222" "HC02222" "MNXM91491" "m02485m" "m02485m"
"MAM02484m" "MAM02484" "" "C00229" "" "CHEBI:64479" "" "PROTEIN" "" "HC02223" "HC02223" "MNXM128788" "m02484m" "m02484m"
"MAM02485c" "MAM02485" "" "C03688" "" "CHEBI:29999" "" "PROTEIN" "" "HC02222" "HC02222" "MNXM59538" "m02485c" "m02485c"
"MAM02485m" "MAM02485" "" "C03688" "" "CHEBI:29999" "" "PROTEIN" "" "HC02222" "HC02222" "MNXM59538" "m02485m" "m02485m"
"MAM02486m" "MAM02486" "" "C00343" "" "CHEBI:18191" "" "" "" "HC02225" "trdox" "MNXM148" "m02486m" "m02486m"
"MAM02487c" "MAM02487" "" "C00342" "" "CHEBI:15967" "" "" "" "HC02224" "trdrd" "MNXM96993" "m02487c" "m02487c"
"MAM02487m" "MAM02487" "" "C00342" "" "CHEBI:15967" "" "" "" "HC02224" "trdrd" "MNXM96993" "m02487m" "m02487m"
Expand Down