Merge pull request #650 from JHL-452b/fix-LipidMaps

Fix duplicate metabolites identified by LipidMaps IDs
SysBioChalmers · Jun 28, 2023 · dc74c65 · dc74c65
2 parents 4670c79 + 209e86f
commit dc74c65
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diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2228,3 +2228,4 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "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"
+"MAM00759c"	"MAM00759"	""	"C13712"	""	""	""	"LMST02030130"	""	""	"M00759"	"MNXM3494"	"m00759c"	"m00759c"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -9937,14 +9937,6 @@
       - charge: -1
       - inchis: ""
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM00759c"
-      - name: "3alpha-hydroxy-5alpha-pregnan-20-one"
-      - compartment: "c"
-      - formula: "C21H34O2"
-      - charge: 0
-      - inchis: ""
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM00760c"
       - name: "3-amino-propanal"
@@ -123346,8 +123338,8 @@
       - id: "MAR02003"
       - name: "3alpha-hydroxy-5alpha-pregnan-20-one:NADP+ 3-oxidoreductase (A-specific)"
       - metabolites: !!omap
-          - MAM00759c: -1
           - MAM01072c: 1
+          - MAM01314c: -1
           - MAM02039c: 1
           - MAM02554c: -1
           - MAM02555c: 1
@@ -218810,7 +218802,6 @@
           - MAM00660c: -1
           - MAM00660r: -1
           - MAM00747r: -1
-          - MAM00759c: -1
           - MAM00828r: -1
           - MAM00830c: -1
           - MAM00925c: -1
@@ -218829,6 +218820,7 @@
           - MAM01001x: -1
           - MAM01011c: -1
           - MAM01012c: -1
+          - MAM01314c: -1
           - MAM01792r: -1
           - MAM01794r: -1
           - MAM02469c: -1

diff --git a/model/metabolites.tsv b/model/metabolites.tsv
@@ -118,9 +118,9 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM00054m"	"MAM00054"	""	""	""	""	""	""	""	""	"M00054"	""	"m00054m"	"m00054m"
 "MAM00055c"	"MAM00055"	""	""	""	""	""	""	""	""	"M00055"	""	"m00055c"	"m00055c"
 "MAM00056m"	"MAM00056"	""	""	""	"CHEBI:76292"	""	""	""	""	"M00056"	"MNXM170116"	"m00056m"	"m00056m"
-"MAM00057c"	"MAM00057"	"od2coa"	"C16218"	"HMDB0006529"	"CHEBI:50570"	"53477850"	"LMFA07050055"	""	""	"od2coa"	"MNXM954"	"m00057c"	"m00057c"
-"MAM00057m"	"MAM00057"	"od2coa"	"C16218"	"HMDB0006529"	"CHEBI:50570"	"53477850"	"LMFA07050055"	""	""	"od2coa"	"MNXM954"	"m00057m"	"m00057m"
-"MAM00057x"	"MAM00057"	"od2coa"	"C16218"	"HMDB0006529"	"CHEBI:50570"	"53477850"	"LMFA07050055"	""	""	"od2coa"	"MNXM954"	"m00057p"	"m00057p"
+"MAM00057c"	"MAM00057"	"od2coa"	"C16218"	"HMDB0006529"	"CHEBI:50570"	"53477850"	"LMFA07050385"	""	""	"od2coa"	"MNXM954"	"m00057c"	"m00057c"
+"MAM00057m"	"MAM00057"	"od2coa"	"C16218"	"HMDB0006529"	"CHEBI:50570"	"53477850"	"LMFA07050385"	""	""	"od2coa"	"MNXM954"	"m00057m"	"m00057m"
+"MAM00057x"	"MAM00057"	"od2coa"	"C16218"	"HMDB0006529"	"CHEBI:50570"	"53477850"	"LMFA07050385"	""	""	"od2coa"	"MNXM954"	"m00057p"	"m00057p"
 "MAM00058c"	"MAM00058"	""	"C05751"	""	""	""	""	""	"HC01594"	"HC01594"	"MNXM23766"	"m00058c"	"m00058c"
 "MAM00059m"	"MAM00059"	""	"C05276"	""	"CHEBI:27537"	"46173358"	"LMFA07050024"	""	"HC01415"	"HC01415"	"MNXM784"	"m00059m"	"m00059m"
 "MAM00059x"	"MAM00059"	""	"C05276"	""	"CHEBI:27537"	"46173358"	"LMFA07050024"	""	"HC01415"	"HC01415"	"MNXM784"	"m00059p"	"m00059p"
@@ -1240,7 +1240,6 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM00758m"	"MAM00758"	"dhcholestanate"	"C04554"	"HMDB0000359"	"CHEBI:48467"	"53477686"	"LMST04030066"	""	"HC01313"	"dhcholestanate"	"MNXM162671;MNXM688"	"m00758m"	"m00758m"
 "MAM00758x"	"MAM00758"	"dhcholestanate"	"C04554"	"HMDB0000359"	"CHEBI:48467"	"53477686"	"LMST04030066"	""	"HC01313"	"dhcholestanate"	"MNXM162671;MNXM688"	"m00758p"	"m00758p"
 "MAM00758r"	"MAM00758"	"dhcholestanate"	"C04554"	"HMDB0000359"	"CHEBI:48467"	"53477686"	"LMST04030066"	""	"HC01313"	"dhcholestanate"	"MNXM162671;MNXM688"	"m00758r"	"m00758r"
-"MAM00759c"	"MAM00759"	""	"C13712"	""	""	""	"LMST02030130"	""	""	"M00759"	"MNXM3494"	"m00759c"	"m00759c"
 "MAM00760c"	"MAM00760"	""	"C05665"	""	"CHEBI:58374"	"75"	""	""	""	"bamppald"	"MNXM43758"	"m00760c"	"m00760c"
 "MAM00761m"	"MAM00761"	""	""	""	""	"3081084"	""	"CE3038"	""	"CE3038"	"MNXM6853"	"m00761m"	"m00761m"
 "MAM00762g"	"MAM00762"	"cs_hs_linkage"	"C04903"	""	"G00157"	""	""	""	""	"cs_hs_linkage"	"MNXM147451"	"m00762g"	"m00762g"
@@ -1427,14 +1426,14 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM00890m"	"MAM00890"	"3ohodcoa"	"C16216"	"HMDB0006498"	"CHEBI:50571"	"22833663"	""	""	""	"3ohodcoa"	"MNXM513"	"m00890m"	"m00890m"
 "MAM00890x"	"MAM00890"	"3ohodcoa"	"C16216"	"HMDB0006498"	"CHEBI:50571"	"22833663"	""	""	""	"3ohodcoa"	"MNXM513"	"m00890p"	"m00890p"
 "MAM00891c"	"MAM00891"	""	"C05750"	""	""	""	""	""	"HC01593"	"HC01593"	"MNXM28031"	"m00891c"	"m00891c"
-"MAM00892m"	"MAM00892"	""	"C05267"	""	"CHEBI:28264"	"11966162"	"LMFA07050016"	""	"HC01406"	"HC01406"	"MNXM706"	"m00892m"	"m00892m"
-"MAM00892x"	"MAM00892"	""	"C05267"	""	"CHEBI:28264"	"11966162"	"LMFA07050016"	""	"HC01406"	"HC01406"	"MNXM706"	"m00892p"	"m00892p"
+"MAM00892m"	"MAM00892"	""	"C05267"	""	"CHEBI:28264"	"11966162"	"LMFA07050249"	""	"HC01406"	"HC01406"	"MNXM706"	"m00892m"	"m00892m"
+"MAM00892x"	"MAM00892"	""	"C05267"	""	"CHEBI:28264"	"11966162"	"LMFA07050249"	""	"HC01406"	"HC01406"	"MNXM706"	"m00892p"	"m00892p"
 "MAM00893m"	"MAM00893"	""	""	""	""	""	""	"CE5160"	"HC10858"	"HC10858"	"MNXM150997"	"m00893m"	"m00893m"
 "MAM00893x"	"MAM00893"	""	""	""	""	""	""	"CE5160"	"HC10858"	"HC10858"	"MNXM150997"	"m00893p"	"m00893p"
 "MAM00894m"	"MAM00894"	""	""	""	""	"440601"	""	"CE0853"	"HC10853"	"CE0853;HC10853"	"MNXM166250"	"m00894m"	"m00894m"
 "MAM00894x"	"MAM00894"	""	""	""	""	"440601"	""	"CE0853"	"HC10853"	"CE0853;HC10853"	"MNXM166250"	"m00894p"	"m00894p"
-"MAM00895m"	"MAM00895"	"3ohdcoa"	"C05259"	""	"CHEBI:15491"	"169621"	"LMFA07050016"	""	"HC01398"	"3ohdcoa"	"MNXM738"	"m00895m"	"m00895m"
-"MAM00895x"	"MAM00895"	"3ohdcoa"	"C05259"	""	"CHEBI:15491"	"169621"	"LMFA07050016"	""	"HC01398"	"3ohdcoa"	"MNXM738"	"m00895p"	"m00895p"
+"MAM00895m"	"MAM00895"	"3ohdcoa"	"C05259"	""	"CHEBI:15491"	"169621"	"LMFA07050250"	""	"HC01398"	"3ohdcoa"	"MNXM738"	"m00895m"	"m00895m"
+"MAM00895x"	"MAM00895"	"3ohdcoa"	"C05259"	""	"CHEBI:15491"	"169621"	"LMFA07050250"	""	"HC01398"	"3ohdcoa"	"MNXM738"	"m00895p"	"m00895p"
 "MAM00896c"	"MAM00896"	""	""	""	""	""	""	""	""	"M00896"	""	"m00896c"	"m00896c"
 "MAM00897m"	"MAM00897"	""	""	""	""	""	""	""	""	"M00897"	""	"m00897m"	"m00897m"
 "MAM00898c"	"MAM00898"	""	""	""	""	""	""	""	""	"M00898"	""	"m00898c"	"m00898c"
@@ -2084,7 +2083,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM01311x"	"MAM01311"	"akgp_hs"	"C03715"	""	"CHEBI:17197"	""	""	""	""	"akgp_hs"	"MNXM9595"	"m01311p"	"m01311p"
 "MAM01312c"	"MAM01312"	""	"C00499"	"HMDB0001209"	"CHEBI:30837"	"203"	""	""	""	"alltt"	"MNXM584"	"m01312c"	"m01312c"
 "MAM01313c"	"MAM01313"	""	"C01551"	"HMDB0000462"	"CHEBI:15676"	"204"	""	""	""	"alltn"	"MNXM612"	"m01313c"	"m01313c"
-"MAM01314c"	"MAM01314"	""	"C13712"	"HMDB0001449"	"CHEBI:50169"	"92786"	"LMST02030130"	"CE2211"	""	"CE2211"	"MNXM3494"	"m01314c"	"m01314c"
+"MAM01314c"	"MAM01314"	""	"C13712"	"HMDB0001449"	"CHEBI:50169"	"92786"	"LMST02030130"	"CE2211"	""	"CE2211"	"MNXM3494"	"m01314c"	"m01314c;MAM00759c"
 "MAM01315c"	"MAM01315"	""	"C07599"	"HMDB0002818"	"CHEBI:730073"	"5781"	""	"CE0074"	""	"CE0074"	"MNXM15828"	"m01315c"	"m01315c"
 "MAM01315e"	"MAM01315"	""	"C07599"	"HMDB0002818"	"CHEBI:730073"	"5781"	""	"CE0074"	""	"CE0074"	"MNXM15828"	"m01315s"	"m01315s"
 "MAM01316c"	"MAM01316"	"decdp"	""	""	""	""	""	""	""	"decdp"	"MNXM1721"	"m01316c"	"m01316c"
@@ -4538,10 +4537,10 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02646l"	"MAM02646"	"ocdcea"	"C00712"	"HMDB0000207"	"CHEBI:30823"	"5460221"	"LMFA01030002"	""	"HC00510"	"ocdcea"	"MNXM306;MNXM727011"	"m02646l"	"m02646l"
 "MAM02646r"	"MAM02646"	"ocdcea"	"C00712"	"HMDB0000207"	"CHEBI:30823"	"5460221"	"LMFA01030002"	""	"HC00510"	"ocdcea"	"MNXM306;MNXM727011"	"m02646r"	"m02646r"
 "MAM02646e"	"MAM02646"	"ocdcea"	"C00712"	"HMDB0000207"	"CHEBI:30823"	"5460221"	"LMFA01030002"	""	"HC00510"	"ocdcea"	"MNXM306;MNXM727011"	"m02646s"	"m02646s"
-"MAM02647c"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5280355"	"LMFA07050055"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647c"	"m02647c"
-"MAM02647m"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5280355"	"LMFA07050055"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647m"	"m02647m"
-"MAM02647x"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5497111"	"LMFA07050055"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647p"	"m02647p"
-"MAM02647r"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5280355"	"LMFA07050055"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647r"	"m02647r"
+"MAM02647c"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5280355"	"LMFA07050356"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647c"	"m02647c"
+"MAM02647m"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5280355"	"LMFA07050356"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647m"	"m02647m"
+"MAM02647x"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5497111"	"LMFA07050356"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647p"	"m02647p"
+"MAM02647r"	"MAM02647"	"odecoa"	"C00510"	"HMDB0001322"	"CHEBI:15534"	"5280355"	"LMFA07050356"	""	"HC00400"	"odecoa"	"MNXM1848;MNXM686"	"m02647r"	"m02647r"
 "MAM02648c"	"MAM02648"	"eicostet"	""	"HMDB0002177"	""	"11722594"	"LMFA01030176"	""	""	"eicostet"	"MNXM11474"	"m02648c"	"m02648c"
 "MAM02648l"	"MAM02648"	"eicostet"	""	"HMDB0002177"	""	"11722594"	"LMFA01030176"	""	""	"eicostet"	"MNXM11474"	"m02648l"	"m02648l"
 "MAM02648r"	"MAM02648"	"eicostet"	""	"HMDB0002177"	""	"11722594"	"LMFA01030176"	""	""	"eicostet"	"MNXM11474"	"m02648r"	"m02648r"
@@ -5788,7 +5787,7 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM02385x"	"MAM02385"	"lgnc"	"C08320"	"HMDB0002003"	"CHEBI:28866"	"11197"	"LMFA01010024"	""	"HC01788"	"lgnc"	"MNXM3297;MNXM8841"	""	"m02385p"
 "MAM00890r"	"MAM00890"	"3ohodcoa"	"C16216"	"HMDB0006498"	"CHEBI:50571"	"22833663"	""	""	""	"3ohodcoa"	"MNXM513"	""	"m00890r"
 "MAM00793r"	"MAM00793"	""	""	""	""	"24906329"	""	"CE2248"	""	"CE2248"	"MNXM1309"	""	"m00793r"
-"MAM00057n"	"MAM00057"	"od2coa"	"C16218"	"HMDB0006529"	"CHEBI:50570"	"53477850"	"LMFA07050055"	""	""	"od2coa"	"MNXM954"	""	"m00057n"
+"MAM00057n"	"MAM00057"	"od2coa"	"C16218"	"HMDB0006529"	"CHEBI:50570"	"53477850"	"LMFA07050385"	""	""	"od2coa"	"MNXM954"	""	"m00057n"
 "MAM00793n"	"MAM00793"	""	""	""	""	"24906329"	""	"CE2248"	""	"CE2248"	"MNXM1309"	""	"m00793n"
 "MAM02941n"	"MAM02941"	"stcoa"	"C00412"	"HMDB0001114"	"CHEBI:15541"	"439229"	"LMFA07050004"	""	"HC00338"	"stcoa"	"MNXM272"	""	"m02941n"
 "MAM02158e"	"MAM02158"	""	""	""	""	"124985"	""	"CE2011"	""	"CE2011"	"MNXM57006"	""	"m02158s"