Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix: miscellaneous curations #325

Merged
merged 6 commits into from
Oct 20, 2021
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
22 changes: 11 additions & 11 deletions model/metabolites.tsv
Original file line number Diff line number Diff line change
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 Expand Up @@ -4618,8 +4618,8 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02678m" "MAM02678" "pmtcoa" "C00154" "HMDB01338" "CHEBI:15525" "15667" "LMFA07050002" "" "HC00150" "pmtcoa" "MNXM88" "m02678m" "m02678m"
"MAM02678p" "MAM02678" "pmtcoa" "C00154" "HMDB01338" "CHEBI:15525" "15667" "LMFA07050002" "" "HC00150" "pmtcoa" "MNXM88" "m02678p" "m02678p"
"MAM02678r" "MAM02678" "pmtcoa" "C00154" "HMDB01338" "CHEBI:15525" "15667" "LMFA07050002" "" "HC00150" "pmtcoa" "MNXM88" "m02678r" "m02678r"
"MAM02679c" "MAM02679" "ptth" "C00154" "HMDB01338" "CHEBI:15525" "15667" "" "" "HC00554" "ptth" "MNXM1154" "m02679c" "m02679c"
"MAM02679m" "MAM02679" "ptth" "C00154" "HMDB01338" "CHEBI:15525" "15667" "" "" "HC00554" "ptth" "MNXM1154" "m02679m" "m02679m"
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Why was the associated metBiGGID ptth removed? I think that association was correct.

Copy link
Member Author

@haowang-bioinfo haowang-bioinfo Oct 20, 2021

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

yes, ptth does appear to be correctly annotated in BiGG.

This removal was due to the wrong annotation to metRecon3DID id ptth, which probably should be removed?

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ah, very interesting case - so the ptth entry is correct in BiGG but incorrect in VMH. Although I would like to maintain the association with the Recon3D ID, it may be better to remove it to avoid confusion...

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yes, it is.

Now the BiGG id was added back, while the erroneous Recon3D id excluded.

"MAM02679c" "MAM02679" "ptth" "C00831" "HMDB0003426" "CHEBI:16753" "439322" "" "" "HC00554" "" "MNXM727034" "m02679c" "m02679c"
"MAM02679m" "MAM02679" "ptth" "C00831" "HMDB0003426" "CHEBI:16753" "439322" "" "" "HC00554" "" "MNXM727034" "m02679m" "m02679m"
"MAM02680c" "MAM02680" "pnto__R" "C00864" "HMDB00210" "CHEBI:7916" "988" "" "" "HC00568" "pnto_R" "MNXM364" "m02680c" "m02680c"
"MAM02680s" "MAM02680" "pnto__R" "C00864" "HMDB00210" "CHEBI:7916" "988" "" "" "HC00568" "pnto_R" "MNXM364" "m02680s" "m02680s"
"MAM02681c" "MAM02681" "pap" "C00054" "HMDB00061" "CHEBI:17985" "159296" "" "" "HC00059" "pap" "MNXM45" "m02681c" "m02681c"
Expand Down