Fix/update_IDs #220
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Fix/update_IDs #220
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…X and KEGG) New reaction IDs are found during manual curation of reactions in the model. These IDs either replace the current model IDs or are added into the model (if no IDs were originally present). Inappropriately annotated or deprecated IDs have also been removed. Details of the changes, such as the rationale for the addition of IDs or changes of IDs are recorded in modifyID.tsv, under the various notes.
…aNetX, KEGG and ChEBI) New metabolite IDs are found during manual curation of metabolites in the model. These IDs either replace the current model IDs or are added into the model (if no IDs were originally present). Details of the changes, such as the rationale for the addition of IDs or changes of IDs are recorded in modifyID.tsv, under the various notes.
With the function mapIDsViaMNXref from RAVEN, model.rxnMetaNetXID is mapped as follows: 1) rxnMetaNetXID -> rxnKEGGID 2) rxnMetaNetXID -> rxnMetaCycID -> rxnKEGGID 3) rxnMetaNetXID -> rxnSEEDID -> rxnKEGGID Total unique rxnKEGGID added: 134
With the function mapIDsViaMNXref from RAVEN, model.metMetaNetXID is mapped as follows: 1) metMetaNetXID -> metKEGGID 2) metMetaNetXID -> metMetaCycID -> metKEGGID 3) metMetaNetXID -> metSEEDID -> metKEGGID Total unique metKEGGID added: 15
model.metChEBIID and model.metKEGGID is mapped to find new MNXMID(s). New MNXMID(s) will only be added if 1 of the following 3 criteria is met: a) Both metKEGGID and metChEBIID is mapped to the same MNXMID b) Only metKEGGID mapped to MNXMID, metFormula of new MNXMID matches model.metFormula c) Only metChEBIID mapped to MNXMID, metFormula of new MNXMID matches model.metFormula Total unique MNXMIDs added: 52
eiden309
added
enhancement
…yID.tsv Added lines 135 – 137, 168 – 170, 203 – 205 to remove metabolite ID annotation in model, based on modifyID.tsv. Minor correction made to modifyID.tsv: 1) Remove unnecessary metabolite and alternative metabolite ID entries which causes duplicated or lengthy notes 2) Correct errors generated when importing deprecated IDs into modifyID.tsv.
edkerk
reviewed
May 16, 2020
edkerk
requested changes
May 16, 2020
feiranl
reviewed
May 17, 2020
feiranl
reviewed
May 17, 2020
feiranl
reviewed
May 17, 2020
feiranl
reviewed
May 17, 2020
feiranl
reviewed
May 17, 2020
Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
New mapKEGGID.m is able to check whether MetaCyc or modelSEED data is downloaded/imported successfully, and clear warning message will be displayed if download/import is unsuccessful.
BenjaSanchez
approved these changes
May 20, 2020
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also looks good from my side, and the model changes don't conflict with the work in #188 (close to finishing my work there)
feiranl
approved these changes
May 20, 2020
This was referenced May 27, 2020
Merged
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Main improvements in this PR:
1. After manual curation of deprecated IDs and selected unbalanced reactions (details found in modifyID.tsv), used script
modifyID.mto:*Numbers reported corresponds to the number of unique IDs updated, added or removed
**Addresses #215 metabolite and reaction annotation mistake, as well as #205 KEGG reaction annotation issue (r_0198, r_0911, r_4245, r_2116, r_4254 and r_4255)
Summary of issues resolved for #205 :
r_0198r_0911r_0911since it is an incorrect reaction annotation. However, this remains an issue as there is no way of incorporating 2 rxnKEGGIDs (R07404 and R07405) into the model.r_4245R09645removed from the model since it cannot be found in KEGG, as mentioned in #205.r_2116r_4254nitric oxide, NADH2:oxygen oxidoreductaser_4255nitric oxide, NADPH2:oxygen oxidoreductase2.
mapKEGGID.mscript written to search for new rxnKEGGIDs and metKEGGIDs through ID mapping, added 134 unique rxnKEGGIDs and 15 unique metKEGGIDs*Note that MNXref version 3.2 is used
3.
mapMNXMID.mscript written to search for new metMNXMIDs through ID mapping, added 52 unique MNXMIDs. After new MNXMIDs are added,mapKEGGID.mis run again to add 6 unique metKEGGIDs*Note that MNXref version 3.2 is used
**Addresses #197 lack of MNXMID annotations for some metabolites
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