Major mass-rebalance of HumanGEM - #131
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This PR should not be merged until after #130 has been merged. |
No reason to have this metabolite in as part of this media formulation for this metabolic task.
2 tasks
- These files had been dealt with in #141, now only keep the xlsx version.
- Newly assigned KEGG rxn id to HMR_4284 through manual curation
- adjust and use this function for updating grRules and other related fields - add notes to the model change log files
haowang-bioinfo
approved these changes
Nov 20, 2019
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| metNames newFormula newCharge | ||
| alpha-D-mannosyl-beta-D-mannosyl-diacetylchitobiosyldiphosphodolichol C128H210N2O27P2 -2 | ||
| beta-D-mannosyldiacetylchitobiosyldiphosphodolichol C122H200N2O22P2 -2 | ||
| dehydrodolichol C100H162O 0 | ||
| dehydrodolichol-diphosphate C100H161O7P2 -3 | ||
| dehydrodolichol-phosphate C100H161O4P -2 | ||
| dolichol C100H164O 0 |
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This file contains significant updates to metabolite formulas and charges. It would very nice to add two more columns: oldFormula and oldCharge (which actually can be found in the model change log files).
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| HMR_5164 ENSG00000072274 | ||
| HMR_5154 ENSG00000084674 | ||
| HMR_5159 ENSG00000110245 | ||
| HMR_5162 ENSG00000122194 | ||
| HMR_5165 ENSG00000130203 | ||
| HMR_5157 ENSG00000130208 | ||
| HMR_5160 ENSG00000171560 | ||
| HMR_5163 ENSG00000180210 | ||
| HMR_5152 ENSG00000196136 | ||
| HMR_5153 ENSG00000197249 | ||
| HMR_5158 ENSG00000234906 |
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If there are references that support these grRule changes, the pmid and suggested confidenceScores can be added as additional columns in this file.
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This was referenced Nov 25, 2019
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Main improvements in this PR:
This PR implements a substantial re-balancing of reactions in
HumanGEM, resulting in a model that is 93.4% charge-balanced, 99.4% mass-balanced, and 100% stoichiometrically consistent. The changes also address issues #43, #58, and #60.The manual curation process identified and implemented the following changes:
The changes are implemented in the
rebalanceHumanGEMscript, which reads change information organized into 12 different tsv files located in the/ComplementaryData/modelCuration/fullRebalancedirectory.Other changes in this PR:
rxnHMRIDis added to thehumanGEMRxnAssoc_lip.JSONreaction annotation file, which contains HMR1 and HMR2 reaction IDs associated with each reaction (if there are any). This provides more explicit association to these models, and was also necessary to document the removal of some duplicated HMR reactions.I hereby confirm that I have:
develas a target branch