Human-GEM
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SysBioChalmers
Non-standard metabolite names
Description of the issue:
Hi, some metabolites in the model seem to have a list of compound names separated by semi-colon as name, here the list:
| ID | NAME |
|---|---|
| 12dhchol_c | 12-Dehydrocholic acid; 12-Oxodeoxycholic acid; 12oxo-3alpha,7alpha-Dihydroxy-5beta-cholan-24-oic acid |
| 12dhchol_s | 12-Dehydrocholic acid; 12-Oxodeoxycholic acid; 12oxo-3alpha,7alpha-Dihydroxy-5beta-cholan-24-oic acid |
| 3dhcdchol_c | 3-Dehydrochenodeoxychollyc acid; 7oxo-3alpha-hydroxy-5beta-cholan-24-oic acid |
| 3dhcdchol_s | 3-Dehydrochenodeoxychollyc acid; 7oxo-3alpha-hydroxy-5beta-cholan-24-oic acid |
| 3dhchol_c | 3-Dehydrocholic acid; 3oxo-7alpha,12alpha-Dihydroxy-5beta-cholan-24-oic acid |
| 3dhchol_s | 3-Dehydrocholic acid; 3oxo-7alpha,12alpha-Dihydroxy-5beta-cholan-24-oic acid |
| 7dhcdchol_c | 7-Dehydrochenodeoxycholic acid; 7oxo-3alpha-hydroxy-5beta-cholan-24-oic acid |
| 7dhcdchol_s | 7-Dehydrochenodeoxycholic acid; 7oxo-3alpha-hydroxy-5beta-cholan-24-oic acid |
| 7dhchol_c | 7-Dehydrocholic acid; 7-Oxodeoxycholic acid; 7oxo-3alpha,12alpha-Dihydroxy-5beta-cholan-24-oic acid |
| 7dhchol_s | 7-Dehydrocholic acid; 7-Oxodeoxycholic acid; 7oxo-3alpha,12alpha-Dihydroxy-5beta-cholan-24-oic acid |
| hyochol_c | Hyocholic acid; gamma-Muricholate |
| hyochol_r | Hyocholic acid; gamma-Muricholate |
| hyochol_s | Hyocholic acid; gamma-Muricholate |
| icdchol_s | Isochenodeoxycholic acid; 3beta,7alpha-Dihydroxy-5beta-cholanic acid |
| icdchol_c | Isochenodeoxycholic acid; 3beta,7alpha-Dihydroxy-5beta-cholanic acid |
| isochol_c | Isochenodeoxycholic acid; 3beta,7alpha,12alpha-Trihydroxy-5beta-cholanic acid |
| isochol_s | Isochenodeoxycholic acid; 3beta,7alpha,12alpha-Trihydroxy-5beta-cholanic acid |
| thyochol_c | Taurohyocholic acid; N-(3alpha,6alpha,7alpha-Trihydroxy-5beta-cholan-24-oyl)taurine |
| thyochol_s | Taurohyocholic acid; N-(3alpha,6alpha,7alpha-Trihydroxy-5beta-cholan-24-oyl)taurine |
| uchol_c | Ursocholic acid; 3alpha,7beta,12alpha-Trihydroxy-5beta-cholan-24-oic acid; 3alpha,7beta,12alpha-Trihydroxy-5beta-cholanic acid; 7beta-Hydroxyisocholic acid; 7-Epicholic acid |
| uchol_s | Ursocholic acid; 3alpha,7beta,12alpha-Trihydroxy-5beta-cholan-24-oic acid; 3alpha,7beta,12alpha-Trihydroxy-5beta-cholanic acid; 7beta-Hydroxyisocholic acid; 7-Epicholic acid |
Expected feature/value/output:
Beware that 7oxo-3alpha-hydroxy-5beta-cholan-24-oic acid and Isochenodeoxycholic acid are duplicated in the table above, and Taurohyocholic acid is already an existing metabolite in the model! So I would suggest to use external databases like ChEBI to get the correct names.
I also noticed that some of the names listed above are found in reaction names, maybe these reaction names should be changed as well.
And needless to say, be sure to not introduce new duplicates when addressing this issue.
Current feature/value/output:
-
Reproducing these results:
-
I hereby confirm that I have:
- [x] Tested my code on my own computer for running the model
- [x] Done this analysis in the
masterbranch of the repository - [x] Checked that a similar issue does not exist already
Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE
@pecholleyc thanks for finding this!
It appeared that these metabolites were inherited from Recon3D.
I guess a better fix for this would be to programmatically adopt the ChEBI name for all metabolites with an associated ChEBI id?
