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[FIX] changed pubchem ID for m01778c #240

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merged 3 commits into from
Mar 15, 2021
Merged

[FIX] changed pubchem ID for m01778c #240

merged 3 commits into from
Mar 15, 2021

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jorgemlferreira
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Main improvements in this PR:

Fixed pubchem ID for m01778c

I hereby confirm that I have:

  • Tested my code on my own computer for running the model
  • Selected devel as a target branch

@haowang-bioinfo haowang-bioinfo linked an issue Mar 11, 2021 that may be closed by this pull request
Pubchem compound id duplicated/wrong #239
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@haowang-bioinfo
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In addition to PubChem, should other metabolite ids (e.g. KEGG, MetaNetX) be modified as well? @jorgemlferreira

@jorgemlferreira
Changelog:
d268ce0 
For elaidate:
	- Most of this changes are based on the fact that elaidate (CHEBI:30825) is conjugate base of elaidic acid (CHEBI:27997), so I don't know if there is need for this change or if it is necessary to introduce another metabolite into the model
	- CHEBI differences on the InChI which made the change in the CHEBI identifier:
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on CHEBI:30825
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9+ elaidic acid on CHEBI:27997
	- Remove KEGG annotation from m01778 since there is no entry to it in the KEGG database (only its acid form)
	- Removed HMDB since there is no annotation for this specific metabolite and:
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9+ Elaidic acid on HMDB0000573
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on CHEBI:30825
	- Removed LipidMaps entry since there is no entry to in in its database
	- Changed the metMetaNetXID to the correct form based on the InCHi presented on the database:
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on CHEBI:30825
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on MNXM727012
For oleate:
	- Most of this changes are based on the fact that oleate (CHEBI:30823) is conjugate base of oleic acid (CHEBI:16196)
	- CHEBI differences on the InChI which made the change in the CHEBI identifier:
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate)
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9- in CHEBI:16196 (oleic acid)
	- Remove KEGG annotation from m02646 since there is no entry to it in the KEGG database (only its acid form)
	- Removed HMDB since there is no annotation for this specific metabolite and:
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9- in Oleic acid on HMDB00207
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate)
	- Removed LipidMaps entry since there is no entry to in in its database and
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9- on LMFA01030002 (Oleic acid)
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate)
	- Changed the metMetaNetXID to the correct form based on the InCHi presented on the database:
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- on MNXM727011 ((9Z)-octadecenoate)
		InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate)
@jorgemlferreira
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Hello again @Hao-Chalmers. So I've made a few changes that are present in the changelog provided on the commit. I think this part may be debatable, since most of the IDs provided by the model led to the conjugate base form of the metabolite. I don't know if this is the kind of identifiers you want in your model, so it's up for debate, since I believe most of the fatty acids are treated in the same manner. However, the initial change to the pubchem IDs are needed, and to be changed in all the compartments (I didn't do it in my first commit).

Please let me know if you just want changed the pubchem IDs, I'll rollback to the original .tsv and change only that.

Best regards

@haowang-bioinfo
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@jorgemlferreira the changes you made look okay based on the provided Changelog. But we'll need more time to evaluate them, and will come back to you later.

@jorgemlferreira
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@Hao-Chalmers Hi again. No problem. I'll assume this kind of changes could lead to a high amount of work, and may not even be necessary, depending on how you want the model to work (specially in fatty acids metabolism).

Best

@haowang-bioinfo
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@jorgemlferreira thanks for the input with detail changelog and accurate InChI mapping! Really surprised by that the commit message could be so long, and can be a good way of log changes.

The modifications to PubChem and CHEBI ids are good. I would suggest to keep the ids from HMDB and LipidMaps though. Because CHEBI and PubChem have very detail classification, while the others don’t. The HMDB and LipidMaps ids are acceptable and good for inclusiveness. In this sense, the KEGG id for ocdcea should also be retained. What do you think?

@jorgemlferreira
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@Hao-Chalmers Hello again, and thank you for the kind words. I agree with you, mainly due to how the fatty acids metabolism is built in the model. However, at some point in the future (maybe when another significant breakthrough is done in this area) it should be considered to revisit and rebuild the whole fatty acids metabolism, as a community effort.

I agree with only changing the PubChem and CHEBI ids, since the others are not 100% incorrect. I'll rollback the changes and only change the ids mentioned before.

Best,

Jorge Ferreira

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@jorgemlferreira I am also very much in support of a complete redesign of the fatty acid metabolic network portion of Human-GEM, though I realize this is no small task.

@jorgemlferreira
Changelog:
e9be6b3 
For elaidate:
	Reverted changes to the original information, asides from the CHEBI and PubChem identifiers. Also, added an extra identifier for the metanext ids. So after reverting to the original ids present in Human-GEM/model/metabolites.tsv in commit f8c74a5 in the master branch:
		- CHEBI differences on the InChI which made the change in the CHEBI identifier -> elaidic acid (CHEBI:27997) to elaidate (CHEBI:30825):
			InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9+ elaidic acid on CHEBI:27997
			InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on CHEBI:30825
		- PubChem from 445639 to 5461071
		- Added metMetaNetXID MNXM727012 to the ones already present based on their InChI:
			InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on CHEBI:30825
			InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ elaidate on MNXM727012

For oleate:
	Reverted changes to the original information, asides from the CHEBI and PubChem identifiers. Also, added an extra identifier for the metanext ids. So after reverting to the original ids present in Human-GEM/model/metabolites.tsv in commit f8c74a5 in the master branch:
		- CHEBI differences on the InChI which made the change in the CHEBI identifier -> oleic acid (CHEBI:16196) to oleate (CHEBI:30823):
			InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9- in CHEBI:16196 (oleic acid)
			InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate)
		- PubChem from 445639 to 5460221
		- Added metMetaNetXID MNXM727011 to the ones already present based on their InChI:
			InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- on MNXM727011 ((9Z)-octadecenoate)
			InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9- in CHEBI:30823 (oleate)
@jorgemlferreira
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@JonathanRob I think everyone wins in this scenario. You've made an important step in making this model and allowing the community to contribute in every way they can. And yes, I know this is not a simple and/or easy task, but a collaboration between the main and small developers/users of human metabolic models could make an integrated effort to improve this, and this repository is an important tool for that. Let's hope this can happen, and if it happens, I'll gladly help in anything I can.

Best,

Jorge

@haowang-bioinfo haowang-bioinfo merged commit b8e89a3 into SysBioChalmers:develop Mar 15, 2021
@haowang-bioinfo haowang-bioinfo mentioned this pull request Apr 16, 2021
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Pubchem compound id duplicated/wrong
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