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

Feat: added smiles and inchi of metabolites #731

Merged
merged 2 commits into from
Jan 10, 2024

Conversation

JHL-452b
Copy link
Collaborator

Main improvements in this PR:

This PR added a document of SMILEs and inchi information of metabolites to data/modelCuration as discussed in #728 . To ensure completeness, in addition to SMILEs, inchi information is also added to TSV.

I hereby confirm that I have:

  • Tested my code on my own computer for running the model
  • Selected deXvelop as a target branch
  • Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

Added metabolite SMILES and Inchi Information
@haowang-bioinfo
Copy link
Member

haowang-bioinfo commented Nov 23, 2023

@JHL-452b looks nice

In order to properly evaluate this PR, please provide more detail information about data source(s) and manipulation, preferably with extraction code

just curious about the column of InChIkey which was not mentioned in #728, if it's redundant to InChI?

@JHL-452b
Copy link
Collaborator Author

JHL-452b commented Nov 26, 2023

In order to properly evaluate this PR, please provide more detail information about data source(s) and manipulation, preferably with extraction code

Data source(s) and main manipulation:

Firstly, I downloaded and collated metabolite information from various databases(including KEGG, ChEBI, PubChem(Api), HMDB, Lipidmaps, Recon3D). The collected information of metabolites contains ID and SMILEs, so I used ID mapping relationship in metabolites.tsv to extract SMILEs. Then, the functions of MolToInchiKey and MolToInchi in RDKit was used to convert SMILEs to inchiKey and inchi, respectively.

Results

metabolites SMILEs inchiKey inchi
All 8460 7141 6435 6435
Unique 4163 3399 2973 2973

just curious about the column of InChIkey which was not mentioned in #728, if it's redundant to InChI?

Inchi is better for accurately representing and comparing chemical substances, while InChIKeys could serve mainly as shortcuts that point back to the original InChI. So I think using both together provides optimal capabilities - InchIKey for fast lookup and matching, with the original InchI storing the richer chemical structure details.

Of course, it's just my opinion.

@haowang-bioinfo
Copy link
Member

Inchi is better for accurately representing and comparing chemical substances, while InChIKeys could serve mainly as shortcuts that point back to the original InChI. So I think using both together provides optimal capabilities - InchIKey for fast lookup and matching, with the original InchI storing the richer chemical structure details.

thanks for the info, sounds good to have both Inchi and InChIKeys

Firstly, I downloaded and collated metabolite information from various databases(including KEGG, ChEBI, PubChem(Api), HMDB, Lipidmaps, Recon3D). The collected information of metabolites contains ID and SMILEs, so I used ID mapping relationship in metabolites.tsv to extract SMILEs. Then, the functions of MolToInchiKey and MolToInchi in RDKit was used to convert SMILEs to inchiKey and inchi, respectively.

would be nice to also have the relevant code uploaded to code/modelCuration as references

@feiranl
Copy link
Collaborator

feiranl commented Jan 3, 2024

@JHL-452b It would be great if you could upload the code into the code/modelCuration as suggested by Hao. Then we can start review this. Thanks!

@JHL-452b
Copy link
Collaborator Author

JHL-452b commented Jan 4, 2024

Sorry late for uploading the code. Thanks for reminding.

@haowang-bioinfo
Copy link
Member

@JHL-452b thanks

@haowang-bioinfo haowang-bioinfo merged commit 4b80d74 into SysBioChalmers:develop Jan 10, 2024
4 checks passed
@JHL-452b JHL-452b mentioned this pull request May 30, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants