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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease #261

Closed Omabekee closed 4 months ago

Omabekee commented 8 months ago

Curcumin Regulates Gut Microbiota and Exerts a Neuroprotective Effect in the MPTP Model of Parkinson's Disease -- Zhu et al. -- Evid Based Complement Alternat Med https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9715342/

MyleeeA commented 8 months ago

Hi @Omabekee @SvetlanaUP Can I be assigned to this?

Thank you 🙏

SvetlanaUP commented 8 months ago

@MyleeeA could you please share your curation of https://github.com/waldronlab/BugSigDBcuration/issues/214 ?

MyleeeA commented 8 months ago

Okay @SvetlanaUP I will Although I’m hoping to share the paper during this weeks office hour as there a few things I’m unsure of and @Omabekee @Folakunmi21 @Peacesandy asked that I share it to get more insights

Would I still be able to edit it once I share it for review?

SvetlanaUP commented 8 months ago

@MyleeeA sure!

MyleeeA commented 8 months ago

Hi @SvetlanaUP this curation is ready for for review Thank you 🙏🏾

SvetlanaUP commented 8 months ago

https://bugsigdb.org/Study_960 ready for review

Scholarpat commented 4 months ago

Hi @MyleeeA,

This is a wonderful curation. Curating all those signatures must have taken a lot of effort. Well done! 🙌

I tried to resolve some of the taxa but couldn't make headway. 😅

Here are my observations:

  1. I noticed that for signature 2 of experiment 3, Candidatus Saccharimonadas (highlighted in orange) was curated. Can you kindly recheck that? What is reported in the study is Candidatus Saccharimonas (TXID - 1331051).

  2. I think the source description should be more descriptive. Rather than 'Analysis of specie differences by Lefse,' it would be better to use something like 'Differential distribution of gut microbiota in ABC vs. XYZ,' depending on the groups in each experiment.

Thank you very much.

SvetlanaUP commented 4 months ago

Let's see what's @MyleeeA's opinion!

MyleeeA commented 4 months ago

Thank you for your observations @Scholarpat

I agree with your points, Candidatus Saccharimonadas was possibly curated in error as Candidatus Saccharimonas already exists amongst the taxas Now I remember the curation process was really tasking, it makes me happy I didn’t make so many mistakes. Thanks again for your observation and I can change the description to what you are proposing because it sounds more descriptive.

SvetlanaUP commented 4 months ago

Please do let me know when the curation is complete @MyleeeA Thanks!

MyleeeA commented 4 months ago

All done @SvetlanaUP, Thanks! Thank you again @Scholarpat

SvetlanaUP commented 4 months ago

https://bugsigdb.org/Study_960 reviewed.