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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients #352

Closed fiddyhamma closed 1 month ago

fiddyhamma commented 5 months ago

Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients Nana Wei https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10166687/

fiddyhamma commented 5 months ago

I found this study while researching and curating on oral lichen planus, looking forward to the curation 😊

Junie06 commented 5 months ago

Can I be assigned to curate this paper @SvetlanaUP My name is Isoken Ibizugbe

Scholarpat commented 4 months ago

Hello @Junie06

Hope you're doing well. I noticed this curation is available on BugSigDB under 'Studies without signatures'. Are you still working on it or do you need help completing it?

Kindly awaiting your response.

Best Regards Scholastica Urua

Buraah commented 1 month ago

Hi @SvetlanaUP, @Scholarpat Can I complete and review this curation?

SvetlanaUP commented 1 month ago

@Buraah Sure! https://bugsigdb.org/Study_1040 is in your hands now :)

Buraah commented 1 month ago

Thank you! @SvetlanaUP

Buraah commented 1 month ago

Hi @SvetlanaUP, I am done completing and reviewing this study.

Here are the things I changed and why;

  1. Statistical test

    • I changed the statistical test from t-test and Mann-Whitney to Lefse. Under 'Statistical analysis' and Phylogenetic profiles of oral bacteria in recovered patients with COVID-19'. The study explains the use of Lefse to identify bacteria that differed between the groups

  2. Condition

    • I changed the condition from 'COVID-19' to 'Microbiome measurement'. The study compared the oral bacterial and fungal microbiomes between recovered COVID-19 patients and healthy controls.

  3. MHT Correction

    • I changed the MHT correction to 'yes'. The discussion under 'Statistical analysis' explained the correction through FDR.

  4. Signatures

    • I added signatures 1 and 2 from Figure 3a and Figure 6a of the study.

  5. Group names

    • I changed the Group 0 and Group 1 names from HCs and RPs to 'HCs (Healthy Controls)' and 'RPs (Recovered Patients)' to make them more descriptive.

The other curated data are in order. Thank you.

SvetlanaUP commented 1 month ago

Excellent review and corrections, @Buraah!

https://bugsigdb.org/Study_1040 is reviewed.