waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Increased diversity of a cervical microbiome associates with cervical cancer #375

Open Junie06 opened 7 months ago

Junie06 commented 7 months ago

https://pubmed.ncbi.nlm.nih.gov/36249017/ I chose this topic because it issue hit close to home for me. Finding out about the HPV vaccine late made me realize there's a gap in awareness and education where I come from. HPV and cervical cancer are a serious health concern, especially for women in Nigeria where it's the third most common cancer.

Junie06 commented 7 months ago

@SvetlanaUP

Analyst-Joan commented 7 months ago

Thanks for adding this @Junie06 @cmirzayi @lwaldron @Omabekee Please can this be assigned to me for curation? Thank you

Analyst-Joan commented 7 months ago

Thanks @SvetlanaUP

Analyst-Joan commented 7 months ago

Good morning @SvetlanaUP This Study has been curated and is ready for review at Study_1038

MyleeeA commented 3 months ago

Hi @SvetlanaUP

can I review this study?

SvetlanaUP commented 3 months ago

Sure @MyleeeA, enjoy!

MyleeeA commented 2 months ago

Hi @Analyst-Joan

This is an excellent curation, and I agree with your curation.

However I'm curious as to how you interpreted Table 3 because you recorded signatures from there for Experiments 5 and 6, it isn't so clear to me

Thank you in anticipation for your response

SvetlanaUP commented 4 days ago

@Analyst-Joan @MyleeeA any update on this curation? Thanks!

MyleeeA commented 4 days ago

Hi @SvetlanaUP

I haven't gotten a response for my only concern on the curation, However every other thing seems to be in order.

SvetlanaUP commented 4 days ago

@AleruDivine https://github.com/AleruDivine could you please review this curation https://bugsigdb.org/Study_1038, next week?

AleruDivine commented 4 days ago

Yes I’d be happy to @SvetlanaUP Thank you so much and good afternoon!

AleruDivine commented 7 hours ago

Hi @Analyst-Joan, great job on this curation, your descriptions are very well detailed and I really commend your attention to detail. @MyleeeA excellent work on the review as well.

I have a few suggestions that I would like you both to look at.

  1. Condition in Experiments 1 and 2: The contrast in these experiments seems to be between samples from healthy controls and pre-treatment groups (before radiation therapy). I don't think "response to radiation" should be used as the condition here. Instead, I would suggest curating the condition as Cervical squamous cell carcinoma (which is already available on BugSigDB), as the samples were collected before the radiation therapy (RT).
  2. @MyleeeA I understand your concerns about the curation of the signatures in experiments 5 and 6. I believe these should be curated as one experiment. See the excerpt, "On the genus level, 31 genera differentiated pre- and post-radiation samples, while only 2 differentiated pre-radiation and follow-up samples" and in Table 3, only 31 genera are listed. The description of Table 3 states, "Bacteria on the genus level differentiating pretreatment samples and posttreatment samples (after treatment and 3-month post-treatment)." I think this suggests the post-treatment group and 3-month follow-up group were combined in the table.

My suggestion is to curate experiments 5 and 6 as one experiment. The alpha diversity would remain unchanged.

Let me know what you think of these suggestions, thank you both so much!