Association between clinical and environmental factors and the gut microbiota profiles in young South African children

[Scholarpat]

Association between clinical and environmental factors and the gut microbiota profiles in young South African children - Kristien Nel Van Zyl – Scientific Reports https://www.nature.com/articles/s41598-021-95409-5

[ToluwalaseAO]

@SvetlanaUP , can I get this issue assigned to me?

[ToluwalaseAO]

Hi! @SvetlanaUP, I signed up to create an account, but I have not yet received the password to access the curation site.

[SvetlanaUP]

Hi @ToluwalaseAO,

this is a question to be posted in our dedicated Slack channel (all communication is there, not related to this specific GitHub issue). Answer to your question is here: https://community-bioc.slack.com/archives/C04RATV9VCY/p1727940469459309?thread_ts=1727940203.037609&cid=C04RATV9VCY

I just checked it and all requests have been approved.

[ToluwalaseAO]

Okay . Thank you!

[ToluwalaseAO]

Hi. @SvetlanaUP my second contribution is ready for review. Thank you.

[SvetlanaUP]

https://bugsigdb.org/Study_1156 ready for review.

[SvetlanaUP]

@ToluwalaseAO thank you for your contribution. Unfortunately this curation needs more work and careful revision of all curation points.

• Study information left "Incomplete"
• Copy-Pasting text/paragraphs from the paper should be changed with concise and accurate descriptions
• V4 region of 16S rRNA gene was sequenced
• Figure 5 with ANCOM results indicate 3 experiments etc. etc.

Item	Description	max	points
1	All elements marked "Needs review" (none "Incomplete")	1	0
2	Correct study design	1	1
3	Entered all relevant experiments and no irrelevant experiments	1	0
4	Body site correctly identified (i.e. does not include multiple sites)	1	1
5	Condition entered according to contrast (correct EFO ontology)	1	0
6	Contrast groups correctly identified	1	0
7	Groups correctly labeled as 1 and 0 (1=cases, 0=controls)	1	1
8	Antibiotic exclusion correctly identified	1	1
9	Correctly identified sequencing details	2	1
10	Identified correct statistical test	1	0
11	Identified MHT correction	1	0
12	Correctly recorded matched on factors	1	0
13	Entered correct number of statistical tests per experiment	1	0
14	All diversity measures identified	1	1
15	Diversity results correctly entered as increased/decreased/unchanged	1	1
16	All signature sources correctly identified (-1 for each error)	2	0
17	Abundance direction correctly selected	1	0
18	Members of Signatures identified correctly	2	0
19	Correct use of NCBI taxonomy	2	2
	TOTAL	23	8

[TheTosin]

@SvetlanaUP I would like to collaborate to resolve this pending issue. @ToluwalaseAO you can reach me as “Adeshile Oluwatosin” on slack.

[ToluwalaseAO]

@SvetlanaUP , I'll take this feedback into account and collaborate with @TheTosin to address and improve the curation. Thank you.

[AleruDivine]

Hi @ToluwalaseAO I'd also love to collaborate with you to review this curation and make corrections if that's okay with you. Thank you so much!

[SvetlanaUP]

@AleruDivine you could help in here https://github.com/waldronlab/BugSigDBcuration/issues/447

This curation is now supported by @TheTosin

[AleruDivine]

Got it @SvetlanaUP I'll proceed with helping out on the issue #447.

[TheTosin]

Hello @SvetlanaUP This study is ready for review

https://bugsigdb.org/Study_1156

[SvetlanaUP]

@TheTosin all good, thank you for corrections. Study reviewed by @Buraah https://github.com/Buraah

[TheTosin]

Welcome ma’am @SvetlanaUP That’s good to hear. Happy to do more reviews and curate more articles. Kindly tag me to more articles that I can collaborate in.