Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum

[Scholarpat]

Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum - Mie Korslund Wiinblad Crusell – Microbiome

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0472-x

[Onyin-o]

Hi @SvetlanaUP i’d like to claim this issue for curation. Thank you

[Rahila-me]

Good morning @Onyin-o @SvetlanaUP , Onyin please I am open for collaboration i just wanted to know if you need help to finish up this paper. Waiting for your reply.. Thank you

[Rahila-me]

@SvetlanaUP @Onyin-o I have looked up this paper in bugsigdb and it shows it has not be created in the wiki, Should i still wait for the original owner to start before offering help @SvetlanaUP

[SvetlanaUP]

@Rahila-me go ahead with curation of this paper, thanks!

[Rahila-me]

@SvetlanaUP okay thank you

[MyleeeA]

Hi @Rahila-me

I have completed my second contribution and I am currently awaiting grading

I am available to collaborate with you on this, if that is okay Thank you 🙏🏾

[Rahila-me]

@MyleeeA Chia i am just seeing this now, and i have finished the curation. The only reason i have not added the link was because this is weekend. Will add the link to the completed curation tomorrow. Thanks for reaching out

[MyleeeA]

That sounds great @Rahila-me

Well done on your curation 👏🏾 Is this your second contribution? Do you need peer review on it?

[Rahila-me]

@MyleeeA No, The initial owner did not curate it.

[Rahila-me]

@SvetlanaUP Good evening, This paper is ready for a review: https://bugsigdb.org/Study_1169

[MyleeeA]

Oh Yes

I’ve read the previous messages and I see that Well done again 👏🏾

[SvetlanaUP]

https://bugsigdb.org/Study_1169 ready for review.

[Buraah]

Hi @SvetlanaUP, I want to review this.

[Buraah]

Hi @Rahila-me, Thank you for doing a good work. Here are a few things I noted:

1. The data transformation for 'Wald test' is 'Raw counts'. This is because it is a negative binomial test, just like DESeq2.
2. The group 1 definitions for experiments 7, 8, 9 and 10 describe the signature source instead of defining the group.
3. There's a signature 3 under experiment 9. Please ask for it to be deleted.
4. Experiments 11 & 12 are a duplicate of 1 & 2.
5. The Group 0 sample size for experiment 1 is 157 from the paper. You can make corrections and ask for a final review. Thank you. Overall, this is a great curation. Well done!

Curation results: S/N	Criteria	Total Points	Points Earned
1	All elements marked "Needs review" (none "Incomplete")	1	1
2	Correct study design	1	1
3	Entered all relevant experiments and no irrelevant experiments	1	0.5
4	Body site correctly identified (i.e. does not include multiple sites)	1	1
5	Condition entered according to contrast (correct EFO ontology)	1	1
6	Contrast groups correctly identified	1	0.5
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	2
10	Identified correct statistical test	1	1
11	Identified MHT correction	1	1
12	Correctly recorded matched on factors	1	1
13	Entered correct number of statistical tests per experiment	1	1
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	1
17	Abundance direction correctly selected	1	1
18	Members of signatures identified correctly	2	2
19	Correct use of NCBI taxonomy	2	2
	TOTAL	23	22

Reviewed @SvetlanaUP

[Rahila-me]

@Buraah Thank you for the review. I will make the necessary correction.

[Rahila-me]

@Buraah @SvetlanaUP I have made the correction pointed out, so please raising it up again for a final review.

[Buraah]

Hi @SvetlanaUP, The second review is done.

Thank you @Rahila-me