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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota #126

Closed SvetlanaUP closed 9 months ago

SvetlanaUP commented 1 year ago

Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota – Eri Komori – Scientific Reports 2023

https://www.nature.com/articles/s41598-023-43108-8

AleruDivine commented 1 year ago

Aleru Divine

I want to claim this article for curation as my third contribution. @cmirzayi @lwaldron @SvetlanaUP

SvetlanaUP commented 1 year ago

Assigned.

AleruDivine commented 1 year ago

@SvetlanaUP Thank you so much!

AleruDivine commented 1 year ago

Hi! @cmirzayi @SvetlanaUP I have completed my curation and here's the link: https://bugsigdb.org/Study_824 I am looking forward to your review. Thank you so much!

SvetlanaUP commented 1 year ago

Marked as ready for review.

AleruDivine commented 1 year ago

Thank you so much! @SvetlanaUP

cmirzayi commented 1 year ago

Some small feedback. Otherwise this was an excellent curation! I made these changes myself so no need for revisions.

Prospective cohort study, not cross-sectional.

LEfSe generally doesn't control for factors. Smoking was not controlled for (I penalized 1 point under matched on factors).

Item Description max points
1 All elements marked "Needs review" (none "Incomplete") 1 1
2 Correct study design 1 0
3 Entered all relevant experiments and no irrelevant experiments 1 1
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 1
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 0
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 2
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 21
AleruDivine commented 1 year ago

Thank you so much for the review and for making the changes @cmirzayi