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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study #80

Closed SvetlanaUP closed 9 months ago

SvetlanaUP commented 1 year ago

Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study – Kristin Gravdal et al. – BMC Endocrine Disorders 2023 DOI: 10.1186/s12902-023-01432-0 https://bmcendocrdisord.biomedcentral.com/articles/10.1186/s12902-023-01432-0

Kadeniyi23 commented 1 year ago

Hello. Im Adeniyi Kabirat. @SvetlanaUP Id like to claim this article for curation

cmirzayi commented 1 year ago

Assigned.

Kadeniyi23 commented 1 year ago

Hey @lwaldron @SvetlanaUP @cmirzayi Im happy to submit my curated paper for review. the link is https://bugsigdb.org/Study_786

cmirzayi commented 1 year ago

Marked as ready for review.

cmirzayi commented 1 year ago

Excellent curation. It just needs some small changes as well as some fixes to clarify the difference between experiments 1 and 2 compared to experiment 3 (which uses a different sequencing platform).

Case-control study

One experiment was done using GA-map 131-plex not Illumina.

"Dorea spp." is not the same thing as "Dorea." This is true for many of the curated taxa and needs to be corrected.

Experiment 3 comes from table 2 but is labeled table 3.

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 1
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 0
TOTAL 23 18
Peacesandy commented 9 months ago

https://bugsigdb.org/Study_786

Reviewed