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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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The gut microbiota and metabolite profiles are altered in patients with spinal cord injury #3

Closed cmirzayi closed 1 year ago

cmirzayi commented 1 year ago

Condition: Spinal Cord Injury URL: https://molecularbrain.biomedcentral.com/articles/10.1186/s13041-023-01014-0

kahvecirem commented 1 year ago

Hello, I'd like to contribute to this article.

anshikabhatt commented 1 year ago

Hello, I am interested to work on this article.

cmirzayi commented 1 year ago

@kahvecirem assigned!

BlessingKaz commented 1 year ago

@cmirzayi a please can I get assigned to this task or another one? I'm interested in this article as well. Noticed all issues have been assigned.

ftzohra22 commented 1 year ago

@BlessingKaz please claim an article without the label "assigned". Thank you

BlessingKaz commented 1 year ago

@ftzohra22 alright thank you

kahvecirem commented 1 year ago

Curated Article for review: https://bugsigdb.org/Study_730

Best Regards

claregri commented 1 year ago

Hi there, good start with this curation! I noticed that you picked the incorrect abundance direction (in Figure 2e, the red is increased in controls and the blue is increased in SCI patients). Also, you labeled both of the signatures in Experiment 1 as Figure 3e, but I think you meant 2e based on the curation. Thirdly, it looks like you started a second experiment - you should curate figures 2b-c as they also document differential abundance between the groups (using a different statistical test). Though this paper goes into analyses of the blood, none of them are curatable by our standards so make sure to update the details of Experiment 2 to reflect figures 2b-c. Please see my grading below.

  1. All elements marked "Needs review" (none "Incomplete") (1 point): 1
  2. Correct study design (1 point): 1
  3. Entered all relevant experiments and no irrelevant experiments (1 point): 0
  4. Body site correctly identified (i.e. does not include multiple sites) (1 point): 1
  5. Condition entered according to contrast (correct EFO ontology) (1 point): 1
  6. Contrast groups correctly identified (1 point): 1
  7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 1
  8. Antibiotic exclusion correctly identified (1 point): 1
  9. Correctly identified sequencing details (2 points): 2
  10. Identified correct statistical test (1 point): 1
  11. Identified MHT correction (1 point): 0
  12. Correctly recorded matched on factors (1 point): 1
  13. Entered correct number of statistical tests per experiment (1 point): 1
  14. All diversity measures identified (1 point): 0
  15. Diversity results correctly entered as increased/decreased/unchanged (1 point): 0
  16. All signature sources correctly identified (-1 for each error) (2 points): 1
  17. Abundance direction correctly selected (1 point): 0
  18. Members of Signatures identified correctly (2 points): 0 (be sure to go through and check that you got all the possibly curatable taxa, I think a few were missed)
  19. Correct use of NCBI taxonomy (2 points): 0 (you'll notice that in Signature 1, Lachnospirales is highlighted in orange. I couldn't find it in the NCBI database, so you should remove it)

Total (maximum 23 points): 13

atrayees commented 1 year ago

Corrected the abundance direction, entered the new experiment and signatures, corrected MHT.