waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Influence of aerobic exercise training on mice gut microbiota in Parkinson’s disease #207

Open Folakunmi21 opened 4 months ago

Folakunmi21 commented 4 months ago

Influence of aerobic exercise training on mice gut microbiota in Parkinson’s disease - Fan et al - Turk J Biol https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10388120/

nwakaegovincent26 commented 4 months ago

Hello @SvetlanaUP , kindly assign this paper to me for curation thank you

nwakaegovincent26 commented 4 months ago

kindly review my paper @SvetlanaUP @Folakunmi21 Thank you

nwakaegovincent26 commented 4 months ago

https://bugsigdb.org/Study_923 here is the link to the study

Folakunmi21 commented 3 months ago

Hello @nwakaegovincent26 unfortunately, this curation was poorly done. Here are a few corrections to note: -Figure 4A and table S1 are not curatable -You entered the wrong condition -Entered MHT correction as yes when there was none -Wrong sequencing details -There were no confounders controlled for in the paper but you entered some please check the corrected curation to see the other changes I made.

CUARTION RESULT

  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): 0
  6. Contrast groups correctly identified (1 point): 0
  7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 0
  8. Antibiotic exclusion correctly identified (1 point): 0
  9. Correctly identified sequencing details (2 points): 1
  10. Identified correct statistical test (1 point): 0.5
  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): 0
  14. All diversity measures identified (1 point): 1
  15. Diversity results correctly entered as increased/decreased/unchanged (1 point): 1
  16. All signature sources correctly identified (-1 for each error) (2 points): 0
  17. Abundance direction correctly selected (1 point): 0
  18. Members of Signatures identified correctly (2 points): 0
  19. Correct use of NCBI taxonomy (2 points): 2

Total (maximum 23 points): 9.5

@SvetlanaUP study 923 reviewed

nwakaegovincent26 commented 3 months ago

thank you for the review feedback . all the correction is well noted and hopefully i will do better in my other curation @SvetlanaUP @Folakunmi21