The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival

[SvetlanaUP]

The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival – Philipp Licht – NPJ Biofilms Microbiomes https://www.nature.com/articles/s41522-024-00542-4

[masembebrian]

id like to have this assigned to curate

[SvetlanaUP]

Hi @masembebrian, have you completed your first contribution https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE ?

[Jayybb]

I would love to be assigned this

[Jayybb]

Thank you so much

[Jayybb]

i'd like to review my project @SvetlanaUP https://bugsigdb.org/Study_1126 https://bugsigdb.org/Study_1126/Experiment_1/Signature_1 https://bugsigdb.org/Study_1126/Experiment_1/Signature_2

thank you

[SvetlanaUP]

https://bugsigdb.org/Study_1126 https://bugsigdb.org/Study_1126/Experiment_1/Signature_1 https://bugsigdb.org/Study_1126/Experiment_1/Signature_2 ready for review.

[SvetlanaUP]

@Peacesandy please review this curation, thanks!

[Peacesandy]

Okay, I'll take this up Thank you so much @SvetlanaUP

[Peacesandy]

Hi @Jayybb this is a nice curation attempt 🎉

However, there were some errors; Here are some points to take note ✍️

• Sequencing type = PCR
• MHT correction - Yes
• No matched on was recorded in the study
• No confounders were recorded in the study
• The differential abundance was obtained from fig 2b, d-g

N/B: I've made all the necessary corrections. Please go through the reviewed curation and the paper again for ease. This will help you gain a better understanding for future curations.

CURATION RESULTS

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): 1
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): 0
10. Identified correct statistical test (1 point): 1
11. Identified MHT correction (1 point): 0
12. Correctly recorded matched on factors (1 point): 0
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): 1
19. Correct use of NCBI taxonomy (2 points): 2

Total (maximum 23 points): 14

@SvetlanaUP https://bugsigdb.org/Study_1126 Reviewed and corrected

[SvetlanaUP]

https://bugsigdb.org/Study_1126 reviewed.

[Jayybb]

Thank you . I will implement the corrections 👏

[SvetlanaUP]

@Jayybb please note corrections are already implemented. NO need for any further edits.

[Jayybb]

@SvetlanaUP i noticed after I sent the reply 🤭🤭🤭. I'm giving it my all next time 😊😊😊😊

[Jayybb]

@SvetlanaUP please can this issue be used for my final project ?

[SvetlanaUP]

@Jayybb please ask this question in Slack channel #bugsigdb.

[Jayybb]

@SvetlanaUP Okay ma. Thank you 👏