Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis

[SvetlanaUP]

Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis – Shuwen Han – Microbiology Spectrum https://journals.asm.org/doi/10.1128/spectrum.01593-22

[imalovee]

Hello please @SvetlanaUP the previous paper I was assigned which was already halfway worked on by an older intern has a completely different experimental procedures carried out in it which is highly distinct from the questions that we need to respond to...it uses different tests and methods..I can assume the other other intern left it half way because of the same issue. Please can I be assigned to this paper thank you.

[allieniola1]

Hello @SvetlanaUP . I would love to curate this article. Thank you.

[AdegboyeRukayat]

@SvetlanaUP please may I be assigned to this paper to be curated?

[allieniola1]

Hello, does this mail means the article has been assigned to me?

On Thu, 7 Mar 2024, 5:59 am AdegboyeRukayat, @.***> wrote:

Adegboye Rukayat

— Reply to this email directly, view it on GitHub https://github.com/waldronlab/BugSigDBcuration/issues/190#issuecomment-1982349245, or unsubscribe https://github.com/notifications/unsubscribe-auth/A32HLBVSSBSO6UZ4TBMFA5DYW7XZZAVCNFSM6AAAAABEJY3UCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBSGM2DSMRUGU . You are receiving this because you commented.Message ID: @.***>

[Iphenn]

Hello @SvetlanaUP, I would love to curate this article. Thank you

[SvetlanaUP]

Assigned to @imalovee

[imalovee]

Thank you @SvetlanaUP

[imalovee]

Hello Mentors @SvetlanaUP @Omabekee I am through with my second task of curating this paper, here is the link: https://bugsigdb.org/Study_907 Thank you.

[imalovee]

@Scholarpat, @MyleeeA, @BarakatAA here is my paper..thank you

[BarakatAA]

Alright Ima

[imalovee]

hello @Kwennb thank you for going through my paper, I have noted your observations.

[MyleeeA]

@imalovee 👍

[kwennB]

You are welcome @imalovee thank you so much for doing the same as well.

[Peacesandy]

This is a great second curation attempt @imalovee. Here are some of the errors you made.

1. The sequencing detail was not correctly identified, you left it blank. In the paper, the sequencing type used is WMS - metagenomic sequencing, the study used metagenomic analysis.
2. No matched on factor was mentioned in the study.
3. The differential abundance was gotten from fig 2G and 2H. All signatures were not entered you omitted a lot of signatures.
4. Abundance direction is incorrect.
5. The signatures you entered as increased and decreased abundance in colorectal cancer are incorrect.

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): 1
12. Correctly recorded matched on factors (1 point): 0
13. Entered correct number of statistical tests per experiment (1 point): 1
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): 1
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): 1

Total (maximum 23 points): 15

@SvetlanaUP https://bugsigdb.org/Study_907 Reviewed ✅

[imalovee]

Oops!!. This is an awesome review, to be honest. I am better informed now, though I lowkey wish it came before my second paper but it's all fine still. Pumped and ready to nail the next curation. Thank you for the opportunity @Peacesandy and @SvetlanaUP

[Peacesandy]

Glad you found it helpful