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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing #246

Closed SvetlanaUP closed 1 month ago

SvetlanaUP commented 5 months ago

Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing – Xiao et al. – Microbiology Spectrum https://journals.asm.org/doi/10.1128/spectrum.01901-21

B612Spac commented 5 months ago

Hello @SvetlanaUP Please I'd like to be assigned to this article, thanks

eve10111 commented 5 months ago

Hi @SvetlanaUP , can you kindly assign this to me to curate? Thank you very much

B612Spac commented 5 months ago

Thank you @SvetlanaUP 🫶🏾

B612Spac commented 5 months ago

Hello @SvetlanaUP thank you for assigning me to this paper. I'd appreciate if you can help me review it and let me know if it needs to be editted. I enjoyed working on this project and it made me realise my little contribution to bugsigdb is for a greater cause. I'd continue to contribute after now and get more conversant with working with Open Source. Thanks for the opportunity

https://bugsigdb.org/Study_988

SvetlanaUP commented 5 months ago
Item Description max points
1 All elements marked "Needs review" (none "Incomplete") 1 1
2 Correct study design 1 1
3 Entered all relevant experiments and no irrelevant experiments 1 0
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 0.5
7 Groups correctly labeled as 1 and 0 (1=cases, 0=controls) 1 0.5
8 Antibiotic exclusion correctly identified 1 1
9 Correctly identified sequencing details 2 1
10 Identified correct statistical test 1 0.5
11 Identified MHT correction 1 1
12 Correctly recorded matched on factors 1 0
13 Entered correct number of statistical tests per experiment 1 1
14 All diversity measures identified 1 0
15 Diversity results correctly entered as increased/decreased/unchanged 1 1
16 All signature sources correctly identified (-1 for each error) 2 0
17 Abundance direction correctly selected 1 1
18 Members of signatures identified correctly 2 1
19 Correct use of NCBI taxonomy 2 1
TOTAL 23 13.5

The main errors here are due to the missing fact that we are not curating relative abundance results. We are interested only in differential abundance results.

B612Spac commented 5 months ago

Thanks for the feedback @SvetlanaUP can I use your corrections to make changes on the study?

SvetlanaUP commented 4 months ago

@B612Spac yes please :) and do make notes here what and how you make changes. Thank you!

B612Spac commented 4 months ago

Thank you @SvetlanaUP I'll get started with it

Buraah commented 4 months ago

Hello @B612Spac Good day and hope you're doing well. I noticed you haven't started correcting this study yet. If you don't mind collaborating on it, you can reach out to me, I'd be glad to help.

SvetlanaUP commented 4 months ago

@Buraah go ahead with this correction! Thanks.

Buraah commented 4 months ago

Okay @SvetlanaUP I'll get to it

B612Spac commented 4 months ago

Hello @Buraah thanks for wanting to assist with the task...I actually got started on it but couldn't continue as I didn't fully understand what I was supposed to. I'd appreciate if you can fully take on it because I'm preoccupied with other activities at the moment. Thank you

Buraah commented 4 months ago

Okay @B612Spac No problem...Thank you for your response.

Buraah commented 4 months ago

Hello @SvetlanaUP I am done implementing the feedback for this study and it's ready for a second review.

Here are the things I changed:

  1. I removed the previously inputted matched-on factors.
  2. I deleted experiment 4 because it was irrelevant.
  3. I added the sequencing details and statistical test details that were missing in the first curation.
  4. I changed the signature sources and curated all signatures from Fig 3c and Fig 4d.
  5. I changed the contrast group definitions.
Scholarpat commented 1 month ago

Hi @Buraah,

I noticed that in this study, the signatures were presented using LEfSe analysis in a "one against all" format. Therefore, the signatures should be represented as follows:

Figure 3C

  1. HCG (group 0) vs. UTG and LCG (group 1)
    • Red bars: Decreased
  2. LCG and HCG (group 0) vs. UTG (group 1)
    • Blue bars: Increased
  3. HCG and UTG (group 0) vs. LCG (group 1)
    • Green bars: Increased

Figure 4D

  1. TTG and CTG (group 0) vs. UTG (group 1)
    • Blue bars: Increased

What do you think about this representation?

Buraah commented 1 month ago

Hi @Scholarpat, I think we should follow your suggestion; it makes more sense to curate as 'one against all'.

Scholarpat commented 1 month ago

@Buraah Should I proceed with making the corrections, or would you prefer to handle it yourself?

Buraah commented 1 month ago

Yes, please proceed with making the corrections. I'm a little bit occupied. Thank you so much!

Scholarpat commented 1 month ago

Hi @Buraah,

I noticed that in this study, the signatures were presented using LEfSe analysis in a "one against all" format. Therefore, the signatures should be represented as follows:

Figure 3C

  1. HCG (group 0) vs. UTG and LCG (group 1)

    • Red bars: Decreased

  2. LCG and HCG (group 0) vs. UTG (group 1)

    • Blue bars: Increased

  3. HCG and UTG (group 0) vs. LCG (group 1)

    • Green bars: Increased

Figure 4D 4. TTG and CTG (group 0) vs. UTG (group 1)

  • Blue bars: Increased

What do you think about this representation?

Hi @SvetlanaUP,

I've curated this study as specified above. Signature 1 of exp. 4 is not displaying but has been curated. Please kindly delete Signature 2 of exp. 1 and 2. https://bugsigdb.org/Study_988

Thank you!

SvetlanaUP commented 1 month ago

https://bugsigdb.org/Study_988 reviewed.