Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study

[lwaldron]

Initiated at https://bugsigdb.org/Study_708. Note - there are no guarantees that information already entered here (such as study design) is correct, so please proceed as you would for a new study with no information pre-entered.

[sopeadeniji]

@lwaldron @cmirzayi @ftzohra22 Please, I will like to complete study 708

[cmirzayi]

Hi @sopeadeniji I see you are claiming this one as well as: https://github.com/waldronlab/BugSigDBcuration/issues/48. Could you please choose one to start? We'd like to review your work first before you perform multiple curations. Thank you!

[sopeadeniji]

@cmirzayi . It's now been curated at https://bugsigdb.org/Study_708

[sopeadeniji]

@cmirzayi please review https://bugsigdb.org/Study_708. Thanks.

[Mehak-4545]

@lwaldron @cmirzayi I would like to take up this study please, can it be assigned to me?

[Mehak-4545]

@lwaldron @cmirzayi I would like to take up this study please, can it be assigned to me?

@lwaldron Thanks! I am facing the same issue and am unable to join the public slack channel. Can I get an invite to it? My mail address is : mehaksharma2303@gmail.com

[ftzohra22]

@sopeadeniji Thank you for your effort on this paper. There were some error in your curation. Please review and make the necessary changes.

1. All elements marked "Needs review" (none "Incomplete") (1 point): 1
2. Correct study design (1 point): 0 (The study title says what type of study this is)
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): 0 (Contrast group for experiment 2 is not correctly identified. Please follow figure 7 which is showing the groups being compared and reported. RA vs. Control and RA vs. PD)
7. Groups correctly labelled as 1 and 0 (1=cases, 0=controls) (1 point): 1
8. Antibiotic exclusion correctly identified (1 point): 1
9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): 2
10. Identified correct statistical test (1 point): 1
11. Identified MHT correction (1 point): 1
12. Correctly recorded matched on factors (1 point): 1
13. Entered correct number of statistical tests per experiment (1 point): 0 (this was tricky, but there shouldn't be more than one value in this field. Only enter the statistical test used for differential abundance testing)
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): 1
18. Members of Signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): 0 (Signature 1 and 2 can never have the same bacteria, missing signature section for experiment 2, missing signature from Figure 7 in experiment 1)
19. Correct use of NCBI taxonomy (don't deduct if can't easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): 0

Total (maximum 24 points): Not scored due to incorrect curationn

[cmirzayi]

Hi @sopeadeniji Thank you so much for your contributions to the BugSigDB project. I wanted to check to see if you wanted to finish this curation. I understand that with the Outreachy applicant selection process over, you may no longer wish to help out with BugSigDB or have other priorities right now.

If not, I will open it up to other curators to finish the curation.

[sopeadeniji]

Hi Chloe,

Please, open up the curation for other curators to finish. I have other priorities at this time and can no longer work on BugSigDB project.

Best,

Sophy

Sent from Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 for Windows

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From: Chloe Mirzayi @.> Sent: Wednesday, May 10, 2023 1:22:47 PM To: waldronlab/BugSigDBcuration @.> Cc: sopeadeniji @.>; Mention @.> Subject: Re: [waldronlab/BugSigDBcuration] Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study (Issue #46)

Hi @sopeadenijihttps://github.com/sopeadeniji Thank you so much for your contributions to the BugSigDB project. I wanted to check to see if you wanted to finish this curation. I understand that with the Outreachy applicant selection process over, you may no longer wish to help out with BugSigDB or have other priorities right now.

If not, I will open it up to other curators to finish the curation.

— Reply to this email directly, view it on GitHubhttps://github.com/waldronlab/BugSigDBcuration/issues/46#issuecomment-1542624136, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALICVGCH6KVAH56B6AHNQGLXFPMHPANCNFSM6AAAAAAVZECD7U. You are receiving this because you were mentioned.Message ID: @.***>

[atrayees]

I have finished this curation. Also @cmirzayi @ftzohra22 @lwaldron could you please delete signatures 3 and 4 for Experiment 1? I have combined all the signatures for this experiment into Signatures 1 and 2. Thank you!