Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease

[lwaldron]

Initiated at https://bugsigdb.org/Study_539. 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 Please, assign study 539 to me.

[sopeadeniji]

@cmirzayi. Can I work on this study after reviewing https://bugsigdb.org/Study_708?

[ftzohra22]

@sopeadeniji We'll assign this after we reviewed all your previous curations.

[sopeadeniji]

@ftzohra22 got you.

[mockingjay13]

I would like to get this article assigned to me for complete curation. Thank you! Name: Aditi SIngh

[lwaldron]

@mockingjay13 I've assigned you #28 - after you receive feedback for that you can request another article.

[BlessingKaz]

@cmirzayi and @Iwaldron can i work on this ?

[Kiiki015]

@cmirzayi I'll like to work on this, please.

[Kiiki015]

@ftzohra22 can I work on this please?

[Anthonyqueencode]

@lwaldron @ftzohra22 please can I be assigned this study. Thank you

[ObafemiBlessing]

@lwaldron one of my work has been reviewed #43, I would like to work on this to help me work on my corrections

[ftzohra22]

@Kiiki015 and @Anthonyqueencode #13 and #37 not assigned to anyone, please pick from those. or you could wait till more options are available.

[Anthonyqueencode]

okay @ftzohra22 please @ftzohra22 I just commented on the issue #13 please can I be assigned to it. I will be waiting for your response. Thank you

[Kiiki015]

@Kiiki015 and @Anthonyqueencode #13 and #37 not assigned to anyone, please pick from those. or you could wait till more options are available.

Thank you

[BlessingKaz]

thanks so much @ftzohra22 for assigning this to me.

[BlessingKaz]

hello @ftzohra @cmirzayi and @lwaldron please kindly review my work. I really need your feedbacks about my curation.

[claregri]

Hi Blessing, good start on this curation! Be sure to thoroughly review the captions before curating a figure or table - Figure 2 is characterizing the metabolites in the samples, not statistically comparing taxon abundance. Please note that the LDA field should be blank; though they used LDA in their analysis, it was not done for any curatable experiment so is not applicable to what you curated.

1. All elements marked "Needs review" (none "Incomplete") (1 point): 0
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): 0
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): 0
11. Identified MHT correction (1 point): 1
12. Correctly recorded matched on factors (1 point): 1 (they did not adjust for the match factors in the analysis, so those should not be listed as confounders in the experiment)
13. Entered correct number of statistical tests per experiment (1 point): 1
14. All diversity measures identified (1 point): 0 (too many identified)
15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): 1
16. All signature sources correctly identified (-1 for each error) (2 points): not scored due to incorrect curation
17. Abundance direction correctly selected (1 point): not scored due to incorrect curation
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): not scored due to incorrect curation
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): not scored due to incorrect curation

Total (maximum 24 points): not scored

[BlessingKaz]

@claregri thank you so much for the feedback I appreciate. the corrections are noted I would carefully work on them.

[cmirzayi]

Hi @BlessingKaz 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

From: Chloe @.> Sent: Wednesday, May 10, 2023 1:23 PM To: @.> Cc: @.>; @.> Subject: Re: [waldronlab/BugSigDBcuration] Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease (Issue #48)

Hi @BlessingKazhttps://github.com/BlessingKaz 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/48#issuecomment-1542625191, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALICVGE6P34OLMVFBCX5E7DXFPMLHANCNFSM6AAAAAAVZEPX7M. You are receiving this because you were mentioned.Message ID: @.***>

[atrayees]

I made the following changes:

1. Corrected the diversity measures
2. Corrected the antibiotic exclusion
3. Curated figure 1 for the experiment, and deleted the signatures containing non-curatable data.