Airway Microbiome and Serum Metabolomics Analysis Identify Differential Candidate Biomarkers in Allergic Rhinitis

[Folakunmi21]

Airway Microbiome and Serum Metabolomics Analysis Identify Differential Candidate Biomarkers in Allergic Rhinitis - Yuan et al. - Frontiers

https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.771136/full

[AdejokeOgunyinka]

@SvetlanaUP I'd love to be assigned this. My full name is Adejoke Ogunyinka. I'm an Outreachy applicant.

[Abiola-Salako]

Hello, @SvetlanaUP May I get assigned to this project, please?

[SvetlanaUP]

@Abiola-Salako this paper is already assigned. Please choose another one.

[Isioma20]

Good morning @AdejokeOgunyinka , I hope you are doing well. I noticed this issue has been assigned for over 3 weeks for your second contribution and since this is the final week of contributions, I just want to know if you'd need help or want to collaborate or if you're done and need peer reviews . I'm willing to help out.

Thank you so much!

[AdejokeOgunyinka]

Good morning @Isioma20. I'm doing okay. Thank you. I noticed on the second week of contributions that Bioconductors had closed contributions, so I assumed I had lost my chance to contribute to the project. I had a hard time following the project, so I eventually gave up after seeing contributions were closed. I just realized I should've reached out. I apologize. Thank you for reaching out instead.

[Isioma20]

I'm quite certain you can still contribute to the project. Do you want to go ahead with the curation?I can collaborate or help you out if you do. You can @idiaruangela on the slack channel #BugSigDB. Thanks

[omojokunoluwatomisin10]

@AdejokeOgunyinka, Hope you are good. Are you still working on your study or did you forget to ask mentors for a review

[Nana-Habiba]

@SvetlanaUP May I work on this study, the owner has abandon it.

[omojokunoluwatomisin10]

@Nana-Habiba, we can collaborate on the study if @SvetlanaUP assigned you to it

[SvetlanaUP]

@Nana-Habiba @omojokunoluwatomisin10 sure!

[omojokunoluwatomisin10]

@Nana-Habiba, you can chat me up on slack omojokunoluwatomisin

[Nana-Habiba]

@SvetlanaUP this is ready for review: https://bugsigdb.org/Study_1076

[Nana-Habiba]

@omojokunoluwatomisin10 Good morning just came online now to see your messages, I started working on the paper immediately I requested for it yesterday, I have finished the curation, however you can check it on the above link. And know if there's any input you can point out. Thank you. Maybe we can collaborate on future papers

[SvetlanaUP]

@Nana-Habiba this is not ok, you should wait for official approval and then collaborate with @omojokunoluwatomisin10

[omojokunoluwatomisin10]

In experiment 1 signature 1 proteobacteria should be changed to Pseudomonata https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1224&lvl=3&lin=f&keep=1&srchmode=1&unlock

Bacteroidetes changed to [Bacteroidia] (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=200643&lvl=3&srchmode=1&keep=1&unlock)

[SvetlanaUP]

@omojokunoluwatomisin10 please do make corrections. Thanks!

[SvetlanaUP]

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	1
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	1
7	Groups correctly labeled as 1 and 0 (1=cases, 0=controls)	1	1
8	Antibiotic exclusion correctly identified	1	1
9	Correctly identified sequencing details	2	2
10	Identified correct statistical test	1	1
11	Identified MHT correction	1	1
12	Correctly recorded matched on factors	1	1
13	Entered correct number of statistical tests per experiment	1	1
14	All diversity measures identified	1	1
15	Diversity results correctly entered as increased/decreased/unchanged	1	1
16	All signature sources correctly identified (-1 for each error)	2	2
17	Abundance direction correctly selected	1	1
18	Members of signatures identified correctly	2	2
19	Correct use of NCBI taxonomy	2	1
	TOTAL	23	22

• correct NCBI taxonomy for Pelomonas is Roseateles (corrected)

Well done @Nana-Habiba @omojokunoluwatomisin10

[Nana-Habiba]

@Svetlana Ugarcina Perovic @.**> Thank you for the review, I have taken note of this: Pelomonas is Roseateles*

On Mon, Apr 8, 2024 at 2:03 PM Svetlana Ugarcina Perovic < @.***> wrote:

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 1 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 1 7 Groups correctly labeled as 1 and 0 (1=cases, 0=controls) 1 1 8 Antibiotic exclusion correctly identified 1 1 9 Correctly identified sequencing details 2 2 10 Identified correct statistical test 1 1 11 Identified MHT correction 1 1 12 Correctly recorded matched on factors 1 1 13 Entered correct number of statistical tests per experiment 1 1 14 All diversity measures identified 1 1 15 Diversity results correctly entered as increased/decreased/unchanged 1 1 16 All signature sources correctly identified (-1 for each error) 2 2 17 Abundance direction correctly selected 1 1 18 Members of signatures identified correctly 2 2 19 Correct use of NCBI taxonomy 2 1 TOTAL 23 22

• correct NCBI taxonomy for Pelomonas is Roseateles (corrected)

Well done @Nana-Habiba https://github.com/Nana-Habiba @omojokunoluwatomisin10 https://github.com/omojokunoluwatomisin10

— Reply to this email directly, view it on GitHub https://github.com/waldronlab/BugSigDBcuration/issues/180#issuecomment-2042706300, or unsubscribe https://github.com/notifications/unsubscribe-auth/BFNINYLRSNSFDD72SX7X6MDY4KITFAVCNFSM6AAAAABEIYQXRCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBSG4YDMMZQGA . You are receiving this because you were mentioned.Message ID: @.***>

[Nana-Habiba]

@Svetlana Ugarcina Perovic @.***> Good morning My bad was just going through my inbox, then I came across this. So Sorry about this, I moved too fast. This won't repeat itself ever again. Thank you very much for this correction.

On Sun, Mar 31, 2024 at 10:19 AM Svetlana Ugarcina Perovic < @.***> wrote:

@Nana-Habiba https://github.com/Nana-Habiba this is not ok, you should wait for official approval and then for @omojokunoluwatomisin10 https://github.com/omojokunoluwatomisin10

— Reply to this email directly, view it on GitHub https://github.com/waldronlab/BugSigDBcuration/issues/180#issuecomment-2028613155, or unsubscribe https://github.com/notifications/unsubscribe-auth/BFNINYLA6KLGWM2N7HCVNV3Y27IJ5AVCNFSM6AAAAABEIYQXRCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRYGYYTGMJVGU . You are receiving this because you were mentioned.Message ID: @.***>