Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease

[ftzohra22]

Condition: Inflammatory bowel disease URL: https://pubmed.ncbi.nlm.nih.gov/36198385/

[Bahati308]

hello, can i do this task please

[Bahati308]

and under your guidance please cause i am an outreachy applicant, any assistance offered will be highly appreciated

[Bahati308]

I am Bahati308, i would like to do this please. thanks

[ftzohra22]

Assigned

[Bahati308]

hello thanks for assigning me the issue, i am new and would like to get the steps on how to accomplish this should i clone it first

On Fri, 10 Mar 2023 at 15:55, Fatima Zohra @.***> wrote:

Assigned

— Reply to this email directly, view it on GitHub https://github.com/waldronlab/BugSigDBcuration/issues/21#issuecomment-1463764453, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP44QVEFBSYLMIVI3PQAOZDW3MQCTANCNFSM6AAAAAAVVRJBJY . You are receiving this because you were assigned.Message ID: @.***>

[Bahati308]

thanks for this opportunity, ill do my best to make a contribution

[Bahati308]

Thanks I followed instructions and I'm soon submitting

On Sun, Mar 12, 2023, 01:30 Bahati Brian Patrick @.***> wrote:

hello thanks for assigning me the issue, i am new and would like to get the steps on how to accomplish this should i clone it first

On Fri, 10 Mar 2023 at 15:55, Fatima Zohra @.***> wrote:

Assigned

— Reply to this email directly, view it on GitHub https://github.com/waldronlab/BugSigDBcuration/issues/21#issuecomment-1463764453, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP44QVEFBSYLMIVI3PQAOZDW3MQCTANCNFSM6AAAAAAVVRJBJY . You are receiving this because you were assigned.Message ID: @.***>

[Bahati308]

hello @ftzohra22 please review my curate and advise me https://bugsigdb.org/Study_739. thanks

[Bahati308]

@ftzohra22 , thanks please so how can i improve on it please

[Bahati308]

what is missing, I request your advise.

[Bahati308]

@ftzohra22 , i request your review on this please https://bugsigdb.org/Study_739. thanks a lot

[lwaldron]

Note @Bahati308 has also curated #36

[Bahati308]

@lwaldron does it mean it was a successful curate,

[Bahati308]

@lwaldron any comments are welcome

[ftzohra22]

@Bahati308 I was not able to score your curation as most of the fields were entered incorrectly. Please go over the article again and revise your curation. Attaching the full PDF here. Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease.pdf

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): 0 (there should be more than one experiment in this study)
4. Body site correctly identified (i.e. does not include multiple sites) (1 point): 0 (body site refers to where the samples were collected from)
5. Condition entered according to contrast (correct EFO ontology) (1 point): 0 (condition refers to the condition the participants)
6. Contrast groups correctly identified (1 point): 0
7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 0
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): 0
10. Identified correct statistical test (1 point): 0
11. Identified MHT correction (1 point): 0
12. Correctly recorded matched on factors (1 point): 0
13. Entered correct number of statistical tests per experiment (1 point): 0
14. All diversity measures identified (1 point): 0
15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): 0
16. All signature sources correctly identified (-1 for each error) (2 points): 0
17. Abundance direction correctly selected (1 point): Incorrect
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): Incorrect
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): Incorrect

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

[cmirzayi]

Hi @Bahati308 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.

[Bahati308]

it is alright, other people can work on it. thanks

On Wed, 10 May 2023 at 21:18, Chloe Mirzayi @.***> wrote:

Hi @Bahati308 https://github.com/Bahati308 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 GitHub https://github.com/waldronlab/BugSigDBcuration/issues/21#issuecomment-1542619411, or unsubscribe https://github.com/notifications/unsubscribe-auth/AP44QVBGIBND2WNBVQ6F6HLXFPLV5ANCNFSM6AAAAAAVVRJBJY . You are receiving this because you were mentioned.Message ID: @.***>

[atrayees]

I have made several changes on the Study (https://bugsigdb.org/Study_739), but I'm still quite confused as to whether my curations are correct or not, would you please take a look at this particular study? Thanks a lot

@cmirzayi @ftzohra22 @lwaldron

[cmirzayi]

I'll review momentarily.

[cmirzayi]

Ok I can see why this was troublesome. They do not consistently state whether the decreases/increases they observed are statistically significant or not. When they do state significance, they do not state whether the significance was between the two arms of the study or within the same arm but before and after treatment. The use of a chi-squared statistical test doesn't really make sense for this analysis either, but it's the only statistical test they say they use.

Given these ambiguities, my feeling is that trying to figure this out would be troublesome and I'm not confident that we would be able to do so. I would remove the signatures from BugSigDB, mark the curation as incomplete, and add a discussion noting that the article in its present form is not curatable.

[atrayees]

Noted. I've marked the curation as incomplete and have added the discussion. Should I go ahead and close this issue?

[lwaldron]

Yes let's close this odyssey!