Salivary microbiota and inflammation-related proteins in patients with psoriasis

[lwaldron]

Initiated at https://bugsigdb.org/Study_710. 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.

[shallockh02]

I Kelvin Joseph can curate this one

[lwaldron]

We'll wait until https://github.com/waldronlab/BugSigDBcuration/issues/27 is reviewed before assigning another issue to you @shallockh02.

[shallockh02]

It has been reviewed can i proceed to make this my third curation

[Kiiki015]

Hello, @lwaldron please can I work on this?

[lwaldron]

Sorry @shallockh02 how do you know #27 has been reviewed? I don't see a review there. @Kiiki015 is this your first "second contribution" ?

[Kiiki015]

Sorry @shallockh02 how do you know #27 has been reviewed? I don't see a review there. @Kiiki015 is this your first "second contribution" ?

It's my first contribution.

[shallockh02]

Got my response on how I performed on the curation

On Wed, Mar 22, 2023, 11:41 PM Kiiki015 @.***> wrote:

Sorry @shallockh02 https://github.com/shallockh02 how do you know #27 https://github.com/waldronlab/BugSigDBcuration/issues/27 has been reviewed? I don't see a review there. @Kiiki015 https://github.com/Kiiki015 is this your first "second contribution" ?

It's my first contribution.

— Reply to this email directly, view it on GitHub https://github.com/waldronlab/BugSigDBcuration/issues/47#issuecomment-1480232384, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5EMEOLMPDVDIW4BSAGMZBTW5NPV3ANCNFSM6AAAAAAVZEGM2Q . You are receiving this because you were mentioned.Message ID: @.***>

[Bahati308]

hello, @lwaldron , can i take over this

[Ellajessica]

@cmirzayi @lwaldron @cmirzayi @fbeghini . Please can this be assigned to me please. Worked on one without signatures before.

[Ellajessica]

@ftzohra22. Please can you assign this to me

[cmirzayi]

@Kiiki015 assigned

[Ellajessica]

https://bugsigdb.org/Study_710. I Have worked on these. Got a Mail from @cmirzayi that this has been assigned to me only to get here and see that it was assigned to another user. Can i get review for it. Since i'm done working on it just few hours ago @lwaldron @cmirzayi @Bahati308

[ftzohra22]

@Ellajessica Good effort on this curaton. You start was good, however none of the signatures you curated from figure 2 were correct. We have to make sure that we are entering the bacteria upto the species level as it appears on the figure not just part of it. Also you did not enter all the experiments that were being compared. Please review the rest of the feedback and make the necessary changes. Thank you.

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 2 experiments one comparing P vs. PS and one comparing HC vs. PS)
4. Body site correctly identified (i.e. does not include multiple sites) (1 point): 0 (the samples are saliva samples. "saliva" should be the correct term)
5. Condition entered according to contrast (correct EFO ontology) (1 point): 0 (condition should be whatever the case group is, if group 1 is psoraisis, condition should say psoriasis)
6. Contrast groups correctly identified (1 point): 11
7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 1
8. Antibiotic exclusion correctly identified (1 point): 1 (just entering the time period i.e. 3 months is fine)
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): 0 (matching only applies if it was specifically mentioned)
13. Entered correct number of statistical tests per experiment (1 point): 1
14. All diversity measures identified (1 point): 0 (diversty measures were incorrectly identified, there was only one measure used)
15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): 0 (results were wrong. please review result section again)
16. All signature sources correctly identified (-1 for each error) (2 points): 0
17. Abundance direction correctly selected (1 point): 0
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
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 curation

[Ellajessica]

@ftzohra22 . i have corrected it . for the body site, i wasnt able to see saliva

[ftzohra22]

Thank you @Ellajessica

[atrayees]

Study 710 Added a new experiment recording differentially abundant taxa in healthy controls vs. Periodontitis patients in the Signature.