Genomic investigations of acute munitions exposures on the health and skin microbiome composition of leopard frog (Rana pipiens) tadpoles

[lwaldron]

Genomic investigations of acute munitions exposures on the health and skin microbiome composition of leopard frog (Rana pipiens) tadpoles

https://www.sciencedirect.com/science/article/pii/S0013935120311427?casa_token=AMHUTxrSEO0AAAAA:TyUcWOzlElLI3kYk4gN8Q-IWLVscUMrmG18_MCs6quxO-zrvP4Al9kUJ7oL_StcNYT1KBzQD49BB

[Kehindeadebisi]

Kehinde Adebisi

[Kehindeadebisi]

Hi @lwaldron I'll like to curate this article

[cmirzayi]

Assigned.

[Buraah]

@SvetlanaUP I'm trying to pick a second article to curate since the first one I picked wasn't curatable. It seems it is the case with this one too, I don't think this is also curatable. Can you please take a look at it?

[SvetlanaUP]

@Buraah this paper provides bacterial signatures that are curatable.

[Buraah]

@Buraah this paper provides bacterial signatures that are curatable.

Oh, that is true. I can see more details now after downloading the pdf. Thank you for assigning it to me.

[Buraah]

Hello @SvetlanaUP I am unable to start curating this because it seems it is already in the database.

[SvetlanaUP]

@Buraah please try it again. It should be fixed now.

[Buraah]

@Buraah please try it again. It should be fixed now.

Yes, it works now. Thank you for your quick response!

[Buraah]

Hello @SvetlanaUP, I am done curating this article.

[Buraah]

Thank you for reviewing my work @AleruDivine

[Buraah]

Hello @keamybams, @flourishralph thank you!

[Buraah]

Here is the link to my curation https://bugsigdb.org/Study_900

[Omabekee]

Overall this was a really good second curation @Buraah , some points to take note:

1. You got almost all correctly except the group sizes and condition. It's good to search the ontology site for the closest match to the condition found, however, in cases where you don't see anything close as in this case, another trick is to read through the paper again for any clue. E.g. I couldn't find Nitroguanidine on the site, but I read in the paper that this is an environmental contaminant, therefore I entered that as the condition.

2. We don't curate relative abundance in BugSigDB, differential abundance results only. I understand that this can be confusing sometimes, Esther shared a thread in the Slack community where Chloe gave a detailed explanation of the difference between the two.

CURATION RESULTS

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): 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): 0
6. Contrast groups correctly identified (1 point): 0.5
7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 0.5
8. Antibiotic exclusion correctly identified (1 point): 1
9. Correctly identified sequencing details (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): 1
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 (2 points): 1
19. Correct use of NCBI taxonomy (2 points): 2 Total = 19

@SvetlanaUP review of study 900 complete. ✅

[Buraah]

Overall this was a really good second curation @Buraah , some points to take note:

1. You got almost all correctly except the group sizes and condition. It's good to search the ontology site for the closest match to the condition found, however, in cases where you don't see anything close as in this case, another trick is to read through the paper again for any clue. E.g. I couldn't find Nitroguanidine on the site, but I read in the paper that this is an environmental contaminant, therefore I entered that as the condition.
2. We don't curate relative abundance in BugSigDB, differential abundance results only. I understand that this can be confusing sometimes, Esther shared a thread in the Slack community where Chloe gave a detailed explanation of the difference between the two.

CURATION RESULTS

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): 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): 0
6. Contrast groups correctly identified (1 point): 0.5
7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 0.5
8. Antibiotic exclusion correctly identified (1 point): 1
9. Correctly identified sequencing details (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): 1
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 (2 points): 1
19. Correct use of NCBI taxonomy (2 points): 2 Total = 19

@SvetlanaUP review of study 900 complete. ✅

Thank you so much @Omabekee. For the group sizes, I thought I had to add up every Tadpole in the different munition concentrations to make up group 1 size. This was a little confusing, so instead of inputting the wrong figure, I left it blank awaiting review. But thank you for clarifying this, I understand better now.

The exact conditions weren't on EFO too, I tried to use Munition and Exposure to munition too. I understand this better now too, thank you so much. I'll be sure to take note of these on my next curation.

[SvetlanaUP]

https://bugsigdb.org/Study_900 reviewed.