Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome

[Scholarpat]

Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome - T Goolam Mahomed – BMC Microbiology

https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02288-x

[AnushaR-star]

Hello @SvetlanaUP and @Scholarpat i would like to contribute could u pls assign this

[TheTosin]

Hi @AnushaR-star

How is your day going? Do you need help in completing this curation. I am happy to assist. You can as well reach me as Adeshile Oluwatosin on slack.

[KateRasheed]

Hello @AnushaR-star . Good morning to you. I see that you haven't created a study on this article. Are you experiencing any blocker? We are here to help if you need anything. Do have a great day.

[AleruDivine]

Good morning, @AnushaR-star. I hope you are doing okay. This study is yet to be added to BugSigDB, and I am wondering if you are having any difficulties with the curation.

I went through the paper this morning and identified 1 potential experiment to be curated (the comparison of targeted metagenomics and IS-Pro methods) and signatures from DESeq2 analysis. We are all available to help and collaborate to tackle the difficulties you are facing. You can reach out to me on Slack @AleruDivine or to any of the applicants who have offered to help before me.

Thank you so much!

[SvetlanaUP]

@TheTosin @AleruDivine @KateRasheed please work on this curation together.

[TheTosin]

Noted! @SvetlanaUP Good Afternoon

[AleruDivine]

Got it @SvetlanaUP thank you so much!

[KateRasheed]

Thank you so much @SvetlanaUP .

[TheTosin]

@AleruDivine @KateRasheed Please let’s create a group on slack for easy communication and team work 🙏

[vandana123maddi]

Good morning @AnushaR-star i found this paper intresting and if u need any help that u think i could add value u can approach me in slack if collaboration I love to do if there is a chance do consider me ! Have a good day

[AleruDivine]

Hi @vandana123maddi this study has been reassigned to me, @TheTosin and @KateRasheed to work on by @SvetlanaUP. You're welcome to join us to complete the curation🤗

[SvetlanaUP]

@AleruDivine What's the status of this curation? Thanks!

[TheTosin]

Good afternoon, @SvetlanaUP it’s ready for review

https://bugsigdb.org/Study_1159

[SvetlanaUP]

Great team effort! I corrected descriptions of the groups: please see how you should provide precise details and also abbreviations first time mentioned.

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	0.5
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	2
	TOTAL	23	22.5

[TheTosin]

Thank you so much @SvetlanaUP Noted.

[KateRasheed]

Thank you so much for this @SvetlanaUP . We will take note of the descriptions in case of next time.

[AleruDivine]

Duly noted! Thank you so much for the review and for the correction @SvetlanaUP. 🙏 Great work @TheTosin @KateRasheed 🙌🏽