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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection #484

Closed Scholarpat closed 2 weeks ago

Scholarpat commented 3 months ago

Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection – Duy M Dinh – The Journal of Infectious Diseases

https://academic.oup.com/jid/article/211/1/19/801451

Agatha-Chineke commented 1 month ago

I am interested in curating this work "Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection #484"

I did appreciate if it is assigned to me

Agatha-Chineke commented 1 month ago

Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection – Duy M Dinh – The Journal of Infectious Diseases

https://academic.oup.com/jid/article/211/1/19/801451

Please assigned this work to me for curation

Thank you

KateRasheed commented 1 month ago

Hi @Agatha-Chineke . How is this curation going? Would you like me to assist in any way?

Agatha-Chineke commented 1 month ago

Hi Kate, thank you for reaching out

Yeah I definitely need your help. I have been not been able to keep up with others because I fell sick but now, I am better

Please do let me know when you are available, I have a couple of questions to ask. Thank you

On Fri, 11 Oct 2024, 12:05 Kate Rasheed, @.***> wrote:

Hi @Agatha-Chineke https://github.com/Agatha-Chineke . How is this curation going? Would you like me to assist in any way?

— Reply to this email directly, view it on GitHub https://github.com/waldronlab/BugSigDBcuration/issues/484#issuecomment-2407174848, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3LCYYEHW4ICXJT4XTMREPDZ26WIVAVCNFSM6AAAAABMN2PSRWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBXGE3TIOBUHA . You are receiving this because you were mentioned.Message ID: @.***>

KateRasheed commented 1 month ago

Ohh. Great. What is your slack name let me send a DM.

KateRasheed commented 1 month ago

@Agatha-Chineke Can you share your slack name so I can reach out to you.

Agatha-Chineke commented 1 month ago

Agatha

On Sat, 12 Oct 2024, 12:17 Kate Rasheed, @.***> wrote:

Ohh. Great. What is your slack name let me send a DM.

— Reply to this email directly, view it on GitHub https://github.com/waldronlab/BugSigDBcuration/issues/484#issuecomment-2408527090, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3LCYYGWG7JCCNYKJUX7SZLZ3EAOJAVCNFSM6AAAAABMN2PSRWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBYGUZDOMBZGA . You are receiving this because you were mentioned.Message ID: @.***>

KateRasheed commented 1 month ago

@Agatha-Chineke Good afternoon to you. The last time we communicated on slack, you mentioned you were adding signatures. I would like to know the progress of your curations, are you done entering the experiments and signatures?

KateRasheed commented 1 month ago

Greetings again @Agatha-Chineke . I see that you have added an experiment and a signature. Can I collaborate with you so we can complete this curation?

Agatha-Chineke commented 3 weeks ago

@SvetlanaUP , please how do I submit my work for review and grading?

SvetlanaUP commented 3 weeks ago

@Agatha-Chineke by writing a comment here: https://bugsigdb.org/Study_1152 ready for review.

Agatha-Chineke commented 3 weeks ago

@SvetlanaUP this work is ready for a review:

https://bugsigdb.org/Study_1152

Thank you

SvetlanaUP commented 3 weeks ago

Hi @Agatha-Chineke, thank you for your contribution. This was a good start of curation but critical curation points finally were missed. Please see the details below and revise in collaboration with @KateRasheed.

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 0
11 Identified MHT correction 1 0
12 Correctly recorded matched on factors 1 1
13 Entered correct number of statistical tests per experiment 1 0
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 0
17 Abundance direction correctly selected 1 0.5
18 Members of Signatures identified correctly 2 0
19 Correct use of NCBI taxonomy 2 0.5
TOTAL 23 14
KateRasheed commented 3 weeks ago

Ohh. Thank you @SvetlanaUP . We'll get to work.

KateRasheed commented 3 weeks ago

Good day @SvetlanaUP . Corrections have been made to the study. I would like to state that for the MHT correction, I did not see any indication of multiple hypothesis testing.

Thank you so much. @Agatha-Chineke

SvetlanaUP commented 2 weeks ago

Well done!

https://bugsigdb.org/Study_1152 reviewed.