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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age #392

Open Scholarpat opened 1 month ago

Scholarpat commented 1 month ago

Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age

https://pubmed.ncbi.nlm.nih.gov/33789672/

Buraah commented 1 month ago

Hello @SvetlanaUP Please I would love to be assigned to this. Thank you.

Buraah commented 1 month ago

Thank you @SvetlanaUP

Buraah commented 4 weeks ago

Hello @SvetlanaUP , @Scholarpat I should have been done with this curation, but the figures pose a huge challenge for me.

This study has 14 experiments, 6 of which I have curated from the first figure showing differential abundance (figure 6). There are 8 more experiments to go, but the figure I will curate from is not visible. So currently I am at a roadblock with this study.

SvetlanaUP commented 4 weeks ago

@Scholarpat can you please go through this curation https://bugsigdb.org/Study_1083

SvetlanaUP commented 4 weeks ago

@Buraah What do you mean by not visible figure?

Scholarpat commented 4 weeks ago

I'll check it out @SvetlanaUP

Buraah commented 4 weeks ago

@Buraah What do you mean by not visible figure?

The names of the microorganisms are blurry, it is difficult to figure them out. ( mostly figure 7). I will share a screenshot of how it looks from my end.

Scholarpat commented 4 weeks ago

It is also blurry from my end too @Buraah. So sorry for the stress. Should have checked it out very well before creating the issue.

I can't make out most of the signatures from the LeFse figure @SvetlanaUP .

Buraah commented 4 weeks ago

![Uploading Screenshot (62).png…]()

Buraah commented 4 weeks ago

It is also blurry from my end too @Buraah. So sorry for the stress. Should have checked it out very well before creating the issue.

I can't make out most of the signatures from the LeFse figure @SvetlanaUP .

Yeah, and mostly the signatures in Figure 7. I could see the ones in Figure 6.

SvetlanaUP commented 4 weeks ago

Ok, I understand it now. I will contact the authors and CC you both to the email.

SvetlanaUP commented 1 week ago

@Scholarpat @Buraah after emailing the authors and a kind reminder for the email sent >10 days ago we did not get any response from the authors, we decide to proceed with curation based on what we have now "visible".

Please finalize curation with a note of poor quality of the figures as the challenge for this curation.

Buraah commented 1 week ago

Okay @SvetlanaUP I'll finalize the curation and get back here when I'm done.

I might take a few days, I lost family last night. It's a long day for me. Thank you

SvetlanaUP commented 1 week ago

@Buraah sorry for your loss, and please take your time!

Scholarpat commented 1 week ago

@Buraah so sorry for your loss

Buraah commented 1 week ago

Hi @SvetlanaUP I have finalized this curation and it's ready for review. Study link: https://bugsigdb.org/Study_1083