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waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
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Large-scale characterization of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population #381

Closed Nana-Habiba closed 5 months ago

Nana-Habiba commented 7 months ago

Large-scale characterization of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population - Sherrianne Ng- nature https://www.nature.com/articles/s41522-021-00261-0?fromPaywallRec=false

Rahila-me commented 7 months ago

@SvetlanaUP May i curate this paper. Thank you

Rahila-me commented 6 months ago

Seen, Thanks

Rahila-me commented 6 months ago

@SvetlanaUP please this curation needs review: Link: https://bugsigdb.org/Study_1034

Scholarpat commented 6 months ago

Hi @SvetlanaUP , please can I review this curation?

Scholarpat commented 6 months ago

Thank you!

Scholarpat commented 6 months ago

Hi @Rahila-me,

This is a great curation. You have done wonderful work here. I have made a few observations/suggestions below:

1. Group 1 definition: This should be altered slightly for clearer understanding. I suggest using "Women with high vaginal sialidase activity, which is often associated with bacterial vaginosis (BV)" rather than "Women with high sialidase activity had significantly higher prevalence of Lactobacillus species depleted microbiota."

2. Source description: This should be consistent for both signatures 1 and 2 in an experiment. I noticed slight differences in your curation. Rather than making both signature source descriptions different, you can merge them. For example, "LDA analysis in vaginal microbiota of women with leukocyte low (grades I-II, green) versus leukocyte high (grades III-IV, red)" would be a better fit for both signatures 1 and 2 source description of experiment 2.

3. Missing taxa: I noticed you excluded the taxa Bacteroidetes in signature 1 of experiment 1. I understand this might be because Bacteroidia (rank = class), a heterotypic synonym of Bacteroidetes, is already present. However, Bacteroidota (rank = phylum) is a homotypic synonym of Bacteroidetes, and both should be curated since they are of different taxonomic ranks. Additionally, in signature 2 of experiment 2, the taxa Actinobacteria is not curated.

I hope these suggestions are helpful. Well done on your curation!

SvetlanaUP commented 6 months ago

Hi @Rahila-me, good job! Would you like to correct your curation based on @Scholarpat's feedback?

Scholarpat commented 5 months ago

Hi @SvetlanaUP, I have effected the corrections to this curation.

It is now complete.

SvetlanaUP commented 5 months ago

https://bugsigdb.org/Study_1034 reviewed.