VMAP: Vaginal Microbiome Atlas during Pregnancy
File(s)
Published version
Author(s)
Type
Journal Article
Abstract
Objectives
To enable interactive visualization of the vaginal microbiome across the pregnancy and facilitate discovery of novel insights and generation of new hypotheses.
Material and Methods
Vaginal Microbiome Atlas during Pregnancy (VMAP) was created with R shiny to generate visualizations of structured vaginal microbiome data from multiple studies.
Results
VMAP (http://vmapapp.org) visualizes 3880 vaginal microbiome samples of 1402 pregnant individuals from 11 studies, aggregated via open-source tool MaLiAmPi. Visualized features include diversity measures, VALENCIA community state types, and composition (phylotypes, taxonomy) that can be filtered by various categories.
Discussion
This work represents one of the largest and most geographically diverse aggregations of the vaginal microbiome in pregnancy to date and serves as a user-friendly resource to further analyze vaginal microbiome data and better understand pregnancies and associated outcomes.
Conclusion
VMAP can be obtained from https://github.com/msirota/vmap.git and is currently deployed as an online app for non-R users.
To enable interactive visualization of the vaginal microbiome across the pregnancy and facilitate discovery of novel insights and generation of new hypotheses.
Material and Methods
Vaginal Microbiome Atlas during Pregnancy (VMAP) was created with R shiny to generate visualizations of structured vaginal microbiome data from multiple studies.
Results
VMAP (http://vmapapp.org) visualizes 3880 vaginal microbiome samples of 1402 pregnant individuals from 11 studies, aggregated via open-source tool MaLiAmPi. Visualized features include diversity measures, VALENCIA community state types, and composition (phylotypes, taxonomy) that can be filtered by various categories.
Discussion
This work represents one of the largest and most geographically diverse aggregations of the vaginal microbiome in pregnancy to date and serves as a user-friendly resource to further analyze vaginal microbiome data and better understand pregnancies and associated outcomes.
Conclusion
VMAP can be obtained from https://github.com/msirota/vmap.git and is currently deployed as an online app for non-R users.
Date Issued
2024-10-01
Date Acceptance
2024-09-09
Citation
JAMIA Open, 2024, 7 (3)
ISSN
2574-2531
Publisher
Oxford University Press
Journal / Book Title
JAMIA Open
Volume
7
Issue
3
Copyright Statement
© The Author(s) 2024. Published by Oxford University Press on behalf of the American Medical Informatics Association. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/ by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/39345789
PII: ooae099
Subjects
16S rRNA sequencing
bioinformatics
data integration
DIVERSITY
Health Care Sciences & Services
Life Sciences & Biomedicine
Medical Informatics
microbiome
Science & Technology
visualization
Publication Status
Published
Coverage Spatial
United States
Article Number
ARTN ooae099
Date Publish Online
2024-09-27