If you use BugSigDB in published research, please cite:
Geistlinger L, Mirzayi C, Zohra F, Azhar R, Elsafoury S, Grieve C, Wokaty J, Gamboa-Tuz SD, Sengupta P, Hecht I, Ravikrishnan A, Gonçalves RS, Franzosa E, Raman K, Carey V, Dowd JB, Jones HE, Davis S, Segata N, Huttenhower C, Waldron L: BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures. Nat. Biotechnol. 2023. https://doi.org/10.1038/s41587-023-01872-y (download citation as .ris file)
For a short summary of the work, see the associated Research Briefing BugSigDB — a database for identifying unusual abundance patterns in human microbiome studies or Press Release CUNY SPH researchers unveil comprehensive database of published microbial signatures.
What is BugSigDB?
BugSigDB.org is an editable Semantic Mediawiki that provides manually-curated, expert-reviewed, syntax-standardized reporting of the published literature on microbial signatures. Curators standardize taxa to the NCBI taxonomy and standardize key information about the studies, experiments, and analytical methods that generated these signatures using data entry forms, controlled vocabulary, and ontologies. BugSigDB standardizes published microbiome literature including:
- geography, health outcomes, host body sites, and experimental, epidemiological, and statistical methods using controlled vocabulary,
- results on microbial diversity,
- microbial signatures standardized to the NCBI taxonomy, and
- identification of published signatures where a microbe has been reported.
To get started, please see our collection of video tutorials, which includes:
- a summary of what BugSigDB is and why it might be useful for you,
- an overview of BugSigDB functionality, including how to use the wiki, how to search for studies, and how to export BugSigDB data for external analysis,
- a step-by-step walk-through of how to add a new study through the curation interface of BugSigDB, and
- a demo of how to work with BugSigDB data in R using the bugsigdbr R/Bioconductor package.
Why and how would I contribute?
You too can enter studies and signatures into BugSigDB.org, and doing so provides benefits:
- the ability to compare to previously published signatures either directly on BugSigDB.org, through the bugsigdbr R/Bioconductor package, or through bulk text export and analysis in the software of your choice. Shortly after you enter or edit a signature, it is exportable and analyzable: see https://waldronlab.io/bugSigSimple/ for several example analyses.
- standardized reporting of study results with a citable URL. Posting your experimental results here is straightforward, vastly more usable than a supplemental table, and allows you to compare your signatures to the rest of bugsigdb.org.
- bulk copy-paste signature entry if you use comma-separated NCBI taxonomy IDs.
- Automatic hyperlinking to the NCBI taxonomy and taxonomy-aware organization and analysis.
It is our goal to incorporate all published host-associated microbiome differential abundance signatures. To start contributing, see the information for curators and create a BugSigDB account.
The BugSigDB Team
CUNY Graduate School of Public Health and Health Policy
- Dr. Levi Waldron
- Dr. Heidi Jones
Harvard Medical School
- Dr. Ludwig Geistlinger
Colorado University Medical Center
- Dr. Sean Davis
Harvard TH Chan School of Public Health
- Dr. Curtis Huttenhower
University of Trento
- Dr. Nicola Segata
The following CUNY SPH staff have contributed extensively through reviewing the work of curators, creating data validation rules, and curation.
- Rimsha Azhar, MS
- Shaimaa El-Safoury, MPH
- Fatima Zohra, MPH
- Chloe Mirzayi, MPH (PhD candidate)
- Clare Grieve, MPH
The following curators have contributed significantly content as part of their master's program fieldwork.
- Mary Bearkland
- Ifeanyi Kalu
- Jessica Shudy
- Sharmila Chunduri
- Umadevi Yokeeswaran
- Jacquelyn Shevin
- Joyessa Dey
- Frans Cuevas
- Martha Martin
- Clare Grieve
- Samara Khan
- Tangirul Islam
- Kweku Amoo
- Philippe Michael Lutete
- Mst Afroza Parvin
- Victoria Goulbourne
- Zyaijah Bailey
- Cynthia Anderson
- William Lam
- Nadine Ulysse
- Lucille Mellor
- Utsav Patel
- Marianthi Thomatos
- Phyu Han
- Lora Kasselman
- Fatima Zohra
- Shaima El Safoury
- Yaseen Javaid
- Lana Park
- Madhubani Dey
- Valentina Pineda
- Yu Wang
- Manuela Hoyos
- My Nguyen
- Titas Sil
Get in touch
We can train student interns and other volunteers, and guide focused projects on an area of your interest in the literature. Contact Levi Waldron to get involved.
BugSigDB: A Comprehensive Database of Published Microbial Signatures is funded primarily by the National Cancer Institute of the National Institutes of Health, 5R01CA230551 "Exploiting public metagenomic data to uncover cancer-microbiome relationships" to Levi Waldron.
These data are made available under the Open Data Commons Attribution License: http://opendatacommons.org/licenses/by/1.0/. You are free:
- To share: To copy, distribute and use the database.
- To create: To produce works from the database.
- To adapt: To modify, transform and build upon the database.
As long as you:
- Attribute: You must attribute any public use of the database, or works produced from the database, in the manner specified in the license. For any use or redistribution of the database, or works produced from it, you must make clear to others the license of the database and keep intact any notices on the original database.
This is not a license. It is simply a handy reference for understanding the ODC-BY 1.0 — it is a human-readable expression of some of its key terms. This document has no legal value, and its contents do not appear in the actual license. Read the full ODC-BY 1.0 license text for the exact terms that apply.
The software powering this site and downstream analyses of the data are licensed under various FSF-approved Open Source licenses, please see individual software packages for information.