From BugSigDB

Information for users[edit]

Video tutorials[edit]

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.

Quality control flags for studies and for taxa (!X?)[edit]

How and why Quality Control flags are set: Help:Quality_control

  • Study-level flags (retracted paper, contamination issues suspected, batch effect issues suspected, uncontrolled confounding suspected, results are suspect (various reasons)) are set manually by wiki editors.
  • Taxon-level flags for potential contaminants (!), not host-associated (X), and body site-typical (prevalent) (?) are set automatically by matching to site-wide lists

Information for curators[edit]

How can I get involved?[edit]

First, request an account. You can immediately start contributing as much or as little as you want, and your edits will become part of BigSigDB (About). See a table of recent contributions and curators, and Testimonials from other curators.

  • For a detailed explanation of the process of entering studies, experiments, and signatures, refer to the Curation Policy.
  • To participate in regular curator meetings, contact To join discussions with administrators and curators, join the #bugsigdb channel of the community-bioc Slack team.
  • See/edit the presentation schedule at PresentationSignup.
  • Join the User Forum on Google Groups for curation and wiki-related discussions and announcements.

Where can I start?[edit]

You can enter a new study by clicking Add a Study at the top of the page. But there are also other ways to contribute:

Do I need permission to add a study to BugSigDB?[edit]

Since bugsigdb doesn't publish copyrighted material, we don't require permission from publishers or authors to curate information from published studies. If you are unsure whether a study is within scope for BugSigDB, see the Curation Policy or ask on the #bugsigdb channel of the community-bioc Slack team.

TODO for reviewers[edit]

Reviewers double-check BugSigDB for accuracy and consistency. Some key links:

Other important links for reviewers[edit]

Contact to request to become a reviewer of contributed data.

NCBI cleanup[edit]

  • Signatures with missing NCBI ID: These are taxa names that original curators were unable to match to a valid NCBI identifier and name, and may benefit from additional expert review.

Information for administrators[edit]

Key links for administrators:

Finally, MediaWiki general help.

Information for data analysts and tool developers[edit]

The data in BugSigDB are made available under the Creative Commons Attribution 4.0 International (CC BY 4.0). Please feel free to copy, redistribute, and adapt, even commercially, as long as you provide attribution and do not apply additional restrictions. Semantic MediaWiki software and customizations made for this website are licensed under GPL>=2.0.

Some useful links:

For other information, see About BugSigDB.

Citing BugSigDB[edit]

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. (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.