Help:Contents

Information for users[edit source]

Video tutorials[edit source]

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 source]

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 source]

How can I get involved?[edit source]

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 waldronlab@gmail.com. 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 source]

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:

Help match unknown names to the NCBI taxonomy.
Complete Studies that have no experiments (these are usually studies of interest that have not yet been curated).
Fix improper values, such as matching study conditions to the Experimental Factor Ontology, body sites to the Uber-anatomy Ontology, and other vocabulary to BugSigDB-defined values. Sometimes it requires requesting that an administrator add a missing term.
Work on a previously identified Paper to Curate.

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

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 source]

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

Help:Needs_review: identifies pages that have never been reviewed ("Missing review"), have been edited since the previous review ("Stale reviews"), or have been manually flagged for review ("Flagged for review").
Help:Cleanup: identifies pages with outstanding issues, such as missing or invalid data. It makes heavy queries so it may take a while to load or purge.
Incomplete pages (marked as incomplete by curator)
Pages with missing NCBI ID
Pages with a disallowed value

NCBI cleanup[edit source]

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 source]

Key links for administrators:

Editing using the API and the API sandbox
Help:Admin: Edit auto-complete fields
Help:Quality_control: Edit QC flags
Special:SpecialPages: All special pages
Special:CreateAccount: Create accounts
Special:ConfirmAccounts: Approve/reject account requests
Special:ListUsers: list users and roles
Special:UserRights: change roles for one of the above users (requires knowing user name, can be found above).
Special:Log: site-wide log
User Forum on Google Groups: Discussion Board

Finally, MediaWiki general help.

Information for data analysts and tool developers[edit source]

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:

Access BugSigDB data in R using the bugsigdbr Bioconductor package. bugsigdbr provides some additional conveniences over raw csv file export, such as harmonizing taxonomic level and selecting on body site or study condition, and provides three options for data source:
- bleeding edge data as csv file exports of bugsigdb.org
- hourly exports
- semi-annual releases on Zenodo, synced with the Bioconductor release cycle
Source code and issue tracking for the bugsigdb.org Semantic MediaWiki site
Example analyses of bugsigdb.org

For other information, see About BugSigDB.

Citing BugSigDB[edit source]

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.