Help:Contents

Information for users

Video tutorials

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⠀?)

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

How can I get involved?

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.

• 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 contact site administrators in a public forum, post to the BugSigDB Google Group.
• 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?

First, request an account. 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.

TODO for reviewers

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

Other important links for reviewers

• Special:ReplaceText: site-wide search and replace
• Special:Log/delete: Deletion log
• Standardize values How to standardize property values
• Information on data transformation Data transformation definitions

Contact waldronlab@gmail.com to request to become a reviewer of contributed data.

NCBI cleanup

• 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

Key links for administrators:

• Special:ApiSandbox: 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

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

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.