Protocol: corpus-level curation statistics for BugSigDB (paper Table 1)

Tier: C (BugSigDB paper) · Type: atomic · Category: Descriptive Statistics

What

Regenerate the database-level summary: number of studies and experiments broken down by study design, subject characteristics, lab analysis (sequencing type, platform, region), statistical analysis method, and alpha diversity reporting — against a pinned bulk export version.

Why it matters

This is the single most obviously updatable analysis in the set: the paper's Table 1 is already out of date and will be out of date again next year. Turning it into a protocol means the next version is a rerun, not a re-derivation. It is also a genuinely easy first protocol for a student who wants to start with descriptive work.

Source material

• waldronlab/BugSigDBPaper — vignettes/Table1.Rmd (pinned to bulk export version 1.0.2; sections for study design, subjects, lab analysis, statistical analysis, alpha diversity)
• waldronlab/BugSigDBStats
• Paper: 10.1038/s41587-023-01872-y

Scope

In: the export version pinning; every reported category and its denominator; how to count experiments vs. studies vs. signatures without double counting; the treatment of missing/unreported fields; the exact table layout so successive versions are comparable.

Out: any inferential statistics.

Frontmatter starting point

type: "atomic"
category: "Descriptive Statistics"
citation: ~   # Descriptive reporting, no originating method. See the note in A2.
tags: [bugsigdb, curation, descriptive-statistics, reporting, table1]

Acceptance criteria

• Every reported number has a stated denominator
• Missing-value handling is defined per field
• Rerunning against the pinned v1.0.2 export reproduces the published Table 1

Cite the method's origin, not its users

PROTOCOL_STANDARD.md is explicit: an atomic protocol carries "strictly 1 citation... corresponding
to the primary literature where the method was originally published." Find the paper that proposed
the method. Do not cite a paper that merely applied it — including the BugSigDB and curatedMetagenomicData
papers, which are the source of the analysis these protocols were extracted from but almost never the
source of the method.

Tracing a method back to its first publication is real work, and it is part of the task, not a
formality. Three things to expect:

• Candidate DOIs in this issue are leads, not answers. Anything marked VERIFY has not been checked.
• Some methods predate modern citation practice or have no single identifiable origin. If that is
  genuinely the case, say so in the pull request rather than reaching for a convenient recent paper.
  Raise it as an issue in waldronlab/agent-protocol-standard — the standard may need a way to express
  "classical method, no primary source".
• If you cannot name one paper that proposed everything the protocol does, it is more than one
  protocol. That test has now split four protocols out of this batch: enrichment into three methods,
  filtering from transformation, LODO from random forest, and PERMANOVA from ANOSIM.

Where the lab's own paper genuinely did propose the method — the oral-to-gut score, and LODO
cross-validation in Pasolli et al. 2016 — citing it is correct. That is the exception, not the pattern.

Before you start

Read CONTRIBUTING.md and
PROTOCOL_STANDARD.md.
The format is defined in the standard repo, not this one. Protocols are prose, not code: they say what to do
and why, precisely enough that two people — or two agents, in two languages — get the same answer. The existing
independent-filtering-variance
protocol is the model to imitate for tone and level of detail.

Validate locally before opening the PR:

git clone https://github.com/waldronlab/agent-protocol-standard.git
Rscript agent-protocol-standard/scripts/validate-protocol.R protocols

Read CONTRIBUTING.md and PROTOCOL_STANDARD.md, then use protocols/independent-filtering-variance/protocol.md as the format model. Inspect BugSigDBPaper/vignettes/Table1.Rmd and the BugSigDBStats source to document the pinned v1.0.2 export, denominators, missing values, and counting rules. Done means the protocol reproduces Table 1 and passes validate-protocol.R.