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Protocol: study characteristics table for a set of curated signatures

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
78/100
Issue type
Documentation
Clarity
Clearly specified
Activity status
Active
Tech stack
r
Domain
documentation

Research direction

Read CONTRIBUTING.md and PROTOCOL_STANDARD.md, then inspect R/describe_curation.R, R/simple.R, and the cited vignettes for study-table behavior. Document the required columns, identifier and DOI rules, missing-value handling, and experiment collapsing without rendering a table. Validate with the provided Rscript command before opening a pull request.

Written by the indexing model from the issue text.

Description

atomic-protocol data-curation good-first-protocol microbiome

Tier: A (fieldwork / first protocol) · Type: atomic · Category: Descriptive Statistics

What

Given a filtered BugSigDB subset, produce the "table of studies" that opens essentially every fieldwork and capstone analysis: one row per study, with study identifier, condition, body site, sequencing type, group sizes, number of signatures, and DOI.

Why it matters

It is the first table in a paper and the first thing a reviewer checks. It is also where the study-identifier convention gets decided — bugSigSimple builds a curatedMetagenomicData-style ID (ZellerG_2014, with .1/.2 disambiguation), which is what makes BugSigDB and cMD analyses joinable later. That convention deserves to be written down as a protocol step rather than buried in an internal helper.

Source material

  • waldronlab/bugSigSimple — R/describe_curation.R (createStudyTable), R/simple.R (.make_unique_study_ID, author: Giacomo Antonello)
  • Vignettes: capstoneanalysis_clare.rmd ("Table of studies"), goldstandard_vignette_peace.Rmd ("Study characteristics")

Scope

In: required columns; the unique-study-identifier construction rule including duplicate suffixing; DOI normalization; how to collapse multiple experiments per study.

Out: taxon-level summaries (see the frequency-table protocol); formatting/typesetting.

Frontmatter starting point

type: "atomic"
category: "Descriptive Statistics"
citation: ~   # No originating method to cite — this is a reporting convention, not a method.
              # `citation` is optional in the standard; leave it empty rather than citing an
              # application paper. Raise it in the standard repo if a reporting protocol needs a
              # different provenance field.
protocols_used: []   # consumes the output of the signature-subset protocol
tags: [bugsigdb, study-table, reporting, study-identifier]

Acceptance criteria

  • The identifier rule is deterministic and stated in prose
  • Says what to do when the first author or year is missing
  • Output is a table specification, not a rendered kable

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
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Getting set up

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

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