Chemical Ontology and Nomenclature Crosswalk Tools • concert

Chemical Ontology & Nomenclature Crosswalk for Entity Registration & Translation.

CONCERT is an R package and Shiny application for cleaning, harmonizing, and registering chemical regulatory and benchmark datasets. It helps users import messy CSV/XLSX files, detect frontmatter, tag chemical and measurement columns, curate identifiers, harmonize units and media, resolve WQX parameter matches, and export reviewable ToxVal-compatible outputs.

Installation

# install.packages("pak")
pak::pak("seanthimons/concert")

GitHub-only dependencies (ComptoxR and a pinned reactable revision) are installed automatically from Remotes in DESCRIPTION.

Launch the App

concert::run_app()

For a fixed local port:

concert::run_app(port = 3838, launch.browser = FALSE)

For a visual guide to source DTXSID evidence, mixture correspondence, scoped acceptance, and session restore, read Reviewing a source chemical identity. It includes the complete long Override dialog as overlapping screenshots.

Headless Curation

concert::curate_headless(
  input = "path/to/input.xlsx",
  output = "path/to/output.xlsx",
  tag_map = list(
    chemical_name = "Name",
    casrn = "CASRN"
  ),
  harmonize = TRUE
)

Names that CompTox leaves unresolved are looked up in the chemi resolver. Its hits are review candidates and are checked against a local copy of the public DSSTox database. That copy is about 800 MB, so CONCERT never downloads it unprompted; without it, hits are marked unverified. To install it once and keep it current:

options(concert.dsstox_install = TRUE)  # or run ComptoxR::dss_install() yourself

For agent-driven curation, the package ships a runner script and a skill:

system.file("scripts/curate_loop.R", package = "concert")
system.file("skills/concert-curate/SKILL.md", package = "concert")

Export Re-Import

CONCERT exports include a Pipeline Config sheet with a concert_export marker. Legacy export markers from the former package name are no longer accepted.

Upload an exported workbook through the ordinary file-upload control and choose Resume Session to restore its review decisions, source evidence and applied cleaning choices. Treat as Raw Data starts a new workflow. Sidebar Import Configuration restores selected configuration rather than the full session.

Development

From a checkout, start R (4.5.1) in the repository root; renv bootstraps on first launch. Restore the locked environment, which includes test dependencies:

renv::restore()
devtools::load_all()

After deliberately changing dependencies, run renv::snapshot() and commit renv.lock. renv::status() checks for drift.

Routine CI runs the locked review and module-rendering tests on Windows with R 4.5.1 and the dependencies in renv.lock, plus commit and secret checks. The Linux, Windows, and macOS package-check matrix runs only when R-CMD-check is started manually in GitHub Actions. The release workflow independently runs R CMD check on Linux and rejects errors or warnings before publishing. Run devtools::test() locally for the full regression suite; package archives currently exclude tests/, so package checks do not run those tests.

To benchmark the review table on the 8,216-row case:

source("scripts/benchmark_review_results.R")
benchmark_review_results()
run_review_benchmark_app()

Source identifiers can be configured explicitly in headless workflows with tag_map = list(chemical_name = "Name", source_dtxsid = "DTXSID"). The DTXSID role validates IDs through EPA CompTox chemical details and retains raw values, normalized candidates, validation status, authority, and timestamp as review evidence. Registry membership does not establish correspondence to the source name or chemical scope and does not automatically assign consensus. Unavailable validation remains distinct from a definitive missing record.

Retained identifier columns without this role produce unused-column diagnostics. Use ignored_identifier_cols = "dtxsid_metadata" to deliberately keep an identifier column as metadata. This configuration is preserved in generated replay scripts and workbook Pipeline Config. Raw columns named dtxsid or dtxsid_* remain input data and cannot become lookup votes through their names. Other retains its generic name-search behavior; it does not provide source ID validation.