Skip to contents

metasalmon

metasalmon logo

R package for creating portable, ontology-aware Salmon Data Packages. Wrap your analysis-ready tables into Frictionless Data Packages extended with semantic fields (IRIs, concept schemes) that link to the DFO Salmon Ontology.

Features

  • Dictionary inference: Automatically propose starter dictionaries from your data frames
  • Dictionary validation: Validate dictionary schemas and semantic fields
  • Data transformation: Apply dictionaries to rename columns, coerce types, and apply factor levels
  • Package creation: Assemble Frictionless Data Packages with salmon-specific semantic extensions
  • Package reading: Load packages back into R as tidy tibbles with metadata

Quick Start 

# install remotes and metasalmon project
install.packages('remotes')
remotes::install_github('dfo-pacific-science/metasalmon')

library(metasalmon)

# Load your data
df <- readr::read_csv("your-data.csv")

# Infer a starter dictionary
dict <- infer_dictionary(df, dataset_id = "my-dataset", table_id = "my-table")

# Validate it
validate_dictionary(dict)

# Create a package
resources <- list(main_table = df)
dataset_meta <- tibble::tibble(
  dataset_id = "my-dataset",
  title = "My Dataset",
  description = "Description here"
)
table_meta <- tibble::tibble(
  dataset_id = "my-dataset",
  table_id = "main_table",
  file_name = "main_table.csv"
)

pkg_path <- create_salmon_datapackage(
  resources, dataset_meta, table_meta, dict,
  path = "output-package"
)

Data Package Format

A Salmon Data Package is a Frictionless Data Package extended with semantic fields that link to the DFO Salmon Ontology.

Conceptual Structure

Components:

  • datapackage.json: Package metadata and resource schemas defining columns with semantic IRIs
  • CSV tables: Data files (one per resource)
  • codes.csv: Optional code lists for categorical fields
  • Semantic IRIs: Links in field schemas connecting columns to DFO Salmon Ontology concepts

Installation 

# Install from GitHub (once published)
devtools::install_github("dfo-pacific-science/metasalmon")

Documentation

DFO Salmon Ontology

This package links your data to the DFO Salmon Ontology using semantic IRIs. Key ontology terms include:

  • Classes: ConservationUnit, Stock, EscapementMeasurement, BroodYear, CatchYear
  • Schemes: WSPBiologicalStatusZoneScheme (Green/Amber/Red zones), SalmonOriginScheme, EnumerationMethodScheme, EstimateMethodScheme
  • Metrics: RelativeAbundanceMetric, LongTermTrendMetric, PercentChangeMetric

See the full ontology and repository for all available terms.

Development

  1. Install R (>= 4.4.0) and required packages:
install.packages(c("devtools", "roxygen2", "testthat", "knitr", "rmarkdown", 
                   "tibble", "readr", "jsonlite", "cli", "rlang", "dplyr", 
                   "tidyr", "purrr", "withr", "frictionless"))
  1. Build and check:
devtools::document()
devtools::test()
devtools::check()
devtools::build_vignettes()
pkgdown::build_site()

Package Structure

  • R/: Core functions for dictionary and package operations
  • inst/extdata/: Example data files (NuSEDS coho sample)
  • tests/testthat/: Automated tests
  • vignettes/: Long-form documentation
  • docs/: pkgdown site output

Roadmap