Use research software taxonomy terms

[andrew]

Refresh the vendored oss-taxonomy terms after ecosyste-ms/oss-taxonomy#20 and apply the research vocabulary to the science tool detectors. Map Nextflow, Snakemake, and targets to function:workflow-orchestration; DVC to function:data-provenance and function:data-version-control; MultiQC and publishing tools to report generation and literate programming; and Dockstore to role:registry. Add the new technology and domain terms, plus a mapping test for the affected tools.

[Copilot]

Pull request overview

This PR updates the knowledge base’s oss-taxonomy classifications to incorporate newly added “research software” terms and applies those terms consistently across research/science-related tool detectors, alongside a regression test to lock in the expected mappings.

Changes:

• Updated taxonomy facets for workflow/orchestration, data provenance/version control, and publishing/reporting tools (including new domain:*, function:*, role:*, and technology:* terms).
• Refreshed the vendored oss-taxonomy term list to include the newly referenced terms.
• Added a KB mapping test covering the updated research/science tools.

Reviewed changes

Copilot reviewed 19 out of 19 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
knowledge/r/targets.toml	Reclassifies targets as function:workflow-orchestration and adds domain:research.
knowledge/r/rmarkdown.toml	Adds literate-programming and report-generation functions for R Markdown.
knowledge/r/knitr.toml	Adds literate-programming and report-generation functions for knitr.
knowledge/julia/runic.toml	Adds technology:julia taxonomy tag.
knowledge/julia/juliaformatter.toml	Adds technology:julia taxonomy tag.
knowledge/julia/documenter.toml	Adds technology:julia taxonomy tag.
knowledge/julia/benchmarktools.toml	Adds technology:julia taxonomy tag.
knowledge/fortran/fortitude.toml	Adds technology:fortran taxonomy tag.
knowledge/_shared/snakemake.toml	Maps Snakemake to function:workflow-orchestration, domain:research, and adds technology:snakemake.
knowledge/_shared/quarto.toml	Adds literate-programming, report-generation, and technology:quarto.
knowledge/_shared/nf-test.toml	Adds technology:nextflow taxonomy tag.
knowledge/_shared/nf-core.toml	Expands domain to include bioinformatics and adds technology:nextflow.
knowledge/_shared/nextflow.toml	Maps Nextflow to function:workflow-orchestration, domain:research, and adds technology:nextflow.
knowledge/_shared/multiqc.toml	Adds function:report-generation and domain:bioinformatics.
knowledge/_shared/jupyter.toml	Adds function:interactive-computing, function:literate-programming, and technology:jupyter.
knowledge/_shared/dvc.toml	Maps DVC to function:data-provenance and function:data-version-control.
knowledge/_shared/dockstore.toml	Reclassifies Dockstore as role:registry (removing prior CLI/deployment classification).
kb/testdata/oss-taxonomy-terms.txt	Updates vendored term list to include new domain/function/role/technology terms used by KB.
kb/kb_test.go	Adds TestResearchToolTaxonomy to verify the updated taxonomy mappings.

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