Curation of Bioconductor package metadata, targeting EDAM ontology and ELIXIR bio.tools metadata schemas

Vincent J. Carey, stvjc at channing.harvard.edu

June 24, 2026

Introduction

This vignette is derived almost entirely from collaborative code supplied by Anh Nguyet Vu of Sage Bionetworks. The purpose is to illustrate usage of LLM-based transformation to provide systematic organization and tagging of content available for Bioconductor packages.

Code in this vignette requires that ANTHROPIC_API_KEY be defined.

Example 1: tximeta

We start with the transformation of vignette content, which may be in HTML or PDF, based on the structured data extraction code examples given in a vignette for the ellmer package on CRAN. We prompt Claude to produce a concise and objective summary of at most 450 words, which is placed in the focus component of the returned data.

if (nchar(Sys.getenv("ANTHROPIC_API_KEY"))>0) {
library(biocEDAM)
content = vig2data("https://bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta.html")
str(content)
nchar(content$focus)
}

## List of 5
##  $ author    : chr [1:4] "Michael I. Love" "Charlotte Soneson" "Peter F. Hickey" "Rob Patro"
##  $ topics    : chr [1:33] "RNA-seq" "transcript quantification" "salmon" "oarfish" ...
##  $ focused   : chr "The tximeta package extends tximport functionality by automating annotation and metadata attachment during RNA-"| __truncated__
##  $ coherence : int 88
##  $ persuasion: num 0.75

## [1] 3033

We then use LLM-based inference to produce associated EDAM tags; see the edamize function for details.

if (nchar(Sys.getenv("ANTHROPIC_API_KEY"))>0) {
substr(content$focus,1,250)
ans = edamize(content$focus, retrieve_k=NULL)
DT::datatable(mkdf(ans))
}

## Connected to SemanticSQL database: /Users/vincentcarey/Library/Caches/org.R-project.R/R/BiocFileCache/16883554f1d39_edam.db

## Primary ontology prefix: EDAM

Example 2: MSnbase

if (nchar(Sys.getenv("ANTHROPIC_API_KEY"))>0) {
mm = vig2data("https://bioconductor.org/packages/release/bioc/vignettes/MSnbase/inst/doc/v05-MSnbase-development.html")
uu = edamize(mm$focus, retrieve_k=NULL)
if (is.null(uu)) uu = edamize(mm$focus, retrieve_k=NULL)  # second try
DT::datatable(mkdf(uu))
}

## Connected to SemanticSQL database: /Users/vincentcarey/Library/Caches/org.R-project.R/R/BiocFileCache/16883554f1d39_edam.db

## Primary ontology prefix: EDAM

Caveats

Sometimes there is no result. This pertains to indeterminacy in the LLM response. Often a second try will get a result. If you have persistent trouble, please file an issue.