using semantic sql in R: a vignette #106

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   documentationImprovements or additions to documentationImprovements or additions to documentation

   on Mar 22, 2026
2. github-actions commented on Mar 22, 2026

   

   github-actionsBot

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   Summary

   This issue is a community contribution from @vjcitn (Vince Carey, Bioconductor core), announcing that the ontoProc2 R package provides an R/RSQLite interface to semantic-sql databases. The package is expected to appear in Bioconductor 3.23 (April 2026), with the current version available on GitHub only.

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   What ontoProc2 Does

   ontoProc2 is a modernized Bioconductor package that wraps semantic-sql SQLite databases for use in R workflows. It mirrors a significant portion of the semantic-sql Jupyter tutorial but in R idioms.

   Key capabilities demonstrated in the vignette:

   Feature	Details
   DB connection	semsql_connect() — connects to pre-built semantic-sql .db files
   Table access	Queries the 100+ views/tables via dplyr + DBI
   Label search	Pattern matching against rdfs_label (e.g., find "apoptosis" terms)
   Direct edges	Subject–predicate–object graph traversal
   Entailed edges	Uses entailed_edge table for inferred (transitive closure) relationships
   Cross-ontology	Joins across CL, UBERON, GO, RO, CHEBI

   Headline example:

   Find all forebrain neurons — filters 185 CL cell types located in forebrain that are subclasses of neuron, returning specialized neuron types across brain regions.

   R packages used:

   ontoProc2, dplyr, DBI, DT, S7, ontologyIndex

   Ontologies demonstrated:

   Gene Ontology (GO), Cell Ontology (CL), UBERON, Relational Ontology (RO), ChEBI

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   Significance

   This is notable as it substantially lowers the barrier for Bioconductor/R users to work with OBO ontologies via semantic-sql — a large community that previously had no first-class path to the semantic-sql infrastructure. The entailed_edge table (pre-computed transitive closures from relation-graph) is particularly powerful for graph traversal in R without needing Python/OAK.

   Worth considering: linking this from the semantic-sql README or tutorial index once the Bioc 3.23 release lands.
3. cmungall commented on Jul 2, 2026

   

   cmungall

   on Jul 2, 2026

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   Thanks for this! Do you want to make a PR to add this to the README?
4. vjcitn commented on Jul 2, 2026

   

   vjcitn

   on Jul 2, 2026

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   I will do this once it passes review in Bioconductor.