Package: ontoProc2 0.99.24

Vincent Carey

ontoProc2: Ontology Facilities Based on INCAtools Semantic SQL

This package provides ontology facilities based on INCAtools Semantic SQL. Tooling is provided to retrieve and cache SQLite databases representing curated ontologies. ontologyIndex ontology_index instances can be produced. Anthropic's Claude was used in the development of S7 classes and methods and in the production of documentation.

Authors:Vincent Carey [aut, cre], Anthropic-Claude Sonnet4.6 [eng], NIH NHGRI 2U24HG004059-17 [fnd]

ontoProc2_0.99.24.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ontoProc2/json (API)

# Install 'ontoProc2' in R:
install.packages('ontoProc2', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vjcitn/ontoproc2/issues

Datasets:
  • cn2tag - A named vector with mapping from cell type phrase to CURIE for CL.owl of 2025-12-17
  • ncit_map - A named vector with values rdfs labels in NCI thesaurus, and names the corresponding formal ontology tags
  • tag2cn - A named vector with mapping from CURIE to cell type phrase for CL.owl of 2025-12-17

On CRAN:

Conda:

infrastructuredatarepresentationpathwayssinglecell

4.86 score 1 packages 16 scripts 38 exports 49 dependencies

Last updated from:5198642dfe. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING192
linux-devel-x86_64OK345
source / vignettesOK314
linux-release-x86_64OK327
macos-release-arm64OK286
macos-oldrel-arm64OK231
windows-develOK569
windows-releaseOK474
windows-oldrelOK386
wasm-releaseOK169

Exports:bbop_sqlite_db_gzcells_with_pmpcount_by_prefixcount_descendantsdescribe_tabledisconnectfind_by_restrictionfind_intersectionget_ancestorsget_ancestors_partonomyget_definitionget_descendantsget_descendants_partonomyget_direct_edgesget_direct_subclassesget_direct_superclassesget_labelget_prefixget_present_pmpget_restrictionsget_synonymsget_term_infoimprove_nodesis_connectedlist_tablesmake_graphNEL_from_ontology_plotonto_plot2PREDICATESreconnectreportretrieve_semsql_connrun_querysearch_labelssemsql_connectsemsql_to_oisemsql_urlSemsqlConnwith_connection

Dependencies:askpassBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrdigestdplyrfastmapfilelockgenericsgluegraphhttr2lifecyclemagrittrmemoiseontologyIndexontologyPlotopensslpaintmappillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6rappdirsRgraphvizrlangRSQLiteS7stringistringrsystibbletidyrtidyselectutf8vctrswithrxml2

ontoProc2 -- leveraging semantic SQL for ontology analysis in Bioconductor
Introduction | Installation | Acquiring ontologies | Make a connection | Make a report | Probe the back end | Use tidy methods | Transformation to ontology_index instances | Background | Searching in label text | Exploring concept properties with 'edge tables' | Generalizing a concept: Ancestors | Working with multiple ontologies | Session information
Rendered fromontoProc2.Rmdusingknitr::rmarkdown

Last update: 2026-05-11
Started: 2025-10-27

celltoprotein -- connecting Cell and Protein Ontologies
Introduction | Given a cell type, what proteins are noted as parts of its plasma membrane? | Given a protein, what cell types are asserted to possess it as a membrane part? | Some details | Session information
Rendered fromcelltoprotein.Rmdusingknitr::rmarkdown

Last update: 2026-03-31
Started: 2026-03-25

uberonpeek -- a look at UBERON ontology, etc., with ontoProc2
Introduction | Parent-child relations | EFO and NCI thesaurus | Session information
Rendered fromuberonpeek.Rmdusingknitr::rmarkdown

Last update: 2026-03-31
Started: 2023-09-07

Readme and manuals

Help Manual

Help pageTopics
retrieve and cache all filenames of Semantic SQL ontologies available, checking for updated content relative to cache via ETagbbop_sqlite_db_gz
produce a table with cells exhibiting given proteins on plasma membrane according to CLcells_with_pmp
a named vector with mapping from cell type phrase to CURIE for CL.owl of 2025-12-17cn2tag
Count labeled terms grouped by CURIE prefixcount_by_prefix
Count the number of descendants of a termcount_descendants
Describe the columns of a table in a SemsqlConn databasedescribe_table
Disconnect a SemsqlConn from its databasedisconnect
Find terms that have a given OWL someValuesFrom restrictionfind_by_restriction
Find terms that are descendants of a superclass and have a given restrictionfind_intersection
Get all ancestors of a term via entailed edgesget_ancestors
Get ancestors traversing both is-a and part-of relationshipsget_ancestors_partonomy
Get the text definition for a termget_definition
Get all descendants of a term via entailed edgesget_descendants
Get descendants traversing both is-a and has-part relationshipsget_descendants_partonomy
Get direct edges in the ontology graph for a termget_direct_edges
Get direct subclasses of a termget_direct_subclasses
Get direct superclasses of a termget_direct_superclasses
Get the rdfs:label for a termget_label
Retrieve the ontology prefix from a SemsqlConnget_prefix
produce a table with list of proteins from protein ontology identified as present on cell membranes for input cell type CURIEsget_present_pmp
Get OWL someValuesFrom restrictions for a termget_restrictions
Get synonyms for a termget_synonyms
Retrieve a summary of information about a termget_term_info
inject linefeeds for node names for graph, with textual annotation from ontologyimprove_nodes
Test whether a SemsqlConn has a valid open connectionis_connected
List tables in a SemsqlConn databaselist_tables
obtain graphNEL from ontology_plot instance of ontologyPlotmake_graphNEL_from_ontology_plot
a named vector with values rdfs labels in NCI thesaurus, and names the corresponding formal ontology tagsncit_map
high-level use of graph/Rgraphviz for rendering ontology relationsonto_plot2
Standard predicate CURIEs used in OBO ontologiesPREDICATES
Show method for SemsqlConn. Concise one-line summary displayed when a 'SemsqlConn' object is auto-printed at the R prompt.print
Reconnect a SemsqlConn to its databasereconnect
Display a detailed report of a SemsqlConn objectreport report,ontoProc2::SemsqlConn-method
return a SQLite connection (read only) to an INCAtools Semantic SQL ontologyretrieve_semsql_conn
Run an arbitrary SQL query against a SemsqlConn databaserun_query
Search term labels in a SemsqlConn databasesearch_labels
Create a SemsqlConn connectionsemsql_connect
produce an ontology_index instance from semantic sql sqlite connectionsemsql_to_oi
produce INCAtools distribution URLsemsql_url
SemsqlConn: S7 connection wrapper for SemanticSQL databasesSemsqlConn
a named vector with mapping from CURIE to cell type phrase for CL.owl of 2025-12-17tag2cn
Execute code with an automatically managed SemsqlConnwith_connection