uberonpeek – a look at UBERON ontology, etc., with ontoProc2
Introduction
The ontoProc2 package is designed to give convenient access to the ontologies that are transformed to “semantic SQL” in the INCAtools project.
We’ll start by retrieving the current UBERON ontology and examining some tables and “statements”.
library(ontoProc2)
library(DBI)
library(dplyr)
ubss <- semsql_connect(ontology = "uberon")
report(ubss)##
## ============================================================
## SemsqlConn Object
## ============================================================
##
## Connection Details:
## ----------------------------------------
## Database path: /github/home/.cache/R/BiocFileCache/11d4cd2265b_uberon.db
## Ontology prefix: UBERON
## Status: ✓ Connected
##
## Database Statistics:
## ----------------------------------------
## Labeled terms: 28,764
## Direct edges: 80,942
## Entailed edges: 6,421,630
## Definitions: 23,007
##
## Terms by Prefix (top 5):
## ----------------------------------------
## UBERON: 16,067
## GO: 7,433
## CL: 1,477
## _: 1,260
## CHEBI: 917
##
## Key Tables Available:
## ----------------------------------------
## ✓ rdfs_label_statement
## ✓ has_text_definition_statement
## ✓ edge
## ✓ entailed_edge
## ✓ rdfs_subclass_of_statement
## ✓ owl_some_values_from
## ✓ has_oio_synonym_statement
##
## ============================================================
## Use methods like search_labels(), get_ancestors(), etc.
## Run ?SemsqlConn for documentation.
## ============================================================## [1] "all_problems" "annotation_property_node"
## [3] "anonymous_class_expression" "anonymous_expression"
## [5] "anonymous_individual_expression" "anonymous_property_expression"## # A query: ?? x 8
## # Database: sqlite 3.53.2 [/github/home/.cache/R/BiocFileCache/11d4cd2265b_uberon.db]
## stanza subject predicate object value datatype language graph
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 obo:uberon.owl obo:uberon.owl foaf:home… <NA> http… xsd:any… <NA> <NA>
## 2 obo:uberon.owl obo:uberon.owl rdfs:comm… <NA> Aure… <NA> <NA> <NA>
## 3 obo:uberon.owl obo:uberon.owl oio:treat… <NA> ZFS … <NA> <NA> <NA>
## 4 obo:uberon.owl obo:uberon.owl oio:treat… <NA> ZFA … <NA> <NA> <NA>
## 5 obo:uberon.owl obo:uberon.owl oio:treat… <NA> XAO … <NA> <NA> <NA>
## 6 obo:uberon.owl obo:uberon.owl oio:treat… <NA> WBls… <NA> <NA> <NA>
## 7 obo:uberon.owl obo:uberon.owl oio:treat… <NA> WBbt… <NA> <NA> <NA>
## 8 obo:uberon.owl obo:uberon.owl oio:treat… <NA> TGMA… <NA> <NA> <NA>
## 9 obo:uberon.owl obo:uberon.owl oio:treat… <NA> TAO … <NA> <NA> <NA>
## 10 obo:uberon.owl obo:uberon.owl oio:treat… <NA> TADS… <NA> <NA> <NA>
## # ℹ more rowsParent-child relations
CRAN’s ontologyIndex package provides a familiar representation that simplifies visualization.
## Warning in ontologyIndex::ontology_index(name = nn, parents = pl): Some parent
## terms not found: BFO:0000001, COB:0000502, CARO:0000000 (4 more)## Ontology with 25854 terms
##
## Properties:
## id: character
## name: list
## parents: list
## children: list
## ancestors: list
## obsolete: logical
## Roots:
## CHEBI:24432 - biological role
## CHEBI:51086 - chemical role
## CHEBI:33232 - application
## CHEBI:23367 - molecular entity
## BFO:0000003 - occurrent
## CHEBI:24433 - group
## CHEBI:33250 - atom
## BFO:0000002 - continuant
## UBERON:0035943 - life cycle temporal boundary
## CARO:0000007 - immaterial anatomical entity
## ... 3 more## $`NCBITaxon:9935`
## [1] "Ovis"
##
## $`NCBITaxon:9963`
## [1] "Caprinae"
##
## $`NCBITaxon:9971`
## [1] "Pholidota"
##
## $`NCBITaxon:9972`
## [1] "Manidae"
##
## $`NCBITaxon:9975`
## [1] "Lagomorpha"
##
## $`NCBITaxon:9989`
## [1] "Rodentia"
##
## $`PATO:0000001`
## [1] "quality"A sense of the variety of ontological cross-references present can be given by tabling the tag prefixes.
## prefs
## BFO BSPO CARO CHEBI CL COB GO IAO
## 14 12 5 915 1474 5 7428 5
## NBO NCBITaxon PATO PR RO UBERON
## 37 474 159 353 1 14972By using the ancestors component we can obtain a view of is-a relations (presumably developed from rdfs:subClassOf predicates). We’ve chosen as terminal tags the tags for heart, kidney, and cortex of kidney.
onto_plot2(
uboi,
unlist(uboi$ancestors[c(
"UBERON:0002189",
"UBERON:0002113", "UBERON:0000948"
)])
)
EFO and NCI thesaurus
On cursory inspection, the EFO ontology has considerable information about anatomic locations of diseases.
We’ll use the entailed edges table in EFO to find all statements that have ‘heart’ (UBERON:0000948) as object.
## Connected to SemanticSQL database: /github/home/.cache/R/BiocFileCache/11d4355bc84c_efo.db## Primary ontology prefix: EFO# nciref = semsql_connect("ncit") # > 500MB, block
htab <- tbl(eforef@con, "entailed_edge") |>
filter(object == "UBERON:0000948") |>
as.data.frame()
head(htab)## subject predicate object
## 1 UBERON:0000948 rdfs:subClassOf UBERON:0000948
## 2 EFO:0009285 IAO:0000136 UBERON:0000948
## 3 EFO:0600032 IAO:0000136 UBERON:0000948
## 4 EFO:0008398 IAO:0000136 UBERON:0000948
## 5 EFO:0009291 IAO:0000136 UBERON:0000948
## 6 EFO:0009290 IAO:0000136 UBERON:0000948It is tedious to see these formal tags. We have assembled a simple character vector map that covers many tags.
## IAO:0000112 IAO:0000114 IAO:0000115
## "example of usage" "has curation status" "definition"
## IAO:0000116 IAO:0000117 IAO:0000232
## "editor note" "term editor" "curator note"What are the predicates of the heart table above?
## <NA> IAO:0000136
## NA "is_about"
## <NA> RO:0002502
## NA "depends on"
## BFO:0000066 RO:0002131
## "occurs in" "overlaps"
## RO:0001025 RO:0002314
## "located_in" "inheres in part of"
## BFO:0000050 EFO:0000784
## "part_of" "has_disease_location"
## RO:0000052 RO:0004027
## "inheres_in" "disease has inflammation site"To enumerate and decode the terms with disease location (EFO:0000784) in heart, we have
Session information
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] S7_0.2.2 DBI_1.3.0 dplyr_1.2.1 DT_0.34.0
## [5] ontoProc2_0.99.24 BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] utf8_1.2.6 rappdirs_0.3.4 sass_0.4.10
## [4] generics_0.1.4 xml2_1.6.0 RSQLite_3.53.2
## [7] digest_0.6.39 magrittr_2.0.5 evaluate_1.0.5
## [10] grid_4.6.1 fastmap_1.2.0 blob_1.3.0
## [13] R.oo_1.27.1 jsonlite_2.0.0 ontologyIndex_2.12
## [16] R.utils_2.13.0 ontologyPlot_1.7 graph_1.91.0
## [19] BiocManager_1.30.27 purrr_1.2.2 crosstalk_1.2.2
## [22] Rgraphviz_2.57.0 codetools_0.2-20 httr2_1.2.3
## [25] jquerylib_0.1.4 paintmap_1.0 cli_3.6.6
## [28] rlang_1.2.0 dbplyr_2.6.0 R.methodsS3_1.8.2
## [31] bit64_4.8.2 withr_3.0.3 cachem_1.1.0
## [34] yaml_2.3.12 otel_0.2.0 tools_4.6.1
## [37] memoise_2.0.1 filelock_1.0.3 BiocGenerics_0.59.7
## [40] curl_7.1.0 buildtools_1.0.0 vctrs_0.7.3
## [43] R6_2.6.1 stats4_4.6.1 BiocFileCache_3.3.0
## [46] lifecycle_1.0.5 htmlwidgets_1.6.4 bit_4.6.0
## [49] pkgconfig_2.0.3 pillar_1.11.1 bslib_0.11.0
## [52] glue_1.8.1 xfun_0.59 tibble_3.3.1
## [55] tidyselect_1.2.1 sys_3.4.3 knitr_1.51
## [58] htmltools_0.5.9 rmarkdown_2.31 maketools_1.3.2
## [61] compiler_4.6.1