Last updated: 2025-02-14
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 10c2f0c | Dave Tang | 2025-02-14 | Cell Ontology |
From Cell Ontology (CL):
Cell Ontology (CL) is an ontology designed to classify and describe cell types across different organisms. It serves as a resource for model organism and bioinformatics databases. The ontology covers a broad range of cell types in animal cells, with over 2700 cell type classes, and provides high-level cell type classes as mapping points for cell type classes in ontologies representing other species, such as the Plant Ontology or Drosophila Anatomy Ontology. Integration with other ontologies such as Uberon, GO, CHEBI, PR, and PATO enables linking cell types to anatomical structures, biological processes, and other relevant concepts.
The Cell Ontology was created in 2004 and has been a core OBO Foundry ontology since the start of the Foundry. Since then, CL has been adopted by various efforts, including the HuBMAP project, Human Cell Atlas (HCA), cellxgene platform, Single Cell Expression Atlas, BRAIN Initiative Cell Census Network (BICCN), ArrayExpress, The Cell Image Library, ENCODE, and FANTOM5, for annotating cell types and facilitating cellular reference mapping, as documented through various publications and examples.
Complete ontology, plus inter-ontology axioms, and imports modules.
cl_url <- 'https://purl.obolibrary.org/obo/cl.obo'
cl_obo <- paste0("data/", basename(cl_url))
if(!file.exists(cl_obo)){
download.file(url = cl_url, destfile = cl_obo)
}Use {ontologyIndex} a package for reading Ontologies into R.
install.packages("ontologyIndex")Load library.
suppressPackageStartupMessages(library(ontologyIndex))The function get_ontology() can read
ontologies encoded in OBO format into R as
ontology_index objects. By default, the properties id,
name, obsolete, parents, children and ancestors are populated.
cl <- get_ontology(cl_obo)
clOntology with 16496 terms
format-version: 1.2
data-version: releases/2025-02-13
ontology: cl
Properties:
id: character
name: character
parents: list
children: list
ancestors: list
obsolete: logical
equivalent_to: list
Roots:
SO:0001260 - sequence_collection
GO:0008150 - biological_process
GO:0050878 - regulation of body fluid levels
RO:0002323 - mereotopologically related to
GO:0003674 - molecular_function
RO:0002328 - functionally related to
RO:0002222 - temporally related to
has_participant - has participant
GO:0010817 - regulation of hormone levels
GO:0042391 - regulation of membrane potential
... 141 moreStructure.
str(cl, max.level = 1)List of 7
$ id : Named chr [1:16693] "CHEBI:24431" "PR:000000001" "CHEBI:46858" "CL:0000000" ...
..- attr(*, "names")= chr [1:16693] "CHEBI:24431" "PR:000000001" "CHEBI:46858" "CL:0000000" ...
$ name : Named chr [1:16693] NA "protein" NA "cell" ...
..- attr(*, "names")= chr [1:16693] "CHEBI:24431" "PR:000000001" "CHEBI:46858" "CL:0000000" ...
$ parents :List of 16693
$ children :List of 16693
$ ancestors :List of 16693
$ obsolete : Named logi [1:16693] FALSE FALSE FALSE FALSE FALSE TRUE ...
..- attr(*, "names")= chr [1:16693] "CHEBI:24431" "PR:000000001" "CHEBI:46858" "CL:0000000" ...
$ equivalent_to:List of 16693
- attr(*, "class")= chr "ontology_index"
- attr(*, "version")= chr [1:115] "format-version: 1.2" "data-version: releases/2025-02-13" "subsetdef: abnormal_slim \"\"" "subsetdef: added_for_HCA \"\"" ...Name.
as.data.frame(cl$name) |>
head() cl$name
CHEBI:24431 <NA>
PR:000000001 protein
CHEBI:46858 <NA>
CL:0000000 cell
CL:0000001 primary cultured cell
CL:0000002 obsolete immortal cell line cellLook for T-cell.
grep(pattern = "^t[- ]cell$", x = cl$name, ignore.case = TRUE, value = TRUE)CL:0000084
"T cell"
sessionInfo()R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 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-r0.3.20.so; LAPACK version 3.10.0
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] ontologyIndex_2.12 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] jsonlite_1.8.9 compiler_4.4.1 promises_1.3.0 Rcpp_1.0.13
[5] stringr_1.5.1 git2r_0.35.0 callr_3.7.6 later_1.3.2
[9] jquerylib_0.1.4 yaml_2.3.10 fastmap_1.2.0 R6_2.5.1
[13] knitr_1.48 tibble_3.2.1 rprojroot_2.0.4 bslib_0.8.0
[17] pillar_1.9.0 rlang_1.1.4 utf8_1.2.4 cachem_1.1.0
[21] stringi_1.8.4 httpuv_1.6.15 xfun_0.48 getPass_0.2-4
[25] fs_1.6.4 sass_0.4.9 cli_3.6.3 magrittr_2.0.3
[29] ps_1.8.1 digest_0.6.37 processx_3.8.4 rstudioapi_0.17.1
[33] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.1 glue_1.8.0
[37] whisker_0.4.1 fansi_1.0.6 rmarkdown_2.28 httr_1.4.7
[41] tools_4.4.1 pkgconfig_2.0.3 htmltools_0.5.8.1