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++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@@ -451,7 +451,7 @@
The results in this page were generated with repository version -e6f0a05. +10c2f0c. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
@@ -472,8 +472,9 @@@@ -522,6 +523,40 @@