Welcome to uberon-go, where the anatomy ontology UBERON meets the Gene Ontology (GO) to programatically download their relations.
An R script is provided to obtain, relative to an anatomy ontology term:
- descendant anatomic terms;
- related Gene Ontology (GO) Biological Process (BP) terms;
- related genes.
Sample results for some UBERON terms (nervous system UBERON:0001016; immune system, UBERON:0002405) are in the examples folder.
The term id can be searched at the Ontology Lookup Service (OLS).
Children and further descendants from an anatomic ontology term are obtained from OLS through the R package rols.
The descendants generally include anatomic terms (UBERON), cell terms from cell ontology (CL), and cellular component terms (GO CC).
The input parent term is included for familiar completeness.
For large families (hundreds of descendants), it may take several minutes to complete the OLS queries.
Example:
| id | label |
|---|---|
| UBERON:0001016 | nervous system |
| CL:0002319 | neural cell |
| CL:1001602 | cerebral cortex endothelial cell |
For each term of the obtained anatomic descendants, the related GO terms are obtained from OLS through the R package rols.
The term names, root node (BP/CC/MF) classification, and descendants of the obtained terms are retrieved with the R package GOfuncR.
For large families (hundreds of descendants), it may take several minutes to complete the OLS queries.
Example:
| id | label |
|---|---|
| GO:0050877 | nervous system process |
| GO:0007399 | nervous system development |
| GO:0007610 | behavior |
A table with the anatomic terms, related GO terms and relationship between them is available in an optional section (_GO-relations.txt). This could optionally be used to filter the terms by relationship.
For each term of the obtained anatomic descendants, the list of related genes are obtained from the GO annotations for Homo sapiens, available at http://current.geneontology.org/products/pages/downloads.html. Annotations for other organisms can also be used.
Please note that no relationship filters are currently applied (in development).
- Mungall, C. J.; Torniai, C.; Gkoutos, G. V.; Lewis, S. E.; Haendel, M. A. Uberon, an Integrative Multi-Species Anatomy Ontology. Genome Biology 2012, 13 (1), R5. https://doi.org/10.1186/gb-2012-13-1-r5.
- Ashburner et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000 May;25(1):25-9. https://doi.org/10.1038/75556.
- The Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics. 2023 May 4;224(1):iyad031. https://doi.org/10.1093/genetics/iyad031.
- Gatto L (2024). rols: An R interface to the Ontology Lookup Service. https://doi.org/10.18129/B9.bioc.rols, R package version 3.0.0, https://bioconductor.org/packages/rols.
- Grote S (2024). GOfuncR: Gene ontology enrichment using FUNC. https://doi.org/10.18129/B9.bioc.GOfuncR, R package version 1.24.0, https://bioconductor.org/packages/GOfuncR.
- Wickham H (2023). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.5.1, https://CRAN.R-project.org/package=stringr.
- Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.4, https://CRAN.R-project.org/package=dplyr.