Gene Ontology annotations user-friendly and customizable

About

The Gene Ontology (GO) is a structured vocabulary of biological functions. The ontology is divided into three domains: biological processes, cellular components, and molecular functions. In total, the ontology contains over 40,000 terms. GO annotations link a gene to a specific GO term to indicate when a gene is associated with a specific biological function.

GO annotations are frequently incorporated into bioinformatics analyses; however, parsing the ontology and annotations can be difficult. This website aims to simplify the process of retreiving GO annotations. The annotations are current (see last updated date) and customizable to an individual user’s needs. Annotations are provided separately for each species.

Please share any feedback, suggestions, or bug reports. See the ThinkLab discussion to learn more or comment. The project is open source and contributions are welcome.

Annotation Options

• Evidence: GO annotations are assigned evidence codes denoting the type of work or analysis underlying a annotation. The default option includes annotations of all evidence codes. The second option restricts annotations to experimental evidence codes (IEP, IPI, IMP, EXP, IGI or IDA). While computational annotations generally have good accuracy, they can introduce biases when used to train other computational approaches.
• Propagation: In general, genes (or gene products) are annotated to the most specific GO term possible. Propagation refers to transmitting a term’s annotations to each ancestor of that term. We propagate along is_a and part_of relationships. For most use cases, propagated (inferred) annotations are desired.

All Evidence Experimental Evidence Only

Inferred Direct

Download Annotations

Download Format

Annotation downloads are tsv-formatted. The first row contains column names. Genes are pipe (|) delimited. Below is an example of the formatting:

go_id	go_name	go_domain	tax_id	annotation_type	size	gene_ids	gene_symbols
GO:0000050	urea cycle	biological_process	9606	inferred	2	445|5009	ASS1|OTC
GO:0000053	argininosuccinate metabolic process	biological_process	9606	inferred	1	445	ASS1
GO:0000054	ribosomal subunit export from nucleus	biological_process	9606	inferred	4	5901|6209|7514|51068	RAN|RPS15|XPO1|NMD3
GO:0000055	ribosomal large subunit export from nucleus	biological_process	9606	inferred	3	5901|7514|51068	RAN|XPO1|NMD3

Source Files

Last updated on 2018-10-26 14:49:34. This resource updates frequently, so make note of this date for version information.

Citations

This resource is published under a CC-BY license. Please cite:

• Gene-Ontology: Initial Zenodo Release
  Daniel Himmelstein, Casey Greene, Venkat Malladi, Frederic Bastian, Sergio Baranzini
  Zenodo (2015-07-28) https://doi.org/f3mqvj
  DOI: 10.5281/zenodo.21711

The project was created as part of Project Rephetio:

• Systematic integration of biomedical knowledge prioritizes drugs for repurposing
  Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini
  eLife (2017-09-22) https://doi.org/cdfk
  DOI: 10.7554/elife.26726 · PMID: 28936969 · PMCID: PMC5640425

And benefitted from the contribution of several community participants:

• Compiling Gene Ontology annotations into an easy-to-use format
  Daniel Himmelstein, Casey Greene, Venkat Malladi, Frederic Bastian
  ThinkLab (2015-03-12) https://doi.org/f3mqt9
  DOI: 10.15363/thinklab.d39

This resource relies on the following projects:

• Gene Ontology: tool for the unification of biology
  Michael Ashburner, Catherine A. Ball, Judith A. Blake, David Botstein, Heather Butler, J. Michael Cherry, Allan P. Davis, Kara Dolinski, Selina S. Dwight, Janan T. Eppig, … Gavin Sherlock
  Nature Genetics (2000-05) https://doi.org/b9gp96
  DOI: 10.1038/75556 · PMID: 10802651 · PMCID: PMC3037419

• Entrez Gene: gene-centered information at NCBI
  Donna Maglott Jim Ostell Kim D. Pruitt Tatiana Tatusova
  Nucleic Acids Research (2004-12-17) https://doi.org/dm9v88
  DOI: 10.1093/nar/gki031 · PMID: 15608257 · PMCID: PMC539985