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Merge pull request #529 from geneontology/suzialeksander-patch-102
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Update download-go-annotations.md
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suzialeksander authored Apr 9, 2024
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# Download annotations

### Getting annotations for a selected organism

This page has instructions for getting GO annotations for almost any organism. If your organism is not available in the [official GO products]((http://current.geneontology.org/products/pages/downloads.html)), [UniProt GAFs by proteome](https://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/){:target="blank"}, or [NCBI RefSeq](https://ftp.ncbi.nlm.nih.gov/genomes/refseq/){:target="blank"}, we recommend using the latest version of [InterProScan](https://interproscan-docs.readthedocs.io/en/latest/){:target="blank"} for unannotated organisms.

#### Required Files
Most tools that use GO annotations take two input files:
1. a file with the **annotations** (in Gene Annotation Format, or GAF)
2. a file with the GO **ontology** structure (in Open Biomedical Ontology Format, or OBO)

Because the ontology and annotations are constantly being improved over time, we recommend downloading the latest version of the annotations for your organism and the corresponding ontology file for that GO version. The version should be specified in the header of the annotation file.

#### Citing files
#### Citing GO
To ensure reproducibility for any publication where GO was used at any point in the research, please include:
* [appropriate GO publication(s)](docs/go-citation-policy/)
* [appropriate GO publication(s)- refer to the full GO citation policy](docs/go-citation-policy/)
* the URL where the files were obtained
* the date on the header of the GAF file
* the ontology version number
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