May 8, 2020

Readme for GO annotation files from HGD

If you use these files in your research, please cite the latest HGD publication in Nucleic Acids Research

Walsh AT, Triant DA, Le Tourneau JJ, Shamimuzzaman M, Elsik CG. Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. Nucleic Acids Res. 2021 Nov 8:gkab1018. doi: 10.1093/nar/gkab1018. Epub ahead of print. PMID: 34747465.

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File and directory descriptions:

go.obo = the Gene Ontology file used in computational annotation and creation of GeneMerge description files. Downloaded from https://geneontology.github.io/docs/download-ontology/.
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gaf directory:

GO Annotation format (GAF) files (species-specific)
<species_name>_HGD_go_annotation.gaf

GAF format is described here: http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/

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genemerge directory:

Files formatted for input to command line GeneMerge (http://www.genemerge.net)

Description files (the same files are used for all species):

biological_process_description.txt
molecular_function_description.txt
cellular_component_description.txt

Association files (species-specific):
<species_name>_BP_all.txt
<species_name>_BP_direct.txt
<species_name>_MF_all.txt
<species_name>_MF_direct.txt
<species_name>_CC_all.txt
<species_name>_CC_direct.txt

Note that the "direct" files contain the GO terms provided in the gaf file above. The "all" files contain the direct annotations as well as all of their parent terms, up through the heirarchy. These are comparable to the "direct" and "all" datasets provided on the David website (https://david.ncifcrf.gov).