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Human Gene Ontology annotations

The parent project provides easy-to-use Gene Ontology annotations.

This repository hosts a modified version of the gene ontology annotation script, which has been adapted to focus exclusively on human gene annotations by filtering for tax_id 9606—Homo sapiens.

Execution

conda env create -f environment.yml 

conda activate human-gene-ontology

bash download.sh

python process.py

Input

  • go-basic.obo
    • The Gene Ontology file in OBO format. It contains ontological information in a structured form, describing gene products in terms of their associated biological processes, cellular components, and molecular functions in a species-independent manner.
  • gene2go.gz
    • The file from NCBI that links genes from the Entrez Gene database to Gene Ontology (GO) terms, establishing a connection between gene identifiers and their functional annotations.
  • gene_info.gz
    • The file from NCBI is a compressed archive containing detailed information on genes.

Output

TSV

  • GO_annotations-9606-allev.tsv
    • Contains both inferred and direct annotations with all types of evidence.
  • GO_annotations-9606-expev.tsv
    • Contains both inferred and direct annotations with experimental evidence specifically.

CSV

  • node_{domain}.csv.gz
    • Lists GO terms and names for specific domains (biological process, cellular component and molecular function).
  • edge_gene_to_{domain}.csv.gz
    • Shows gene-GO term relationships for each domain, indicating if annotations are direct or inferred and if the evidence is experimental.

Note: These CSV files are formatted for easy import into Neo4j.