GOparser 1.1

GOparser is a Python framework for working with Gene Ontology (GO) terms and annotations. GOparser is free and open-source software (see License).

Main Features

  • Efficient parsing of GO term information contained in go-basic.obo from the Gene Ontology Consortium.
  • Efficient parsing of GO annotations contained in GAF files from EBI’s GO Annotation Database (UniProt-GOA).
  • Filtering for annotations of protein-coding genes (using genometools).
  • Easy and fast retrieval of all genes annotated with a particular GO term, or all GO terms a particular gene is annotated with.
  • Annotations are fully propagated based on is_a and part_of relations between GO terms.
  • Cross-species support.
  • Support for filtering annotations based on evidence code.

Demo Notebooks

Installation

GOparser can be installed from PyPI using pip:

$ pip install goparser

Missing Features

  • Visualizations (e.g., to show relationships between GO terms).
  • Support for other GO relations, e.g., regulates and has_part.