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
andpart_of
relations between GO terms. - Cross-species support.
- Support for filtering annotations based on evidence code.
Demo Notebooks¶
- Demo.ipynb (
download
): GOparser demo notebook
Missing Features¶
- Visualizations (e.g., to show relationships between GO terms).
- Support for other GO relations, e.g.,
regulates
andhas_part
.