GENE Ontology

Introduction

Understanding our genes e.g., what they do, which processes they are part of, and where the proteins they code for are found, is of utmost importance for many kinds of research, including bioinformatics. To facilitate this, the scientific community has developed Gene Ontology, or just GO, which is an extensive database of

• various properties a gene can have, and
• information on how these properties relate to each other.

This python code reads in the Gene Ontology database in a suitable data structure and processes the data in certain ways. This code could be one of the first steps in creating a web based browser for Gene Ontology and related data resources.

The properties that a gene can have are called GO categories. In the data we will be working with, there are 47,385 different GO categories. Each GO category has an id, e.g. GO:0008150, a more descriptive name, e.g. biological_process, and a few other attributes.

How the GO categories relate to each other is captured in relations that are composed of relationships. There are a number of different relations, and the most important of these is the is_a relation. For example, the GO category with id equal to GO:0000003 and name equal to reproduction forms a relationship in the is_a relation to GO:0008150 (biological_process), i.e. reproduction is_a biological_process. There are a number of other types of relations. Another example is part_of, where one of the relationships is GO:0098687 (chromosomal region) is part_of GO:0005694 (chromosome).

Mathematically speaking, a relationship is a pair of categories, and a relation is a set of relationships.

I implemented invert relation, e.g. creating the relation has_part from part_of by saying that category a has_part category b if category b is part_of category a (note that a and b swapped place).

I also demonstrated how to combine two relations, e.g. you can construct a new relation my_rel from is_aand part_of by saying that two categories are related with my_rel if they are related with at least one of the is_a or part_of relations.

Some relations are transitive, meaning that if a is related to b, and b is related to c, then a is also related to c. The is_a relation is transitive, e.g. we have the relationship GO:0019953 (sexual reproduction) is_a GO:0000003 (reproduction), and as we also have the relationship GO:0000003 (reproduction) is_a GO:0008150 (biological_process), we know that we have the relationship GO:0019953 (sexual reproduction) is_a GO:0008150 (biological_process). However these indirect relationships are not explicitly stated in the Gene Ontology database.

If you are interested, you can look at http://geneontology.org for more information.

Materials

In addition to this document, two other files have been provided:

• Go.obo file was downloaded from http://purl.obolibrary.org/obo/go.obo and is licensed under the Creative Commons Attribution 4.0 International Public License. Please see http://geneontology.org for more information.
• The GO.py file contains code for parsing the go.obo file and storing the information using three classes defined in the GO.py file.
• The file test_GO.py defines a number of functions that help testing the code in GO.py.

Notes

All this code should run with Python 3 on an ordinary PC or server. CPU and memory requirements should be modest.