Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The GO captures many aspects of functional annotations, but there are other alternative complementary sources of protein function information. For example, enzyme functional annotations are described in a range of resources from the Enzyme Commission...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The Evidence and Conclusion Ontology (ECO) is a community resource for describing the various types of evidence that are generated during the course of a scientific study and which are typically used to support assertions made by researchers. ECO des...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The specificity of knowledge that Gene Ontology (GO) annotations currently can represent is still restricted by the legacy format of the GO annotation file, a format intentionally designed for simplicity to keep the barriers to entry low and thus enc...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
This chapter is a tutorial on using Gene Ontology resources in the Python programming language. This entails querying the Gene Ontology graph, retrieving Gene Ontology annotations, performing gene enrichment analyses, and computing basic semantic sim...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
Contemporary techniques in biology produce readouts for large numbers of genes simultaneously, the typical example being differential gene expression measurements. Moreover, those genes are often richly annotated using GO terms that describe gene fun...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The Gene Ontology (GO) is a formidable resource, but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding of its s...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
Gene-category analysis is one important knowledge integration approach in biomedical sciences that combines knowledge bases such as Gene Ontology with lists of genes or their products, which are often the result of high-throughput experiments, gained...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
Gene Ontology-based semantic similarity (SS) allows the comparison of GO terms or entities annotated with GO terms, by leveraging on the ontology structure and properties and on annotation corpora. In the last decade the number and diversity of SS me...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The Gene Ontology Consortium (GOC) produces a wealth of resources widely used throughout the scientific community. In this chapter, we discuss the different ways in which researchers can access the resources of the GOC. We here share details about th...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
A biological experiment is the most reliable way of assigning function to a protein. However, in the era of high-throughput sequencing, scientists are unable to carry out experiments to determine the function of every single gene product. Therefore, ...