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, ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The Gene Ontology (GO) (Ashburner et al., Nat Genet 25(1):25-29, 2000) is a powerful tool in the informatics arsenal of methods for evaluating annotations in a protein dataset. From identifying the nearest well annotated homologue of a protein of int...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computati...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
Collaborations between the scientific community and members of the Gene Ontology (GO) Consortium have led to an increase in the number and specificity of GO terms, as well as increasing the number of GO annotations. A variety of approaches have been ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
In this chapter, we explain how text mining can support the curation of molecular biology databases dealing with protein functions. We also show how curated data can play a disruptive role in the developments of text mining methods. We review a decad...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
Surveys of public sequence resources show that experimentally supported functional information is still completely missing for a considerable fraction of known proteins and is clearly incomplete for an even larger portion. Bioinformatics methods have...