MOTIVATION: Protein subcellular localization prediction has been an important research topic in computational biology over the last decade. Various automatic methods have been proposed to predict locations for large scale protein datasets, where stat...
SUMMARY: The miRBase database is the central and official repository for miRNAs and the current release is miRBase version 21.0. Name changes in different miRBase releases cause inconsistencies in miRNA names from version to version. When working wit...
Database : the journal of biological databases and curation
Jan 1, 2017
UNLABELLED: With ever-increasing amounts of sequence data available in both the primary literature and sequence repositories, there is a bottleneck in annotating molecular function to a sequence. This article describes the biocuration process and met...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The overarching goal of the Gene Ontology (GO) Consortium is to provide researchers in biology and biomedicine with all current functional information concerning genes and the cellular context under which these occur. When the GO was started in the 1...
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...