Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools

Monica Munoz-Torres; Seth Carbon

doi:10.1007/978-1-4939-3743-1_11

Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools

Methods Mol Biol. 2017:1446:149-160. doi: 10.1007/978-1-4939-3743-1_11.

Authors

Monica Munoz-Torres¹, Seth Carbon²

Affiliations

¹ Berkeley Bioinformatics Open-Source Projects, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd. MS 977, Berkeley, CA, 94720, USA. McMunozT@LBL.GOV.
² Berkeley Bioinformatics Open-Source Projects, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd. MS 977, Berkeley, CA, 94720, USA.

PMID: 27812941
DOI: 10.1007/978-1-4939-3743-1_11

Abstract

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 the mechanics of obtaining GO annotations, both by manually browsing, querying, and downloading data from the GO website, as well as computationally accessing the resources from the command line, including the ability to restrict the data being retrieved to subsets with only certain attributes.

Keywords: Access; AmiGO; Annotation; Annotation resources; Biocuration; Bioinformatics; Curation; Gene ontology; Genomics; Ontology; QuickGO; Transcriptomics.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Computational Biology / methods
Databases, Genetic
Gene Ontology*
Humans
Internet
Molecular Sequence Annotation* / methods
Software