title: Combining heterogeneous data sources for accurate functional annotation of proteins.
abstract: Combining heterogeneous sources of data is essential for accurate prediction of protein function. The task is complicated by the fact that while sequence-based features can be readily compared across species, most other data are species-specific. In this paper, we present a multi-view extension to GOstruct, a structured-output framework for function annotation of proteins. The extended framework can learn from disparate data sources, with each data source provided to the framework in the form of a kernel. Our empirical results demonstrate that the multi-view framework is able to utilize all available information, yielding better performance than sequence-based models trained across species and models trained from collections of data within a given species. This version of GOstruct participated in the recent Critical Assessment of Functional Annotations (CAFA) challenge; since then we have significantly improved the natural language processing component of the method, which now provides performance that is on par with that provided by sequence information. The GOstruct framework is available for download at http://strut.sourceforge.net.
authors.affiliation: Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA. sokolov@soe.ucsc.edu
authors.forename: Artem
authors.initials: A
authors.lastname: Sokolov
authors.forename: Christopher
authors.initials: C
authors.lastname: Funk
authors.forename: Kiley
authors.initials: K
authors.lastname: Graim
authors.forename: Karin
authors.initials: K
authors.lastname: Verspoor
authors.forename: Asa
authors.initials: A
authors.lastname: Ben-Hur
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods; D015870:Gene Expression; D051379:Mice; D058977:Molecular Sequence Annotation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D012984:Software; D018875:Vocabulary, Controlled
chemical_list: D011506:Proteins