title: Improving functional annotation for industrial microbes: a case study with Pichia pastoris.
abstract: The research communities studying microbial model organisms, such as Escherichia coli or Saccharomyces cerevisiae, are well served by model organism databases that have extensive functional annotation. However, this is not true of many industrial microbes that are used widely in biotechnology. In this Opinion piece, we use Pichia (Komagataella) pastoris to illustrate the limitations of the available annotation. We consider the resources that can be implemented in the short term both to improve Gene Ontology (GO) annotation coverage based on annotation transfer, and to establish curation pipelines for the literature corpus of this organism.
authors.affiliation: Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
authors.forename: Duygu
authors.initials: D
authors.lastname: Dikicioglu
authors.affiliation: Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
authors.forename: Valerie
authors.initials: V
authors.lastname: Wood
authors.affiliation: Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
authors.forename: Kim M
authors.initials: KM
authors.lastname: Rutherford
authors.affiliation: European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Mark D
authors.initials: MD
authors.lastname: McDowall
authors.affiliation: Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK. Electronic address: sgo24@cam.ac.uk.
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Oliver
mesh_terms: D001709:Biotechnology / Q000379:methods*; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D007218:Industrial Microbiology / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods*; D010843:Pichia / Q000235:genetics / Q000378:metabolism / Q000502:physiology*
chemical_list: D005656:Fungal Proteins
keywords: Komagataella pastoris; Pichia pastoris; functional annotation; industrial microbes; recombinant protein production