title: Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.
abstract: BACKGROUND
  Phenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology. Since its initial publication, we have added new features that address several major bottlenecks in the efficiency of the phenotype curation process: allowing curators during the data curation phase to provisionally request terms that are not yet available from a relevant ontology; supporting quality control against annotation guidelines to reduce later manual review and revision; and enabling the sharing of files for collaboration among curators.
  
  
  RESULTS
  We decoupled data annotation from ontology development by creating an Ontology Request Broker (ORB) within Phenex. Curators can use the ORB to request a provisional term for use in data annotation; the provisional term can be automatically replaced with a permanent identifier once the term is added to an ontology. We added a set of annotation consistency checks to prevent common curation errors, reducing the need for later correction. We facilitated collaborative editing by improving the reliability of Phenex when used with online folder sharing services, via file change monitoring and continual autosave.
  
  
  CONCLUSIONS
  With the addition of these new features, and in particular the Ontology Request Broker, Phenex users have been able to focus more effectively on data annotation. Phenoscape curators using Phenex have reported a smoother annotation workflow, with much reduced interruptions from ontology maintenance and file management issues.
authors.affiliation: National Evolutionary Synthesis Center, Durham, NC USA ; Department of Biology, University of North Carolina, Chapel Hill, NC USA.
authors.forename: James P
authors.initials: JP
authors.lastname: Balhoff
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, SD USA.
authors.forename: Wasila M
authors.initials: WM
authors.lastname: Dahdul
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, SD USA.
authors.forename: T Alexander
authors.initials: TA
authors.lastname: Dececchi
authors.affiliation: National Evolutionary Synthesis Center, Durham, NC USA.
authors.forename: Hilmar
authors.initials: H
authors.lastname: Lapp
authors.affiliation: Department of Biology, University of South Dakota, Vermillion, SD USA.
authors.forename: Paula M
authors.initials: PM
authors.lastname: Mabee
authors.affiliation: National Evolutionary Synthesis Center, Durham, NC USA ; Department of Biology, University of North Carolina, Chapel Hill, NC USA.
authors.forename: Todd J
authors.initials: TJ
authors.lastname: Vision
keywords: Annotation; Character matrix; Curation; Ontology; Phenotypes; Systematics