Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.

Journal Article (Journal Article)


Phenex ( 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.


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.


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.

Full Text

Duke Authors

Cited Authors

  • Balhoff, JP; Dahdul, WM; Dececchi, TA; Lapp, H; Mabee, PM; Vision, TJ

Published Date

  • January 2014

Published In

Volume / Issue

  • 5 / 1

Start / End Page

  • 45 -

PubMed ID

  • 25411634

Pubmed Central ID

  • PMC4236444

Electronic International Standard Serial Number (EISSN)

  • 2041-1480

International Standard Serial Number (ISSN)

  • 2041-1480

Digital Object Identifier (DOI)

  • 10.1186/2041-1480-5-45


  • eng