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

Area of Science:

• Evolutionary biology
• Bioinformatics
• Computational biology

Background:

• Phenex is a desktop application for semantic annotation of phenotypic character matrix datasets.
• New features address bottlenecks in phenotype curation efficiency.
• Enhancements include provisional term requests, quality control, and collaborative file sharing.

Purpose of the Study:

• To improve the efficiency and workflow of phenotype data curation.
• To reduce errors and manual review in the annotation process.
• To facilitate collaboration among researchers annotating phenotypic data.

Main Methods:

• Developed an Ontology Request Broker (ORB) to decouple data annotation from ontology development.
• Implemented annotation consistency checks for quality control.
• Enhanced file sharing reliability through file change monitoring and autosave for collaborative editing.

Main Results:

• The Ontology Request Broker allows provisional term requests, which are later replaced with permanent identifiers.
• Annotation consistency checks reduce common curation errors and the need for revisions.
• Improved reliability with online folder sharing enhances collaborative editing capabilities.

Conclusions:

• New Phenex features, especially the ORB, enable more effective data annotation.
• Phenoscape curators report a smoother annotation workflow with fewer interruptions.
• The software enhances focus on data annotation by minimizing ontology and file management issues.