Software roadmap

Phenotype annotation editor

Enhance Phenote with necessary features to be productively and efficiently used by curators -- March 2008

• [complete] Initial Phenote configuration for PhenoScape data model
• [complete] Specimen List window allowing curators to repeatedly choose one or more taxa for EQ annotation
• [complete] Phylogeny view for selecting taxa to annotate
• [complete] Search field to filter table rows
• [complete] Ontology mode in search field for more advanced table filtering
• [complete] Configuration for editing homology annotations
• [complete] Transition PhenoScape components to Phenote 2 docking windows interface
• [complete] Use standard menus and keyboard shortcuts for Open, Save, Quit, Cut, Copy, Paste, etc.
• [complete] Improved document saving functionality. User should be able to quickly save a document to the same file it was opened from.
• [complete] Rework Specimen List as Taxon List: each taxon has multiple specimens which can be picked from during annotation as supporting evidence
• Choose museum code from pick list when entering specimen IDs
• Character matrix view of annotations: Taxon by Entity+Attribute

Features for the future

• Annotation using temporary terms, when an appropriate term is not available in an ontology. Ability to update these terms to official term once it is available.
• Make DAG view work browsing entire ontology, with drag-and-drop to fields
• Allow user to see what version of ontology is being used
• Create lookup-enabled Publication field (enter DOI or PMID)

Phenote integration with PhenoScape web application and database

• Determine whether to integrate standalone Phenote application with web database, or migrate components into web application

Ontology editor

Curators begin by using OBO-Edit to view and edit project ontologies

• [complete] Curators are using OBO-Edit successfully and no PhenoScape development