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] 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.

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

Development Plan

Timeline	Phenotype Annotation Editor	Ontology Editor
September 2007	Search field for character list tables. Filter out table rows by simple text matching. Complete --jim 16:35, 14 September 2007 (EDT)	Curators use OBO-Edit to view and edit project ontologies.
	Ontology mode for search field. Show only rows using a term descending from the search term. Complete --jim 17:20, 19 October 2007 (EDT)
October 2007	Improved menu handling. User should be able to access common application commands while any window is in front. On Mac, menu should properly use Quit menu and other standard menu items.
	Improved document opening/saving functionality. User should be able to quickly save a document to the same file it was opened from. User should be able to open multiple documents simultaneously.
	Character matrix view of data: species by Entity+Attribute.
November 2007	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.
	Phenote feature-complete to be productively and efficiently used by curators.