Software roadmap

Phenotype annotation editor

[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.
[complete] Choose museum code from pick list when entering specimen IDs.
[complete] Make DAG view work browsing entire ontology, with drag-and-drop to fields.
[complete] Allow user to edit field values directly in the table (especially for Specimen list).
[complete] Allow user to create multiple, temporary annotation template lists while editing. Not savable with current file format, however
[complete] Include preset docking interface configuration for Phenoscape

[complete] Browse and edit characters and character states, edit EQ phenotypes per character state.
[complete] Browse and edit taxa, edit specimens per taxon.
[complete] New post-composition editing interface.
[complete] Load from and save to NeXML file format.

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.
Create lookup-enabled Publication field (enter DOI or PMID).
Character matrix view of annotations: Taxon by Entity+Attribute.
Determine whether to integrate standalone Phenex application with web database, or migrate components into web application.

Character encoding syntax for OBO file format and support in OBO-Edit (for example, UTF-8).