- 1 Phenotype annotation editor
- 1.1 Enhance Phenote with necessary features to be productively and efficiently used by curators -- March 2008 (first Data Jamboree)
- 1.2 Phenex editor (Phenote with custom character-oriented interface) 1.0-beta1 -- July 2008
- 1.3 Phenex 1.0-beta3 -- August 2008
- 1.4 Phenex 1.0-beta4 -- August 2008
- 1.5 Phenex 1.0
- 1.6 Unscheduled features
- 2 Ontology editor
- 3 A database and web application to store and query the taxonomies, ontologies, and phenotype data
Phenotype annotation editor
Enhance Phenote with necessary features to be productively and efficiently used by curators -- March 2008 (first Data Jamboree)
- [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
Phenex editor (Phenote with custom character-oriented interface) 1.0-beta1 -- July 2008
- [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.
Phenex 1.0-beta3 -- August 2008
- [complete] Character matrix panel for viewing and editing.
- [complete] Open NEXUS files.
- [complete] Import data from tab-delimited taxon files.
Phenex 1.0-beta4 -- August 2008
- Import data from tab-delimited character files.
- Interface for user option for whether to update ontologies.
- User-customizable ontology preferences.
- Undo/redo support.
- 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.
Curators begin by using OBO-Edit to view and edit project ontologies -- August 2007
- [complete] Curators are using OBO-Edit successfully.
- Character encoding syntax for OBO file format and support in OBO-Edit (for example, UTF-8).