Software roadmap

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.

Phenex 1.0

• Interface for user option for whether to update ontologies.
• User-customizable ontology preferences.
• Undo/redo support.

Unscheduled features

• 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.

Ontology editor

Curators begin by using OBO-Edit to view and edit project ontologies -- August 2007

• [complete] Curators are using OBO-Edit successfully.

Unscheduled features

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

A database and web application to store and query the taxonomies, ontologies, and phenotype data

• Phenoscape

At present, we have implemented

1. A relational database to hold ontological definitions of concepts from ontologies such as the TTO, TAO, and PATO, and curated data from NeXML files
2. A query API to extract assertions from the database using combinations of taxon, entity, and quality parameters by extending the OBD API
3. A front end application to query the database by Entity Quality (EQ) combinations

This application was demoed at the Data Roundup at Rapid City, SD