Software roadmap

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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