Software roadmap

From phenoscape
Revision as of 20:05, 5 February 2008 by Jpb15 (talk | contribs) (Enhance Phenote with necessary features to be productively and efficiently used by curators -- March 2008)

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
  • Choose museum code from pick list when entering specimen IDs
  • Character matrix view of annotations: Taxon by Entity+Attribute

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.
  • Make DAG view work browsing entire ontology, with drag-and-drop to fields
  • Allow user to see what version of ontology is being used
  • Create lookup-enabled Publication field (enter DOI or PMID)

Phenote integration with PhenoScape web application and database

  • Determine whether to integrate standalone Phenote 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

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