Difference between revisions of "Software roadmap"
From phenoscape
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* '''[complete]''' Browse and edit taxa, edit specimens per taxon. | * '''[complete]''' Browse and edit taxa, edit specimens per taxon. | ||
* '''[complete]''' New post-composition editing interface. | * '''[complete]''' New post-composition editing interface. | ||
| − | * Load from and save to NeXML file format. | + | * '''[complete]''' Load from and save to NeXML file format. |
* Interface for user option for whether to update ontologies. | * Interface for user option for whether to update ontologies. | ||
Revision as of 18:35, 13 August 2008
Contents
- 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 Phenoscape editor (Phenote with custom character-oriented interface) 1.0 -- July 2008
- 1.3 Phenoscape editor 1.1
- 1.4 Unscheduled features
- 1.5 Phenote integration with Phenoscape web application and database
- 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
Phenoscape editor (Phenote with custom character-oriented interface) 1.0 -- 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.
- Interface for user option for whether to update ontologies.
Phenoscape editor 1.1
- 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.
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.
