Difference between revisions of "Software roadmap"
From phenoscape
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==Phenotype annotation editor== | ==Phenotype annotation editor== | ||
===Enhance Phenote with necessary features to be productively and efficiently used by curators -- March 2008 (first Data Jamboree)=== | ===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]''' Initial Phenote configuration for PhenoScape data model. |
| − | * '''[complete]''' Specimen List window allowing curators to repeatedly choose one or more taxa for EQ annotation | + | * '''[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]''' Phylogeny view for selecting taxa to annotate. |
| − | * '''[complete]''' Search field to filter table rows | + | * '''[complete]''' Search field to filter table rows. |
| − | * '''[complete]''' Ontology mode in search field for more advanced table filtering | + | * '''[complete]''' Ontology mode in search field for more advanced table filtering. |
| − | * '''[complete]''' Configuration for editing homology annotations | + | * '''[complete]''' Configuration for editing homology annotations. |
| − | * '''[complete]''' Transition PhenoScape components to Phenote 2 docking windows interface | + | * '''[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]''' 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]''' 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]''' 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 | + | * '''[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=== | ===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. | * 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. | |
| − | * Create lookup-enabled Publication field (enter DOI or PMID) | + | * Determine whether to integrate standalone Phenex application with web database, or migrate components into web application. |
| − | |||
| − | |||
| − | * Determine whether to integrate standalone | ||
==Ontology editor== | ==Ontology editor== | ||
===Curators begin by using OBO-Edit to view and edit project ontologies -- August 2007=== | ===Curators begin by using OBO-Edit to view and edit project ontologies -- August 2007=== | ||
| − | * '''[complete]''' Curators are using OBO-Edit successfully | + | * '''[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== | ==A database and web application to store and query the taxonomies, ontologies, and phenotype data== | ||
| + | * [[Data Jamboree 2/Prototype|Roadmap for prototype]] demoed at the Data Roundup | ||
| + | * [[Roadmap for first iteration]] to be demoed and tested at [http://www.sicb.org/meetings/2009/index.php3 SICB 2009] | ||
| + | * [[Database Roadmap]] to be demoed and tested at [http://www.dce.k-state.edu/conf/jointmeeting/ ASIH 2009] | ||
| − | + | [[Category:Archive]] | |
| − | [[Category: | ||
Latest revision as of 19:26, 11 October 2011
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 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.
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
- Roadmap for prototype demoed at the Data Roundup
- Roadmap for first iteration to be demoed and tested at SICB 2009
- Database Roadmap to be demoed and tested at ASIH 2009
