Difference between revisions of "Software roadmap"

From phenoscape
(→‎Development Plan)
(→‎A database and web application to store and query the taxonomies, ontologies, and phenotype data)
 
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==Development Plan==
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==Phenotype annotation editor==
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===Enhance Phenote with necessary features to be productively and efficiently used by curators -- March 2008 (first Data Jamboree)===
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* '''[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
  
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{| border="1" cellpadding="5"
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===Phenex editor (Phenote with custom character-oriented interface) 1.0-beta1 -- July 2008===
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! Timeline !! Phenote
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* '''[complete]''' Browse and edit characters and character states, edit EQ phenotypes per character state.
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|-
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* '''[complete]''' Browse and edit taxa, edit specimens per taxon.
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! rowspan=2 | September 2007
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* '''[complete]''' New post-composition editing interface.
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| Search field for character list tables. Filter out table rows by simple text matching.
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* '''[complete]''' Load from and save to NeXML file format.
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|-
 
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| Ontology mode for search field.  Show only rows using a term descending from the search term.
 
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|}
 
  
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===Phenex 1.0-beta3 -- August 2008===
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* '''[complete]''' Character matrix panel for viewing and editing.
 +
* '''[complete]''' Open NEXUS files.
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* '''[complete]''' Import data from tab-delimited taxon files.
  
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===September 2007===
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===Phenex 1.0-beta4 -- August 2008===
 +
* Import data from tab-delimited character files.
  
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* Phenote: Search field for character list tables.  Filter out table rows by simple text matching.
+
===Phenex 1.0===
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* Phenote: Ontology mode for search field.  Show only rows using a term descending from the search term.
+
* Interface for user option for whether to update ontologies.
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* Phenote: Character matrix view of entered data.  Read-only.
+
* User-customizable ontology preferences.
 +
* Undo/redo support.
  
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===October 2007===
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===Unscheduled features===
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* Phenote: Improved menu handling.
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* 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.
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** User should be able to access common application commands while any window is in front.
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* Create lookup-enabled Publication field (enter DOI or PMID).
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** On Mac, menu should properly use Quit menu and other standard menu items.
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* Character matrix view of annotations: Taxon by Entity+Attribute.
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* Phenote: Improved document opening/saving functionality.
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* Determine whether to integrate standalone Phenex application with web database, or migrate components into web application.
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** User should be able to quickly save a document to the same file it was opened from.
 
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** User should be able to open multiple documents simultaneously.
 
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* Phenote: Editable character matrix for data entry as well as viewing.
 
  
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===November 2007===
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==Ontology editor==
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* Phenote: 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.
+
===Curators begin by using OBO-Edit to view and edit project ontologies -- August 2007===
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* Phenote: Should be feature-complete for essential character annotation work by curators.
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* '''[complete]''' Curators are using OBO-Edit successfully.
  
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===Early 2008===
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===Unscheduled features===
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* TBD
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* Character encoding syntax for OBO file format and support in OBO-Edit (for example, UTF-8).
  
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==History==
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==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
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* [[Roadmap for first iteration]] to be demoed and tested at [http://www.sicb.org/meetings/2009/index.php3 SICB 2009]
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* [[Database Roadmap]] to be demoed and tested at [http://www.dce.k-state.edu/conf/jointmeeting/ ASIH 2009]
 +
 
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[[Category:Archive]]

Latest revision as of 19:26, 11 October 2011

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

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