Difference between revisions of "Software roadmap"

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(→‎Phenotype annotation editor)
(→‎A database and web application to store and query the taxonomies, ontologies, and phenotype data)
 
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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===
+
===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]''' Transition PhenoScape components to Phenote 2 docking windows interface
+
* '''[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]''' 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.
−
* Character matrix view of annotations: Taxon by Entity+Attribute
+
* '''[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
  
−
===Features for the future===
+
===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.
 
* 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
+
* Create lookup-enabled Publication field (enter DOI or PMID).
−
* Allow user to see what version of ontology is being used
+
* 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.
  
−
===Phenote integration with PhenoScape web application and database===
+
==Ontology editor==
 +
===Curators begin by using OBO-Edit to view and edit project ontologies -- August 2007===
 +
* '''[complete]''' Curators are using OBO-Edit successfully.
  
−
==Ontology editor==
+
===Unscheduled features===
−
===Curators begin by using OBO-Edit to view and edit project ontologies===
+
* Character encoding syntax for OBO file format and support in OBO-Edit (for example, UTF-8).
−
* '''[complete]''' Curators are using OBO-Edit successfully and no PhenoScape development
 
  
 
==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]
  
−
==Development Plan==
+
[[Category:Archive]]
−
 
 
−
{| border="1" cellpadding="5"
 
−
! Timeline !! Phenotype Annotation Editor !! Ontology Editor
 
−
|-
 
−
! rowspan=2 | September 2007
 
−
| Search field for character list tables.  Filter out table rows by simple text matching. ''Complete --[[User:Jpb15|jim]] 16:35, 14 September 2007 (EDT)''
 
−
| style="background:#efefef;" | Curators use OBO-Edit to view and edit project ontologies.
 
−
|-
 
−
| Ontology mode for search field.  Show only rows using a term descending from the search term. ''Complete --[[User:Jpb15|jim]] 17:20, 19 October 2007 (EDT)''
 
−
|-
 
−
! rowspan=3 | October 2007
 
−
|  Improved menu handling. User should be able to access common application commands while any window is in front.  On Mac, menu should properly use Quit menu and other standard menu items.
 
−
|-
 
−
| Improved document opening/saving functionality.  User should be able to quickly save a document to the same file it was opened from.  User should be able to open multiple documents simultaneously.
 
−
|-
 
−
| Character matrix view of data: species by Entity+Attribute.
 
−
|-
 
−
! rowspan=2 | November 2007
 
−
| 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.
 
−
|-
 
−
| style="background:#efefef;" | Phenote feature-complete to be productively and efficiently used by curators.
 
−
|}
 
−
 
 
−
[[Category:Informatics]]
 

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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