Phenoscape web UI

Phenoscape web UI development plan.

2009

February 2009

• Mockup changes to existing interfaces required to incorporate 1/5/09 team feedback on existing interface components
• Taxon search interface Done
  • Mockup interface using dummy data within web application - request group feedback
    • Front page search interface and results table - may include intermediate results summary page
• Interface demo and feedback session - DECAP meeting, Feb. 27, 2009 Done
  • Present screenshots and mockups
  • Possible live demo depending on data service performance progress
    • Services should return in no more than 2 seconds
    • Evaluate feasibility 2 weeks before meeting
• Mockup publication data interface within web application Done
• Mockup "splashy" search entry page - we should have a more graphically capturing entry gateway for exploring the data content
  • One of the following:
    • Hierarchical term explorer
    • Visual explorer, using schematic drawings ("the prototypical fish")
    • Visual explorer using 3D scans of catfish (and eventually zebrafish when done).
  • Should explore various prototypes of these ideas using HTML mockups and get feedback from project team
• Mockup taxonomy-based tree-mapped data perspective
  • View taxonomic phenotype annotation results organized by a phylogenetic tree
  • Group phenotypes as simplistic union of descendant nodes, rather than ancestral reconstruction
  • Use taxonomy as basis for phylogenetic tree
  • Develop HTML mockups in web application

March 2009

• Incorporate 1/5/09 team feedback on existing interface components In progress
  • Anatomy term search results - reorganize according to sketch
  • Gene search results - reorganize according to sketch
  • Taxonomic phenotype results page - add Order column for taxonomic grouping
  • Present various phenotypic results grouped by custom "character slim" done
    • Requires slim development by team members (Wasila, Paula) Done--Pmabee@usd.edu 12:20, 20 March 2009 (EDT)done and service implementation by Cartik
• Taxon search interface
  • Design data service schema to be implemented by Cartik
  • Implement interface using live data service once developed by Cartik

April 2009

• Implement "splashy" search entry page as defined by mockup work
• Incorporate publication data into user interface
  • Incorporate publication links into annotation results displays
    • Columns referencing numbers of taxonomic phenotype or mutant phenotype match results will be accompanied by a column including number of publications referencing the search item
    • Link from publication count to a publication listing
  • Publication listing includes brief citation each of which links to a publication detail page
  • Publication detail page(s)
    • Full citation information
    • Display curator credits
    • Display or link to original matrix including free-text data and specimen listing
    • Display or link to all phenotype annotations resulting from publication
  • Requires publication data implementation in OBD by Cartik
  • Requires specimen data implementation in OBD by Cartik
• Possible user testing session in conjunction with RCN meeting at NESCent

May 2009

• Implement taxonomy-based tree-mapped data perspective
• Implement appropriate scalable deployment of web application Done
  • Multiple application instances and load balancing Done

Release candidate - June 2009

• Project team testing
• Bug fixes
• Overall performance evaluation

2010

February 2010

• Develop overall site revision plan based on feedback from Knowledgebase Beta 1 interface [Done]
• Knowledgebase 2.0 site revision mockup testing [Done]
  • Present mockups to naive users in Eugene, Oregon, February 16-17 [Done]
• Revise mockups using testing session user feedback
• Develop 2.0-beta implementation plans with feedback from Phenoscape stakeholders

March 2010

• Annotation search results pages with editable data filters
• Working taxonomy cladogram data interfaces
• Complete mockups of advanced query interfaces
• Phenoscape meeting at Field Museum, Chicago
  • Conduct user feedback sessions with mockups of forthcoming interfaces, and live testing of implemented pages [Done]
  • Write-up results of feedback and proposed changes
• Generate permanent unique ID for each publication [Done]
• Enter unique IDs for publications into Endnote [Done]
• Data imported KB via Endnote XML files
  • • NOTE: This part was done quite a while ago. However, a slight modification needs to be made to use the new unique IDs for publications
  • citation information as individual semantic pieces (individual authors, title, journal, etc.)
  • abstract
  • DOI if available
• Investigate importing previous names of ZFIN genes
• Gene symbol as primary name
  • NOTE: This was the old status quo before we decided to the display the complete name of the gene, can easily revert to this

April 2010

• Term search results pages incorporating ontology tree browser
• Publication pages with citation and abstract, links to publications from other data types
• Advanced query interface, data download implementation
• type of mutation/defect producing phenotype result (requires feasibility investigation)
• ZFIN publication ID for each phenotype annotation
• import common names for taxa

May 2010

• Publication pages with data matrix (table view and downloadable)
• Publication pages with specimens
• Link to taxonomy cladogram interfaces via data on other pages
• Official release of Phenoscape Knowledgebase 2.0-beta

June 2010

• User testing sessions of Knowledgebase 2.0-beta
• Bug and feedback revisions

July 2010

• Official release of Phenoscape Knowledgebase 2.0