Knowledgebase mockups (Nov 2009)

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Publications

Revision 1

Revision 1 posted on 12/16/09 by Wasila based on amphibanat feedback, Phenoscape conference call (11/20/09), discussion with Paula (12/14/09), and conference call with John Lundberg (12/18/09). The Powerpoint file containing the revisions is on the webdav.

Publication results on anatomy term search pages, revision 1

Pubs1-rev1.png

Comments:
  • John likes separate column for publications (as in previous revision), maybe add 'KB Publications' vs. book icon in taxon column.
  • Tree page, source data box: will need link to Pub page 3, below (case # 1337)
  • Per conference call 12/15/2009: we will use book icon with hover popup text which tells what book means and how many publications user will see.

List of publications, revision 1

Pubs2-rev1.png

Comments:
  • Per conference call 12/15/2009: include indented smaller source character text under each publication to indicate which data caused association of that publication with ontological term on previous page. This text is not clickable, only the publication citation is.

Publication detail page, revision 1

Pubs3-rev1.png

Comments:
  • Per conference call 12/15/2009: Free text character headers and cells are not linked anywhere. There should be a popup accessed by clicking a cell to see the EQ(s) resulting from that character state.
  • Per conference call 12/15/2009: Matrix will show all characters, using horizontal scroll bar. Matrix should be scrolled to start so that character of interest is in view (determined by page user navigates from).

Additional character x taxon matrix mockups

Based on conference call 12/18/09; mockups added on 12/21/09 by Wasila. "how to show character of interest? should entopterygoid be first column (even if author lists as #4 or #79)? or should there be a slider or 'next' arrow that allows users to view additional characters?"

collapse/expand all button

1. Matrix1.png

2. Matrix2.png

advance to next character arrow

Matrix3.png

Comments:

Data downloads: phenotypes for single entity across studies

From 12/18/09 conference call:

  • John’s new use case: obtain data for a single entity across multiple studies. If want to do broad phylogenetic analysis of catfishes, need to look in detail in each pub of how entopterygoid is treated. Want to get just the entopterygoid by taxon data matrix.
    • go back to anatomical term page. Need to get all data for entopterygoid (size, shape, etc.). Will the tree have 'entopterygoid' with 'ento, shape', 'ento, size' etc. beneath it? Will there be a sum/number of the total number of phenotypes for just entopterygoid? if, e.g. '800', click on it, and you would see a matrix with columns, size, shape, etc. with EQ in cells, but mouse-over to see free text. Can DOWNLOAD THIS SELECTION OF DATA ALONE in excel. In the excel file, you would have the free text, publication, and EQ? ...same thing as in genbank data with incomplete stuff, put in alignment program.

Original mockups

Integration of publication data across site.

Publication results on term search pages

  • this shows an entity page (entopterygoid) - could have similar layout on taxon and gene searches
  • for each row (phenotype class) - see how many publication are linked to any EQs of that type
  • click one of the count links to go to a page listing those publications

Pubs1.png

List of publications

  • click one of the links to go to that publication's detail page

Pubs2.png

Publication detail page

  • matrix will usually be much bigger - will be scrollable
  • click column header or cell links to go to a phenotype details page showing all related EQs grouped by taxon (as on existing phenotype pages)

Pubs3.png

Comments

Tree mapping

Map 2 phenotypes on tree

MultiplePhenotypesOnTree.png


November 2009 version from Jim

  • user can enter phenotype specification for each "state"
  • see on tree which branches exhibit one or both of the phenotypes
  • Do users want the tree "pruned"? Or show branches without annotations also? could be a lot of taxa

Trees1.png

Same interface

  • shows that the 2 phenotypes don't have to be obvious alternatives

Trees2.png

Map phenotypes of a given entity on tree

Display qualities using a grid of colored tiles

  • Qualities are displayed with consistent location and color in the grid
  • Desaturated colors are used for qualities of phenotypes that are inferred, rather than annotated
    • Note annotation to Ictaluridae in this and next candidate example
  • The 16 tile designs are intended to support expansion of the list of qualities used in curation - as has already happened.

ColorGridOption1.png

Display qualities using colored icons strung along branches

  • Qualities are displayed with consistent icon, color and relative position along branches
  • As above, desaturated colors are used for inferred qualities
  • Additional icons may be added

IconsOnBranchOption.png

Display qualities using text icons adjacent to taxon names

  • user enters any entity term
  • each of the standard upper-level PATO qualities has some icon
  • each node of tree is annotated with icons for which kinds of phenotypes are exhibited by that node
  • so if you just put in "bone", you could get a "shape" icon at a node for any bone shape phenotype (basihyal bone round, vertebra 1 flat, etc.)

Trees3.png

Comments

Phenotype queries

Entry of phenotype specification

Single Pane Set Algebra interface

ComplexQuery1.png

ComplexQuery2.png

ComplexQueryAlgebraBox.png


Phenotype on Tree Mapping Specification

TreeDisplayQuery.png

Biomart style interface

BioMart1.png

BioMart2.png

November 2009 Version

  • user enters a phenotype specification, presses Done

Queries1.png

Additional phenotype specification

  • bottom of page shows taxa which exhibit first phenotype
  • user pressed "+" under first phenotype and can enter another

Queries2.png

Results

  • taxa exhibiting both phenotypes are shown

Queries3.png

Comments

What should happen upon clicking taxon names? --jim 11:38, 18 November 2009 (EST)