Knowledgebase mockups (Nov 2009)

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

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

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

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

advance to next character arrow

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

List of publications

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

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)

Comments

Tree mapping

Map 2 phenotypes on tree

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

Same interface

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

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.

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

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.)

Comments

Phenotype queries

Entry of phenotype specification

Single Pane Set Algebra interface

Phenotype on Tree Mapping Specification

Biomart style interface

November 2009 Version

user enters a phenotype specification, presses Done

Additional phenotype specification

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

Results

taxa exhibiting both phenotypes are shown

Comments

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

go to taxon’s page?
go to phenotype listing for that taxon and given phenotypes?
I have created pages with multiple versions for Complex Query Specification, Map Multiple Phenotypes on Tree and Map Qualities on Tree – peter 17:39, 19 January 2010