Difference between revisions of "Knowledgebase mockups (Nov 2009)"
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==Publications== | ==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==== | ||
| + | |||
| + | |||
| + | [[Image:Pubs1-rev1.png|700px]] | ||
| + | =====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==== | ||
| + | [[Image:pubs2-rev1.png|700px]] | ||
| + | =====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 ==== | ||
| + | [[Image:pubs3-rev1.png|700px]] | ||
| + | =====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. | ||
| + | [[Image:matrix1.png|700px]] | ||
| + | |||
| + | 2. | ||
| + | [[Image:matrix2.png|700px]] | ||
| + | |||
| + | =====advance to next character arrow===== | ||
| + | [[Image:matrix3.png|700px]] | ||
| + | |||
| + | ====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. | Integration of publication data across site. | ||
| − | ===Publication results on term search pages=== | + | ====Publication results on term search pages==== |
* this shows an entity page (entopterygoid) - could have similar layout on taxon and gene searches | * 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 | * for each row (phenotype class) - see how many publication are linked to any EQs of that type | ||
| Line 9: | Line 56: | ||
[[Image:pubs1.png|700px]] | [[Image:pubs1.png|700px]] | ||
| − | ===List of publications=== | + | ====List of publications==== |
* click one of the links to go to that publication's detail page | * click one of the links to go to that publication's detail page | ||
[[Image:pubs2.png|700px]] | [[Image:pubs2.png|700px]] | ||
| − | ===Publication detail page=== | + | ====Publication detail page==== |
* matrix will usually be much bigger - will be scrollable | * 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) | * 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) | ||
| Line 24: | Line 71: | ||
==Tree mapping== | ==Tree mapping== | ||
===Map 2 phenotypes on tree=== | ===Map 2 phenotypes on tree=== | ||
| + | |||
| + | [[Image:MultiplePhenotypesOnTree.png]] | ||
| + | |||
| + | |||
| + | ==November 2009 version from Jim== | ||
* user can enter phenotype specification for each "state" | * user can enter phenotype specification for each "state" | ||
* see on tree which branches exhibit one or both of the phenotypes | * see on tree which branches exhibit one or both of the phenotypes | ||
| − | * Do | + | * Do users want the tree "pruned"? Or show branches without annotations also? could be a lot of taxa |
[[Image:trees1.png|700px]] | [[Image:trees1.png|700px]] | ||
| Line 36: | Line 88: | ||
===Map phenotypes of a given entity on tree=== | ===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. | ||
| + | [[Image: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 | ||
| + | |||
| + | [[Image:IconsOnBranchOption.png]] | ||
| + | |||
| + | ==Display qualities using text icons adjacent to taxon names== | ||
| + | |||
* user enters any entity term | * user enters any entity term | ||
* each of the standard upper-level PATO qualities has some icon | * each of the standard upper-level PATO qualities has some icon | ||
| Line 46: | Line 117: | ||
==Phenotype queries== | ==Phenotype queries== | ||
| + | ===Entry of phenotype specification=== | ||
| + | |||
| + | ==== Single Pane Set Algebra interface ==== | ||
| + | |||
| + | [[Image:ComplexQuery1.png]] | ||
| + | |||
| + | [[Image:ComplexQuery2.png]] | ||
| + | |||
| + | [[Image:ComplexQueryAlgebraBox.png]] | ||
| + | |||
| + | |||
| + | ==== Phenotype on Tree Mapping Specification ==== | ||
| + | [[Image:TreeDisplayQuery.png]] | ||
| + | |||
| + | ==== Biomart style interface ==== | ||
| + | |||
| + | [[Image:BioMart1.png]] | ||
| + | |||
| + | [[Image:BioMart2.png]] | ||
| + | |||
| + | ==== November 2009 Version ==== | ||
| + | * user enters a phenotype specification, presses Done | ||
| + | |||
[[Image:queries1.png|700px]] | [[Image:queries1.png|700px]] | ||
| + | |||
| + | ===Additional phenotype specification=== | ||
| + | * bottom of page shows taxa which exhibit first phenotype | ||
| + | * user pressed "+" under first phenotype and can enter another | ||
[[Image:queries2.png|700px]] | [[Image:queries2.png|700px]] | ||
| + | |||
| + | ===Results=== | ||
| + | * taxa exhibiting both phenotypes are shown | ||
[[Image:queries3.png|700px]] | [[Image:queries3.png|700px]] | ||
| + | |||
| + | ===Comments=== | ||
| + | What should happen upon clicking taxon names? --[[User:Jpb15|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]] -- [[User:peteremidford@yahoo.com | peter]] 17:39, 19 January 2010 | ||
| + | |||
| + | [[Category:User Interface]] | ||
| + | [[Category: Mockups]] | ||
Latest revision as of 18:49, 21 January 2010
Contents
- 1 Publications
- 2 Tree mapping
- 3 November 2009 version from Jim
- 4 Display qualities using a grid of colored tiles
- 5 Display qualities using colored icons strung along branches
- 6 Display qualities using text icons adjacent to taxon names
- 7 Phenotype queries
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
1.
2.
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
Error creating thumbnail: Unable to save thumbnail to destination
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.
Error creating thumbnail: Unable to save thumbnail to destination
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
Error creating thumbnail: Unable to save thumbnail to destination
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
Error creating thumbnail: Unable to save thumbnail to destination
Error creating thumbnail: Unable to save thumbnail to destination
Error creating thumbnail: Unable to save thumbnail to destination
Phenotype on Tree Mapping Specification
Error creating thumbnail: Unable to save thumbnail to destination
Biomart style interface
Error creating thumbnail: Unable to save thumbnail to destination
Error creating thumbnail: Unable to save thumbnail to destination
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
