Knowledgebase mockups

From phenoscape

Grouping data by using an ontology tree view

Phenotype results

This would be an enhancement to the results currently displayed on a page like

The nearest common ancestor term of the annotated taxon terms is used as the root of the tree display. The only leaf terms displayed are those with annotations. Internal nodes show the union of the annotations to their descendant nodes.

Phenotype ontology tree.png


  • From Paula: start off with taxon tree semi-collapsed (at genus level). Starts semi-collapsed, but not yet at genus level
  • From Paula: Put the number of taxa for which there are annotations in parens behind, e.g., the genus name. Tracked in FogBugz now
  • From Todd: can we avoid repetition of the entity (ie "caudal vertebra") if all the phenotypes concern that one entity, or are you listing it to allow for the possibility of subsumed entities as well? yes indeed, to allow for subsumed entities
  • From Todd: show numbers of taxa with annotations in parens for collapsed entities is this not the same as Paula's comment above?
  • From Todd (cosmetic): italicize species names tracked in FogBugz
  • From Todd: will the names be links to other pages? They are now.

Search summary results

This would be an enhancement to the Phenotypes results currently displayed on a page like

The leftmost column is intended to represent a disclosable tree display. The nearest common ancestor of the represented annotated anatomy terms is used as the root of the tree display. Each anatomy term has a flat list of the qualities annotated for it. Don't pay too much attention to the dummy numbers given in these results.

Root anatomy term "infraorbital" collapsed:

Infraorbital closed ontology tree.png

Root anatomy term "infraorbital" expanded:

Infraorbital open ontology tree.png

Possible further enhancement to page capabilities - redisplay data on a quality tree. The included results would be somewhat different.

Nearest quality ancestor collapsed:

Quality closed ontology tree.png

Quality ancestor expanded:

Quality open ontology tree.png


  • From Paula: Rename 'Entity' 'Anatomy' as per other mockups for consistency
  • From Paula: swap column headings Entity-Quality on Quality tree table (below ' Nearest quality ancestor collapsed" text)
  • From Todd (cosmetic): I'm not sure the alternating colors will be clear when there are multiple rows - those are most useful as an aid to follow horizontally across many columns within a row
  • From Todd: would it be possible to collapse the quality column too (ie to "4 qualities" for a given entity? or "4 anatomical terms" for a given quality)?
  • From Todd: Personally I think having the anatomical entity in the 1st column is a lot more useful than having the quality tree there.

Display of citation and free-text basis for annotations

Here is a list of specific phenotype annotations resulting from a search. There is an added "Source(s)" link next to each one. The yellow bubble is not part of the page.

Phenotypes and sources.png

If the user clicks a "Source(s)" link, the citation information for a particular taxon-phenotype annotation is retrieved and displayed in a page overlay.

Phenotypes and sources open.png

A particular taxon-phenotype annotation may have been asserted from more than one publication:

Phenotypes and 2 sources open.png


  • From Todd (cosmetic): Add more buffer to table cells, with more subtle boundaries between them - you don't want the cells to visually overwhelm the data text.
  • From Todd (big issue): Showing the phenotypes makes me think we really need to list the reference point for them, since "increased size" is explicitly relative. One option would be to list the group to which the data matrix is being applied, so that "increased size" would be interpreted as relative to all catfish, or characiforms, or whatever the inclusive taxon was for that study.
  • From Todd: Shouldn't the reference be specific to each annotation, rather than to each taxon? I would suggest making a little icon to represent source/publication, and displaying it immediately after the phenotype annotation in the same cell, kind of like a superscript footnote. And I wouldn't have guessed that I would see the original character state description from the name "Source" - before I clicked it, I assumed it was just going to show me the citation.
  • From Paula: I think we need to add comments where there are some (if possible would be best not to see an empty comments field where there are not comments). E.g., in Siebert (1987), the matrix code "0" conflicts with the assessment of the condition in the text. So we'd like to leave the original coding in the matrix, but make sure that the comment appears to users. The comment is: "Gyrinocheilidae: text states pg 75 "An Ipb IV could not be positively identified as a separate element in my material." Fig 24 has "IpbIV?" This could go right below state and above curated by.

Simple display of homology information

Anatomy pages can make use of homology information from the database to list possible homologous terms. This mockup adds a list of homologous terms to the term info panel. The user can click one of these term links to go to the anatomy page about that term.

Homology list.png


  • From Todd: include evidence string
  • From Paula: I agree with Hilmar, that under 'Possible homologs' it should say 'accessory neural arch in TAXON' Then maybe a "evidence" button that links to the pub?