Bookmark a search result/state → and vice versa show bookmark in search results

Steps

• Open Gene list
• Add Single Score Column
• Select a cell line

Expected

The selected cell line should be tracked and available for retrieval.

Search for state metadata (e.g., states that are 2 days ago)

The best match should have an indicator in the state sequence.

Steps

• Open Gene view
• Select "EGFR" and open "Copy Number" detail view
• Filter for tumor type "breast cancer" and sort by "Copy Number"

Expected
The retrieval should provide a list of used filters.

Implement the provenance retrieval for Ordino.

When showing search results the previous states could be collapsed.

• At the moment selected items are only accessible via the Top 10 list
• Generate a property with selected items for genes, cell lines, etc. from all states of the provenance graph

Search view without prov view → could switch to CLUE presentation mode, to avoid forks from clicks by mistakes

Alternative: Ask the user if he wants to continue the analysis from the search results and switch to exploration mode.

Reproduce

1. Select gene TP53 (ENSG00000141510) in copy number view
2. This gene is added as additional column in the new mutation view
3. Select cell line A549 in mutation view
4. Open Cosmic view

Expected
Also dynamically added columns from selections in the context view should be tracked in the VisState.

Currently, only Ensembl IDs are tracked, however, many people would search by gene symbol.

The image shows the total sequence length of 8 states, but the compressed states in the glyph must be 6, since the start and end state are indicated as circles.

Searching for cell line name → dropdown shows “Selected cellline” and “Selected externalItem” → the latter one is confusing

Collection for all issues for Ordino from the BI feedback session

At the moment all available views in Ordino are added to the Select2

However it's better to show only the views that are used and stored in the provenance graph.

Several key words used for the search can appear in multiple categories.
E.g., Relative Copy Number can belong to Selected Data Types, Selected Data Subtypes, Selected Copy Numbers, and maybe others.
It would be nice if one could decide whether the search term should be restricted to a specific category or not.

When searching and jumping to a search result, the user needs a back button to continue where she left. This button is especially important when provenance panel is closed.

The query-by-example is not usable if the provenance panel is closed. Therefore we need a different solution to filter the select2 only be the current visible view.

Problem description

In this example the parameter data_subtype changed from TPM to Raw Counts:

As you can see all states are grouped into one sequence.

Expected

If a parameter changes the result should be two different sequences. In the image above one with 5 states for TPM and a second sequence with 2 states for Raw Counts.

Both highlighted buttons should be available if the panel are collapsed.

Like so:

Improvements that are not application specific, but rather general.

Click on search-by-example show select2 suggestions filtered by “instate” (marked with an orange dot).

At the moment all set properties are compared in one big set. However, this doesn't make sense, if you have parameter and selections of different idtypes, that should be compared.

Improvement
Group the SET properties and only compare these groups among each other.

• Rename tooltip to “Active in current view” (not state)
• Select2 usage bar: add baseline to the left border and don't round corners
• Rename “Provenance” panel to “Current session history”
• Rename Search panel header → “Search current session”
• Add label to x from “Remove all search terms”

When selecting the magnifier icon the select2 is not open and filtered anymore.

• The search result as box should be clickable
• Hover over box should highlight the sequence in prov view
• Click on box should jump to first result
• Top result must then look a bit different
• Open sequence with click on glyph is unintuitive → adding a small arrow?
• Current search result as top result doesn’t provide visual feedback on hover

This doesn't make sense:

Make them more salient or don't encode the similarity score as opacity.

At the moment the user doesn't get feedback if the search result (also in the sequence) is currently active.

Remove all “x” was confusing and interpreted as a broken searchterm.

A trash can might be better or adding a label.

Switch the flat property model to a tree and search for it using Sam's algorithm:

Datamodel (Tree)
root
tags = union of all children tags + selection tags
selection = tags of the selection
children
vis type for this child
tags = current set of tags for this child

Search
query … set of tags to search for
similarity(q, t) … similarity between query q and current tags t
union(a, b) … union of two tag sets
intersect(a, b) … intersection of two tag sets
possible(vistype) … returns the list of possible tags for an idtype

score(q, root) => {
  const max = root.children.map((c) => {
     //just the possible query tags
     const possible = intersect(q, possible(c.vistype));
     //the more possible the better
     const weight = possible.length / q.length;
     const similarity = similarity(possible, c.tags);
     const score = weight * similarity;
     return {score, c};
   }).reduce((max, current) => {
     //select the maximum considering the weighted similarity result
     if (max === null || (max.score < current.score) {
       return current;
     }
     return max;
   }, null);

  //just consider the tags of the winning child
  const actual = union(max.c.tags, root.selection);
  return similarity(q, actual);
}

Goal
What terms occurs together → meta-analysis (e.g., A was analyzed with B, and A with C → the system could recommend a new visualization with B and C)

Gapminder prototype with preloaded Stories from Hans Rosling
https://gapminder-retrieval.caleydoapp.org

Instead of mixing all kinds of property values it would be helpful to categorize them.

Expected

Views: Genes, UniProt
Genes: *ENSG00000256030*, ENSG00000269149, ENSG00000169347, ENSG00000146648, ENSG00000023839, ENSG00000213107, ENSG00000242529, ENSG00000186352