allen-cell-animated / cell-line-catalog Goto Github PK

Implement sorting of rows by a given column (ex. cell line, protein, structure, gene symbol, etc)

Create a search bar so that users can do text searches without being limited by the filter drop downs.

Filtering is broken for multi-edit lines and does not behave as expected for these multi-edit lines. Multi-edits (ex. FBL/NPM1) should not appear in the filter dropdown, instead only the single gene symbols from the second tab in Irina's spreadsheet (see attached; Filter Gene Symbol tab) should appear. A single gene filter (ex. FBL) should retrieve both single edit and multi-edit lines (ex. FBL should retrieve AICS14, 84, 86, and 89).

Acceptance criteria:

• "Filter by Gene" is changed to "Filter by Gene Symbol"
• Filter by Gene Symbol dropdown contains only genes listed in Irina's spreadsheet (see attached; Filter Gene Symbol tab)
• filtering works for multi-edit lines (each gene symbol filter should retrieve the list of lines in Irina's spreadsheet; (see attached -> Filter Gene Symbol tab)
• gene symbols are in alphabetical order in dropdown
  Cell Catalog corrections and filters.xlsx

Filtering is broken for multi-edit lines and does not behave as expected for these multi-edit lines. Multi-edits (ex. mEGFP/mTagRFP-T) should not appear in the filter dropdown, instead only the single fluorophores from the 5th tab in Irina's spreadsheet (see attached; Filter Fluorophore) should appear. A single fluorophore filter (ex. mEGFP) should retrieve both single edit and multi-edit lines (ex. TagBFP should retrieve AICS89 and 90).

Acceptance criteria:

• Filter by Gene Fluorophore dropdown contains only fluorophores listed in Irina's spreadsheet (see attached; Filter Fluorophore tab)
• Fluorophores in dropdown should appear in same order as in Irina's spreadsheet (see attached; Filter Fluorophore tab)
• filtering works for multi-edit lines (each fluorophore filter should retrieve the list of lines in Irina's spreadsheet; (see attached -> Filter Fluorophore tab)
• EGFP and mEGFP should be combined into a single entry in the dropdown -> (m)EGFP and should retrieve the list of lines in Irina's spreadsheet
  Cell Catalog corrections and filters.xlsx

Multi-edit gene symbols are currently stored like this:

The Main_gene_symbol gets displayed in the cell line table view:

and the Main_gene_symbol1, 2, and 3 are displayed here:

Goal is to remove the redundancy and convert Main_gene_symbol to store a list that gets used to populate both the entry in the cell line table view and the individual line view. New implementation should work for both single gene edit lines and multi-gene edit lines like the example above

Add the following new Addgene and hpscreg links:

AICS-0093
https://hpscreg.eu/cell-line/UCSFi001-A-48

AICS-0095
https://hpscreg.eu/cell-line/UCSFi001-A-46
https://www.addgene.org/164499/

AICS-0096
https://hpscreg.eu/cell-line/UCSFi001-A-47
https://www.addgene.org/164500/

Irina created a spreadsheet of the structure names that should be used for each line. Corrections should be made to match the names in the spreadsheet, and they should be all lower case. Required changes are color coded orange in attached spreadsheet.

Acceptance criteria:
structure names, column names, and capitalization in catalog matches exactly what Irina has in first tab of attached spreadsheet
Cell Catalog corrections and filters.xlsx

Create a clickable button next to the dropdown filter options that clears all filter selections

• Created

Filtering is broken for multi-edit lines and does not behave as expected for these multi-edit lines. Multi-edits (ex. Endoplasmic reticulum/nuclear envelope) should not appear in the filter dropdown, instead only the single structures from the 4th tab in Irina's spreadsheet (see attached; Filter Structure tab) should appear. A single structure filter (ex. endoplasmic reticulum) should retrieve both single edit and multi-edit lines (ex. endoplasmic reticulum should retrieve AICS10, 46, 59).

Acceptance criteria:

• Filter by Gene Structure dropdown contains only structures listed in Irina's spreadsheet (see attached; Filter Structure tab)
• filtering works for multi-edit lines (each structure filter should retrieve the list of lines in Irina's spreadsheet; (see attached -> Filter Structure tab)
• structures are in alphabetical order in dropdown
  Cell Catalog corrections and filters.xlsx

Create a protein name filter using protein names list in Irina's spreadsheet (Filter Protein Name tab in attached)

Acceptance criteria:

• protein filter called "Filter by Protein"
• protein filter is populated with entries from Irina's list in alphabetical order
• protein filter works for multi-edit lines
• each protein name retrieves cell lines listed in Irina's spreadsheet (Filter Protein Name tab)
  Cell Catalog corrections and filters.xlsx

When navigating cell lines and tabs on the Cell Catalog, multiple tabs get displayed at the same time when doing the following:

1. Click on any line from the list. By default, the Gene editing tab will be displayed.
2. Click over to any other tab (ex. Cellular Validation)
3. Scroll up to the top and click Return to full list (goes back to table view of cell lines)
4. Click on a new cell line
5. In addition to the Gene editing tab, the last tab you clicked on for the previous cell line (ex. Cellular Validation from step 2 above) will be displayed under the Gene editing tab

This behavior is undesirable and only one tab should be displayed at a time.

Acceptance criteria: only one tab is displayed at all times

Some cell lines have multiple isoforms that are displayed in the gene editing tab:

These are separate entries in the data/cell_line_catalog.json but should be implemented as a list instead

Acceptance criteria:
NCBI isoforms should be stored in the following format in the json:

Format should work for single gene edit lines and multi-gene edit lines; each gene can have 1 or more isoforms

We want to make a caveat document available to users for some lines.

Acceptance criteria:

• optional caveat button on main page of cell line
• caveat button links to pdf on Coriell's website
• button is name "???" [waiting on Caroline for name]