Improve metabolite page

[yosefdroth]

Hi all,

Can you please give feedback on the metabolites page --http://datanator.info/metabconcs/Adenosine%20triphosphate/Escherichia%20coli

[lzy7071]

Is it possible for "custom stats" to display the four values in four rows, each row for each value?

[lzy7071]

Can the height of the table be increased so that it fills most of the screen?

[yosefdroth]

added breaks to "custom stats" and renamed it "consensus"

[jonrkarr]

Unfortunately, I don't see the page due to server errors.

[jonrkarr]

Rename "consensus" --> "Stats". Consensus is a bit too forward, especially given that the measurements are from scattered organisms and conditions. I think its more accurate to call the box plot a statistical summary of the display/selected measurements. Consensus suggests that Datanator extrapolates measurements to a specific organism. I think this is inaccurate and could irritate some users. See #39.

[jonrkarr]

• Remove copyright from bottom of page or apply to all pages

• Add 2rem margin to content

  • Organize content into a single div

    <div class="total_container">
    <div class="bp3-navbar bp3-fixed-top bp3-dark navbar">...</div>
    <div class="metabolite_definition_data">...</div>
    <div class="ag_chart">...</div>
    </div>

    -->

    <div class="total_container">
    <div class="bp3-navbar bp3-fixed-top bp3-dark navbar">...</div>
    <div class="content">
     <div class="metabolite_definition_data">...</div>
     <div class="ag_chart">...</div>
    </div>
    </div>

  • Change style

    .content {
    max-width: 1000px;
    margin: calc(50px + 2rem) auto 2rem auto;
    }
    
    .metabolite_definition_data {
     margin-top: 0px;
     border-radius: 0px;
    }

• Set vertical spacing between top section and grid to 2rem

  .ag_chart {
    margin-top: 2rem;
  }

• Add same box shadow as section to grid

  .ag_chart {
    box-shadow: 3px 3px 5px rgba(0,0,0,.4);
  }

• Change the heading of the top section to the name of the metabolite

• The top section should present metadata about the metabolite

  • Textual description (from ECMDB)
  • Synonyms (from ECMDB)
  • InChI/SMILES
  • Picture of the structure
  • Use can use the NIH service described here to generate images from InChI or SMILES
  • Chemical formula, charge, molecular weight
  • List of similar metabolites and their tanimoto similarity. This doesn't need to display the chemical formula of each metabolite.
  • List of identifiers in other databases (e.g, ChEBI, KEGG, etc.)

• Format chemical formulas with subscripts (<sub>x</sub>)

• Rename "Consensus" to "Stats"

• Just about the grid I think we should put the title "Intracellular Concentration" in the same style as the heading of the first section

• Grid

  • Disable pivot mode, row groups, aggregate values
  • Disable second header row with filters. This is redundant with the filters tool bar.
  • Make column headings grammatically consisent
    • Concentrations --> Concentration
    • Error --> Uncertainty
    • Tanimoto Similarity --> Chemical Similarity
    • Conditions --> Condition
    • Source Link --> Source
  • Display units of concentrations
  • Reorder columns
  • Move Tanimoto Similarity to before Organism column
  • Move Source Link to last column
  • In Source Link column, display id within source (e.g, ECMDB: XX)
  • Right align concentrations
  • Replace numeric taxonomic distance with semantically meaningful string (genus, class, kingdom, etc.)
  • Set filter types of columns
  • Numeric: concentrations
  • Set: molecule, organism, growth phase
  • Consensus tool
  • Change title "Concentrations" --> "Concentration (μM)"
  • Shorten "Standard deviation" --> "Std Dev"
  • Rename "Total" --> "All"
  • Does the box plot use the same blue as in the color palette we've chosen?
  • Fix double border between tool panel and grid content

    .ag-theme-balham .ag-root {
    border-left: none;
    }

[jonrkarr]

Closing because this is now covered by several smaller individual issues.