WEBVTT

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Welcome to the Integrated Chemical
Environment, also known as ICE.

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This video offers a guide to viewing
results of a query run

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in the ICE Curve Surfer tool.

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As discussed in the previous video,
this tool lets you view and interact

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with concentration-response curves
from in vitro high-throughput screening

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data, (referred to as cHTS data),
in ICE that have been curated by NICEATM.

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We will be viewing the results of a
Curve Surfer query built in that video;

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if you have not yet viewed it, you may
want to do so before watching this one.

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Once the query is run,
the window will switch to Results view.

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Curve Surfer results provide individual
concentration-response graphs for every

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chemical-assay combination from the query
for which there are cHTS data in ICE.

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This lets you query, retrieve,
and review data for multiple chemicals

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and/or multiple assays in one query.

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The main feature
of the Curve Surfer results page is

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a series of cards containing graphs.

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Each graph represents one chemical-assay
concentration-response curve.

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The orange dots on the graph indicate
individual data assay points.

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If a chemical was active in a particular
assay, the solid curved line represents

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the modeled winning curve
derived

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from the US Environmental Protection
Agency's ToxCast Pipeline or

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tcpl processing algorithm.

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The color of the curve identifies
the best fit model type.

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A blue line indicates the best fit model
was a Hill model,

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while a yellow line indicates
that the best fit was a gain–loss model.

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The best fit model type is also identified
in the metadata below the curve

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and in the figure legend.

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In addition to the concentration-response
curve, we can see some other features

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in the plot for an active chemical.

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A gray vertical small-dashed line denotes
the ACC, the activity

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concentration at cutoff.

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A black vertical large-dashed line denotes
the AC50, the half-maximal

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activity concentration.

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A purple horizontal small and large-dashed
line indicates the cutoff value.

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A green horizontal large-dashed
line indicates the top-of-curve value.

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Chemical-assay combinations that were
inactive or marked by NICEATM as "Flag-Omit"

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or "QC-Omit" will lack some summary values.

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For more details on NICEATM curation,
please refer to the "Curve/assay-based

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Curation" section of the cHTS data set page.

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Hover the mouse over a plot area
to display a menu of tools in the top

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right corner that can be used to adjust
the graph display or export

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the graph to a PNG file.

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Metadata are provided below each graph.

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The CASRN is a hyperlink that can be used
to search data on that chemical

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in the National Toxicology Program's
Chemical Effects

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in Biological Systems, or CEBS, database.

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Click on the DTXSID to view information
on the chemical

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in the US Environmental Protection
Agency's CompTox Chemicals Dashboard.

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The metadata field also provides the name
of the assay, the assay's mechanistic

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target, and the winning curve fit model.

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If curves have an active call, then
the AC50, ACC, and top-of-curve are given.

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If assays have an inactive call or have
been tagged as "Flag-Omit" or "QC-Omit"

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assays, then the ACC, AC50s,
and top-of-curve are marked as NA.

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If assays have been tagged as "Flag-Omit" or
"QC-Omit",

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detailed information on the flag
associated with each chemical-assay

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pair is provided as "Flag-Information".

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If more than 10 curves are returned
from the query,

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the Results view will initially show
the first 10 concentration-

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response curves for the query.

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You can view the page count
and select or browse page changes by using

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the arrows and dropdown
list under "Select Page".

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Use the "Sort Results By" dropdown list
to choose from seven sorting criteria

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and "Direction" to display curves
in ascending or descending order.

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You can use the filtering options
at the top of the page to refine results

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or focus on data of interest.

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Use the "Select Filter to add to Chain"
dropdown list to choose

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from several filtering options.

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For this example, we are applying filters
for call and assay system and filtering

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on a numerical range of AC50 values.

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Select the filter option to open a dialog
box allowing you to set specific

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criteria for that filter type.

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When you select your criteria and click
"Apply Filter",

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a colored box will appear describing
the applied filter and summarizing

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the number of curves in the results
meeting the chosen criteria.

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You can add additional filtering criteria,
for which additional boxes

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will appear in an ordered chain.

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You can click and drag the boxes
to reorder them or click the "x" in the top

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right corner to remove a filter.

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A pie chart to the left of the dropdown
shows the number of curves meeting

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the criteria in each layer of filtering.

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Click the "Clear Filters"
button to clear all filters.

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In addition to filtering,
you can manually select curves of interest

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and sort to view the selected curves.

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Click on the "Select this Item" box
on the top of each tile to select

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the curves you are interested in.

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You can "Select All Filtered" to select all
the filtered curves and "Clear

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Selected" to unselect all.

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The number of curves selected will appear
as "Selected Items" at the far

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right of the display.

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You can overlay multiple curves to compare
across chemicals and/or assays

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in one interactive, downloadable plot.

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Click "Overlay Selected" if you have
a manual selection of curves that you'd

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like to see together in one plot.

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Alternatively, click "Overlay Filtered"
to overlay all curves that remain

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after applying filters.

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Overlay views are limited to 50 curves.

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Once either option is selected,
a new popup window will open

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with a curve overlay graph.

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Only assays that have the selected
response units will appear on the graph.

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To place curves with different response
units on one graph, select

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"scaled response" as the response unit.

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Scaled response is calculated for each
data point as the response divided

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by the curve's concentration cutoff.

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The dropdown menu next to "Select AC50 or
ACC" allows you to toggle between

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displaying AC50 or ACC curves.

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Hovering over an individual curve will
provide information about which chemical-

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assay combination the curve represents.

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Click on the legend to remove
individual curves from this display;

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click again to restore them.

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As for individual curves,
you can hover over the graph area

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to display a menu of tools in the top
right corner that can be used

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to adjust the graph display.

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Clicking the camera icon will export the
graph to a publication quality PNG file.

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Click the "3-D" checkbox in the top left
corner to display a 3-D view of the graph.

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This may take a few seconds to display.

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The 3D plot is interactive.

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You can click and drag the plot to rotate
it to view the curves

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from a different perspective.

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Query results can be downloaded using
the download tools at the top of the page.

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Any sorting,
filtering, and/or selections applied

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to this display will be
applied to the downloads.

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Use the "Clear Filter" or "Clear Selected"
buttons to clear any sorts,

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filters, or selections.

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Clicking the "TXT" icon will export your
results to a tab-delimited text file.

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Data in this file are organized as one
row per chemical-assay combination.

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Clicking the "XLSX" icon
will export your results to an Excel file.

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This file includes the same data
in the same formatting as the tab-

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delimited text file described above.

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Clicking the "PDF" icon will export your
results to a PDF file that will capture

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each graph and assorted data exactly
as it appears on the webpage.

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The file will show one graph per page.

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You can also use the "Send filtered results
to" dropdown list next to the download

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button to send the chemical-assay
combinations to other ICE tools

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to run additional queries.

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For details on the use and output of these
tools, refer to their

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respective user guides.

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You can also also copy a list
of chemical identifiers to the clipboard.

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A new feature on all ICE tool web
pages streamlines the citation of ICE.

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The "Cite ICE" button leads
to an Acknowledgement webpage where you can

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find ICE citation formats,
examples of citations, and references.

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Thank you for watching our video
on viewing Curve Surfer query results in ICE.

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For more detailed information on the tool,
go to "Help" and select User Guides.