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

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results of a query run
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 with concentration-response curves
from in vitro high-throughput screening

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data in ICE that have
been curated by NICEATM.

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These are referred to as "cHTS data."

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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 results 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,

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and review data from multiple chemicals
and/or multiple assays in one query.

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The main feature

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of the Curve Surfer Results page is
a series of tiles containing graphs.

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

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The red dots on the graphs indicate

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experimental data points if chemical
was active in a particular assay.

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The solid curved line represents

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the modeled winding curve
derived from the

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U.S. Environmental Protection Agency's ToxCast
pipeline, or 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 best fit was a gain-loss model.

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The best fit model type is also identified

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in the metadata below the curve
and in the figure legend.

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In addition to the concentration response

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curve, we can see some other features
in the plot for an active chemical.

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A gray vertical dashed line denotes

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the ACC, the activity
concentration and cutoff.

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A black vertical dashed line denotes

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the AC50, the half-maximal
activity concentration.

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A green horizontal batch line indicates

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the top-of-curve value.
For chemical-assays combinations that were

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inactive or marked by NICEATM as

"flag omit" or "QC omit,"

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not all of summary values will appear.

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

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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.

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Display or export the graph to a PNG file.

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Click the "expand" button in the top left

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corner of the plot area to open
a larger viewing window for the graph.

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Metadata are provided below each graph.

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The CASRN is a hyperlink that can be used

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to search data on that chemical
in the National Toxicology Program's

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Chemical Effects in Biological Systems,
or CEBS database.

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Click on the DTXSID to view
information on the chemical in the

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U.S. Environmental
Protection

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Agency's Computational Toxicology
, or CompTox Chemicals Dashboard.

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The meditative field

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also provides curve summary values such as
AC50 on top of curve and lists

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the mechanistic target terms
as annotated to the assay.

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If more than 10 curves are returned
from your query, the Results view will

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initially show the first 10
concentration-response curves

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for the query.
You can view the page count and select or

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browse pages using the arrows
and drop down 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

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at the top of the page to refine
results or focus on data of interest.

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Use the "Select Filter to add the chain"

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dropdown list to choose
from several filtering options.

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For this example, we are applying filters

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for call and assay format, and filtering
on a numerical range of AC50 values.

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Select the filter option to open a dialog

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box allowing you to set specific
criteria for that filter type.

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When you select your criteria and click
"Close," a colored box will appear

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describing the applied filter
and summarizing the number of curves

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in the results meeting the chosen
criteria. You can add additional filtering

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criteria, for which additional boxes
will appear in an ordered chain.

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You can click and drag the boxes

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to reorder them, or click the "x" in the top
right corner to remove a filter.

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A pie chart to the left of the dropdown

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shows the number of curves meeting
the criteria in each layer of filtering.

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Click the "Clear Filters" button to clear
all filters. In addition to filtering,

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you can manually select
curves of Interest and sort

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to view the selected curves.
Click on the "Select this item" box

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at the top of each tile to select
the curves you are interested in.

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You can "Select All Filtered" to select all

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the filtered curves
and "Clear Selected" to unselect all.

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Any number of curves selected will appear

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as "Selected item(s)" at the far
right of the display.

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You can overlay multiple curves to compare

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across chemicals and/or assays in one
interactive, downloadable plot.

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Click "Overlay Selected" if you have

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a manual selection of curves that you'd
like to see together in one plot.

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Alternatively, click "Overlay Filtered"

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to overlay all curves that remain
after applying filters.

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Overlay views are limited to 50 curves.

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Once either option is selected

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a new popup window will open
with a curve overlay graph.

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This graph displays all curves plotted

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using a "Scaled Response" to overcome unit
differences across different assay

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platforms, such as
fold change vs. percent inhibition.

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Above this graph,

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the dropdown menu allows you to select
only assays with a specific data type.

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Hovering over an individual curve will

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provide information about which chemical-
assay combination the curve represents.

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

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click again to restore them.

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As for individual curves,

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you can mouse over the graph 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.

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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

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it to view the curves
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

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applied to the display will
be applied to the downloads.

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Use the "Clear Filter" or "Clear Selected"

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buttons to clear any sorts,
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 for 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

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in the same formatting as the
tab-delimited text file described above.

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

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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"

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dropdown list next to the download
button to send the chemical-assay

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combinations to other ICE tools
to run additional queries.

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For details on the use and outputs

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of these tools, refer to their
respective user guides.

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

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Thank you for watching our video

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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."