WEBVTT

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

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In this video, we will show you how
to understand and interpret

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results from the ICE Search tool.

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We will be viewing the results of a search
built in the previous video

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on building a query in ICE.

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If you have not yet viewed that video,
you may want to do so

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before watching this one.

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Once the Search query is run,
the "Results" tab will open.

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On the top, there are
three expandable headings.

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The first heading gives the names of the
Chemical Quick Lists selected by the user.

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The second heading shows the names
of the assay selected by the user,

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and the last heading gives the identifiers
that were not returned by the query.

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Identifiers may not be returned because
the chemical had no data for the assays

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selected or the specific identifier
was not available in the database.

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Three buttons beneath the expandable
headings allow you to view or

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download the results from your query.

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Clicking the "Data Table" button displays
a long view of the table with individual

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record data for each
substance–endpoint pair.

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You'll need to drag the scroll bar
to the right to view the entire table.

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Each data table can be filtered
by clicking the filter icons in the table

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heading and selecting a subset
of your results in the dialog box.

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For this example, we select the chemical

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"Propylparaben" and the mixture "Swagger".

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You can interact with elements
of the table to obtain more information

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about each individual chemical or mixture.

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Click on the chemical's
CASRN to be directed to the available

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test article page about the chemical
in the NTP Chemical Effects

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and Biological System
(CEBS) database.

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You can also click on the DTXSID to be
directed

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to the US Environmental Protection
Agency's CompTox Chemicals

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Dashboard entry for that chemical.

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For mixtures, the CASRNs
and DTXSIDs are provided for the active

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ingredients in the substance,
along with the percentage of the active

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ingredient in the reported formulation.

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The Data Table can be downloaded as a
tab-delimited text file or Excel file

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by using the buttons above the table.

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Any filters applied to the displayed data
will also be applied to the download.

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So if you need all the data, make sure
you clear any filters before downloading.

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Clicking the "Data Summary" button displays
a wide view of that table that summarizes

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results for each substance–endpoint pair.

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The first column of the "Data Summary" table
displays a "View Details"

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button for each substance.

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Let's look at the details
for the chemical propylparaben by clicking

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on the button in the first column,
which will open a new window.

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This new view contains two tabs:
"Substance Details" and "Curve Surfer".

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Under the "Substance Details" tab,
you can find the chemical structure,

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physicochemical properties,
and plots summarizing the active

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and inactive calls from binary endpoints.

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If any cHTS assays were selected, results
may also be shown as "QC-Omit" or "Flag-Omit".

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The pie chart represents results
for the specific chemical

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with all endpoints combined.

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The stacked bar plot on the right displays
call counts by assay or cHTS term.

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You can change the format of this plot
from stacked bar to pie chart

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and display assay call count as
percentages by selecting

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the different options under "Plot Type".

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Double click the graph for any assay that
has an active call to view AC50 plots.

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Click on the graph legend to remove or add
specific results from the graph view or

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specify what assay types should
be included in the graph view.

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Now, let's investigate
the "Curve Surfer" tab.

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The "Curve Surfer" tab allows you to view
and interact with

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concentration-response curves from cHTS data.

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You use the dropdowns to filter
the view or reorder the graphs.

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Curve Surfer is also a stand-alone tool.

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You can check the User Guide
and Help page to learn more about it.

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To see how this process works
for a mixture,

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click on the "Detail View" for swagger.

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Under "Mixture Details" on the top left,
we have information on the active

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ingredient of the mixture

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and on the right,
we get the chemical structure

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and the physicochemical properties
for each active ingredient if available.

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On bottom left,
we have a box plot that shows the AC50

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and LD50 values for each
active ingredient.

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Clicking "x" in the top right of the Detail
View and Data Summary tables will

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return you to the Search results page.

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Directly beneath the "View Data Tables"
section is an

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"Interact with Results" section.

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This section allows you to explore
the results using interactive

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tables and visualizations.

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Multiple filtering options are
provided to narrow down your search.

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At the top of this section,
you can use the dropdown list to apply

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a chain of filters for various parameters.

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Below this on the left,
you can use the data navigation

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map to filter results by data set;

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please note that filtering this way will
not be reflected in the above

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data tables or download features.

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To the right of the navigation map,
two bar charts summarize the number

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of substances and records
returned in the data set.

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Below this,
two tables summarize the results

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by selected quick list or
by individual substance.

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At the bottom, a plot displays
the endpoint data for all chemicals.

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The "Assay Calls Summary" has interactive
information that can be displayed as

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a stacked bar or pie chart with additional
filters and features to further view

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additional data,
including AC50 box and whisker

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plots, by clicking on any
endpoint with an active call.

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Applying filters will update the tables
and visualizations shown

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throughout the page.

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We'll first take a look
at the filter chain.

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The
filter chain allows you to filter results

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based on chemical or
assay-specific parameters.

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In the dropdown menu,
select "Chemical Name".

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A dialog box is shown with a selection
list for chemical name and a figure

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summarizing the number of results
available by chemical name.

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Let's select "Propylparaben"
and "Swagger" and click on "Apply Filter".

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The figures and tables on the page are
updated to show only results

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for the two selected substances.

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A box below the filter chain dropdown
menu shows details about

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the applied filter.

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You can apply additional filters
using the filter chain dropdown menu.

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Use the "Clear Filters" button
to remove all filters.

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Click the "x" in the top right
of the individual filter chain boxes

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to remove specific filters.

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Below the filtered chain,
an interactive data navigation map

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shows the distribution of records
returned across the data sets selected.

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The nested boxes in the map represent
subsets of the results according

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to data type hierarchy.

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Hovering over a box will display
the number of records in the results

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that correspond to that data subset.

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Click on boxes within the map to zoom
in on a data type and view the specific

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endpoint data available
for a selected data type subset.

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As you zoom into the map,
your location within the map's hierarchy

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is displayed as sequential
banners above the map.

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Click on the banners above the map to zoom
back out to a higher level in the map.

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All panels in the data graph section
will update to reflect only the subset

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of data you are zoomed in on.

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Please be aware that filters applied
while a user is located in a lower

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hierarchy within the navigation
map will trigger a warning message.

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Acknowledging the message will reset
the user's position to the highest level

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in the navigation map while the bottom
of the screen will populate

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with visualizations of data
specific to the chosen filter.

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The user can then continue to easily
navigate to any level within the

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navigation map to interact with results.

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Navigating through the data navigation map
will populate the bottom of the screen

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with graphs that are grouped
into individual individual cards

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which are specific to the selected
data subset and data type.

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As you navigate through the data
navigation map, the graphs will update

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to reflect your selection in the map.

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Your location in the data navigation map
will dictate the information

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displayed in the information cards below.

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We'll click on "Acute Lethality" in the data
navigation map to display

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results split by data subset.

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The first card shows cHTS results
for the selected acute lethality

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mode of action terms.

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In the second, categorical endpoints are
summarized within boxes of varying

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hues of the same color family.

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Hover over the boxes to show the number
of records with a specific classification.

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Below the bars, density plots show the
distributions for LC50 or LD50 results.

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Hover over individual points to view
the chemical name and associated value.

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Query results can be downloaded through
several options on the Results page.

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Any sorting,
filtering, and/or selections

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applied to the query results will
also be applied to the downloads.

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If you need all the data,
make sure to use the "Clear Filter" or "Clear

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Selected" buttons to clear any sorts,
filters, or selections

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prior to downloading.

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Three download options are available once
you click the "Download" button

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in the "View Data Tables" section.

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The "Summary Data" includes a single row
for each chemical, with a summary of all

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assays run on that chemical
given in the columns.

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A second option, "Wide Format Data",
returns summary data with the individual

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cHTS assays if there is a cHTS
assay group specified in the query.

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The "Long Format Data" returns the
substance-endpoint data table.

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You can also use the "Send filtered results
to" dropdown list below 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 copy a list of chemical
identifiers to the clipboard.

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Once you have downloaded all your results,
a new feature on all ICE tool

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webpages streamlines the citation of ICE.

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

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will find ICE citation
formats and references.

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Thank you for watching our
video on Search results in ICE.

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For more detailed information
on the Search tool, go to the "Help"

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top menu item and select "User Guides"