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 build a query in the ICE Search tool.

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A second video will help you understand
and interpret ICE search results.

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The ICE Search tool allows you

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to integrate data from different models
and testing systems to provide an overall

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view of chemical activity for
regulatory endpoints of interest.

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To compare or evaluate methods,
users typically need to view data

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from chemicals of interest
from multiple assays.

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Furthermore, combining biologically
related datasets can support weight

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of evidence assessments of chemical
safety and bioactivity.

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However, the process of identifying

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desired data for multiple biologically
relevant assays or datasets can be

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daunting for those without domain
expertise in either biological endpoints

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or data processing.
You can use ICE to explore different

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properties and endpoints to get
a summary view of a chemical's toxicity.

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The tool gives you access to data
for over 800,000 chemicals.

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Selecting Search on the top
menu or from the icon below

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the graphics takes you to the ICE Search
page. Located throughout the tool are green

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information buttons to help you better
understand key features and results.

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When you hover over a button,

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brief explanatory text will appear.
When you click a button

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more details will appear in a text box

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that can be resized
and relocated on the screen.

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If you encounter a problem using a tool,

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click the "Report and Issue" button
on the left side of the display

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to generate an email to ICE support.

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To run a search, you must specify at least

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one assay or chemical
or combination of both.

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ICE Search queries can access and integrate

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bioactivity data for over 10,000
chemicals, as well as in silico

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predictions of properties
and bioactivities for over 800,000

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chemical structures
from EPA's DSSTox database.

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You can add chemicals to your query using
one or both of two input methods

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in the chemical input field
on the left side of the screen.

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ICE gives you the option of using

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Chemical Quick Lists,
which are list of chemicals that have been

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found useful for evaluating
specific types of toxicities.

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They're useful when you don't have

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a specific set of chemicals
in mind to look at.

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For more information on these quick lists,

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you can use the information boxes
available in the selection box

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and also check the descriptions
under the data tab on the top right.

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You can also enter your own list

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of chemical Identifiers in the User
Chemical Identifier box.

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You can do this by typing in one or
more individual chemical identifiers.

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For this example, we can type in 50-28-2,

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the CASRN for the chemical estradiol.

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You can also paste in a list
of chemical Identifiers.

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You can use any combination of the following

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identifiers, CASRNs, DTXSIDs,
SMILES, and InChikeys.

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An example of these identifiers are

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provided under the information box
located in the chemical input field.

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You can run a search in ICE
without specifying chemicals.

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If you don't add any
chemicals to your query,

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your results will include all chemicals
with data for your selected assays.

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To select assays for your query,
click on "Select Assays" from the Assay

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Input field.
In the dialog box that appears,

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select a category of interest
from the tabs and then select the assays

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and endpoints of interest
in the window that opens.

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Data in ICE is organized in categories

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around toxicity or target endpoints
of regulatory interest,

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such as acute lethality, irritation
and corrosion, or developmental

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and reproductive toxicity,
with additional categories allowing

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queries specific to cHTS,
and physicochemical property data.

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This organization of assays makes it easy
for users to identify and explore all data

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from both animal and non-animal
tests relevant to that endpoint.

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ICE also provides documentation
with detailed information on endpoints,

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sources, and curations so
that users have full provenance.

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Check the descriptions under
the data tab on the top right.

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For this example, we are going to select

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the acute lethality assay type and select
all the dermal and inhalation endpoints.

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We can also open the mode of action

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drop down and select P53 Signaling

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Pathway, Oxidative Stress,
and Neuronal Transmission.

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Use the check boxes to the left of each

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list to select or deselect
assays in the category.

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You can select different assays
from different categories.

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When you are done
selecting assays and endpoints,

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select "Finished" on the bottom
left of the dialog box.

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You can run a search in ICE
without specifying assays.

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If you don't add any assays to your query,

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your results will include all assays
with data for your selected chemicals.

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Before we run the search, let's look
at two more options provided by ICE.

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On the bottom, you will see
that we have the option,

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"Add chemicals with identical
QSAR structures".

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Checking this box will add chemicals
available in ICE to your query that have

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the same QSAR structure as
a chemical you have specified.

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We provide this option because one

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of the challenges associated
with identifying relevant data for test

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chemical is a different salts
of the chemical are often an assayed.

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ICE provides the option to include results

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from chemicals with the same two-
dimensional desalted structures based

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on the InChi keys of the
"QSAR-ready" structures.

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The broader query based on the parent
structure, as opposed to a specific salt

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form, can help expand the data
returned for a specific structure.

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ICE also gives you two options
to define the scope of your search.

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The default option, Union, returns
all assay results available in ICE

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for all chemicals specified in the search.

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The more restrictive option, Intersection,
returns assay results only for chemicals

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that were tested in all
the selected assays.

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Now that we have built our query,
we can run our search.

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See the results video for an overview of
understanding and interpreting results.

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Thank you for watching our video
on how to build a Search query in ICE.

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For more detailed information

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on the Search tool, go to the Help
top menu and select "User Guides".