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
to integrate data from different models

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and testing systems to provide an overall
view of chemical activity

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for regulatory endpoints of interest.

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

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for chemicals of interest
from multiple assays.

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Furthermore, combining biologically
related data sets can support

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weight-of-evidence assessments
of chemical safety and bioactivity.

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However, the process of identifying
desired data for multiple biologically

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relevant assays or data sets can be
daunting for those without domain

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expertise in either the biological
endpoint or data processing.

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To assist users in this process,
this version of ICE now includes updated

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curated high throughput screening (or cHTS
data) with annotations

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to OBO Foundry ontologies
so you can more easily pair chemicals

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with biologically relevant assays.

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Once you've identified chemicals
and assays of interest,

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ICE allows you to explore different
properties and endpoints to get a summary

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view of each chemical's toxicity.

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Let's head over to the ICE Search tool
by selecting "Search"

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on the top right-hand panel.

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Located throughout the tool are green
information buttons to help you better

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understand key features and results.

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When you hover over a button, brief
explanatory text will appear.

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When you click a button,
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,
click the "Report an Issue" button

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on the left side of the display
to generate an email to ICE support.

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To build a search,
you must specify at least one data set

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or chemical or a combination of both.

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ICE Search queries can access
and integrate curated toxicity data

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for thousands of chemicals,
as well as chemical properties

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and human exposure predictions.

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

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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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The first input method gives you
the option of using Chemical Quick Lists,

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which are lists of chemicals that are
relevant to specific biological effects

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or toxicological research efforts.

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They are useful when you don't have
a specific set of chemicals

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in mind to look at.

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To select chemical quick lists for your
query, click on "Select Chemicals"

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from the Chemical Input field.

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For more information on these quick lists
you can click on the green information

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buttons available in the dialog box
and also check the descriptions

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under the "Data" tab in the top right.

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These lists can also be downloaded
using the icon on the far right.

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Use the check boxes to the left of each
list to select or deselect

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the chemical lists of interest.

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For this example query, we can select
the quick list, "A Demo List of Chemicals".

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Click "Finished" to populate the chemical
input field on the left with chemical

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identifiers from the selected quick list.

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The second input method allows you to type
or paste in your own list

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of chemical identifiers

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in the User
Chemical Identifiers box.

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Enter one chemical per line.

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You can use any combination
of the following identifiers:

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chemical names, CASRNs,
DTXSIDs, SMILEs, and InChIKeys.

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An example of these identifiers is
provided next to the information box

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located in the Chemical Input field.

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For this example query, let's type
in the chemical name "propylparaben".

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If you don't add any chemicals to your
query, however, your results will include

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all chemicals with data in ICE
for your selected data sets.

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To select data sets for your query,
click on "Select Data Sets"

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from the Select Data Sets Input field.

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In the dialog box that appears, select
a category of interest from the tabs.

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Use the check boxes to the left of each
list to select or deselect the assays or

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endpoints of interest
within your chosen tab.

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Data in ICE are organized in categories
along toxicity or target endpoints

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of regulatory interest,
such as acute lethality,

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irritation and corrosion, or
developmental and reproductive toxicity.

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Additional categories allow
queries specific to cHTS, chemical

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property data, and exposure predictions.

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For this query example,
we are going to select

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the "Acute Lethality" data set tab
and select all the "Dermal" endpoints.

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We can also select
cHTS assays within the "Acute Lethality" tab

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by opening the "Mode of Action" dropdown
and selecting

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"AcuteTox Neuronal Transmission",

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"AcuteTox p53 Signaling Pathway",

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and "AcuteTox Cellular Response
to Oxidative Stress".

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Selecting these terms will return results
from the cHTS assays annotated

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to the specific term.

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You can also select different
data sets from different categories.

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Under the "Endocrine" tab, we can select
In vivo and in vitro estrogen assays.

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We will also select the parent term
for sensitization in the "Sensitization" tab

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so that the in vivo and in vitro skin
sensitization assay

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child terms are selected.

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When you're done selecting data sets
and endpoints, select "Finished"

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on the bottom left of the dialog box.

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Click on the green information buttons for
a description of a data set or endpoint.

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ICE also provides documentation
with detailed information on data

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provenance, including endpoints,
sources, and curation.

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To view this, click on the descriptions
under the "Data" tab on the top right.

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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 "Add chemicals

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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 quantitative structure-activity
relationship, (or QSAR), structure

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as a chemical you have specified.

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We provide this option because one
of the challenges associated

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with identifying relevant data for a test
chemical is that different salts

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of the chemical are often assayed.

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ICE provides the option to include results
from chemicals with the same

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two-dimensional desalted structures based
on the InChIKeys of the

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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 for all

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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
on the Search tool, go to the "Help"

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top menu and select "User Guides".