WEBVTT

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

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In this video,
we will go over how to build a query

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in the ICE Curve Surfer tool.

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This tool lets you view and interact
with concentration-response curves

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from in vitro high throughput screening
data, referred to as cHTS data,

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in ICE that have been curated by NICEATM.

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To run a Curve Surfer query,
you must specify at least one assay

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or chemical or a combination of both.

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Select chemicals for your query
in the "Chemical Input" field on the left.

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You can choose an ICE Chemical Quick List
by clicking on the

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"Select Chemicals" button.

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For this example, For this example,
we will select the AR In Vitro

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Agonist Chemical Quicklist.

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Click Finished when you are done
selecting chemical quick lists.

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You can also enter chemical identifiers
in the User Chemical

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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 the list
of chemical identifiers.

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You can use any combination of these
identifiers: chemical names,

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CASRNs, DTXSIDs, SMILES, and InChIKeys.

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An example of these identifiers is
provided in the information box

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located in the Chemical Input field.

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ICE has cHTS data
for thousands of chemicals.

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Only chemicals with cHTS data return
results for a Curve Surfer query.

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Chemicals without cHTS data in ICE
will simply be omitted from the output;

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no error message or list of chemicals
with missing data will be returned.

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ICE allows you to run a Curve Surfer query
without specifying chemicals,

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but we advise against doing this.

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If you don't add any chemicals to your
query, the query will return results

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for all chemicals with data for your
selected assays, which will

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result in a very large output.

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Add in vitro assay data to your query
by using the "Data Input" field

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to the right of the "Chemical Input" field.

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To select cHTS assays,
click the "Select Assays" button.

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A dialog box will open showing two tabs:
"cHTS" and "Mode of Action".

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Click on the "cHTS" tab to view curated
in vitro high-throughput

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screening assays

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from ToxCast and Tox21 organized
into mechanistic target categories

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that have been annotated to help clarify
the biological interpretation

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of assay readouts.

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Click on the "Mode of Action" tab
to view curated in vitro high-throughput

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screening assays from ToxCast
and Tox21 organized by mode of action.

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The mode of action categories
group assays to inform on pathways

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and functions known to potentially
contribute to toxicological

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endpoints of regulatory relevance.

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Use the check boxes to select the assay
annotation terms

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of interest under each tab.

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Only assays with cHTS data in ICE
will shown as options for selection.

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For this example, under the "cHTS" tab,
we will choose the assays annotated

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to "Thyroid Hormone Metabolic Process".

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When you're finished selecting
Selecting Assays, click on "Finished".

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The assay annotation terms you have
selected will be displayed in a text box.

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ICE will allow you to run a Curve Surfer
query without specifying assays.

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However, such a query will return all cHTS
data for the specified chemicals in the

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query, resulting in a very large output.

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Click on "Run" to execute your query.

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You can navigate back to the input page
and modify selections as necessary.

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The session will remember
the selections made.

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To reset query parameters, select "Reset".

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See the results video for a guide
to viewing query results.

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

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For more detailed information about
the Curve Surfer tool,

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go to "Help" and select "User Guides".