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Update learn.mdx (#3256)
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Updated to remove references to Gen3 and replace with the AnVIL Data Explorer.
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acliffe38 authored Oct 15, 2024
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Expand Up @@ -52,18 +52,17 @@ This section covers:

All you need is a Google account to register with Terra and browse AnVIL’s publicly accessible workspaces.

Likewise, with a Google account, you can register with Gen3 and browse publicly accessible datasets or register with
Likewise, with a Google account, you can register with the AnVIL Data Explorer and browse publicly accessible datasets or register with
Dockstore and browse tools and workflows.

To send artificial cohorts from Gen3 to Terra for Analysis, you will need to link your Gen3 and Terra accounts.
To send artificial cohorts from to Terra for Analysis, you will need to use the same Google ID for your Data Explorer and Terra accounts.

To allow your dbGaP data request approvals to flow through to Terra and Gen3, you will need to link your eRA commons ID
To allow your dbGaP data request approvals to flow through to Terra and the Data Explorer, you will need to link your eRA commons ID
with both platforms.

<Alert icon={false} severity="info">
For instructions on setting up accounts in Google, Terra, Gen3, and linking
them together see [Overview of Account
Setup](/learn/account-setup/overview-of-account-setup).
For instructions on setting up accounts in Google, Terra, the AnVIL Data Exlplorer, and linking
them together see [How to register in Terra on GCP (Google SSO)](https://support.terra.bio/hc/en-us/articles/360028235911-How-to-register-on-Terra-Google-SSO).
</Alert>

### Obtaining Access to AnVIL Data
Expand All @@ -74,12 +73,12 @@ To obtain access to controlled-access data sets, you must either be a member of
data-sharing agreement among consortium members or have been granted access to a study through the dbGaP Data Access
Request process.

Once you have been granted access, and assuming you have linked your eRA commons ID with Terra and Gen3, you will be
able to see your new studies in Gen3 and new data-oriented workspaces in Terra.
Once you have been granted access, and assuming you have linked your eRA commons ID with Terra, you will be
able to see your new studies in the Data Explorer and new data-oriented workspaces in Terra.

AnVIL’s open-access datasets such
as [1000 Genomes High Coverage 2019](https://anvil.terra.bio/#workspaces/anvil-datastorage/1000G-high-coverage-2019) can
be accessed in Terra or Gen3 immediately after account creation.
be accessed in Terra or teh Data Explorer immediately after account creation.

For a detailed listing of available datasets searchable by disease, data type, consent type, and consortia, see
AnVIL’s [Dataset Catalog]({portalURL}/data/consortia).
Expand Down Expand Up @@ -111,7 +110,7 @@ analysis you require.
There are several types of workspaces to consider when thinking about cloning a workspace to start your project.

**Data-Oriented Workspaces** - These workspaces hold data for AnVIL open or controlled-access data sets or cohorts
exported from Gen3. They may contain documentation in the dashboard about the study that generated the data set and data
exported from the Data Explorer. They may contain documentation in the dashboard about the study that generated the data set and data
tables holding sample and subject phenotypic metadata with links to the genomic data files.

**Analysis Oriented Workspaces** - Analysis-oriented workspaces showcase a specific analysis or tool such
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