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51 changes: 36 additions & 15 deletions docs/user-guide/doc-odm-user-guide/quickstart_user.md
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@@ -1,4 +1,10 @@
# User Quick Start Guide
# Start

On this page we briefly show main pages of the ODM: Dashboard, Study Browser, Metadata Editor.

For more details about Study Browser and Metadata Editor functionality refer to corresponding guide page.

![StartGIF](doc-odm-user-guide/gif/start.gif)

The first thing you see when logging in to Open Data Manager is the Dashboard:

Expand All @@ -11,28 +17,43 @@ link from the dashboard takes you to the Study Browser to help you do this.

## Study Browser

![image](doc-odm-user-guide/images/quickstart_user_studybrowser.png)
!!! info "Limitation"
Only Studies you have permission to observe (Studies created by you or Studies shared with your group of users
by another user) are displayed as default.

By default all studies are shown that you have permission to see, but since you aren’t expected to scroll through
thousands of studies there are, of course, search and filtering options to help you find studies of interest.
These are given in the left hand panel of the Study Browser and they allow you to search by study name, accession or
by the text present in any metadata field.
There is search and filtering options to help you find studies of interest.
Facets in the left hand panel of the Study Browser and Search bar allow you to search by study name, accession or
by any value presented in any metadata field.

#### NOTE
!!! tip
Harmonising your Study and its child entities (Samples, Libraries, Preparations, Data) Metadata values by using
configurable validation rules helps you to find all relevant values by preventing missed results due to
non-standard terms usage.

Harmonising your study and sample data (metadata) texts by using controlled vocabularies and ontologies helps searches find all relevant data by preventing missed results due to misspellings or non-standard term usage
The search is also aware of controlled dictionary/ontology and will expand results to include synonyms, with optional
extension to include child terms.
Click on the question mark next to the search bar to open `Help` with more details about advanced search functionality.

The search is also controlled vocabulary/ontology aware and will expand results to include synonyms, with optional extension to include child terms. You can use asterisks (\*) to allow any positive number of wildcard characters: “*ale” will find “male” and “female” for example. Click on the question mark next to the search bar to open \*\*Help\** with more details about advanced search functionality.
![SearchHelpGIF](doc-odm-user-guide/gif/search_help.gif)

The facets beneath the search bar allow you to filter down the results of a search based on the samaple data (metadata) fields that
are present in your results.
The facets on the left side allow you to filter down the results of a search based on the metadata fields that
are presented in your results.

To access more details about a study and to explore it further click the name of the study which will launch
the Metadata Editor in a new tab.
![FacetsGIF](doc-odm-user-guide/gif/facets.gif)

You can find more about Search functionality on [Study Browser](../doc-odm-user-guide/studybrowser.md) page
of this guide.

## Metadata Editor

To access more details about a study and to explore it further click the name of the study which will launch
the **Metadata Editor** in a new tab.

![image](doc-odm-user-guide/images/quickstart_user_studymetainfoeditor.png)

The Metadata Editor allows you to see all the information about a study, the samples contained in the study and any
signal data types associated with the study, for example, expression or variant data.
The Metadata Editor allows you to see all the information about a Study metadata, Samples, Libraries, and Preparations
metadata contained in the Study and any Data Classes (signal data and attached files) associated with the Study,
for example, expression or variant data.

You can find more about this functionality on [Metadata Editor](../doc-odm-user-guide/metadata-editor.md) page
of this guide.
2 changes: 1 addition & 1 deletion docs/user-guide/index.md
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Expand Up @@ -65,7 +65,7 @@ Want to know more? Learn more by watching our videos below.

## In Depth User Guide Articles

* [User Quick Start Guide](doc-odm-user-guide/quickstart_user.md)
* [Start](doc-odm-user-guide/quickstart_user.md)
* [Dashboard](doc-odm-user-guide/quickstart_user.md#dashboard)
* [Study Browser](doc-odm-user-guide/quickstart_user.md#study-browser)
* [Metadata Editor](doc-odm-user-guide/quickstart_user.md#metadata-editor)
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2 changes: 1 addition & 1 deletion mkdocs.yml
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Expand Up @@ -22,7 +22,7 @@ nav:
- About Genestack: https://genestack.com/
- Advanced Guide:
- user-guide/index.md
- Quick Start Guide: user-guide/doc-odm-user-guide/quickstart_user.md
- Start: user-guide/doc-odm-user-guide/quickstart_user.md
- User Setup: user-guide/doc-odm-user-guide/setup.md
- Create New Study: user-guide/doc-odm-user-guide/create-study.md
- Import Data on ODM: user-guide/doc-odm-user-guide/import-samples-spreadsheet.md
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