diff --git a/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/gif/facets.gif b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/gif/facets.gif new file mode 100644 index 00000000..d927cf06 Binary files /dev/null and b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/gif/facets.gif differ diff --git a/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/gif/search_help.gif b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/gif/search_help.gif new file mode 100644 index 00000000..ca071da2 Binary files /dev/null and b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/gif/search_help.gif differ diff --git a/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/gif/start.gif b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/gif/start.gif new file mode 100644 index 00000000..a7df72f1 Binary files /dev/null and b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/gif/start.gif differ diff --git a/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/quickstart_user_studymetainfoeditor.png b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/quickstart_user_studymetainfoeditor.png index c6b9f6ce..add6b3ef 100644 Binary files a/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/quickstart_user_studymetainfoeditor.png and b/docs/user-guide/doc-odm-user-guide/doc-odm-user-guide/images/quickstart_user_studymetainfoeditor.png differ diff --git a/docs/user-guide/doc-odm-user-guide/quickstart_user.md b/docs/user-guide/doc-odm-user-guide/quickstart_user.md index 2bb48cfb..432451eb 100644 --- a/docs/user-guide/doc-odm-user-guide/quickstart_user.md +++ b/docs/user-guide/doc-odm-user-guide/quickstart_user.md @@ -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: @@ -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. diff --git a/docs/user-guide/index.md b/docs/user-guide/index.md index b0553d26..a4108c52 100644 --- a/docs/user-guide/index.md +++ b/docs/user-guide/index.md @@ -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) diff --git a/mkdocs.yml b/mkdocs.yml index 835ed2c7..1fe0932f 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -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