Updated Metadata Editor

docs/release-notes/v1.50-v1.59.md

@@ -585,6 +585,7 @@ Please review the documentation, as these changes may impact your integrations.
         ??? example "Response example"
       ![RN](1.58/1-58-4.png)
 
+
           * ??? danger "Affected endpoints (for both as-curator and as-users)"
 
 

docs/user-guide/doc-odm-user-guide/metadata-editor.md

@@ -1,10 +1,10 @@
 # Metadata Editor
 
-The **Metadata Editor** allows you to explore study, sample and data information and metadata and validate it against templates, correcting/curating it if needed.
+The Metadata Editor allows you to explore study, sample, data information, and associated metadata.
 
-## Getting to the Metadata Editor
+## Accessing the Metadata Editor
 
-To open an existing experiment with Metadata Editor, click on the study name in the search results in the Study Browser application.
+To open the Metadata Editor, click on **Browse Studies** and select the study of interest. You can apply filters or use keywords to search for specific studies.
 
 ![quickstart_user_dashboard.gif](doc-odm-user-guide/gifs/quickstart_user_dashboard.gif)
 
@@ -19,158 +19,54 @@ templates etc.) to any experiments.
 
 ## Exploring the Metadata Editor
 
-![image](doc-odm-user-guide/images/open-me-2.png)
+Once you have selected the study, click on its title to open and explore the metadata.
 
-When you click on the study name, a drop-down menu will appear allowing you to:
+!!! info
+    For more information on study browsing, filters, and bookmarked studies, refer to the [Study Browser](studybrowser.md) section.
 
-![image](doc-odm-user-guide/images/me-dropdown-2.png)
+![2ExploreStudies.png](doc-odm-user-guide/images/2ExploreStudies.png)
+<figcaption>Explore studies. Apply filters and click on the selected study to explore it further</figcaption>
 
-- **Share** data with your colleagues
+## **Study**
 
-![image](doc-odm-user-guide/images/share.png)
+This tab shows the study metadata, including:
 
-- **Export** data by creating a link that can be used to download data and can be shared with your colleagues
+* **Genestack:accession** number (automatically assigned)
+* Metadata regarding the study type, design, and contributor details (name, email, country, etc.).
 
-![image](doc-odm-user-guide/images/export-data-link.png)
+!!! note
+    The yellow highlighted fields indicate metadata currently checked against your currently applied data template and non-highlighted fields are not checked against the template. For more information click on the [Template Editor](template-editor.md) section
 
-You can also click the Export button near the top right of any Metadata editor tab.
+![3Overview.png](doc-odm-user-guide/images/3Overview.png)
+<figcaption>Overview of the Study Tab. The tab includes the study metadata details. Data in yellow represents metadata currently checked against the applied template</figcaption>
 
-![image](doc-odm-user-guide/images/export_button.png)
+## Samples
 
-- **Rename** study
+This tab contains all the sample metadata that are associated with this study. The information regarding the samples is displayed with columns representing features and rows representing samples. Key columns include:
 
-![image](doc-odm-user-guide/images/rename.png)
+* **Genestack:accession number**: Automatically assigned to each row.
+* **Sample Source ID**: A unique identifier linked to the experimental data.
 
-- **Copy accession** of the study
+![4Samples.png](doc-odm-user-guide/images/4Samples.png)
+<figcaption>Overview of the Samples tab. This section shows the sample metadata. The attributes (columns) highlighted in yellow represent the metadata currently checked against the template</figcaption>
 
-![image](doc-odm-user-guide/images/copy-accession.png)
+## Data
 
-- **Get more information** about the study. For example, you can learn when the study is created and modified, who is
-  the owner and which groups it is shared with.
+This tab details the files linked or attached to the study. It includes:
 
-![image](doc-odm-user-guide/images/more-info.png)
+* Details of the indexed data files linked (e.g., transcriptomics, pathways, proteomics, any TSV file)
+* Information on data attached in any format
+* Metadata of the study, including platform, path, version, etc
+* Details of non-indexed file attachments (e.g., PDF, PPT)
 
-- **Explore and change metadata template** by clicking on “Explore” and “Apply another…”
-  option in the drop-down menu.
+![5Data.png](doc-odm-user-guide/images/5Data.png)
+<figcaption>Overview of the Data tab. The Data tab contains the linked experimental data and attached files</figcaption>
 
-![image](doc-odm-user-guide/images/template_selection.png)
+## Limitations to the Metadata Editor
 
-There are several tabs that can be shown on the Metadata Editor page, namely Study, Samples, Expression (optional),
-Variants (optional) which represent metadata describing experiment, samples and processed files,
-such as transcriptomics data (GCT) and genomics data (VCF).
+All users, can explore data, visualize data, and export data. However, if you are not part of the **Curator group**, you cannot make edits or curate data. These functionalities are reserved for Curators. 
 
-### Study tab
+Learn more about users and permissions in the [User Setup](setup.md) section.
 
-Study tab provides general information about the study, namely experiment description, contributors and their contact
-details and so on.
-
-![image](doc-odm-user-guide/images/study-tab.png)
-
-To rename the study, click on the study title link at the top of the page and select “Rename”. Type in the new name and click the blue “Rename” button.
-
-Columns containing invalid metadata are highlighted in red and **Invalid metadata** flag is specified.
-
-![image](doc-odm-user-guide/images/study-invalid-metadata.png)
-
-### Samples tab
-
-Sample tab represents metadata describing each sample in the study. For example, here can be provided information about
-organism, cell line, disease. Metadata columns coming from the applied template are highlighted in yellow.
-
-**Add and delete samples**
-
-When you create a new study, by default it contains four samples. You can add more samples or delete samples if necessary.
-To add them, click on the “+” button, then in the appeared window specify number of samples you would like to add to the study and click “Add”.
-
-![image](doc-odm-user-guide/images/add-samples-1.png)![image](doc-odm-user-guide/images/add-samples-2.png)
-
-To remove samples from your study, hover over samples you would like to exclude, select them, and click on the “Delete” button.
-
-![image](doc-odm-user-guide/images/delete-samples.png)
-
-**Filter samples by metadata**
-
-If you need to narrow the list of samples shown in the study (for example, filter by organism to get only samples obtained
-from H. sapiens). To do so, click on the “Filters” button in the upper-left corner. This will show a metadata summary, where for
-each metadata field the list of values and the number of samples with this values are specified.
-
-![image](doc-odm-user-guide/images/filters-1.png)
-
-You can also start typing metadata value of your interest (“H. sapiens” in this case) to show only needed checkbox in the list of suggested meatadata values.
-
-![image](doc-odm-user-guide/images/filters-4.png)
-
-Then, click on the “Apply” button.
-
-![image](doc-odm-user-guide/images/filters-2.png)
-
-As a result only samples obtained from H. sapiens are shown in the Samples tab.
-
-![image](doc-odm-user-guide/images/filters-3.png)
-
-### Data tab
-
-The remaining tab in the Metadata Editor display metadata for the data files associated with a study. If more than one version of an omics file is available the different versions can be toggled.
-
-![image](doc-odm-user-guide/images/data-versions.png)
-
-## Metadata validation and curation
-
-**Curators** can not only view but also validate and edit metadata.
-
-Metadata fields are checked against a specific template, each template contains specific list of metadata fields and
-rules for the Study, Samples and processed/experimental metadata tabs. If some required metadata fields are missing,
-have typos or entered values don’t match the applied template, an **Invalid metadata flag** is shown in the upper right corner. Also,
-invalid fields themselves are highlighted in red.
-
-![image](doc-odm-user-guide/images/invalid-metadata.png)
-
-To **correct metadata manually**, click the field you wish to change and type a new value.
-
-![image](doc-odm-user-guide/images/correct-manually.png)
-
-When all the fields in a tab have been corrected the Invalid metadata flag will be replaced with a green
-**Metadata is valid** flag.
-Metadata fields for which **dictionaries or ontologies** are specified in the template allow you to click the
-arrow and select a term from a list of suggested terms from the associated dictionary.
-You can also start typing a term and auto-complete will help you to select an appropriate term from the dictionary.
-
-![image](doc-odm-user-guide/images/autocomplete.png)
-
-Values matching dictionary terms will be marked in green.
-
-![image](doc-odm-user-guide/images/green-term.png)
-
-Values in the metadata columns can be propagated by dragging the bottom-right corner of a cell.
-
-![image](doc-odm-user-guide/images/drug.png)
-
-To replace multiple values you can use **bulk replace** function. To do so, you should click the name a metadata field
-including incorrect values and select “Bulk replace” option in the drop-down list.
-
-![image](doc-odm-user-guide/images/bulk-replace-1.png)
-
-This will open **Replace values** window where you can specify correct values.
-
-![image](doc-odm-user-guide/images/bulk-replace-2.png)
-
-If the field is controlled by a dictionary then auto-complete suggestions will also appear
-so that you can select a term from a dictionary. Click **Replace in…** button to replace the incorrect metadata values
-with the new terms.
-
-![image](doc-odm-user-guide/images/bulk-replace-3.png)
-
-If there are any filters applied, you can choose to replace values only for the samples
-that match your filter. As a result, values for only the filtered samples will be changed.
-
-Clicking on the Invalid metadata link opens the **Validation Summary** pop-up window where the
-invalid metadata terms will be shown. Click on a term you would like to update, immediately, **Replace values**
-window will open, allowing you to type in the correct value.
-
-There are special terms “Not applicable” and “Not recorded” that can be entered if you wish the value to always pass validation.
-
-As well as editing metadata manually you can also import and validate the metadata. Click on the “Import” icon in
-the upper-right corner and select a local TSV file containing metadata you would like
-to associate with the imported files.
-
-![image](doc-odm-user-guide/images/import-from-spreadsheet.png)
+![6Limitations.png](doc-odm-user-guide/images/6Limitations.png)
+<figcaption>All users can access studies and explore the tabs. However, only members of the curator group can view, make edits and curate data</figcaption>