Merge pull request ITISFoundation#21 from KZzizzle/classifier_tag

Add Classifiers vs Tags

_sidebar.md

@@ -11,7 +11,8 @@
   * [Data](/docs/platform_introduction/core_elements/Data.md)
   * [Services](/docs/platform_introduction/core_elements/services.md)
   * [User Preferences](/docs/platform_introduction/main_window_and_navigation/user_setup/profile.md)
-  * [Security & DAT-Core](/docs/platform_introduction/main_window_and_navigation/user_setup/security_details.md)
+  * [Security & Tokens](/docs/platform_introduction/main_window_and_navigation/user_setup/security_details.md)
+  * [Annotations](/docs/platform_introduction/annotations.md)
 * Quick Start Guide
   * [Creating a Study](/docs/study_setup/create_study.md)
   * [Loading Data](/docs/study_setup/loading_data/loading_data.md)
@@ -22,7 +23,6 @@
   * [Visualization](/docs/study_setup/postpro_viewer_types.md)
   * [Retrieving Files](/docs/study_setup/loading_data/retrieving_files.md)
   * [Sharing Studies](/docs/study_setup/sharestudy.md)
-  * [Filtering](/docs/platform_introduction/main_window_and_navigation/filtering.md)
 * Tutorials
   * [Cardiac Tissue Models](/docs/tutorials/uc_davis.md)
   * [2D Visualization](/docs/tutorials/2d_plot.md)

docs/platform_introduction/annotations.md

@@ -0,0 +1,20 @@
+# Annotations
+One important aspect of *osparc* is its adherence to [**FAIR**](https://www.nature.com/articles/sdata201618) (**F**indable **A**ccessible **I**nteroperable **R**eusable) data and code-based artifacts (e.g. models, simulations, data processing modules). To that end, we enable several different features to promote FAIR principles. 
+
+## Classifiers
+Classifiers are annotations that can be attached to either **Studies** or **Services** in *osparc*. These classifiers are based on curated resource identifiers, defined in greater detail at https://scicrunch.org/resources. Adding classifiers to your published studies allows other users to find your work and identify other possibly compatible submissions. Each **Classifier** is a resource with unique identifying number. 
+
+To add a **Classifier** to your study, follow the steps below,
+1. Navigate to the **Studies** tab of the **Dashboard**
+2. Click the  3-dot icon on the upper right hand corner of your study card
+3. Click the **Classifiers** option in the popup menu.
+4. A new menu will appear with a checklist of previously-used classifiers. If the classifier you would like to assign is on this list, skip to step **8**. 
+![classifier](https://user-images.githubusercontent.com/33152403/102335522-54792c80-3f90-11eb-92f8-8ff0787ba46b.png)
+5. If your desired classifier is not on the pre-populated list, find its RRID on [SciCrunch](https://scicrunch.org/resources) by clicking the ```RRID``` link.
+6. Enter your desired RRID into the ```RRID:    ``` text field and then click ```Add Classifier```
+7. If your desired RRID exists on the SciCrunch-connected databases, it will be validated and added to the list of classifiers.
+8. To assign one or more of these classifiers, simply click the empty checkboxes next to the appropriate classifiers (click again to deselect).
+9. Click ```Save``` on the lower right hand side of the window to  assign the classifier(s). 
+
+## Classifiers vs. Tags
+Classifiers and [Tags](/docs/platform_introduction/main_window_and_navigation/user_setup/profile.md) are two different Ways to annotate studies. However, classifiers come from a *curated* set of resources and are common to all SPARC researchers. when you annotate a study with a classifier and publish or share it, that classifier assignment is persistent for other users. On the other hand, tags are *specific to your account* - publishing a study with one of your tags will not make it visible for anyone else. Tags are meant to be used to organize studies on your account. They are also colorful so you can think of them as sticky notes!

docs/platform_introduction/core_elements/dashboard.md

@@ -11,7 +11,13 @@ Within the Dashboard a number of important sections and elements can be are high
    This button allows you to return to the Dashboard and Overview at any time from anywhere within the platform.
 
 2. **Study Filter and Search** <br/>
-   This tool allows you to filter studies (either your own or submitted by others) by tags that you have applied to your studies.
+   This tool allows you to filter studies, templates, and services (either your own or submitted by others) on the **Studies** and **Discover** tabs. You can filter by:
+      * string, name
+      * keywords
+      * [tags](/docs/platform_introduction/main_window_and_navigation/user_setup/profile.md)
+      * classifiers
+
+   The filtered items are then either highlighted in the flowchart, shown/hidden within services catalogues, etc. 
 
 3. **Dashboard Menu** <br/>
    The menu tabs give you quick access to a set of core elements of the platform, namely the Studies, the Services and the [Data](/docs/platform_introduction/core_elements/Data.md).

docs/platform_introduction/core_elements/studies.md

@@ -11,8 +11,8 @@ There are a number of operations that are specific to studies, accessible by the
 These options are:
 1. **Select:** allows you to select this study and/or others, primarily useful for deletion
 2. **More Info:** allows you to view and edit metadata for a study including its title, description and icon
-3. **Classifiers** allows you to assign classifiers (descriptors) for a study which can then be used for search and filtering using the filter tool on the [Dashboard](docs/platform_introduction/core_elements/dashboard.md)
-4. **Permissions** allows you view who the study is shared with and to add collaborators to the study
+3. **Classifiers** allows you to assign classifiers (curated descriptors) for a study which can then be used for search and filtering using the filter tool on the [Dashboard](docs/platform_introduction/core_elements/dashboard.md). See [Annotations](/docs/platform_introduction/annotations.md) for more details. 
+4. **Permissions** allows you view who the study is shared with and to add collaborators to the study. See [Sharing Studies](/docs/study_setup/sharestudy.md) for more details.
 5. **Publish as Template** if selected, you will be allowed to create a copy of the study in its current state which will appear as a template study in the [Discover](docs/platform_introduction/core_elements/Discover.md) tab for users you share the template with.* 
 6. **Delete** as you may guess, this will delete the particular study, with a confirmation popup
 

docs/platform_introduction/main_window_and_navigation/user_setup/profile.md

@@ -26,7 +26,7 @@ Entering the preferences dialog, a separate window pops up which allows the user
   ![prefs](../../../../_media/preference_exp.png) <br/>
 
 * __Tags__ <br/>
-  Here you may define custom tags, or labels, for your studies. Once you have created the tags, you may assign them by editing the metadata of a study. To do this, follow the steps below:
+  Here you may define custom tags, or labels, for your studies, that are only visible to you. Tagging a study and then sharing it does provide the same tag for those you have shared it with. Once you have created the tags, you may assign them by editing the metadata of a study. To do this, follow the steps below:
   1. Navigate to the **Studies** tab of the **Dashboard**
   2. Choose the study options (3-dot button) on the study you would like to assign a tag to
   3. choose **More Info** option

docs/platform_introduction/main_window_and_navigation/user_setup/security_details.md

@@ -1,4 +1,4 @@
-# Security & DAT-Core Access
+# Security & Tokens
 
 In this section and as an addition to the last section on user preferences, we'd like to particularly highlight how the user can specify access tokens for the DAT-Core/Blackfynn platform.