Data Page

The Data page is the hub for each project. Collections, datasets, and raw data files are accessible here. The data organization system implements familiar concepts of paths and folders to organize and access data in Orion. A user can view both their own projects and data for their organization.

The Programming Guide has additional technical details about data handling in Orion.

Organizing and Sharing Data in Folders

Users can organize the data according to the way they would like to share data among team members in a project. In addition, there are controlled data sharing capabilities among members in the project. To achieve these objectives, the following main folders are available to users.

My Data

The data in this location are private and only accessible by the user. However, these data still can be shared by moving the data to a Shared Space workspace. Data are put in My Data unless you specify otherwise in your upload.

Only you can see the data until you share it to the Team or Shared folders.

Team Data

The data in this location are available to all project members.

Shared Spaces

The data in this location are available to the project members selected by the user.

../_images/data_page.png — **Figure 1.** The Data page in **Orion**.

Orion provides automatic intraspection of files: hovering gives a depiction of the first structure if the file contains small molecules, or a protein schematic if amino acids are present. Selecting one or more datasets creates an active dataset. Active datasets are carried forward to any feature domain (for example, moving to the Analyze page automatically populates the spreadsheet). The Data page also shows which filters are currently applied to the active data.

**Data Page Layout**
Name	Description
Add Data button	Allows users to add data by uploading files, sketching, or importing biomolecules.
Search	Allows users to search for collections, datasets, or files by name or tag.
Show drop-down	Allows users to show any assortment of collections, datasets, and files.
Sort by drop-down	Allows users sort by one of several options.
Dataset Table	Lists project datasets, sorted as specified by the ‘Sort by:’ drop-down.
Trash Can	Repository for deleted datasets. To restore the dataset, click on the Trash Can, select the dataset, and drag it to the appropriate folder.

Tile View

Another form of intraspection is available for small molecule files: the tile view. Activate the tile view by clicking the icon to the left of a dataset name. On completion of the browsing of structures, click “Cancel,” and you will be returned to the originating page.

../_images/cardview.png — **Figure 2.** The tile view for a file of structures.

The tile view displays a panel list of structures in 2D or 3D, with associated properties. It can be configured to display single structures, a side-by-side view, a grid compare view, or a grid view. Entries can be sorted by properties selected from all those available within the dataset. The tile view is designed for fast traversal; selected structures can form the basis of a selected set on leaving the page.

Manipulating Data

Data can be uploaded, downloaded, moved, and otherwise manipulated within the Data page in Orion. These features are described below.

Searching for Data

You can search for datasets by entering a tag or resource name in the search bar. Select the main folder or space you would like to search. Next, enter the tag or resource name and click on that name. The results will appear at the bottom of the page. In addition, you will be able to see the path where this data can be found.

Uploading Data

You can specify a path when uploading a file into Orion. To specify a path, select the folder or subfolders as applicable. Alternatively, you can go up a directory by clicking on the up arrow or using the backspace key. Also, you can create a new subfolder by entering the name and then clicking the “Create a new folder” button.

CXSMILES Data

Data can be uploaded in CXSMILES format. (Data/My Data/+Add Data/Upload….)

Downloading and Exporting Data

You can download data, and it will be converted to a canonical format if necessary.

Select dataset > More Actions > Export.
In the Export pop-up, choose your preferred file format, then click Export.
In the notification panel, you can check the status of your exports.
After download, optionally move or delete the exported file from My Data Exports.

Moving Data Between Projects

Data (datasets, files and collections) can be moved between projects, folders or subfolders. To do this, select the data you would like to move and click the bi-directional line icon or the ellipsis (...) icon and select Move. Then, choose the destination or path, and click the Move button. The selected data will be moved to the specified destination or path.

Note

Multiple datasets can be moved at once.

Deleting Data

To delete data, first select the data you want to delete by clicking on the square box on the left side to the folder or subfolder name. Next, click the icon on the far right or in the top menu. Multiple data can be selected and deleted at once. These data will be moved to the Trash space. The items in the trash will be automatically deleted after 30 days.

Preserving Data of a Removed User

Customers can open a support request to remove a user from an organization, which transfers ownership of that user’s data to project owners or an organization administrator.

Necessary Actions for Accounts on Pre-2021 Versions of Orion

If you have a pre-2021 Orion account, you will need to take some action on the shared data from previous Orion versions.

Decide how to organize the data.
Move all previously shared items into the appropriate folders.
Assign collections to a project.

AWS Representation

Datasets are stored within an AWS Postgres database. Files and collections are stored on AWS S3. If datasets, files, or collections are deleted, they are sent to the Trash Can. Anything in the Trash Can is deleted automatically after 30 days. In addition, users can delete items in the Trash Can immediately by selecting the “Delete permanently” option. Please consult the Orion Admin Guide for further details.

Data Page Video Tutorial

For more information on the use of the project data facilities, see the tutorial video.

Subfolders

To create a new subfolder, first select the place (My Data, Team Data or Shared Spaces) where you want to create a new subfolder. Then click on the icon next to the path (example: My Data). In the pop-up window, enter the folder name and click “OK.” A new subfolder will be created with the specified name in the selected path.

You can create a new folder or subfolder in the same window you use to upload data or when starting a floe run. To do this, select the path you want. A bar will appear to select a subfolder or to create a new folder. Type a name to create a new folder, and the new folder or subfolder will show up on the path specified.

Favorite Subfolders

To quickly access a subfolder, you can mark it as a favorite by clicking on the star next to the folder, and it will be added to the Favorite Folders area in the left side column.

Deleting Subfolders

To delete a subfolder, select the subfolder you want to delete and click on the icon. The subfolder and all the contents in this subfolder will be moved to the Trash space. The items in the trash will be automatically deleted after 30 days.

Moving a Subfolder

A subfolder can be moved to another path or location. To do this, select the folder you would like to move, and click either the bi-directional line icon on top or the ellipsis icon, and select Move. Then, choose the destination or path and click the Move button. The subfolder (and its contents) will be moved to the specified destination or path.

Note

Multiple subfolders can be moved at once.

Shared Spaces

To share data, use the Shared Spaces main folder.

You can start by creating a workspace in Shared Spaces. Click on the + icon next to the path. A pop-up window named Workspace Name will appear. Enter the name of the workspace you want to create and click OK.

The new subfolder will appear in Shared Spaces. If you click on this workspace, then you will have the option to add members with whom you want to share the data.

Click on the icon and then enter the name of the project member you want to add. In this window, you will have the option to set the permissions (write, delete) you want for that user to have. All the data in this workspace will be shared with the selected project members.

Alternatively, if you would like all project members to have access to the data, save the data in the Team Data folder.

The workspaces in Shared Spaces resemble folders, but they are actually file systems in their own right. The user interface enforces the differences between workspaces and folders.

Note

With folders, access to data by others is determined by the folder you choose to use. For example, items in the Team Data folder are accessible to all members of the project team. For the workspaces within Shared Spaces, you can define a subset of users who have access to the workspace and its data. You can pick the users by use of the icon.

Move, Drag-and-Drop: The user interface does not show these actions for workspaces in the list of workspaces because they cannot be performed.
Create and Rename and Delete: You can perform these actions on workspaces.
Inside a workspace: Folders created within a workspace behave as other folders do.

../_images/data_workspace_list.png — **Figure 4.** The list of workspaces in Shared Data.

../_images/data_workspace_contents.png — **Figure 5.** The contents of a workspace.

Collection Metadata

Some collections feature an information icon () that displays pregenerated metadata about the collection. The information may be helpful in working with collections, because you can see the metadata immediately, without having to run a floe.

../_images/data_page_metadata.png — **Figure 3.** Collection metadata.

Discussion Boards

You often need not only to share data with team members but also to discuss the results with them.

Discussion boards are accessed by the “chat” icon () on the Data page. If you select the icon, you get a display on the right side of the screen that will be familiar from other chat experiences you have used.

You can share links and images along with text comments. A snapshot from the Analyze or 3D Modeling pages can be included on a discussion board. Discussions are preserved so you can revisit them. The discussion board autosaves users’ edits.

For an introduction, see this training video: Introducing Discussion Boards

You can see further information in this training video: Using Discussion Boards.

Organization Data Page

../_images/data_page_orgdata.png — **Figure 6.** The data available to an organization can hold many projects and collections, as shown in this folder within the Organization Data files.

The Organization Data space allows for admin users to share datasets and collections with the entire organization.

OpenEye Data Subfolder

The OpenEye folder contains data curated and provided by Cadence/OpenEye Molecular Sciences for FastROCS and Gigadock searches.

Policy for Curation of Databases

OpenEye, Cadence Molecular Sciences is dedicated to offering high-quality vendor databases to enhance virtual screening for our customers. Vendor data provided by OpenEye for searches in Orion is regularly updated as new versions become available from vendors. If a particular vendor collection is not currently available on Orion, please let us know, and we will assess the feasibility of adding the library to our platform.

When new versions of existing FastROCS and Gigadock collections become available in the Organization Data/OpenEye Data directory, the following process will be implemented:

The new version will replace the previous version of the collection in the Organization Data/OpenEye Data directory.
The previous version of the collection will be moved to the Deprecated subfolder.
The version of the collection that had been stored in the Deprecated subfolder will be permanently deleted and will no longer be available.

To ensure that our customers have access to the most current vendor data, and to optimize vendor fulfillment, OpenEye reserves the right to permanently delete any vendor data older than two years.