From ca0ec3e3245ec531614b60a6698360d707b82454 Mon Sep 17 00:00:00 2001 From: Henry Luetcke Date: Wed, 26 Jun 2024 14:04:14 +0200 Subject: [PATCH] add notes for CEDAR --- vault/pid.cedar.md | 91 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 vault/pid.cedar.md diff --git a/vault/pid.cedar.md b/vault/pid.cedar.md new file mode 100644 index 00000000000..00868df4485 --- /dev/null +++ b/vault/pid.cedar.md @@ -0,0 +1,91 @@ +--- +id: 6nza83uq5nwts16z6oh6egu +title: Cedar +desc: '' +updated: 1719403435555 +created: 1719392040347 +--- + +# CEDAR: The Metadata Center + +## Links +https://metadatacenter.org/ + +https://github.com/metadatacenter + +## Summary +- Focuses on enhancing metadata creation in scientific research. +- Supports FAIR data principles. +- Provides tools like the CEDAR Workbench for creating and managing metadata. +- Offers templates and controlled vocabularies to help scientists submit well-annotated datasets. +- Aims to improve data submission to repositories and enhance data accessibility for analysis. + +## Activity log - ETH SIS + +### First steps +- Logged Into CEDAR +- Watched CEDAR video tutorials +- Joined CEDAR Mailing List +- CEDAR website: https://metadatacenter.org/#about +- CEDAR User Manual: https://metadatacenter.readthedocs.io/en/latest/user-overview/ +- Orientation for the CEDAR Workbench: https://more.metadatacenter.org/tools-training/orientation + +### CEDAR Workbench Usage tutorial +- How to search for an available template +- How to populate (use) a template +- How to edit a template + +### Using CEDAR +1. Create an Account and Log In + - Sign Up: Go to the CEDAR website and sign up for an account. + - Log In: Once your account is created, log in with your credentials. +2. Familiarize Yourself with the Interface + - Dashboard: The dashboard is your central hub for accessing different features. Take some time to explore the layout and available options. +3. Create Metadata Templates + - Navigate to Templates: Go to the “Templates” section from the dashboard. + - Create New Template: Click on the option to create a new template. + - Design Template: Use the drag-and-drop interface to add fields, such as text boxes, drop-down lists, and checkboxes. Customize these fields to match your metadata requirements. + - Incorporate Ontologies: Integrate relevant ontologies and controlled vocabularies to ensure standardization. You can search and import these from within CEDAR. + - Save Template: Once you have designed your template, save it for future use. +4. Annotate Metadata Using Templates + - Select Template: Choose the appropriate template you created for annotating your data. + - Fill in Metadata: Input your metadata values into the fields defined in the template. Make sure to follow any guidelines or standards applicable to your data. + - Validate Metadata: Use the built-in validation tools to check for completeness and compliance with the template rules. +5. Collaborate and Share + - Share Templates and Metadata: CEDAR allows you to share your templates and annotated metadata with other users or groups. Use the sharing options to grant access to collaborators. + - Collaborative Editing: Multiple users can work on the same metadata template or annotation, facilitating teamwork and consistency. +6. Manage and Reuse Metadata + - Metadata Repository: Store and manage your metadata in the CEDAR repository. + - Search and Retrieve: Use the search functionality to find and retrieve specific metadata records or templates. + - Export Metadata: Export your metadata in various formats for use in other systems or for publication. +7. Integrate with Other Systems + - APIs: Utilize CEDAR’s APIs to integrate metadata management with other data systems and workflows in your organization. + - Interoperability: Ensure that your metadata complies with standards to enable interoperability with other tools and platforms. +8. Ensure Data Security and Privacy + - Access Controls: Set up appropriate access controls to protect your metadata. Define roles and permissions to manage who can view or edit your templates and metadata. + - Regular Backups: Ensure that your metadata is regularly backed up to prevent data loss. + +#### Populating templates +**Populating a template** in the CEDAR tool refers to the process of filling out a pre-defined data template with specific information. CEDAR is designed to help researchers and scientists create, share, and reuse structured data templates for metadata annotation. Here's a step-by-step overview of what it means to populate a template in CEDAR: + +1. Template Selection: Choose or create a data template that fits the data you need to annotate. Templates in CEDAR are structured forms that define the fields and types of data required. + +2. Access the Template: Open the selected template within the CEDAR interface. The template will have various fields and sections that need to be filled out. + +3. Fill Out the Fields: Enter the relevant information into each field of the template. Fields might include text boxes, drop-down menus, checkboxes, date pickers, and more, depending on how the template is designed. + +4. Validation: Ensure that the data entered meets the specified requirements and constraints of each field. CEDAR may provide validation checks to ensure the data conforms to expected formats or values. + +5. Save or Submit: Once all required fields are filled and validated, save or submit the populated template. This might involve saving it to a database, exporting it in a particular format, or sharing it with other users or systems. + +6. Reuse and Share: Populated templates can be reused for similar data entries or shared with other researchers or systems that need access to the structured data. + +### CEDAR Test Project and Test Meta Data Template +**Created Test Project and Test Meta Data Template in the Personal Space on the CEDAR Workbench Platform** +- Registered a new Project in My Workspace +- Found a Public Meta Data Template to be used in the project +- Registered a new Meta Data Field and Element +- Extended the Meta Data Template with newly created Field and Element +- Populated (used) the Template to register a new entity in the project + +Next Action: explore how to organize/represent a scientific project \ No newline at end of file