Open Data Manager user guide¶
Welcome to the Open Data Manager (ODM) User Guide.
File Management vs. Data Management¶
Our ODM workspace enhances productivity across various data-related projects in the Life Sciences, from Agritech to Genomics. With such a broad scope, it’s easy to get confused about the specifics of Data Management and File Management. Although they may seem similar, they have fundamental differences that are crucial to understand.
File Management is prevalent across many industries, but when it comes to scientific data, it is often insufficient. Why? Check out our detailed article here.
Important
Data Management has specific requirements, which are explained in this short introductory video: Familiarize yourself with the basics of ODM.
With an understanding of Data Management under the belt, the next question is onboarding. When considering what ODM can do for you; context is key. What kind of user are you? An admin, a data contributor, a data consumer? All three? We have onboarding guides for each flow below.
User Admins¶
User management and administration can be grueling work when attempting without the proper software to help you on the path! Find out how ODM makes administration easy below.
In this video you will find out:
- Who are the two user classes: contributors and consumers
- How to create users and assign permissions
- How to create user groups and assign curator groups
- How to enable sharing and editing
Guide for data contributors¶
ODM’s main purpose for your contributors is to get them straight into all of the data available at your organization via a single access point. Data however, can still come from different sources; be it outside the organization or from within, generated by different teams and even through legacy data!
To make your data findable, you need to pass it through a curation (aka harmonization) procedure by applying defined guidelines to your datasets in order to make them easy for anyone with access to reach at any time!
Still unsure? Learn more by watching our videos below.
- What a data template is
- How to work with dictionaries and ontologies
- How to create a Study and upload your data
- How to curate your data
Guide for data consumers¶
Those who are data all-consuming have one goal in mind when using ODM - generating that key insight!
Want to know more? Learn more by watching our videos below.
In Depth User Guide Articles¶
- Start
- User setup
- Create new study
- Import Data in ODM
- Import Data Using API
- Import Data Using Python Script
- Exporting Data
- Cross-reference Mapping
- What can I import?
- Importing a cross-reference mapping
- Querying cross-reference mappings
- Retrieving the mapping for a given gene in a study
- Performing OMICS queries using gene/transcript IDs
- Checking a mapping is available for a given expression data file
- Checking which expression data files are linked to a given mapping file
- Updating a mapping file
- Removing a mapping file
- Who can do what?
- Study Browser
- Metadata Editor
- Template Editor
- Curator Guide
- Metadata Versioning
- Sharing Studies
- Getting a Genestack API token
- Supported File Formats
- Working with Single Cell Data