Base
Introduction to Base
Base is a genomics data aggregation and knowledge management solution suite. It is a secure and scalable integrated genomics data analysis solution which provides Information management and knowledge mining. Users are able to analyze, aggregate and query data for new insights that can inform and improve diagnostic assay development, clinical trials, patient testing and patient care. For this, all clinically relevant data generated from routine clinical testing needs to be extracted and clinical questions need to be asked across all data and information sources. As a large data store, Base provides a secure and compliant environment to accumulate data, allowing for efficient exploration of the aggregated data. This data consists of test results, patient data, metadata, reference data, consent and QC data.
Base User Personas and Use Cases
Base can be used by different user personas supporting different use cases:
Clinical and Academic Researchers:
Big data storage solution housing all aggregated sample test outcomes
Analyze information by way of a convenient query formalism
Look for signals in combined phenotypic and genotypic data
Analyze QC patterns over large cohorts of patients
Securely share (sub)sets of data with other scientists
Generate reports and analyze trends in a straightforward and simple manner.
Bioinformaticians:
Access, consult, audit, and query all relevant data and QC information for tests run
All accumulated data and accessible pipelines can be used to investigate and improve bioinformatics for clinical analysis
Metadata is captured via automatic pipeline version tracking, including information on individual tools and/or reference files used during processing for each sample analyzed, information on the duration of the pipeline, the execution path of the different analytical steps, or in case of failure, exit codes can be warehoused.
Product Developers and Service Providers:
Better understand the efficiency of kits and tests
Analyze usage, understand QC data trends, improve products
Store and aggregate business intelligence data such as lab identification, consumption patterns and frequency, as well as allow renderings of test result outcome trends and much more.
Base Action Possibilities
Data Warehouse Creation: Build a relational database for your Project in which desired data sets can be selected and aggregated. Typical data sets include pipeline output metrics and other suitable data files generated by the ICA platform which can be complemented by additional public (or privately built) databases.
Report and Export: Once created, a data warehouse can be mined using standard database query instructions. All Base data is stored in a structured and easily accessible way. An interface allows for the selection of specific datasets and conditional reporting. All queries can be stored, shared, and re-used in the future. This type of standard functionality supports most expected basic mining operations, such as variant frequency aggregation. All result sets can be downloaded or exported in various standard data formats for integration in other reporting or analytical applications.
Detect Signals and Patterns: extensive and detailed selection of subsets of patients or samples adhering to any imaginable set of conditions is possible. Users can, for example, group and list subjects based on a combination of (several) specific genetic variants in combination with patient characteristics such as therapeutic (outcome) information. The built-in integration with public datasets allows users to retrieve all relevant publications, or clinically significant information for a single individual or a group of samples with a specific variant. Virtually any possible combination of stored sample and patient information allow for detecting signals and patterns by a simple single query on the big data set.
Profile/Cluster patients: use and re-analyze patient cohort information based on specific sample or individual characteristics. For instance, they might want to run a next agile iteration of clinical trials with only patients that respond. Through integrated and structured consent information allowing for time-boxed use, combined with the capability to group subjects by the use of a simple query, patients can be stratified and combined to export all relevant individuals with their genotypic and phenotypic information to be used for further research.
Share your data: Data sharing is subject to strict ethical and regulatory requirements. Base provides built-in functionality to securely share (sub)sets of your aggregated data with third parties. All data access can be monitored and audited, in this way Base data can be shared with people in and outside of an organization in a compliant and controlled fashion.
Access
Base is a module that can be found in a project. It is shown in the menu bar of the project.
❗️Before users can access Base:
On the domain level, Base needs to be included in the subscription
On the project level, the project owner needs to enable Base
On the user level, the project administrator needs to enable workgroups to access the Base pages
Permission to Enable Base
The access to activate the Base module is controlled based upon the chosen subscription (full and premium subscriptions give access to Base) when registering the account. This will all happen automatically after the first user logs into the system for that account. So from the moment the account is up and running, the Base module will also be ready to be enabled.
Enable Base
When a user has created a project, they can go to the Base pages and click the Enable button. From that moment on, every user who has the proper permissions has access to the Base module in that project.
Only the project owner can enable Illumina Connected Analytics Base. Make sure that your subscription for the domain includes Base.
Navigate to Projects > your_project > Base > Tables / Query / Schedule.
Select Enable
Access Base pages
Access to the projects and all modules located within the project is provided via the Team page within the project.
Activity
The status and history of Base activities and jobs are shown on the Activity page.
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