1. Bento Glossary¶
ALB: Application Load Balancer - used in the Bento infrastructure to provide access to required resources.
AWS: Amazon Web Services.
AWS CLI: Amazon Web Services Command Line Interface.
AWS Credentials: Credentials required to access an AWS account, usually in the form of a private key.
AWS Security Groups: A security group acts as a virtual firewall for your instance to control inbound and outbound traffic. Security groups act at the instance level
AWS cloud platform: a cloud platform offers access to technology services, such as computing power, storage, and databases, on an as-needed basis from a cloud provider like Amazon Web Services (AWS) for the on-demand delivery of IT resources over the Internet with pay-as-you-go pricing.
Aggregate Count: The Program Level Aggregate Count field allows you to display a Program level count for an key data entity in your data sharing platform.
Alt tag: Alt attribute specifies an alternate text for an image, if the image cannot be displayed.
Amazon Web Services: Amazon Web Services (AWS) is Amazon’s comprehensive cloud platform.
Ansible: Ansible is a simple automation language that is used to alter and update the application infrastructure
Application load balancer: An Application Load Balancer acts as the front end of an application and automatically distributes incoming traffic across multiple targets, such as EC2 instances, containers, and IP addresses based on pre-set rules.
Arm: An Arm of a clinical trial is a group or subgroup of participants that receives a specific intervention/treatment, or no intervention, according to the trial’s protocol. Within the Bento Framework an Arm is considered to represent a subgroup of a Program entity type. The Arm Detail Page template can be used to display details of Projects or Studies that belong to a given program.
Arm Detail Page: The Arm Detail Page provides a summary of a Study/Project/Arm of that belongs to a Program that participates in your data sharing platform
Arm Detail Page Table: An optional table on the Arm Detail Page.
BACKEND_SOURCE_FOLDER: In bento-local the file location used to store bento-backend source files.
BUILD_MODE: In Bento-local the mode used to build docker images locally that can then be exported to a repository.
Back End: The database or API layer of an application.
Bastion Host: A special-purpose computer on a network specifically designed and configured to withstand attacks. This instance generally hosts a single application, in the case of Bento this server allows SSH connections and is used for remote login. All other services are removed or limited to reduce the threat to the instance.
Bento Custodian: The Bento Custodian a role, within an organization, that is responsible for the building and maintaining a data sharing platform.
Bento Data Model: The Bento Data Model is an abstract graphical model that organizes data generated by biological research programs and clinical trials. It models key data entities, their properties and their relationships.
Bento Framework: The Bento Framework consists of a set of reusable and customizable software components for the building of data sharing platforms.
Bento-Local Neo4j container: The container in a bento-local environment that will run the Neo4j graph database.
Bento-Local environment: The combination of code, containers, services, and scripts required to run bento on a local machine.
Bento-local scripts: A collection of scripts used to build and run Bento on a local machine.
Billing account: In AWS the account used to bill for resource usage.
Breadcrumb: A breadcrumb navigation or breadcrumbs allows users to know where they are in a hierarchical structure and navigate back to higher-level pages in the hierarchy.
Call To Action: It’s a phrase that’s used to tell the user exactly what action to take and how to take it.
Cart Workflow: The cart workflow is a mechanism for users to generate a manifest for working with case files.
Cart Workflow Notifications: Stats messages that popup whenever there is an addition / deletion to cart selections.
Case Detail Page: The Case Detail Page lists the key attributes of a case or study subject participating in a clinical study or research program in your data sharing platform.
Case Detail Page Header: The title of case detail page.
Configuration Parameters: Configuration Parameters are the settings that are made available to custodian to update UI components.
Cypher Query: A database query that is written in Cypher (query language for Neo4j) and runs on Neo4j database.
Dashboard: The Dashboard provides the end user with several capabilities (a) filter data entities of in interested via faceted search (b) view graphical summaries of data entities and (c) select data entities for further exploration.
Dashboard Sidebar Filters: The Dashboard Sidebar Filters allow an end user to search for data of interest by applying multiple filters, based on faceted classification, of stored data entities.
Dashboard Table: The Dashboard Table can be configured to list key data entities in your data sharing platform along with a list of key data entity attributes. In the Bento reference implementation the Dashboard Table list the cases (or study subjects) in the program.
Dashboard Widgets: Dashboard Widgets provide a graphical summary of the key data entities in your data sharing platform.
Database Module: A term used to collectively describe the Neo4j database and GraphQL-Neo4j plugin.
Dataloader: A set of scripts used to load Bento data into the database.
Docker: Docker is a set of platform as a service (PaaS) products that use OS-level virtualization to deliver software in packages called containers
Docker Compose: Compose is a tool for defining and running multi-container Docker applications.
Docker Container: A container is a standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another.
Docker Desktop: Docker Desktop is an application for MacOS and Windows machines for the building and sharing of containerized applications and microservices.
Docker Engine: Docker Engine is an open source containerization technology for building and containerizing your applications.
EC2: AWS Elastic Cloud Compute.
EC2 instances: An EC2 instance is a virtual server in Amazon’s Elastic Compute Cloud (EC2) for running applications on the Amazon Web Services (AWS) infrastructure.
ECS cluster: An Amazon ECS cluster is a logical grouping of tasks or services.
ETL (Extract, Transform and Load): A data integration process referring to three distinct but interrelated steps (Extract, Transform and Load) that is used to synthesize data from multiple sources to build a dataset.
Elastic Cloud Compute: Amazon Elastic Compute Cloud (Amazon EC2) is a web service that provides secure, resizable compute capacity in the cloud.
External link: External Links are hyperlinks that point at (target) any domain other than the domain the link exists on (source).
External link icon: Icon that is displayed along with an external link.
FE Redux Architecture: Redux is used to maintain application state. ‘FE Redux Architechture’ is the architechture diagram for FE-Redux.
FRONTEND_SOURCE_FOLDER: In bento-local the file location used to store bento-frontend source files.
Favicon: It is a small 16*16 icon displayed next to application title on any browser tab.
File Count widget: The File count graphic displays the number of Program Level file.
Footer Anchor Links: Hyperlinks listed in the footer.
Front End: The web or UI layer of an application.
GCP: Google Cloud Platform.
GET_ARM_DETAIL_DATA_QUERY: GraphQL query to retrive ARM detail attributes information.
GET_CASE_DETAIL_DATA_QUERY: GraphQL query to retrive Case detail attributes information.
GET_DASHBOARD_TABLE_DATA_QUERY: GraphQL query to retrive Case detail attributes information.
GET_GLOBAL_STATS_DATA_QUERY: GraphQL query to retrive StatsBar information.
GET_LANDING_PAGE_DATA_QUERY: GraphQL query to retrive Landing page statistics.
GET_MY_CASES_DATA_QUERY: GraphQL query to retrive Case attributes and files related to a case.
GET_PROGRAM_DETAIL_DATA_QUERY: GraphQL query to retrive Program detail attributes information.
GitHub: A cloud based code repository
Global Footer: The Global Footer appears at the bottom of every page in a Bento-based application. The Global Footer may be used to display an organization logo and additional links, that may be helpful for the end user, such as documentation, support email and social media platforms.
Global Header: The Global header appears at the top of all Bento-based applications. It displays a platform-specific logo and image.
Global Header Image: The image displayed on home page (below the navBar).
Global Header Logo: The logo displayed on header on the left hand side.
Global Navigation Bar: Navigation Bar allows users to quickly visit any section within the site, dissplayed below header
Global UI Elements: Global UI elements are displayed on every page of a Bento application. These are the (a) Web Browser tab, (b) Global Footer, (c) Navigation Bar and (d) Global Footer. The “Stats” bar, that displays the high-level statistics is a semi-global element as it is displayed only in the Program Listing, Program Detail, Dashboard and Case Detail pages.
GraphQL API: The API (Application Programming Interface) used to handle GraphQL formatted queries.
GraphQL API framework: The framework used to create the backend interface to handle GraphQL formatted queries.
Header: A header is the top margin of each page which includes a logo, image.
Internal Link: Hyperlinks that point to content within the same domain.
Jenkins Server: An extensible open source automation server.
Landing Page Stats Bar: The Landing Page Stats Bar provides the end user with a high level view of the volume and diversity of your stored data, by providing the counts of up to five major data entity types.
Landing Page Tiles: The four Landing Page Tiles provide additional visual and textual description of the mission and capabilities of your data sharing platform.
Landing page: A page which is delivered to browser by navigating to a dns of website. It is also called as home page.
Local Machine: The user’s local computer.
NAT: Network address translation (NAT) is a method of remapping an IP address space into another by modifying network address information in the IP header of packets while they are in transit across a traffic routing device.
NEO4J_PASS: In bento-local a variable used to store the Neo4j password.
NEO4J_USER: In bento-local a variable used to store the Neo4j user name.
Neo4J: A native graph database, built from the ground up to leverage not only data but also data relationships.
Neo4J Database: The specific datastore used by Neo4j when accessing and writing data.
Neo4j: A native graph database built to store data and data relationships.
Neo4j container: In Bento-local the docker container used to store the database.
Organization Logo: The logo displayed on footer on the left hand side.
Page Title: The title for a webpage usually displayed on the top.
Private subnet: In AWS a subnet with no internet access.
Program: A broad framework of goals to be achieved. The Bento Data Model includes “Program” as a key entity type.
Program Detail Left Hand Panel: The Left and Right Hand Panels allow for the display of case attributes as label:value pairs with a set of subsections; related data attributes can be grouped together in a section.
Program Detail Page: A program detail page shall contain case attributes labels, description and aslo associated files and associated samples.
Program Detail Page Table: A configurable table on program detail page.
Project: Any specifically defined piece of work that is undertaken or attempted to meet a single requirement. The Bento Data Model includes a “Project” entity type as a subunit of the “Program” entity type.
REST API: An acronym for REpresentational State Transfer. It is an architectural style for distributed hypermedia systems and was first presented by Roy Fielding in 2000 in his famous dissertation.
Redux: With Redux, the state of application is kept in a store, and each component can access any state that it needs from this store.
S3: AWS Simple Storage Service.
Static Pages: The pages that are listed under ‘ABOUT’ navBar item.
Stats Bar: Navigation Bar allows users to identify stistics of database, displayed below navBar.
Study: A detailed examination, analysis, or critical inspection of a subject designed to discover facts about it. The Bento Data Model includes a “Study” entity type as a subunit of the “Program” entity type.
Tab Title: Defines the document’s title that is shown in a browser’s title bar or a page’s tab.
Terraform: Terraform allows infrastructure to be expressed as code in a simple, human readable language.
The Case Detail Page Table: A configurable table on case detail page.
The Virtual DOM: The virtual DOM (VDOM) is a programming concept where an ideal, or “virtual”, representation of a UI is kept in memory and synced with the “real” DOM by a library such as ReactDOM.
VPC: Virtual Private Cloud.
VPC subnets: In AWS a VPC spans all of the Availability Zones in a Region. After creating a VPC, you can add one or more subnets in each Availability Zone.
Virtual Machines: A virtual machine (VM) is an emulation of a computer system. Virtual machines are based on computer architectures and provide the functionality of a physical computer.
Web Application Containers: Docker containers containing the required code and components to run a Web application.
Web Browser tab: Web browser tabs allow you to have multiple web pages open at the same time. In bento, we allow custodian to configure tab title, favicon that displays on browser tab.
ansible-playbook: A configuration and multinode deployment system for Ansible.
vars.tfvars file: A file used by Terraform to populate variables.