This is a software architecture document for the Ontology Management (ONT) cell. It identifies and explains important architectural elements. This document will serve the needs of stake holders to understand system concepts and give a brief summary of the use of the ONT message format.
Overview

The Ontology Management cell (ONT) is an i2b2 Hive core cell. This cell manages i2b2 vocabulary definitions and contains concepts and information about relationships between concepts for the entire hive. It is accessed by other cells to give semantic meaning to data.
Vocabularies in the ONT cell are organized in hierarchical structures that represent the relationships between terms. The top levels in the hierarchy are called the "parents" or "roots", with the lower levels being their "children". Elements occurring on the same level are known as "siblings". A level in a hierarchy is sometimes referred to as a "node", and a group of related data is called a "category".
A category is defined as a set of data for which there is a common rule or rules for querying against the Clinical Research Chart (CRC). A category is usually represented visually as a table of terms. An example of a category is the "Diagnoses" category shown in the diagram below, which consists of a table of diagnostic terms and uses a single rule to build all diagnostic queries.


Vocabularies in the ONT cell may originate as code from different sources. The ONT cell distinguishes these codes from one another by pre-pending a unique prefix to each code. Each distinct vocabulary and their associated codes are called a scheme.
In Release 1.6, we added modifiers to the ONT cell vocabulary. A modifier may be used to extend the meaning of a concept. An example of modifiers is shown below: the concept 'Smoker' has three modifiers that may be applied to it: 'Heavy', 'Light', and 'Moderate'.


ONT Definitions, Acronyms and Abbreviations

Vocabulary Data Object (VDO)

This object holds vocabulary definitions and information about the relationships between concepts.
Scheme

Each distinct vocabulary and their associated codes is called a scheme. A distinction is made between codes from different sources by pre-pending a unique prefix to each code.

Roles

When and how data is presented to a user is based on their user roles, which are specified in the PM Cell. Each user will have at least two roles per user_id and product_id combination. These two roles can be further defined as a Data Protection role and a Hive Management role.
The data protection role establishes the detail of data the user can see while the hive managment role defines their level of functionality the user has in a project.The following tables summarize the roles in a hierarchical order of least to most access.

• Further details regarding roles can be found in the PM_Design_Document.

Security

Users may access ONT with a user-id and password combination, which is authorized through the Project Management Cell. The implementation detail of Project Management Cell is considered out-of scope to this document.
Scope of the system

Some other participants, currently outside the scope of ONT are:

• Project Management Cell

Assumptions/Constraints

The Ontology metadata database shall not contain protected health information.
Technical Platform

The product is designed to run on the following platform:

• Java 2 Standard Edition 7.0
• Oracle Server 10g/11g database
• SQL Server 2005/2008
• Xerces2 XML parser
• Jboss Application server version 7.1.1
• Spring Web Framework 2.0
• Axis2 1.6.2 web service (SOAP / REST)

Transaction

The ONT system is transactional, leveraging the transaction management model of the J2EE platform.
Security

The application must implement basic security behaviors:

• Authentication: Authenticate using at least a user name and a password
• Authorization: User may only access categories that they are allowed to by role
• Confidentiality: Sensitive data must be encrypted
• Data integrity : Data sent across the network cannot be modified by a tier
• Auditing: In the later releases we may implement logging of sensitive actions

Persistence

This application utilizes JDBC calls to retrieve persisted data.
Reliability/Availability

• The Reliability/Availability will be addressed through the J2EE platform
• Targeted availability is 16/7: 16 hours a day, 7 days a week
• The time left (8 hours) is reserved for any maintenance activities

Performance

The user authentication with project management cell must be under 1 second.
Use Case

The diagram below depicts common use cases a user may perform with the ONT cell.



Operations

The ONT service is designed as a collection of operations or use cases:

Architecture Description

This section provides a description of the architecture as multiple views. Each view conveys the different attributes of the architecture.

1. Components and Connector View
2. Client-Server Style

1. Module View
2. Decomposition Style
3. Uses Style

1. Data View
2. Deployment View

Components and Connector View

A Component and Connector view represents the runtime instances and the protocols of connection between the instances. The connectors represent the properties such as concurrency, protocols and information flows. The diagram shown in the Primary Presentation section represents the Component and Connector view for the multi-user installation. As seen in the diagram, component instances are shown in more detail with specific connectors drawn in different notations.
Client-Server Style

The ONT system is represented using the components and connector client-server view.






Primary Presentation

Metadatai2b2
WorkbenchOntology
Management
ServerProject
Management
ServerREST/SOAPREST/SOAPJDBC*Server*Client

3.1.1.2 Element Catalog

Design Rationale, Constraints

N-tier Architecture
The client-server style depicts an n-tier architecture that separates the presentation layer from the business logic and data access layer.

Module View Type

The module view shows how the system is decomposed into implementation units and how the functionality is allocated to these units. The layers show how modules are encapsulated and structured. The layers represent the "allowed-to-use" relation.
The following sections describe the module view using Decomposition and Uses Styles.
Decomposition Style

The Decomposition style presents system functionality in terms of manageable work pieces. It identifies modules and breaks them down into sub-modules and so on, until a desired level of granularity is achieved.
Primary Presentation

Element Catalog

Context Diagram

Operation ManagerOntology Management Server


Uses Style

The Uses style shows the relationships between modules and sub-modules. This view is very helpful for implementing, integrating and testing the system.
Primary Presentation

Element Catalog