Informatics for Scientific Data Bio-informatics and Medical Informatics Week 9 Lecture notes INF 380E: Perspectives on Information

Medical Informatics Hersh: – the field concerned with the management and use of information in health and medicine

Primary stakeholders in medical informatics patients clinicians payers governments

Types of information patient-specific – information generated and used in the care of patients knowledge-based – the information that comprises the scientific basis of health care

Core themes of medical informatics (Hersh) standards terminology usability demonstrated value

Standards HL7 – a family of standards for the exchange, integration, and retrieval of electronic health information HL7 Mission: – HL7 empowers global health data interoperability by developing standards and enabling their adoption and implementation

Interoperability HIMSS – interoperability is the ability of different information technology systems and software applications to communicate, exchange data, and use information that has been exchanged

Three Levels of Interoperability (HIMSS) 1. foundational allows data exchange from one information technology system to be received by another does not require the ability for the receiving information technology system to interpret the data. System B can “receive” data from System A

Three Levels of Interoperability (HIMSS) 2. structural relies on the syntax of the data exchange. ensures that data exchanges between information technology systems can be interpreted at the data field level. system B can “read in” data from system A

Three Levels of Interoperability (HIMSS) 3. semantic ability of two or more systems or elements to exchange information and to use the information that has been exchanged relies on both the structuring of the data exchange and the codification of the data including vocabulary so that the receiving information technology systems can interpret the data. system B can “understand” data from system A

Electronic Health Records HL7 provides a set of "functional models and profiles that enable the constructs for management of electronic health records."a set The intent is to standardize the objects and functions that represent patient information.

Functional models "A functional model in systems engineering and software engineering is a structured representation of the functions (activities, actions, processes, operations) within the modeled system or subject area."A functional model

Challenges for medical informatics – discussion Find a partner or two and discuss – Do Hersh’s core themes (standards, terminology, usability, demonstrated value) cover all of the challenges for medical informatics? What are some challenges not mentioned by Hersh? What are some opportunities? Are there additional themes?

Interaction between technology and scientific discipline MacMullen and Denn – Argue that molecular biology is driven by and highly reliant on – development of techniques and technology to acquire data

Types of tools for science (MacMullen and Denn) physical tools – instruments to capture data from physical things or phenomena logical tools – mathematical and statistical methods, applied to raw or derived data information tools – databases, ontologies, metadata applied to data

raw data? primary data: – data derived directly from experimentation derived data secondary data data levels

Discussion Find a partner or two and discuss: – Is the interaction between technology and discipline described by MacMullen and Denn unique to molecular biology and closely related fields? Can you think of other examples? Does this change the fundamental nature of a discipline?

Knowledge Representation Issues Sharing and integrating data at a semantic level requires a shared nomenclature – and common usage So we need techniques to rigorously define our terms and document how we will use them

Reference models A reference model is "an abstract framework or domain-specific ontology consisting of an interlinked set of clearly defined concepts... to encourage clear communication" (wikipedia) (wikipedia) Typically a "high-level" model, not specifying particular implementations

Encoding representations directly ontologies for information management and modeling encode a representation of a domain to enable computation

Data curation A discipline to help a variety of discipline with their information problems By defining and developing technical and socio-technical solutions That take the information life cycle of data and related objects into account

The OAIS Reference Model "This Recommended Practice establishes a common framework of terms and concepts which make up an Open Archival Information System (OAIS). It allows existing and future archives to be more meaningfully compared and contrasted. It provides a basis for further standardization within an archival context and it should promote greater vendor awareness of, and support of, archival requirements."

The OAIS Reference Model Originally developed by The Consultative Committee for Space Data Systems (CCSDS) Has become very influential in digital archiving across domains Defines components and roles essential for archival information systems Includes a functional model and an information model.

Information models "An information model in software engineering is a representation of concepts and the relationships, constraints, rules, and operations to specify data semantics for a chosen domain of discourse."information model Information models are commonly expressed with ER diagrams or UML The OpenEHR EHR Information ModelInformation Model

Metadata and data independence Jim Grey argues that metadata can enable data independence What is data independence? How does metadata enable greater data independence?

Data mining These applications enable analysis of large amounts of data Require certain kinds of expertise and rely on a range of technologies.

Scientific data centers NSIDC – provides data – and expertise on the management of data

Discussion Find a partner or two and discuss: – Where are the opportunities for information science research according to MacMullen and Denn? – What do you see as the points of entry for information professionals in scientific data management? Educational roles? Development roles? Implementation roles?