Download 380E_SP16_Week9

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."
• 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."
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)
• 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 models are commonly expressed
with ER diagrams or UML
• The OpenEHR EHR Information 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?