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Information structures and workflows in health care informatics
Umeå University, Faculty of Science and Technology, Department of Computing Science.
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Patient data in health care have traditionally been used to support direct patient care. Although there is great potential in combining such data with genetic information from patients to improve diagnosis and therapy decisions (i.e. personalized medicine) and in secondary uses such as data mining, this is complex to realize due to technical, commercial and legal issues related with combining and refining patient data.

Clinical decision support systems (CDSS) are great catalysts for enabling evidence-based medicine in clinical practice. Although patient data can be the base for CDSS logic, it is often scattered among heterogenous data sources (even in different health care centers). Data integration and subsequent data mining must consider codification of patient data with terminology systems in addition to legal and ethical aspects of using such data. Although computerization of the patient record systems has been underway for a long time, some data is still unstructured. Investigation regarding the feasibility of using electronic patient records (EPR) as data sources for data mining is therefore important.

Association rules can be used as a base for CDSS development. Logic representation affect the usability of the systems and the possibility of providing explanations of the generated advice. Several properties of these rules are relatively easy to explain (such as support and confidence), which in itself can improve end-user confidence in advice from CDSS.

Information from information sources other than the EPR can also be important for diagnosis and/or treatment decisions. Drug prescription is a process that is particularly dependent on reliable information regarding, among other things, drug-drug interactions which can have serious effects. CDSS and other information systems are not useful unless they are available at the time and location of patient care. This motivates using mobile devices for CDSS. Information structures of interactions affect representation in informatics systems. These structures can be represented using a category theory based implementation of rough sets (rough monads).

Development of guidelines and CDSS can be based on existing guidelines with connections to external information systems that validate advice given the particular patient situation (for example, previously prescribed drugs may interact with recommended drugs by CDSS). Rules for CDSS can also be generated directly from patient data but this assumes that such data is structured and representative.

Although there is great potential in CDSS to improve the quality and efficiency of health care, these systems must be properly integrated with existing processes in health care (workflows) and with other information systems. Health care workflows manage physical resources such as patients and doctors and can help to standardize care processes and support management decisions through workflow simulation. Such simulations allow information bottle-necks or insufficient resources (equipment, personnel) to be identified.

As personalized medicine using genetic information of patients become economically feasible, computational requirements increase. In this sense, distributing computations through web services and system-oriented workflows can complement human-oriented workflows. Issues related to dynamic service discovery, semantic annotations of data, service inputs/outputs affect the feasibility of system-oriented workflow construction and sharing. Additionally, sharing of system-oriented workflows increase the possibilities of peer-review and workflow re-usage.

Place, publisher, year, edition, pages
Umeå: Department of Computing Science, Umeå University , 2010. , 108 p.
Series
Report / UMINF, ISSN 0348-0542 ; 10.08
Keyword [en]
Health care informatics, work ows, decision support systems
National Category
Computer and Information Science
Research subject
Computer Science
Identifiers
URN: urn:nbn:se:umu:diva-33829ISBN: 978-91-7459-026-5 (print)OAI: oai:DiVA.org:umu-33829DiVA: diva2:318224
Public defence
2010-06-07, MIT-huset, MA121, Umeå universitet, Umeå, 09:00 (English)
Opponent
Supervisors
Available from: 2010-05-12 Created: 2010-05-06 Last updated: 2010-05-12Bibliographically approved
List of papers
1. On the logic of medical decision support
Open this publication in new window or tab >>On the logic of medical decision support
2006 (English)In: Theory and applications of relational structures as knowledge instruments II: international workshops of COST action 274, TARSKI, 2002-2005, selected revised papers / [ed] Harrie C. M. de Swart, Ewa Orlowska, Gunther Schmidt and Mark Roubens, Berlin: Springer Berlin/Heidelberg, 2006, 50-59 p.Chapter in book (Other academic)
Abstract [en]

Guideline development, implementation, utility and adherence require intelligence and multimedia to interact in decision support environments. However, efforts to combine all these aspects and to connect solutions into a effective, efficient and productive environment are rare. In this paper we use a regional health care perspective on maintenance and analysis of data, information and knowledge. Examples are drawn from cardiac diseases. Analysis and development is viewed from by-pass surgery point of view. Association rules are used for analysis, and we show how these rules take logical forms so as to prepare for development of guidelines.

Place, publisher, year, edition, pages
Berlin: Springer Berlin/Heidelberg, 2006
Series
Lecture Notes in Computer Science, ISSN 0302-9743 (Print) 1611-3349 (Online) ; Vol 4342
National Category
Computer Science
Identifiers
urn:nbn:se:umu:diva-33798 (URN)10.1007/11964810_3 (DOI)978-3-540-69223-2 (print), 978-3-540-69224-9 (Online) (ISBN)
Available from: 2010-05-06 Created: 2010-05-06 Last updated: 2014-02-06Bibliographically approved
2. Mobile pharmacology
Open this publication in new window or tab >>Mobile pharmacology
2006 (English)In: Advances in hybrid information technology: First international conference, ICHIT 2006, Jeju Island, Korea, november 9-11, 2006 / [ed] Marcin S. Szczuka, Daniel Howard, Dominik Slezak, Haeng-Kon Kim, Tai-Hoon Kim, Il Seok Ko, Geuk Lee, and Peter M. A. Sloot, Berlin/Heidelberg: Springer , 2006, 522-533 p.Conference paper, Published paper (Refereed)
Abstract [en]

In mobile usage scenarios, patient care involving point of care considerations build upon increasingly complex information and information structures. Furthermore, communication of information must be enabled regardless of space and time. Decision support and guidelines are expected to communicate with other subsystems, such as those provided by information sources and hardware devices. As also these subsystems may build upon intelligence and involve their own usage scenarios, this implies further complications also the knowledge representation and software engineering tasks. In these developments, public health problems provide case studies with potentially rather huge impacts. Examples are provided e.g. by guidelines involving pharmacological treatment. Knowledge and reasoning need to interact with information management, and often involves utility of various devices. Well organized databases for pharmacological information are necessary for successful engineering of mobile extensions in these case studies. The public is now also one of the driving forces in these developments. As electronic prescriptions and generic substitutes are appreciated by the public, we experience how knowledge in its various forms provide success stories in this field.

Place, publisher, year, edition, pages
Berlin/Heidelberg: Springer, 2006
Series
Lecture Notes in Computer Science, ISSN 0302-9743 (Print) 1611-3349 (Online) ; 4413
National Category
Computer Science
Identifiers
urn:nbn:se:umu:diva-33799 (URN)10.1007/978-3-540-77368-9 (DOI)978-3-540-77367-2 (ISBN)
Conference
ICHIT
Available from: 2010-05-06 Created: 2010-05-06 Last updated: 2010-05-24Bibliographically approved
3. Software development and maintenance strategies for guideline implementation
Open this publication in new window or tab >>Software development and maintenance strategies for guideline implementation
Show others...
2001 (English)In: EUNITE-Workshop: intelligent systems in patient care, Austrian Computer Society , 2001, 26-45 p.Conference paper, Published paper (Refereed)
Abstract [en]

In this paper we discuss various software engineering aspects of guideline computerisation, both from domain oriented as well as technology driven points of view. The discussion includes case studies on pharmacological treatment of hypertension, diagnosis of dementia, and drug interactions.

Place, publisher, year, edition, pages
Austrian Computer Society, 2001
National Category
Computer and Information Science Medical and Health Sciences
Identifiers
urn:nbn:se:umu:diva-33801 (URN)
Conference
EUNITE
Available from: 2010-05-06 Created: 2010-05-06 Last updated: 2010-05-24Bibliographically approved
4. Magallanes: a web services discovery and automatic workflow composition tool
Open this publication in new window or tab >>Magallanes: a web services discovery and automatic workflow composition tool
2009 (English)In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 10, no 334Article in journal (Refereed) Published
Abstract [en]

BACKGROUND:To aid in bioinformatics data processing and analysis, an increasing number of web-based applications are being deployed. Although this is a positive circumstance in general, the proliferation of tools makes it difficult to find the right tool, or more importantly, the right set of tools that can work together to solve real complex problems.RESULTS:Magallanes (Magellan) is a versatile, platform-independent Java library of algorithms aimed at discovering bioinformatics web services and associated data types. A second important feature of Magallanes is its ability to connect available and compatible web services into workflows that can process data sequentially to reach a desired output given a particular input. Magallanes’ capabilities can be exploited both as an API or directly accessed through a graphic user interface.The Magallanes’ API is freely available for academic use, and together with Magallanes application has been tested in MS-WindowsTM XP and Unix-like operating systems. Detailed implementation information, including user manuals and tutorials, is available at http://www.bitlab-es.com/magallanes.CONCLUSION:Different implementations of the same client (web page, desktop applications, web services, etc.) have been deployed and are currently in use in real installations such as the National Institute of Bioinformatics (Spain) and the ACGT-EU project. This shows the potential utility and versatility of the software library, including the integration of novel tools in the domain and with strong evidences in the line of facilitate the automatic discovering and composition of workflows.

Keyword
bioinformatics, service discovery, service composition, service oriented architectures
Identifiers
urn:nbn:se:umu:diva-33819 (URN)http://dx.doi.org/10.1186/1471-2105-10-334 (DOI)
Available from: 2010-05-06 Created: 2010-05-06 Last updated: 2017-12-12Bibliographically approved
5. Workflow repositories for bioinformatics
Open this publication in new window or tab >>Workflow repositories for bioinformatics
Show others...
2008 (English)Report (Other academic)
Abstract [en]

Workflows are crucial instruments to use distributed and heterogeneous resources in a repeatable and well-defined way. Additionally, sharing of workflows promote peer-review and re-usage. This paper describes workflow sharing in the MOWServ client. Researchers can share and enact workflows through a controlled workflow repository and use results from workflow enactments in further processing with MOWServ. Due to a custom workflow enactor, it is possible to perform tasks in workflows that require long time to process. If a web-service is temporarily off-line, the enactor can invoke equivalent web-services instead (when available). Several issues with workflow sharing are discussed in the paper. The use of ontologies for workflow discovery and annotation is crucial but, on the other hand, also requires substantial work to develop and ensure that all workflows are properly annotated.

Place, publisher, year, edition, pages
Department of Computer Architecture, Malaga University, 2008. 14 p.
Keyword
bioinformatics, workflows, service oriented architectures
National Category
Information Science
Research subject
Computer Science
Identifiers
urn:nbn:se:umu:diva-33812 (URN)
Available from: 2010-05-06 Created: 2010-05-06 Last updated: 2010-06-03Bibliographically approved
6. Rough monadic interpretations of pharmacologic information
Open this publication in new window or tab >>Rough monadic interpretations of pharmacologic information
2007 (English)In: ICCS 2007: proceedings of the 15th international workshops on conceptual structures, London: Springer , 2007, 108-113 p.Conference paper, Published paper (Refereed)
Abstract [en]

Public databases for pharmacological information provide rich and complete information for therapeutic requirements. In particular, the ATe code with its unique identification of drug compound is the basis e.g. of modelling of drug interactions. Therapeutic decisions are frequently faced with needs to consider not just drug-drug interactions but also drugs interacting with sets of drugs and even sets of medical conditions. The typing of interactions provides an additional complication as this is an entrance towards management of uncertainties concerning interactions. The hierarchical structure of pharmacological information and its intrinsic uncertainties are in this paper used as an information platformfor the demonstration of the power of rough set modelling. Rough sets in a more general functorial view involving partially ordered monads are able to capture interactionswith respect to different granularities in the information hierarchy.

Place, publisher, year, edition, pages
London: Springer, 2007
National Category
Computer Science
Identifiers
urn:nbn:se:umu:diva-33818 (URN)10.1007/978-1-84628-992-7_15 (DOI)978-1-84628-990-3 (Print) 978-1-84628-992-7 (Online) (ISBN)
Available from: 2010-05-06 Created: 2010-05-06 Last updated: 2010-05-24Bibliographically approved
7. Categorical innovations for rough sets
Open this publication in new window or tab >>Categorical innovations for rough sets
2009 (English)In: Rough set theory: a true landmark in data analysis / [ed] Ajith Abraham, Rafael Falcón, Rafael Bello, Berlin/Heidelberg: Springer Berlin/Heidelberg, 2009, 45-69 p.Chapter in book (Other academic)
Abstract [en]

Categories arise in mathematics and appear frequently in computer science where algebraic and logical notions have powerful representations using categorical constructions. In this chapter we lean towards the functorial view involving natural transformations and monads. Functors extendable to monads, further incorporating order structure related to the underlying functor, turn out to be very useful when presenting rough sets beyond relational structures in the usual sense. Relations can be generalized with rough set operators largely maintaining power and properties. In this chapter we set forward our required categorical tools and we show how rough sets and indeed a theory of rough monads can be developed. These rough monads reveal some canonic structures, and are further shown to be useful in real applications as well. Information within pharmacological treatment can be structured by rough set approaches. In particular, situations involving management of drug interactions and medical diagnosis can be described and formalized using rough monads.

Place, publisher, year, edition, pages
Berlin/Heidelberg: Springer Berlin/Heidelberg, 2009
Series
Studies in Computational Intelligence, ISSN 1860-949X (Print), 1860-9503 (Online) ; 174
Keyword
Engineering
National Category
Computer Science
Identifiers
urn:nbn:se:umu:diva-33821 (URN)10.1007/978-3-540-89921-1_2 (DOI)000266820400002 ()978-3-540-89920-4 (ISBN)978-3-540-89921-1 (ISBN)
Available from: 2010-05-06 Created: 2010-05-06 Last updated: 2013-07-05Bibliographically approved

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CiteExportLink to record
Permanent link

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Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf