Research proposal

The impact of bioinformatical

methods to the

biotechnological advancement Modeling of the efficiency of the computer

application software in medical bioinformatics

Course code: 4IK024

Author: Claudia Halas Semester: Autumn 2013

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Contents

Abstract ____________________________________ 2

1 Introduction _______________________________ 3

1.1 The research problem ___________________________________ 3

1.2 Previous studies review _________________________________ 4

1.2.1 Deficiencies in the previous studies ____________________ 4

1.3 The significance of the study _____________________________ 4

1.4 Purpose and delimitations of the study ______________________ 5

1.5 Hypothesis and research questions _________________________ 5

2 Theoretical framework ______________________ 5

2.1 Methodology and Ethical considerations ____________________ 5

2.1.1 Research design and strategy of inquiry ________________ 6 2.1.2 Role of the researcher _______________________________ 6 2.1.3 Units of analysis ____________________________________ 6

2.1.4 Data collection methods ______________________________ 6 2.1.5 Data analysis methods _______________________________ 7

2.2 Validity and reliability __________________________________ 7

2.3 Expected outcomes _____________________________________ 7

3 References/Tentative references (of the RP) ______ 8

3.1 Books _______________________________________________ 8

3.2 Articles ______________________________________________ 8

4 Appendix 1 Tentative Table of Contents ________ 10

4.1 Appendix 2 Project steps _______________________________ 12

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Abstract Primarily used for administration use, more precisely for the execution of

financial data, the computational processing became involved for the

manipulation of the health records (EHR) for the population only from the

1970’s. The main reason for this was because the organizations did not

already have in place the necessary technology nor the answers concerning

the use or storage of such information. The process of automated work has

therefore intrigued the medical professionals who were considering the

benefits that such new machines could bring in the area of health observation

(Sethi and Theodos, 2009). Nevertheless Walsham (2012) argues that the past

few decades saw the tremendous influence and development of such

technology namely through the increase in personal computer use, graphical

workstations, the development of the new methods for human–computer

interactions, the innovations and changes brought to the storage of mass data,

the Internet or to the wireless communications. The intriguing role of such

technology for the health society is the main attention for this proposal.

Based mainly on previous theoretical studies the theses seeks to show

that a better collaboration between the involved disciplines could not just

simplify but also bring considerable improvements to such an important

domain that paradoxically seems to be the one advancing the less.

After a theory inquiry that helps classify the information, a more

particular analyses is given to the existing technology and the health

informatics research. The means of sharing the electronic data and the recent

developments in genetics, informatics and medical science are an important

step for the understanding the research problem. In order to do this the

analyses follows both qualitative and quantitative approaches and it is

primarily using explanatory and descriptive methods with outcomes from

observational studies or past research cases. Moreover, a closer attention is

given to the analyses, recognition and classification of the existing software

applications by comparatively looking at some of the most used browser and

desktop applications.

A final chapter regards the discussion of the results, the impact of

such study and it makes references for future research.

Keywords: E-health, Bioinformatics, Technology acceptance, Genetics,

Software, Social media, Strategy

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1 Introduction As a transformation of the recent years computer retrieval of information has

been prioritized for being routinely used as memory devices or as computer

assistants. Dahlbom (1996) argues that the recent years have also seen the

challenge of a new strategic planning and competing environment. In this

environment the old paper-based medical records have proven their

inefficiency and frustration when associated with strong instruments such as

self-analysis and strategic planning. The burden of the sharing of the old

paper-based patient health record (Shortliffe et al, 2006, pp. 447-448) have

been of an interest even before being associated to the informational use. As

a result many institutions have tried over the past few years to integrate

solutions for eHealth and have also seeked to develop integrated clinical

workstations. The computational tools should assist both the clinical matters

but the financial and the administrative areas as well. The issue has become

even broader as it also implies sectors such as research or education.

Part of the definition of the human being is the capacity and the

attributes of the human being to create their unique personality and identity,

yet the main attribute of the human side is their belonging to a group of

people. A shared EHR is therefore also challenged by the social side because

it could imply that the computerized system could follow the evidence based

guidelines by gathering information from resources that are not available for

human perception.

1.1 The research problem When referring to the EHR one should consider that in order to acquire good

e-health solutions one must consider all the implications of such records. The

demand for an easy patient information access also regards a good recall of

the clinical technology, a secure share of the patient record, confidential, a

need for effective and specialized tools (Cresswell, Worth and Sheikh, 2012,

pp 252) and also the fact that patient data must be shared by the physicians

themselves (Shortliffe and Blois, 2006).

In this study I want to focus on security and on identification of the

problems that occur the most in connection to the use of EHR. For this

purpose I will consider that the share of the medical records should be a joint

conduct of the patients and of the medical staff as well. The use of automated

shared tools could come of a benefit towards a simplified share of

information but this implies a good manipulation of the existing technology.

My focus will be on determining the main problems that occur from

the use of such technology by looking at it first from the problems that appear

in connection with such information processing and secondly from the

problems that people encounter when using these tools. A final outcome

would thereafter be a conceptual model where both technology and human

cooperation meet for delivering the best existing product so far.

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1.2 Previous studies review Different projects have already been implemented in regard to this

development. Projects initiated by different organizational agencies or

foundations saw to the use of new mechanisms, the creation on new web

interfaces, that could deliver remote access to computing and processing of

data.

Shortliffe and Blois (Shortliffe and Blois, 2006, p. 32) regard the

biomedical informatics as part of the basic sciences where the reliable data is

gathered from the results of past experiences and findings and that this

information, through objective organization and encoding becomes suitable

for processing.

The automation of information sharing in the field of bioinformatics

and medical informatics represent different tools and mechanisms according

to the field of interest of the professionals’ activity:

“To a hospital administrator, it might suggest

the maintenance of medical records using

computers; to a decision scientist, it might

mean the assistance of computers in disease

diagnosis; to a basic scientist, it might mean

the use of computers for maintaining and

retrieving gene-sequencing information.”

(Shortliffe and Blois, 2006, p. 21)

Recent advances in molecular biology have already experienced the

use of solutions exclusively with the use of automated tools (Jenssen, 2002).

It is therefore been showed that the past few years have given more and more

space to professionals being instructed in aspects of both disciplines that

concern the biomedical issues and also the technical and engineering issues.

The organizational issues of such findings can also be a starting point for a

vision for implementation of new prototype web based solutions.

1.2.1 Deficiencies in the previous studies

The field of Information systems as a multidisciplinary field has intrigued

many researchers yet little has been studied so far. Such findings have

showed that the literature focuses mostly on either the technical or the social

aspect. Based on previous studies in this subject the need for such analyses

had arisen. The nowadays literature exploited problems related to the health

informations systems so that a number of models and case analyses can be

closely presented, analyzed and further developed.

1.3 The significance of the study The recent development in the field of bioinformatics shows that with an

increased focus from the emerging technology this could assist even closer

the clinical health professionals. Taking into consideration that the thesis

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refers to such a multidisciplinary field it collects information from all the

related subject fields; it is on the merge of the biomedical and informatics

more precisely it regards the science of genetics and the translational

bioinformatics. The main focus is to contribute to deliver a simplified and

improved prototype.

1.4 Purpose and delimitations of the study The main purpose of this thesis is to measure the efficiency of the various

computational methods for the steps concerning the analysis of the gene

expression data measures. The study takes in considering only past reviews

and studies in order to extract the information but it is limited to the available

automated tools that share the gathered information over the internet. The

studies present that there are deficiencies in the use of software tools that can

be translated in the existence of several products that offer different outcomes

or that require different knowledge.

The study will briefly present the problems related to the

manipulation of the EHR as it will mainly focus on comparing the different

existing software applications or other tools.

1.5 Hypothesis and research questions The thesis will seek to answer three main questions:

Has the advance of the modern computing tools and the Internet

changed the biomedical computing?

What are the problems related to the use of such modern computing

tools for EHR?

Can we affect the biomedicine research in the coming years?

2 Theoretical framework The main goal of the theoretical framework is to make delimitations on the

existing literature by presenting the main concepts. The review starts by

presenting the difficulties related to the use of EHR. The literature overview

continues thereafter with more detailed information about EHR (Edwards,

Stajich and Hansen, 2009, pp. 259-381 and Adak and Srivastava, 2002) and

the processing of such data. Once we have set such information we look at

the existing standards in biomedical informatics (Hammond and Cimino in

Shortliffe et al, 2006, pp 265-311) and we consider thereafter the hospital

environment and the share of information.

2.1 Methodology and Ethical considerations The initial part of the thesis presents the topic of the study; this part is

followed by a brief background and discussion. The continuing part of the

introduction makes the reader acquainted with the purpose of the study and

the research questions. Before providing the reader with a literature review, a

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full theory review is provided. The thesis final chapter deals with the finding

and the questions to be answered in future studies.

A joint conduct is needed as it is not possible to buy the EHR as a

single product which also brings up issues of confidentiality and security.

People' integrity and human rights must take the first place in such studies,

which makes the institutionalized domain of the study the main reason for a

responsible study for the researcher (Pimple, 2002, pp 191).

The literature will follow a qualitative review, not limited by a

geographical delimitation for the articles.

2.1.1 Research design and strategy of inquiry

A special concern is given to the response received from the people involved

within this process. On one hand, using the literature we come with

qualitative methods (Myers and Avison, 2002, pp 5), on the other hand using

quantitative studies from previous online surveys, reviews and case studies

(Creswell, 2009, pp 4 and Kaplan and Duchon, 1988, pp 5) we come

deductively towards solutions that give guidance in advancing in our

research. The use of the research methods see to the modelling of the

communication between the actors, to the advantages or the errors and risks

that occur due to the acceptance or rejection of the communication or

computational systems. The critical analysis is needed for providing the

consumer with the best literature review and the description of the variables

that already exist.

Finally a model of best use is provided where all the processed data

can give answers to the main questions of the theses.

2.1.2 Role of the researcher

The researcher will take a look at the involved actors. On one side there is the

technology and on the other side the hospital personnel and staff and their

interactions. In order to do this, the researcher will look at previous research

in the field and will try to collect information related to the encountered

problems. All the collected data will be analyzed and interpreted under the

supervision of the guiding supervisor. The theses will use interpretative

approach (Myers and Avison, 2002, pp 6) and deductive reasoning for the

outcomes. The researcher will come with a conceptual model after the

problems have been identified and will suggest a low-fi prototype.

2.1.3 Units of analysis

The main units of the analyses will be the desktop applications and the

information that such applications need to process.

2.1.4 Data collection methods

In order to reach valuable results the research will make a number of

qualitative reviews to past case studies. Data will be collected and compared

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in regard to the existing technological tools and with strong concern to

security matters. Quantitative data will be gather from already existing case

studies.

2.1.5 Data analysis methods

The data collection will assume previous online surveys, reviews, examples

and case studies that will be summarized and analyzed.

2.2 Validity and reliability Dalkir (2011) stresses the need for an organizational environment where

sharing the same interests can create a strong organizational culture that is

very benefit especially for the creation of such new environments. The use of

the EHR by specialized people solves problems related to its use but it

requires a good manipulation and deep knowledge. Such problems are

tackled in this theses with regard to arising the problem for future research

(Webster and Watson, 2002). The possibility of finding little information

may account for an uninteresting study or may provide a different orientation

than the given outcomes.

2.3 Expected outcomes The expected outcome of the theses is to come with a conceptual model to

the identified problems. The theses will be limited to the problems and the

gaps that have been identified from the tools and applications that are

processing data valuable for EHR and send this information over the internet.

In order to convince and add support to the use of such means the theses will

look at the organizational culture because we consider it to play an essential

role.

The theses is also focused on supporting future studies by establishing

a vision for implementation of new prototyped web based solution.

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3 References/Tentative references (of the RP) 3.1 Books

Creswell, J. W. (2009) Research design: Qualitative, quantitative,

and mixed methods approaches. (3rd ed.), Thousand Oaks, CA: Sage

Publications.

Dalkir, K. (2011) Knowledge management in theory and practice. (1st

ed.), MIT Press Cambridge, MA, USA.

Edwards, D., Stajich, J., and Hansen, D (2009) Bioinformatics: Tools

and Applications ed ger Available at:

http://www.academia.edu/1537232/Bioinformatics_Tools_and_Applications .

Date accessed: 03 Sept. 2013.

Myers, M. D. and Avison, D. E. (2002) Qualitative research in

information systems. London: Sage Publications.

Shortliffe, EH, Perreault, LE, Wiederhold, G, and Fagan, LM (2006)

Biomedical Informatics: Computer Applications in Health Care and

Biomedicine. 3rd ed. New York, Springer. Available at:

http://link.springer.com/book/10.1007%2F0-387-36278-9. Date accessed: 23

Nov. 2013.

3.2 Articles Adak, S. and Srivastava, B. (2002) 'Bioinformatics: advancing

biotechnology through information technology Part I: molecular biology

databases' Indian Journal of Biotechnology, 1 pp. 101--116. Available at:

http://nopr.niscair.res.in/bitstream/123456789/11294/1/IJBT%202%282%29

%20159-174.pdf. Date accessed: 26 Nov. 2013.

Barrows, R.C., jr. and Clayton, P.D. (1996) ‘Privacy, Confidentiality

and EMR’ Journal of the American Medical Informatics Association 3 (2).

Brown, M. P., Grundy, W. N., Lin, D., Cristianini, N., Sugnet, C. W.,

Furey, T. S., Ares, M. and Haussler, D. (2000) 'Knowledge-based analysis of

microarray gene expression data by using support vector machines'

Proceedings of the National Academy of Sciences, 97 (1), pp. 262--267.

Coiera, E. (1996) 'Clinical communication: a new informatics

paradigm.' p. 17, Jamia, UK.

Coiera, E. (2000) 'When conversation is better than computation'

Journal of the American Medical Informatics Association, 7 (3), pp. 277-286.

Cresswell, K. M., Worth, A. and Sheikh, A. (2012) 'Comparative case

study investigating sociotechnical processes of change in the context of a

national electronic health record implementation' Health informatics journal,

18 (4), pp. 251--270. Available at: http://jhi.sagepub.com/content/18/4/251

Date accessed: 26 Nov. 2013.

Dahlbom, B. (1996) 'The new informatics' Scandinavian Journal of

Information Systems, 8 pp. 29--48. Available at:

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http://iris.cs.aau.dk/tl_files/volumes/volume08/no2/02_dahlbom_p29-48.pdf.

Date accessed: 26 Nov. 2013. De Vaujany, F., Walsh, I. and Mitev, N. (2011) 'An historically

grounded critical analysis of research articles in IS' European journal of

information systems, 20 (4), pp. 395--417.

Hammond, WE, Cimino, JJ ‘FACP Standards in Biomedical

Informatics’ in Shortliffe, EH, Perreault, LE, Wiederhold, G, and Fagan, LM

(2006) Biomedical Informatics: Computer Applications in Health Care and

Biomedicine. 3rd ed. New York, Springer.

Von Alan, R. H., March, S. T., Park, J. and Ram, S. (2004) 'Design

science in information systems research' MIS quarterly, 28 (1), pp. 75--105.

Kaplan, B. and Duchon, D. (1988) 'Combining qualitative and

quantitative methods in information systems research: a case study' MIS

quarterly, pp. 571--586.

Krathwohl, D. R. (1988) 'How to prepare a research proposal:

Guidelines for funding and dissertations in the social and behavioral sciences'

Syracuse University Press Syracuse.

Mueller, M., Gansl, T, T., Frankewitsch, T., Krieglstein, C.,

Senninger, N. and Prokosch, H. (1999) 'Workflow analysis and evidence-

based medicine: towards integration of knowledge-based functions in

hospital information systems.' Germany: University of Muenster, Proc AMIA

Symp. Available at:

http://pubmedcentralcanada.ca/pmcc/articles/PMC2232821/pdf/procamiasym

p00004-0367.pdf. Date accessed: 24 Dec. 2013.

Pimple, K. D. (2002) 'Six domains of research ethics' Science and

Engineering Ethics, 8 (2), pp. 191--205.

Sethi, P. and Theodos, K. (2009) 'Translational bioinformatics and

healthcare informatics: computational and ethical challenges' Perspectives in

health information management/AHIMA, American Health Information

Management Association, 6 (Fall). Available at:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804463. Date accessed: 24

Dec. 2013.

Walsham, G. (1995) 'Interpretive case studies in IS research: nature

and method' European Journal of information systems, 4 (2), pp. 74--81.

Walsham, G. (2012) 'Are we making a better world with ICTs?

Reflections on a future agenda for the IS field' Journal of Information

Technology, pp. 87-93. Available at: http://dx.doi.org/10.1057/jit.2012.4 .

Date accessed: 24 Dec. 2013.

Webster, J. and Watson, R. T. (2002) ‘Analyzing the past to prepare

for the future: writing a literature review’ MIS Quarterly, 26(2), xiii-xxiii.

Young, M., Kuo, F. and Myers, M. D. (2012) 'To share or not to

share: a critical research perspective on knowledge management systems'

European Journal of Information Systems, 21 (5), pp. 496--511. Available at:

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http://www.palgrave-journals.com/ejis/journal/v21/n5/full/ejis201210a.html

Date accessed: 03 Sept. 2013.

Yu, L., Lu, Y. and Zhu, X. (2012) 'Smart Hospital based on Internet

of Things.' Journal of Networks, 7 (10). Available at:

http://ojs.academypublisher.com/index.php/jnw/article/view/8492. Date

accessed: 24 Dec. 2013.

4 Appendix 1 Tentative Table of Contents

Abstract ____________________________________ i Acknowledgements _________________________________________ ii

Chapter 1. Introduction _______________________ 13

1.1 Background __________________________________________ 11

1.2 Purpose And Problem Area _____________________________ 12 1.3 Research Questions ___________________________________ 13

1.4 Limitations Of The Study _______________________________ 14

1.5 Disposition __________________________________________ 15

Chapter 2. Literature Review And Theoretical

Framework ________________________________ 16 2.1 The Nature Of The Modern Medicine And Medical Practice ___ 17

2.1.1 The Nature Of The Clinical Data _____________________ 18

2.1.2 The Humans-Computer Communication ______________ 19

2.1.3 The Arhitecture And Design Of The HIS______________ 20

2.1.4 Privacy And Security Issues _________________________ 21

2.2 Workflow, Decision Support And Data Gathering Practice_____ 17

2.2.1 The Medical Expert Systems ________________________ 22

2.2.2 The Electronic Health Record Systems ________________ 23

2.2.3 Understanding Bioinformatics ____________________ 24

2.3 The Bioinformatics: Sequence And Genome Analysis ________ 25

2.3.1 The Translational And Clinical Bioinformatics ________ 26

2.3.2 Introduction To Genomic Medicine And Techniques ___ 27

2.3.3 Connecting Complex Molecular Information To Decision

Making _______________________________________________ 28

CHAPTER 3. Methodology ___________________ 29

3.1 Research Design ______________________________________ 31

3.1.1 Exploratory Research _____________________________ 32

3.1.2 Descriptive Research ______________________________ 33

3.1.3 Explanatory Research _____________________________ 34

3.2 Research Approach ____________________________________ 35 3.2.1 Qualitative Approach _____________________________ 36

3.2.2 Quantitative Approach ____________________________ 37

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3.2.3 Date Collection Methods ___________________________ 38

Chapter 4. Implementation Strategies ___________ 39

4.1 Technology Acceptance ________________________________ 40

4.1.1 The Technology Acceptance Model (TAM) ____________ 41

4.1.2 Innovation Resistance _____________________________ 42

4.2 Biomedical Informatics ________________________________ 44 4.2.1 The Way We Design IS In Healthcare ________________ 45

4.2.2 Trends In HIS ____________________________________ 46

4.2.3 Cloud Computing In Health ________________________ 47

4.3 What Is Unlearning? ___________________________________ 48 4.3.1 Organizational Unlearning _________________________ 49

4.3.2 Individual Unlearning _____________________________ 50

4.3.3 Demarcation Between Learning And Unlearning _______ 51

4.4 Clinical Communication: A New Informatics Paradigm ______ 52 4.4.1 When Conversation Is Better Than Computation ______ 53

4.4.2 Patient Data Confidentiality And Security ____________ 54

4.4.3 Diagnosis, Standards, Codification ___________________ 55

4.4.4 Summary Of Literature Review _____________________ 55

CHAPTER 5. Empirics And Analytics __________ 56 5.1 The Biomedical Data: Acquisition, Storage, And Use _________ 57

5.1.1 The Technology Applied In Building National Electronic-

Medical Data __________________________________________ 58

5.1.2 The Record Systems Via The World Wide Web ________ 59

5.1.3 Automatic Workflow, Document Extraction ___________ 60

5.2 The Case Platform ____________________________________ 61 5.2.1 Technology Used For Genetics ______________________ 62

5.2.2 Brower And Desktop Applications ___________________ 63

5.2.2 Other Findings ___________________________________ 64

Chapter 6. Conclusion And Discussion __________ 65 6.1 Assimilation Of Automated Practice Into Medical Practice ____ 66

6.1.1 Cases Analysed ____________________________________ 70

6.1.2 Data Gathered Though Retrospective Cases ____________ 75

6.2 Software Performance _________________________________ 78

6.2.1 Interpretation Of Software Apps Vs Classical Statistics _ 80

6.2.2 Research Design Considerations _____________________ 85

Chapter 7. Bibliography ______________________ 91

Chapter 8. Apendix __________________________ 94

8.1 Definitions __________________________________________ 95

8.2 Figures ____________________________________________ 100

8.3 List Of Questionnaires ________________________________ 110 8.4 Statistical Data ______________________________________ 120

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4.1 Appendix 2 Project steps

Step 1 – gather information

Step 2 – prioritize task works for the project and within the

project

Step 3 – draw a figure to summarize the decisions, the results

Information

seeking

Problem

solving

Constant

adaptation