Biomedical subjects

C Kulikowski

Publications and source records attributed to C Kulikowski.

At least 19 recordsLinked to original sources

PubMed2006

Medical informatics and bioinformatics: integration or evolution through scientific crises?

OBJECTIVES: To contribute a new perspective on recent investigations into the scientific foundations of medical informatics (MI) and bioinformatics (BI). To support efforts that could generate synergies and new research directions. METHODS: MI and BI are compared and contrasted from a philosophy of science perspective. Historical examples from MI and BI are analyzed based on contrasting viewpoints about the evolution of scientific disciplines. RESULTS: Our analysis suggests that the scientific approaches of MI and BI involve different assumptions and foundations, which, together with largely non-overlapping communities of researchers for the two disciplines, have led to different courses of development. We indicate how their respective application domains, medicine, and biology may have contributed to these differences in development. CONCLUSIONS: An analysis from the point of view of the philosophy of science is characteristic of established scientific disciplines. From a Kuhnian perspective, both disciplines may be entering a period of scientific crisis, where their foundations are questioned and where new ideas (or paradigm shifts) and a progressive research programme are needed to advance them scientifically. We discuss research directions and trends both supporting and challenging integration of the subdisciplines of MI and BI into a unified field of biomedical informatics (BMI), centered around the evolution of information cybernetics.

Computational Biology↗

PubMed2006

Assessing information technologies for health.

OBJECTIVES: To provide an editorial introduction to the 2006 IMIA Yearbook of Medical Informatics with an overview of its contents and contributors. METHODS: A brief overview of the main theme of 'Assessing Information Technology for Health Care', and an outline of the purposes, readership, contents, new format, and acknowledgment of contributions for the 2006 IMIA Yearbook. RESULTS: Assessing information technology (IT) in biomedicine and health care is emphasized in a number of survey and review articles. Synopses of a selection of best papers for the past 12 months are included, as are original papers on the history of medical informatics by pioneers in the field, and selected research and education programs. Information about IMIA and its constituent societies is given, as well as the authors, reviewers, and advisors to the Yearbook. CONCLUSIONS: The 2006 IMIA Yearbook of Medical Informatics highlights as its theme one of the most significant yet difficult aspects of information technology in health: the assessment of IT as part of the complex enterprise of biomedical research and practice. It is being published in a new format with a wide range of original survey and review articles.

Delivery of Health Care↗

PubMed2005

François Grémy and the birth of IMIA. 1st IMIA/UMIT Medical Informatics Award of Excellence given to Professor Grémy.

In 2001 the International Medical Informatics Association (IMIA) approved the establishment of a Medical Informatics Award of Excellence to be given every three years to an individual, whose personal commitment and dedication to medical informatics has made a lasting contribution to medicine and healthcare through her or his achievements in research, education, development or applications in the field of medical informatics. The first award was given in 2004 to Prof. François Grémy, Uzes, France. As the first chairman and moderator of TC4, François Grémy is considered to be the first President of its renamed and refocused successor, the International Medical Informatics Association. The role of IFIP-TC4 in bringing together early health informaticians cannot be underestimated. Although TC4 was composed in large part of computer professionals interested in medical applications, Grémy recruited the first generation of IMIA officers and members from the medical and healthcare communities. Intellectually as well as organizationally, IFIP-TC4 was the true predecessor of IMIA.

Awards and Prizes↗

PubMed2005

The challenge of ubiquitous computing in health care: technology, concepts and solutions. Findings from the IMIA Yearbook of Medical Informatics 2005.

OBJECTIVES: To review recent research efforts in the field of ubiquitous computing in health care. To identify current research trends and further challenges for medical informatics. METHODS: Analysis of the contents of the Yearbook on Medical Informatics 2005 of the International Medical Informatics Association (IMIA). RESULTS: The Yearbook of Medical Informatics 2005 includes 34 original papers selected from 22 peer-reviewed scientific journals related to several distinct research areas: health and clinical management, patient records, health information systems, medical signal processing and biomedical imaging, decision support, knowledge representation and management, education and consumer informatics as well as bioinformatics. A special section on ubiquitous health care systems is devoted to recent developments in the application of ubiquitous computing in health care. Besides additional synoptical reviews of each of the sections the Yearbook includes invited reviews concerning E-Health strategies, primary care informatics and wearable healthcare. CONCLUSIONS: Several publications demonstrate the potential of ubiquitous computing to enhance effectiveness of health services delivery and organization. But ubiquitous computing is also a societal challenge, caused by the surrounding but unobtrusive character of this technology. Contributions from nearly all of the established sub-disciplines of medical informatics are demanded to turn the visions of this promising new research field into reality.

Biomedical Technology↗

PubMed2004

Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care.

In this paper, we review the results of BIOINFOMED, a study funded by the European Commission (EC) with the purpose to analyse the different issues and challenges in the area where Medical Informatics and Bioinformatics meet. Traditionally, Medical Informatics has been focused on the intersection between computer science and clinical medicine, whereas Bioinformatics have been predominantly centered on the intersection between computer science and biological research. Although researchers from both areas have occasionally collaborated, their training, objectives and interests have been quite different. The results of the Human Genome and related projects have attracted the interest of many professionals, and introduced new challenges that will transform biomedical research and health care. A characteristic of the 'post genomic' era will be to correlate essential genotypic information with expressed phenotypic information. In this context, Biomedical Informatics (BMI) has emerged to describe the technology that brings both disciplines (BI and MI) together to support genomic medicine. In recognition of the dynamic nature of BMI, institutions such as the EC have launched several initiatives in support of a research agenda, including the BIOINFOMED study.

Biotechnology↗

PubMed2004

Towards clinical bioinformatics: advancing genomic medicine with informatics methods and tools.

OBJECTIVES: To summarize the challenges facing clinical applications in the light of growing research results in genomic medicine and bioinformatics. METHODS: Analysis of the contents of the Yearbook of Medical Informatics 2004 of the International Medical Informatics Association (IMIA). RESULTS: The Yearbook of Medical Informatics 2004 includes 32 articles selected from 22 peer-reviewed scientific journals. A special section on clinical bioinformatics highlights recent developments in this field. Several guest editors review the promises and limitations of available methods and resources from biomedical informatics that are relevant to clinical medicine. Integrated data and knowledge resources are generally regarded to be central and key issues for clinical bioinformatics. Further review papers deal with public health implications of bioinformatics, knowledge management and trends in health care education. The Yearbook includes for the first time a section on the history of medical informatics, where the significant impact of the Reisensburg protocol 1973 on international health and medical informatics education is examined. CONCLUSIONS: Close collaboration between bioinformatics and medical informatics researchers can contribute to new insights in genomic medicine and contribute towards the more efficient and effective use of genomic data to advance clinical care.

Computational Biology↗

PubMed2003

Establishing an agenda for biomedical informatics.

OBJECTIVE: To describe potential areas of collaboration between Medical Informatics (BI) and Bioinformatics (BI) and their effects on planning future work in both disciplines. METHODS: Some reflections on the objectives and rationale underpinning MI and BI are given, and preliminary results from the BIOINFOMED workgroup, supported by the European Commission, are introduced. RESULTS: Applications from both subfields suggest topics for sharing and exchange between the subfields within the emerging field of Biomedical Informatics. CONCLUSIONS: We suggest how the nature and degree of collaboration between the sub-disciplines can impact future work in molecular medicine.

Biomedical Research↗

PubMed2003

Medical informatics and the quality of health: new approaches to support patient care - findings from the IMIA Yearbook of Medical Informatics 2003.

OBJECTIVES: The Yearbook of Medical Informatics is published annually by the International Medical Informatics Association (IMIA) and contains a selection of excellent papers on medical informatics research which have been recently published (http://www. yearbook.uni-hd.de). The 2003 Yearbook of Medical Informatics took as its theme the role of medical informatics for the quality of health care. In this paper, we will discuss challenges for health care, and the lessons learned from editing IMIA Yearbook 2003. RESULTS AND CONCLUSIONS: Modern information processing methodology and information and communication technology have strongly influenced our societies and health care. As a consequence of this, medical informatics as a discipline has taken a leading role in the further development of health care. This involves developing information systems that enhance opportunities for global access to health services and medical knowledge. Informatics methodology and technology will facilitate high quality of care in aging societies, and will decrease the possibilities of health care errors. It will also enable the dissemination of the latest medical and health information on the web to consumers and health care providers alike. The selected papers of the IMIA Yearbook 2003 present clear examples and future challenges, and they highlight how various sub-disciplines of medical informatics can contribute to this.

Delivery of Health Care↗

PubMed2002

Medical Imaging Informatics and Medical Informatics: opportunities and constraints. Findings from the IMIA yearbook of Medical Informatics 2002.

OBJECTIVES: The Yearbook of Medical Informatics is published annually by the International Medical Informatics Association (IMIA) and contains a selection of recent excellent papers on medical informatics research (http://www.yearbook.uni-hd.de). The 2002 Yearbook of Medical Informatics took as its theme the topic of Medical Imaging Informatics. In this paper, we will summarize the contributions of medical informatics researchers to the development of medical imaging informatics, discuss challenges and opportunities of imaging informatics, and present the lessons learned from the IMIA Yearbook 2002. RESULTS AND CONCLUSIONS: Medical informatics researchers have contributed to the development of medical imaging methods and systems since the inception of this field approximately 40 years ago. The Yearbook presents selected papers and reviews on this important topic. In addition, as usual, the Yearbook 2002 also contains a variety of papers and reviews on other subjects relevant to medical informatics, such as Bioinformatics, Computer-supported education, Health and clinical management, Health information systems, Knowledge processing and decision support, Patient records, and Signal processing.

Computer-Assisted Instruction↗

PubMed2001

Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation.

Automatic identification of sub-structures in multi-aligned sequences is of great importance for effective and objective structural/functional domain annotation, phylogenetic treeing and other molecular analyses. We present a segmentation algorithm that optimally partitions a given multi-alignment into a set of potentially biologically significant blocks, or segments. This algorithm applies dynamic programming and progressive optimization to the statistical profile of a multi-alignment in order to optimally demarcate relatively homogenous sub-regions. Using this algorithm, a large multi-alignment of eukaryotic 16S rRNA was analyzed. Three types of sequence patterns were identified automatically and efficiently: shared conserved domain; shared variable motif; and rare signature sequence. Results were consistent with the patterns identified through independent phylogenetic and structural approaches. This algorithm facilitates the automation of sequence-based molecular structural and evolutionary analyses through statistical modeling and high performance computation.

Algorithms↗

PubMed2001

Medical informatics and bioinformatics: European efforts to facilitate synergy.

Over the past decade there have been several attempts to rethink the basic strategies and scope of medical informatics. Meanwhile, bioinformatics has only recently experienced a similar debate about its scientific character. Both disciplines envision the development of novel diagnostic, therapeutic, and management tools, and products for patient care. A combination of the expertise of medical informatics in developing clinical applications and the focused principles that have guided bioinformatics could create a synergy between the two areas of application. Such interaction could have a great influence on future health research and the ultimate goal, namely continuity and individualization of health care. This article summarizes current activities related to facilitating synergy between medical informatics and bioinformatics, emphasizing activities in Europe while relating them to efforts in other parts of the world. The report provides examples of the analysis that European investigators are carrying out, aiming to propose new ideas for collaborations between medical informatics and bioinformatics researchers in a variety of areas.

Computational Biology↗

PubMed2001

Digital Libraries and Recent Medical Informatics Research. Findings from the IMIA Yearbook of Medical Informatics 2001.

The Yearbook of Medical Informatics is published annually by the International Medical Informatics Association (IMIA) and contains a selection of recent excellent papers on medical informatics research (http://www.med.uni-heidelberg.de/mi/yearbook/index.htm). The special topic of the just published Yearbook 2001 is "Digital Libraries and Medicine". Digital libraries have changed dramatically and will continue to change the way we work with medical knowledge. The selected papers present recent research and new results on digital libraries. As usual, the Yearbook 2001 also contains a variety of papers on other subjects relevant to medical informatics, such as Electronic Patient Records, Health Information Systems, Health and Clinical Management, Decision Support Systems, Education, as well as Image and Signal Processing. This paper will briefly introduce the contributions covering digital libraries and will show how medical informatics research contributes to this important topic.

Humans↗

PubMed2000

Geometric invariant core for the CL and CH1 domains of immunoglobulin molecules.

A previously developed algorithmic method for identifying a geometric invariant of protein structures, termed geometrical core, is extended to the C(L) and C(H1) domains of immunoglobulin molecules. The method uses the matrix of C(alpha) - C(alpha) distances and does not require the usual superposition of structures. The result of applying the algorithm to 53 Immunoglobulin structures led to the identification of two geometrical core sets of C(alpha) atom positions for the C(L) and C(H1) domains.

Algorithms↗

PubMed2000

HGML: a hypertext guideline markup language.

Existing text-based clinical practice guidelines can be difficult to put into practice. While a growing number of such documents have gained acceptance in the medical community and contain a wealth of valuable information, the time required to digest them is substantial. Yet the expressive power, subtlety and flexibility of natural language pose challenges when designing computer tools that will help in their application. At the same time, formal computer languages typically lack such expressiveness and the effort required to translate existing documents into these languages may be costly. We propose a method based on the mark-up concept for converting text-based clinical guidelines into a machine-operable form. This allows existing guidelines to be manipulated by machine, and viewed in different formats at various levels of detail according to the needs of the practitioner, while preserving their originally published form.

Decision Support Systems, Clinical↗

PubMed1999

Analysis of ribosomal RNA sequences by combinatorial clustering.

We present an analysis of multi-aligned eukaryotic and procaryotic small subunit rRNA sequences using a novel segmentation and clustering procedure capable of extracting subsets of sequences that share common sequence features. This procedure consists of: i) segmentation of aligned sequences using a dynamic programming procedure, and subsequent identification of likely conserved segments; ii) for each putative conserved segment, extraction of a locall homogeneous cluster using a novel polynomial procedure; and iii) intersection of clusters associated with each conserved segment. Aside from their utilit in processing large gap-filled multi-alignments, these algorithms can be applied to a broad spectrum of rRNA analysis functions such as subalignment, phylogenetic subtree extraction and construction, and organism tree-placement, and can serve as a framework to organize sequence data in an efficient and easily searchable manner. The sequence classification we obtained using the method presented here shows a remarkable consistency with the independently constructed eukaryotic phylogenetic tree.

Algorithms↗

PubMed1998

Algorithmic determination of core positions in the VL and VH domains of immunoglobulin molecules.

We introduce a new algorithmic method for identifying the geometrical core of proteins that does not require the usual superposition of structures. A geometrical core is defined as the set of residues such that the C alpha (I) - C alpha (J) atom distances are identical in all structures of the protein family under study, where I and J are secondary structure positions in the structural units--strands, loops, or parts of them. The result of applying the algorithm to 53 Ig structures leads to the identification of two geometrical core sets of C alpha atom positions for the VL and VH domains. Applications of the core sets are described.

Algorithms↗

PubMed1998

Geometric invariant core for the V(L) and V(H) domains of immunoglobulin molecules.

A new algorithmic method for identifying a geometric invariant of protein structures, termed geometrical core, is developed. The method used the matrix of C(alpha)-C(alpha) distances and does not require the usual superposition of structures. The result of applying the algorithm to 53 immunoglobulin structures led to the identification of two geometrical core sets of C(alpha) atoms positions for the V(L) and V(H) domains. Based on these geometric invariants a preferred coordinate system for the immunoglobulin family is constructed which serves as a basis for structural prediction. The X-ray atom coordinates for all available immunoglobulin structures are transformed to the preferred coordinate system. An affine symmetry between the V(L) and V(H) domains is defined and computed for each of the 53 immunoglobulin structures.

Algorithms↗

PubMed1994

Automated sequencing of amino acid spin systems in proteins using multidimensional HCC(CO)NH-TOCSY spectroscopy and constraint propagation methods from artificial intelligence.

We have developed an automated approach for determining the sequential order of amino acid spin systems in small proteins. A key step in this procedure is the analysis of multidimensional HCC(CO)NH-TOCSY spectra that provide connections from the aliphatic resonances of residue i to the amide resonances of residue i + 1. These data, combined with information about the amino acid spin systems, provide sufficient constraints to assign most proton and nitrogen resonances of small proteins. Constraint propagation methods progressively narrow the set of possible assignments of amino acid spin systems to sequence-specific positions in the process of NMR data analysis. The constraint satisfaction paradigm provides a framework in which the necessary constraint-based reasoning can be expressed, while an object-oriented representation structures and facilitates the extensive list processing and indexing involved in matching. A prototype expert system, AUTOASSIGN, provides correct and nearly complete resonance assignments with one real and 31 simulated 3D NMR data sets for a 72-amino acid domain, derived from the Protein A of Staphylococcus aureus, and with 31 simulated NMR data sets for the 50-amino acid human type-alpha transforming growth factor.

Amino Acid Sequence↗