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At least 559 records · Page 31Linked to original sources
PubMed2004

A knowledge based approach for representing and reasoning about signaling networks.

MOTIVATION: In this paper we propose to use recent developments in knowledge representation languages and reasoning methodologies for representing and reasoning about signaling networks. Our approach is different from most other qualitative systems biology approaches in that it is based on reasoning (or inferencing) rather than simulation. Some of the advantages of our approach are, we can use recent advances in reasoning with incomplete and partial information to deal with gaps in signal network knowledge; and can perform various kinds of reasoning such as planning, hypothetical reasoning and explaining observations. RESULTS: Using our approach we have developed the system BioSigNet-RR for representation and reasoning about signaling networks. We use a NFkappaB related signaling pathway to illustrate the kinds of reasoning and representation that our system can currently do. AVAILABILITY: The system is available on the Web at http://www.public.asu.edu/~cbaral/biosignet

Algorithms↗
PubMed1984

Derivation of rule-based knowledge from established medical outlines.

The purpose of this paper is to describe the derivation of a rule base for an expert system from an existing medical auditing method called a criteria map. The criteria map represents the physician's logic in the specialty involved. The system described, EMERGE, is written in the standard Pascal programming language, operates on a microcomputer, and provides a convenient user-interface. All medical knowledge in EMERGE is contained in an independent set of production rules, which are derived from the criteria map.

Diagnosis, Computer-Assisted↗
PubMed2005

Introducing DoT-U2--an XML-based knowledge supported checklist software for documentation of a newborn clinical screening examination.

In a project concerning the German newborn screening examination "U2" we developed a software system called DoT-U2 for concurrent documentation at the point of care. Physicians can enter findings in(to) a tree structured protocol with management of logical dependencies. Additionally, all findings except free text annotations can be entered by speech recognition. The software system program is written in Java and uses separate XML-based modules both for knowledge and language representation. It can, therefore, easily be adapted to other languages and further documentation scenarios. We showed the high flexibility of the software system by integrating it in a completely new setting in Salt Lake City without major problems. We found that modular software development with platform independent Java and XML leads to highly flexible software which can be adapted to very different scenarios without knowing their requirements ahead of time.

Decision Making, Computer-Assisted↗
PubMed2006

Knowledge-based risk assessment under uncertainty for species invasion.

Management of invasive species depends on developing prevention and control strategies through comprehensive risk assessment frameworks that need a thorough analysis of exposure to invasive species. However, accurate exposure analysis of invasive species can be a daunting task because of the inherent uncertainty in invasion processes. Risk assessment of invasive species under uncertainty requires potential integration of expert judgment with empirical information, which often can be incomplete, imprecise, and fragmentary. The representation of knowledge in classical risk models depends on the formulation of a precise probabilistic value or well-defined joint distribution of unknown parameters. However, expert knowledge and judgments are often represented in value-laden terms or preference-ordered criteria. We offer a novel approach to risk assessment by using a dominance-based rough set approach to account for preference order in the domains of attributes in the set of risk classes. The model is illustrated with an example showing how a knowledge-centric risk model can be integrated with the dominance-based principle of rough set to derive minimal covering "if ... , then...," decision rules to reason over a set of possible invasion scenarios. The inconsistency and ambiguity in the data set is modeled using the rough set concept of boundary region adjoining lower and upper approximation of risk classes. Finally, we present an extension of rough set to evidence a theoretic interpretation of risk measures of invasive species in a spatial context. In this approach, the multispecies interactions in an invasion risk are approximated with imprecise probability measures through a combination of spatial neighborhood information of risk estimation in terms of belief and plausibility.

Animals↗
PubMed2001

The accessibility of research-based knowledge for nurses in United Kingdom acute care settings.

BACKGROUND: The successful dissemination of the results of the National Health Service (NHS) research and development strategy and the development of evidence based approaches to health care rely on clinicians having access to the best available evidence; evidence fit for the purpose of reducing the uncertainties associated with clinical decisions. AIM: To reveal the accessibility of those sources of information actually used by nurses, as well as those which they say they use. DESIGN: Mixed method case site, using interview, observational, Q sort and documentary audit data in medical, surgical and coronary care units (CCUs) in three acute hospitals. RESULTS: Three perspectives on accessibility were identified: (a) the humanist--in which human sources of information were the most accessible; (b) local information for local needs--in which locally produced resources were seen as the most accessible and (c) moving towards technology--in which information technology begins to be seen as accessible. Nurses' experience in a clinical specialty is positively associated with a perception that human sources such as clinical nurse specialists, link nurses, doctors and experienced clinical colleagues are more accessible than text based sources. Clinical specialization is associated with different approaches to accessing research knowledge. Coronary care unit nurses were more likely to perceive local guidelines, protocols and on-line databases as more accessible than their counterparts in general medical and surgical wards. Only a third of text-based resources available to nurses on the wards had any explicit research base. These, and the remainder were out of date (mean age of textbooks 11 years), and authorship hard to ascertain. CONCLUSION: A strategy to increase the use of research evidence by nurses should harness the influence of clinical nurse specialists, link nurses and those engaged in practice development. These roles could act as 'conduits' through which research-based messages for practice, and information for clinical decision making, could flow. This role should be explored and enhanced.

Acute Disease↗
PubMed2004

Cardio: a web-based knowledge resource of genes and proteins related to cardiovascular disease.

BACKGROUND: Cardiovascular disease (CVD) is the leading killer for human. In order to understand the linkage between cardiovascular diseases and genes or proteins, it is essential to construct a database to organize the body of knowledge. While the existing molecular biological databases focus on the sequence and structural aspects of biological macromolecules, i.e. DNAs, RNAs and proteins, Cardio is the web-based system we built to provide a knowledge environment with visual interface to integrate information about major cardiovascular diseases in relation to genes and proteins. METHODS: We collected the information from the web by using a group of software we developed and used a relational database management system to manage the information of these data. RESULTS: Cardio consists of six sections: GENE, PROTEIN, DISEASE, DRUG, LINKS, and REFERENCE. Each section contains relevant information about the topic. Using a phenotype-driven approach, we can identify genetic mechanisms underlying the physiology and pathophysiology of specific cardiovascular disease, such as atherosclerosis, hypertension, heart failure, and stroke. CONCLUSION: The website titled "Database of Genes and Proteins Related to Cardiovascular Disease (Cardio)" is available at along with additional information on cardiovascular disease, supplementary materials and related figures.

Cardiovascular Diseases↗
PubMed1996

Knowledge-based image analysis in the precursors of prostatic adenocarcinoma.

OBJECTIVES: It is the objective of this study to present the use of knowledge-guided procedures in quantitative image analysis and interpretation in histopathology. METHODS: The knowledge-guided procedures were implemented in the form of N-gram encoding methods for the search and detection of areas of atypicality or abnormality in histopathologic sections; they were implemented as expert system for automated scene segmentation based on an associative network with frames at each node. The extraction of histometric features from the basal cell layer of prostatic lesions is presented as an example of automated image interpretation. RESULTS: Rapid search algorithms for lesion detection were able to identify approximately 90% of areas labelled as atypical or abnormal by visual assessment, in lesions of colon, prostate and breast. Automated segmentation of very complex histopathologic imagery was possible with a success rate of approximately 80-90%, in sections of prostatic and colonic lesions. Histometry of the deterioration of the basal cell layer in prostatic lesions provided a monotonic trend curve suitable for the measurement of progression or regression. CONCLUSIONS: Knowledge-guided procedures bring external information, not offered by the imagery itself, to bear on image processing and image analytic methods. This has enabled automated analysis and interpretation of very complex imagery, such as from cribriform glands, resulting in quantitative diagnostic information.

Adenocarcinoma↗
PubMed2000

Increasing the knowledge base of asthmatics and their families through asthma clubs along the southwest border.

This study focused on behavior modification and enhancement of knowledge concerning home asthma management. The intervention focused on asthma awareness, severity assessment, medication use, and development of management plans while building a support group. The quasi-experimental design utilized various tools to evaluate knowledge, behavior modification, and self-care management. A 25% increase in knowledge and a 13% decrease in emergency department visits was identified over the 12-month period of the study.

Asthma↗
PubMed1995

SNOMED-based knowledge representation.

A standardized vocabulary and a standardized representation for this vocabulary are necessary prerequisites for the development of a computer-based patient record. A standard conceptual scheme or data structure for this vocabulary must be in place to define clinical events and to share data. SNOMED International is a detailed, fine grained, semantically typed and comprehensive computer processable vocabulary encompassing both human and veterinary medicine. Each term is placed in a standardized data structure that shows the term relationship within its own and other related taxonomic hierarchies. SNOMED International is a standardized vocabulary and data structure suitable for use in the computer-based patient record.

Animals↗
PubMed1998

Knowledge-based technology in the service of health.

The significance of numerical information for decision-making usually has to be assessed on the basis of knowledge that does not readily lend itself to quantification. Computational logic can help to handle the complexity of this process of interpretation without sacrificing the necessary rigour. When this approach is used, health indicators are expressed in the form of a "knowledge map".

Aged↗
PubMed2001

How well do you know the back of your hand? Toward evidence-based knowledge.

Familiarity with the back of one's hand has long been used as a reference criterion for knowledge despite a lack of supporting evidence. The present study prospectively tests normal subjects' knowledge of dorsal hand features. Sixty surgical, medical, and allied hospital employees (30 men, 30 women) were asked 5 questions with binary answers about features on the dorsum of their dominant hands while their hands were concealed. The proportion of correct answers to each question ranged from 0.45 to 0.65, and none was significantly different from 0.50. Similarly, the mean percentage of correct answers for all subjects and all questions was 54%, which was not significantly different from 50%. Thus, the accuracy of the answers approximated random guesses. Hand specialists scored significantly higher (75%) than other occupation groups. Men and women scored equally as a whole. These data refute the use of the hand idiom as a reference criterion for knowledge.

Adult↗
PubMed1988

GESA--a two-dimensional processing system using knowledge base techniques.

The successful analysis of two-dimensional (2-D) polyacrylamide electrophoresis gels demands considerable experience and understanding of the protein system under investigation as well as knowledge of the separation technique itself. The present work concerns the development of a computer system for analysing 2-D electrophoretic separations which incorporates concepts derived from artificial intelligence research such that non-experts can use the technique as a diagnostic or identification tool. Automatic analysis of 2-D gel separations has proved to be extremely difficult using statistical methods. Non-reproducibility of gel separations is also difficult to overcome using automatic systems. However, the human eye is extremely good at recognising patterns in images, and human intervention in semi-automatic computer systems can reduce the computational complexities of fully automatic systems. Moreover, the expertise and understanding of an "expert" is invaluable in reducing system complexity if it can be encapsulated satisfactorily in an expert system. The combination of user-intervention in the computer system together with the encapsulation of expert knowledge characterises the present system. The domain within which the system has been developed is that of wheat grain storage proteins (gliadins) which exhibit polymorphism to such an extent that cultivars can be uniquely identified by their gliadin patterns. The system can be adapted to other domains where a range of polymorpic protein sub-units exist. In its generalised form, the system can also be used for comparing more complex 2-D gel electrophoretic separations.

Algorithms↗
PubMed2005

Knowledge-based computational search for genes associated with the metabolic syndrome.

MOTIVATION: A methodology to search for genes associated with multifactorial diseases by integrating the large amount of accumulated knowledge is seriously needed. A comprehensive understanding derived from a holistic view of gene relationship structures can be gained from our proposed analysis called the cross-subspace analysis (CSA). In this analysis, gene objects are generated by machine learning using their term occurrence patterns in MEDLINE abstracts and the degree of relationship between gene objects is quantified by matching these patterns. RESULTS: Structuralization of relationships of a set of genes was performed using CSA, which were retrieved using the terms, 'obesity', 'diabetes', 'hypertriglyceridemia' and 'hypertension' that refer to diseases comprising metabolic syndrome, on a 2D plane inferring important biomedical concepts from the gene distribution. Then, we prioritized the significance of 6131 well-annotated human genes in terms of the distance on the plane from the centroid of 'metabolic syndrome'-related genes distribution. The validity was confirmed by comparing the knowledge extracted by the ordering with existing medical knowledge.

Abstracting and Indexing↗