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PubMed1991

Extensions to the time-oriented database model to support temporal reasoning in medical expert systems.

Physicians faced with diagnostic and therapeutic decisions must reason about clinical features that change over time. Database-management systems (DBMS) can increase access to patient data, but most systems are limited in their ability to store and retrieve complex temporal information. The Time-Oriented Databank (TOD) model, the most widely used data model for medical database systems, associates a single time stamp with each observation. The proper analysis of most clinical data requires accounting for multiple concurrent clinical events that may alter the interpretation of the raw data. Most medical DBMSs cannot retrieve patient data indexed by multiple clinical events. We describe two logical extensions to TOD-based databases that solve a set of temporal reasoning problems we encountered in constructing medical expert systems. A key feature of both extensions is that stored data are partitioned into groupings, such as sequential clinical visits, clinical exacerbations, or other abstract events that have clinical decision-making relevance. The temporal network (TNET) is an object-oriented database that extends the temporal reasoning capabilities of ONCOCIN, a medical expert system that provides chemotherapy advice. TNET uses persistent objects to associate observations with intervals of time during which "an event of clinical interest" occurred. A second object-oriented system called the extended temporal network (ETNET), is both an extension and a simplification of TNET. Like TNET, ETNET uses persistent objects to represent relevant intervals; unlike the first system, however, ETNET contains reasoning methods (rules) that can be executed when an event "begins", and that are withdrawn when that event "concludes". TNET and ETNET capture temporal relationships among recorded information that are not represented in TOD-based databases. Although they do not solve all temporal reasoning problems found in medical decision making, these new structures enable patient database systems to encode complex temporal relationships, to store and retrieve patient data based on multiple clinical contexts and, in ETNET, to modify the reasoning methods available to an expert system based on the onset or conclusion of specific clinical events.

Diagnosis, Computer-Assisted↗

PubMedDate not supplied

Microcomputer database management for surgical residents.

Surgical residents must record procedures performed and may choose to keep files of photographic slides, bibliographic references, and a curriculum vitae. Four databases that store this information are produced with an inexpensive and easily obtained microcomputer software program. A surgical procedure database is modeled after the procedure list recommended by surgical boards. This list can be viewed while one enters data, thereby enabling production of accurate and complete records. In the second database, photographic slides are assigned sequence numbers and slide content is designated using both procedure codes and key words, allowing structured and personal recall of data. Data can be printed in many report formats, including that used by the boards of surgery for final submission of reports of residents' operations at the completion of residency. The bibliographic and CV databases contain highly segmented citation data. This structure enables manipulation of data to satisfy the sequence requirements of journals or institutions to which articles or CV are submitted. Database maintenance consumes a few minutes daily and requires a minimum of experience with computers. By providing ease of access to organized data, these databases enhance the potential for critical review of clinical experience by both residents and program directors.

General Surgery↗

PubMed1983

A medical record database in radiology.

A database system on the medical records of radiation therapy, computer tomographic and radioisotopic examinations of our department was created in Computing Center of Hokkaido University which has two remote terminals in the department. Old three filing systems which had been kept in three sections of our department independently since 1972 were integrated by the creation of the database. The main functions of our database management system are as follows; 1. data input through two minicomputers in the department; 2. data loading to the database from the minicomputers; 3. production of key word files and link files for generalised data handling. Seven files are defined in the database with total data of 30 Mega bytes at the end of 1981. Many programs for information retrieval and data processings were prepared and every member of the department can share both data and application programs registered. Outline and operation of the database system and some examples of data processings are reported.

Computers↗

PubMed1995

Revelations from a meta database system on environmental health problems.

Harmful effects of environmental pollution to the health status of population is well-known to ecologists and experts on health sciences. However, prevention and protection against such direct environmental hazards to save, or, in a worse case, re-establish the ecological balance are anything but successful. It is true, even if modern monitoring and measuring technology, adequate information systems, and related data bases are available. Precision of measurements and surveys, assessment and evaluation of the relationship between component elements of negative environmental effects on one the one hand, and general health conditions of the population on the other, could be increased by applying methods of informatics i.e., if we carry out a preliminary and professional analysis of the already existing information property. A useful tool for such activities could be the creation and maintenance of an integrated meta-type data base. It is a set sorted by a causal relations group of information that is collected from several databases of different origin, as pre-defined by the task. Our task was to systematize valuable information collected from different fields of science and research (competencies), to compare them with international standard databases, and thus, to discover new inter-relations, create new values. As an input, one could envisage a network of satellite data bases evaluating relevant results of scientists and research institutions. The main database itself could contain standard national and international information on environmental health care. The output of the system could be relational analysis produced by the meta-system on the basis of results provided by the satellite systems. Thus, frequently, even without carrying out a particular survey, one could already suspect that certain environmental health hazards exist, or plan and implement certain measurements and surveys in a more precisely targeted way. An unlimited number of local satellite workstation modules of experts and research institutions may be linked to the meta database. Information property created as a result of special analysis and annotation might create a knowledge basis for free access by participants. Thus not only would their scientific backgrounds be strengthened, but services would also be provided by the meta database which could be diversified continuously. The satellite systems, the sorting and retrieval functions of the database, and its graphical services would provide a loose but flexible micro-computer system that could be linked together by autonomous or networked workstations. Our system is written on FoxPro and uses FoxGraph. At a medium level of capacity, it requires 1 MB free RAM and 14-16 MB fixed memory. The system already shows a certain specialization: the 'PubHealth' system from general issues of environmental health care leans towards problems related to sub-toxic long term effects and correlations to health insurance risk assessment (cost-benefit, risk-benefit analysis). However, new issues are also emerging when experts wish foremost to utilize the philosophy of the system (e.g., epidemiological mental-hygienic surveys related to life style and social status).

Computer Communication Networks↗

PubMed1996

Population groups: indexing, coverage, and retrieval effectiveness of ethnically related health care issues in health sciences databases.

OBJECTIVES: This study examined methods of accessing (for indexing and retrieval purposes) medical research on population groups in the major abstracting and indexing services of the health sciences literature. DESIGN: The study of diseases in specific population groups is facilitated by the indexing of both diseases and populations in a database. The MEDLINE, PsycINFO, and Embase databases were selected for the study. The published thesauri for these databases were examined to establish the vocabulary in use. Indexing terms were identified and examined as to their representation in the current literature. Terms were clustered further into groups thought to reflect an end user's perspective and to facilitate subsequent analysis. The medical literature contained in the three online databases was searched with both controlled vocabulary and natural language terms. RESULTS: The three thesauri revealed shallow pre-coordinated hierarchical structures, rather difficult-to-use terms for post-coordination, and a blurring of cultural, genetic, and racial facets of populations. Post-coordination is difficult because of the system-oriented terminology, which is intended mostly for information professionals. The terminology unintentionally restricts access by the end users who lack the knowledge needed to use the thesauri effectively for information retrieval. CONCLUSIONS: Population groups are not represented adequately in the index languages of health sciences databases. Users of these databases need to be alerted to the difficulties that may be encountered in searching for information on population groups. Information and health professionals may not be able to access the literature if they are not familiar with the indexing policies on population groups. Consequently, the study points to a problem that needs to be addressed, through either the redesign of existing systems or the design of new ones to meet the goals of Healthy People 2000 and beyond.

Abstracting and Indexing↗

PubMed1996

Using concept maps on the World-Wide Web to access a curriculum database for problem-based learning.

Development of medical school curriculum databases continues to be challenging. Representation of the instructional unit is becoming increasingly difficult due to characteristics of the problem-based learning (PBL) curricula. Curriculum databases may be used to store materials for the PBL curricula, and also to provide a delivery mechanism for those materials. However, in order to take advantage of the curriculum database as a tool for PBL, methods for accessing the curriculum database that are better suited to the information needs of students, faculty, and administrators must be developed. Concept maps are directed graph representations of conceptual relationships, and may be used to represent the content of a curriculum database. In this paper, we describe a Web application that uses Java-based concept maps was the user interface to a curriculum database.

Computer Communication Networks↗

PubMed1997

Creating an environment for linking knowledge-based systems to a clinical database: a suite of tools.

A difficulty in using knowledge-based systems has been linking them to clinical databases. The challenge is in making a correct mapping from the data in the knowledge base to the data in the database. At Columbia-Presbyterian Medical Center, we have built a suite of tools developed to create queries that address this challenge. The tools were designed to allow users to easily retrieve data from the database without requiring the users have extensive database and vocabulary knowledge. The tools help users write correct queries (Query Builder), find correct terms in the clinical database (MED Browser), aggregate the resulting data into a useful form (Clinical Database Browser), and allow the user to test the query within the environment of the knowledge-based system (Event Playback). The tools have been in use for one year.

Artificial Intelligence↗

PubMed1998

Diagnosis of acute appendicitis in two databases. Evaluation of different neighborhoods with an LVQ neural network.

The use of an artificial neural network system was studied in the diagnosis of acute abdominal pain, especially acute appendicitis, with patients from Finland and Germany. Separate Learning Vector Quantization (LVQ) neural networks were trained with a training set from each database and also with a combined database. Each neural network was evaluated separately with a test set of cases from each database. With the combined database different neighborhood methods were compared to find the optimal choice for this decision-making problem. The acute appendicitis cases of the Finnish test data set were classified well with all the networks, but the cases of the German test set were difficult to classify for the Finnish network. The use of larger neighborhoods increased the sensitivity of the classification by nearly 10%. The differences in the results of the Finnish and German databases suggest that there are differences in the data collection or patient populations between centers. Therefore, care must be taken when using decision-support systems which have been developed in other centers. Neural networks offer a method to evaluate differences between databases. With the use of larger neighborhoods, the effects of the differences on the accuracy of the classification can be partly diminished.

Abdominal Pain↗

PubMed1997

Sequence database searches via de novo peptide sequencing by tandem mass spectrometry.

A method is described for searching protein sequence databases using tandem mass spectra of tryptic peptides. The approach uses a de novo sequencing algorithm to derive a short list of possible sequence candidates which serve as query sequences in a subsequent homology-based database search routine. The sequencing algorithm employs a graph theory approach similar to previously described sequencing programs. In addition, amino acid composition, peptide sequence tags and incomplete or ambiguous Edman sequence data can be used to aid in the sequence determinations. Although sequencing of peptides from tandem mass spectra is possible, one of the frequently encountered difficulties is that several alternative sequences can be deduced from one spectrum. Most of the alternative sequences, however, are sufficiently similar for a homology-based sequence database search to be possible. Unfortunately, the available protein sequence database search algorithms (e.g. Blast or FASTA) require a single unambiguous sequence as input. Here we describe how the publicly available FASTA computer program was modified in order to search protein databases more effectively in spite of the ambiguities intrinsic in de novo peptide sequencing algorithms.

Algorithms↗

PubMed2000

MuStaR and other software for locus-specific mutation databases.

As the human genome sequencing project nears completion, there has been a vast increase in the rate at which disease and nondisease associated variant sequences are being sought and detected. This has heightened the need for software with which to accumulate allelic variant (mutation) data, and with which to make the data accessible to the scientific community. Many ad hoc solutions have been developed by those interested in specific genes and diseases, and the creation of central databases which hold data for all genes has provided an alternative repository for some of the locus data. Despite this, few specialised software tools exist for researchers to create their own locus-specific allelic variant databases. This article describes methods available to potential curators, including software systems developed with the sole purpose of generating locus-specific mutation databases. In particular, the authors' own software, MuStaRtrade mark, is described. MuStaRtrade mark allows curators to maintain a database on a laptop computer if desired, while being able to export the data to an automatically generated Website which will run on any cgi compliant Web server. Searching the database and the submission of new mutations are made possible through fill-in Web forms. A number of other software tools which may be of use to curators are also described.

Chromosome Mapping↗

PubMed2004

The construction of web database server-client system for functional food factors.

In food, other than known nutrients, such as lipid, carbohydrate, protein, vitamins, and minerals, many substances with physiological function and medicinal action exist, and it is contributing to healthy improvement and/or prevention of illness. Although carotenoid, flavonoid and polyphenol, terpenoid, volatile substance and sulfur compounds, peptide, etc. have the function of illness prevention, and research of those non-nutrient functional food factors (FFF) became globally active, the research of this field is not yet done systematically. We evaluate function of FFF and reappraise known knowledge, and this knowledge is standardized and accumulated, aimed at building a web database server-client system which is easy to use for the people and nutritional research. We also collected related data such as chemical characters of FFF from literatures and other source, and formatted them into the database. We constructed the web database server-client system with MySQL database server and Apache web server based on Linux, and used Tomcat JSP engine for data connecting since they were reliable in stability and speed. We are opening the database at http://www.life-science.jp/FFF for test now.

Database Management Systems↗

PubMed2002

HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server.

We have constructed a relational database of hemoglobin variants and thalassemia mutations, called HbVar, which can be accessed on the web at http://globin.cse.psu.edu. Extensive information is recorded for each variant and mutation, including a description of the variant and associated pathology, hematology, electrophoretic mobility, methods of isolation, stability information, ethnic occurrence, structure studies, functional studies, and references. The initial information was derived from books by Dr. Titus Huisman and colleagues [Huisman et al., 1996, 1997, 1998]. The current database is updated regularly with the addition of new data and corrections to previous data. Queries can be formulated based on fields in the database. Tables of common categories of variants, such as all those involving the alpha1-globin gene (HBA1) or all those that result in high oxygen affinity, are maintained by automated queries on the database. Users can formulate more precise queries, such as identifying "all beta-globin variants associated with instability and found in Scottish populations." This new database should be useful for clinical diagnosis as well as in fundamental studies of hemoglobin biochemistry, globin gene regulation, and human sequence variation at these loci.

Databases, Genetic↗

PubMed2006

An agent- and ontology-based system for integrating public gene, protein, and disease databases.

In this paper, we describe OntoFusion, a database integration system. This system has been designed to provide unified access to multiple, heterogeneous biological and medical data sources that are publicly available over Internet. Many of these databases do not offer a direct connection, and inquiries must be made via Web forms, returning results as HTML pages. A special module in the OntoFusion system is needed to integrate these public 'Web-based' databases. Domain ontologies are used to do this and provide database mapping and unification. We have used the system to integrate seven significant and widely used public biomedical databases: OMIM, PubMed, Enzyme, Prosite and Prosite documentation, PDB, SNP, and InterPro. A case study is detailed in depth, showing system performance. We analyze the system's architecture and methods and discuss its use as a tool for biomedical researchers.

Animals↗

PubMed2006

A specific database for providing local and national level of integration of clinical data in cystic fibrosis.

It has recently been stated that a database is an essential tool in the management of CF. The purpose of this work is to create a specific database allowing optimal performance of storage, search and retrieval functions on patients with CF. A specific database was developed using a Windev licence, for application via Microsoft supported platforms or Intranet system. The database allows real-time point of care data management of medical, investigational and administrative data. It is currently being used in the 6 Belgian reference centres. It represents a useful tool for gathering information on routine clinical and lab data, bacteriology, treatments, complications and specific outcomes for clinical and research purposes. The ongoing evolution of the database includes enhancements toward research data orientation including comparison of patient data between different centres and completeness of the National CF registry questionnaire. A complimentary copy of the software can be provided to multidisciplinary accredited CF centres worldwide upon request.

Belgium↗

PubMed2002

Congenital Heart Surgery Nomenclature and Database Project: update and proposed data harvest.

The first report of The Society of Thoracic Surgeons (STS) National Congenital Heart Surgery Database in 1998 reported the clinical features of 18 congenital heart categories. The report provided a significant amount of important information and also highlighted the strengths and weaknesses of the existing database. Following this report the STS Congenital Heart Surgery Committee in cooperation with the European Association of Cardio-Thoracic Surgery and the European Congenital Heart Surgeons Foundation initiated the International Congenital Heart Surgery Nomenclature and Database Project. The goal was to begin the standardization of nomenclature reporting strategies and establish the foundations for an international congenital heart surgery database. The first report of the International Congenital Heart Surgery Nomenclature Project was published in The Annals of Thoracic Surgery in April 2000. The current report outlines modifications to the minimum dataset as well as the diagnoses and procedure short lists. Plans for the next STS National Congenital Heart Surgery Database harvest are also presented.

Cardiac Surgical Procedures↗

PubMed2002

Designing clinical databases.

Evidence-based medicine has always relied on databases. Anyone who needs to know anything about the outcome of a treatment needs a database, but individual practitioners may feel that database design is beyond them for various reasons. Effective database design does not require complexity. This article seeks to be a practical guide for those who are contemplating development of their own database.

Computer Security↗

PubMedDate not supplied

KID, a Kinase Inhibitor Database project.

The Kinase Inhibitor Database is a small specialized database dedicated to the gathering of information on protein kinase inhibitors. The database is accessible through the World Wide Web system and gives access to structural and bibliographic information on protein kinase inhibitors. The data in the database will be collected and submitted by researchers working in the kinase inhibitor field. The submitted data will be checked by the curator of the database before entry.

Databases as Topic↗

PubMed2003

Phyto-oestrogen levels in foods: the design and construction of the VENUS database.

The objective of the Vegetal Estrogens in Nutrition and the Skeleton (VENUS) project was to evaluate existing data on dietary exposure to compounds with oestrogenic and anti-oestrogenic effects present in plant foods as constituents or contaminants, and to identify and disseminate in vitro and in vivo methodologies to analyse the effects of such compounds on bone. To permit the assessment of exposure to isoflavones in European populations (Italy, the UK, Ireland, The Netherlands), the VENUS database of phyto-oestrogen levels in foods was established. Data on the isoflavone (genistein and daidzein) content of 791 foods, including almost 300 foods commonly consumed in Europe, were collected. Levels of coumestrol, formononetin and biochanin A in a limited number of foods were also included. Lignan levels (secoisolariciresinol and matairesinol) in 158 foods were incorporated into the database, which also contains information on the references sourced for the compositional data, on the analytical methods used by each author and on the number of foods analysed in each reference. The VENUS database was constructed in Microsoft Access 2000, which is widely available as part of Microsoft Office Professional. This paper outlines the procedures used for the selection and evaluation of existing literature data for incorporation into the database. In addition, the design of the database is described, along with the data entry and quality control procedures used in its construction. Limitations of the data are discussed and guidelines for its use are provided.

Database Management Systems↗