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PubMed1993

Using an integrated software package for clinical data analysis on a microcomputer.

An integrated software package was used effectively for entering, organizing and analyzing clinical research data on a microcomputer. Both the database and the spreadsheet components of the package were used in the process. The database component enabled a form to be created for entering the data. The spreadsheet component was used in the organization and analysis of data. Macros were written within the spreadsheet environment for the statistical analysis of data. The purpose of this paper is to illustrate how an integrated software like Symphony could offer features beyond simply the use of a spreadsheet for the analysis of research data. Also highlighted are the other useful features of the integrated software that are not directly related to data analysis.

Adolescent↗
PubMed2000

Gamma knife radiosurgery as a primary treatment for prolactinomas.

OBJECT: The purpose of this study was to estimate the efficacy of gamma knife radiosurgery (GKS) in controlling tumor growth and endocrinopathy associated with prolactinomas. METHODS: Between 1993 and 1997, 164 of 469 patients with pituitary adenomas treated by GKS harbored prolactinomas. The dose to the tumor margin ranged from 9 to 35 Gy (mean 31.2 Gy), and the visual pathways were exposed to a dose of less than 10 Gy. The mean tumor diameter was 13.4 mm. The mean follow-up time for 128 cases was 33.2 months (range 6-72 months). Tumor control was observed in all but two patients who underwent surgery 18 and 36 months, respectively, after GKS. Clinical cure was achieved in 67 cases. Clinical improvement was noted with a decrease in the hyperprolactinemia after GKS. Nonetheless, in 31 (29%) of 108 patients who were followed for more than 2 years no improvement in serum prolactin levels was demonstrated, although this could be normalized by bromocriptine administration after treatment. Nine infertile women became pregnant 2 to 13 months after GKS and all gave birth to normal children. There was no visual deterioration related to GKS. Five women experienced premature menopause. In these patients there was subtotal disappearance of the tumor and an empty sella developed. CONCLUSIONS: Gamma knife radiosurgery as a primary treatment for prolactinomas can be safe and effective both for controlling tumor growth and for normalization of prolactin hypersecretion. A higher margin dose (> or = 30 Gy) seemed to be associated with a better clinical outcome. Gamma knife radiosurgery may make prolactinomas more sensitive to the bromocriptine.

Humans↗
PubMed2004

Integrated analysis of microarray data and gene function information.

Microarray data should be interpreted in the context of existing biological knowledge. Here we present integrated analysis of microarray data and gene function classification data using homogeneity analysis. Homogeneity analysis is a graphical multivariate statistical method for analyzing categorical data. It converts categorical data into graphical display. By simultaneously quantifying the microarray-derived gene groups and gene function categories, it captures the complex relations between biological information derived from microarray data and the existing knowledge about the gene function. Thus, homogeneity analysis provides a mathematical framework for integrating the analysis of microarray data and the existing biological knowledge.

Algorithms↗
PubMed2003

The integration of similar clinical research data collection instruments.

We devised an algorithm for integrating similar clinical research data collection instruments to create a common measurement instrument. We tested this algorithm using questions from several similar surveys. We encountered differing levels of granularity among questions and responses across surveys resulting in either the loss of granularity or data. This algorithm may make survey integration more systematic and efficient.

Algorithms↗
PubMed1998

Database tools for integrating and searching membrane property data correlated with neuronal morphology.

A critical problem in neuroscience is the lack of database tools for integrating neuronal property data. We report here the development of a combined object oriented-relational database (NeuronDB, http://senselab.med.yale.edu/neurondb) that meets these needs by providing tools for integrating data within neurons and comparing data across neurons. It focuses on three types of neuronal properties voltage-gated channels, neurotransmitter receptors, and neurotransmitters. The data are organized in relation to different regions of neurons as represented in canonical forms; using simple canonical models of complex cells as a vehicle for indexing information permits the database to be searchable across different neurons. Using these multidimensional search tools, users can locate specific properties in specific regions of a neuron; obtain integrated summaries of all properties within a region; and carry out searches to compare properties across equivalent compartments in different neurons. These tools thus permit searches of the multidimensional neuron property space equivalent to homology searches of sequence databases. NeuronDB is accessible over the Internet; it provides immediate links to citation indexes and abstracts supporting the deposited data, and annotations that indicate the state of acceptance of the data. Users are encouraged to contribute data. The ability to input the data from NeuronDB directly to NEURON and GENESIS is being developed. As a shared Web resource, NeuronDB should enhance the efforts of neuroscientists and neuronal modellers to analyze and compare the functional operations of different types of neurons.

Automation↗
PubMed2001

Urinary schistosomiasis in southern Ghana: a logistic regression approach to data from a community-based integrated control program.

The data for this analysis are based on the schistosomiasis control project of the Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana, designed to study the feasibility and effectiveness of an integrated schistosomiasis control program. It embraced chemotherapy and health education for community motivation. The study was carried out from 1993 to 1997. This paper presents observations made 24 months after intervention. Eight communities in southern Ghana were grouped into three areas. Individuals in all the areas received praziquantel after the baseline data collection in 1992-1993. Area 1 had passive while Area 3 received active health education. Area 2 received no education. Prevalence of schistosomiasis was the response variable of interest while age, sex, and area were considered as possible influencing variables. The model for the baseline data indicated no significant difference in prevalence among the three areas. The model 24 months after intervention indicated a significant difference among the three areas, suggesting a possible influence of the health education that motivated community participation in the provision of facilities for the control of schistosomiasis.

Adolescent↗
PubMed2003

Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions.

Knowledge discovery from the exponentially growing body of structurally characterised protein-ligand complexes as a source of information in structure-based drug design is a major challenge in contemporary drug research. Given the need for powerful data retrieval, integration and analysis tools, Relibase was developed as a database system particularly designed to handle protein-ligand related problems and tasks. Here, we describe the design and functionality of the Relibase core database system. Features of Relibase include, e.g. the detailed analysis of superimposed ligand binding sites, ligand similarity and substructure searches, and 3D searches for protein-ligand and protein-protein interaction patterns. The broad range of functions provided in Relibase and its high level of data integration, along with its flexible and intuitive interface, makes Relibase an invaluable data mining tool which can significantly enhance the drug development process. An example, illustrating a 3D query for quarternary ligand nitrogen atoms interacting with aromatic ring systems in proteins, a pattern found in pharmaceutically relevant target proteins such as, e.g. acetylcholine-esterase, is discussed.

Animals↗
PubMed1991

An integrated, hospital information system based obstetrical medical record and database.

Described in this paper is the implementation and integration of an obstetrical medical record and database into an existing hospital information system. A unique feature of this system was the integration of existing data captured by the established hospital information systems with the newly implemented obstetrical database to form a complete patient data profile. This complete database integrated data from hospital functions such as demographic data obtained at patient registration, outpatient visits and tests, inpatient admission historical data, tests and procedures, newborn data and miscellaneous data required for birth registration. An important second feature was the utilization of physicians and nurses to enter the obstetrical data. This permitted immediate access to patient data from any hospital information system terminal, immediate retrieval for generating reports, and subsequently, ad hoc queries, statistical analysis and the electronic transfer of birth registration data to the State Vital Statistics Registry.

Academic Medical Centers↗
PubMed1993

Integrality and meaning: essential and orthogonal dimensions of graphical data display.

There are few sound principles, rules, or laws to guide construction of graphic displays of medical data or information. The present paper describes two orthogonal dimensions of data displays: integrality and meaningfulness. These are hypothesized to be both fundamental building blocks of a theory of graphic representation and programmatically useful principles for organizing previously created graphic displays and creating new ones. Examples taken from recent medical informatics literature illustrate high and low integral vs. high and low meaningful displays. If the present analysis is correct, then pattern recognition tasks will be better supported by displays that are high on both integrality and meaningfulness. Integrality, it is hypothesized, increased the degree to which a pattern is apparent. Meaningfulness increases the degree to which a pattern, once detected, is interpretable.

Computer Graphics↗
PubMed2004

Integrative analysis of cancer-related data using CAP.

The development of human cancer is a highly complex process and can be considered the result of several combined events, such as genetic alterations, disturbance of signal transduction, or failure of immunological surveillance. Cancer-related databases usually focus on specific fields of research, e.g., cancer genetics or cancer immunology, whereas the complexity of cancer genesis requires an integrated analysis of heterogeneous data from several sources. Here we present the cancer-associated protein database (CAP), a novel analysis system for cancer-related data. CAP integrates data from multiple external databases, augments these data with functional annotations, and offers tools for statistical analysis of these data. We have employed CAP to analyze genes that have been found to cause an autoimmune response in cancer. In particular, we explored the connection between the autoimmune response, mutations, and overexpression of these genes. Our preliminary results suggest that mutations are not significant contributors to raising an antibody response against tumor antigens, whereas overexpression seems to play a more important role. We hereby demonstrate how different types of data can be integrated and analyzed successfully, providing interesting results. As the amount of available data is growing rapidly, a combined analysis will play an important role in exploring the genetic and immunological basis of cancer. CAP is freely available at the following web site: http://www.bioinf.uni-sb.de/CAP/.

Autoimmunity↗
PubMed2001

Cross sections of (n,p), (n,alpha) and (n,2n) reactions on some isotopes of zirconium in the neutron energy range of 10-12 MeV and integral tests of differential cross section data using a 14 MeV d(Be) neutron spectrum.

Cross sections were measured for the 90Zr(n,alpha)87mSr, 90Zr(n,2n)89m,gZr, 91Zr(n,p)91mY, 92Zr(n,p)92Y, 94Zr(n,alpha)91Sr and 96Zr(n,2n)95Zr reactions over the neutron energy range of 11.4 to 12.4 MeV and for the 94Zr(n,p)94Y reaction from 9.2 to 12.4 MeV. Nuclear model calculations were performed up to 16MeV. The statistical model incorporating precompound effects reproduces excitation functions of the three major threshold reactions, namely (n,p), (n,alpha) and (n,2n), quite well. Spectrum averaged cross sections were measured using a thick target Be(d,n) neutron field at Ed = 14 MeV. For the same neutron field averaged reaction cross sections were deduced using the excitation functions measured in this work as well as those given in the ENDF/B-VI, JEF-2, JENDL-3.2, BROND and ADL-3 data files. A comparison of the experimental and deduced integral data helped validating the differential data.

Journal Article↗
PubMed2000

USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression.

MOTIVATION: SAGE enables the determination of genome-wide mRNA expression profiles. A comprehensive analysis of SAGE data requires software, which integrates (statistical) data analysis methods with a database system. Furthermore, to facilitate data sharing between users, the application should reside on a central server and be accessed via the internet. Since such an application was not available we developed the USAGE package. RESULTS: USAGE is a web-based application that comprises an integrated set of tools, which offers many functions for analysing and comparing SAGE data. Additionally, USAGE includes a statistical method for the planning of new SAGE experiments. USAGE is available in a multi-user environment giving users the option of sharing data. USAGE is interfaced to a relational database to store data and analysis results. The USAGE query editor allows the composition of queries for searching this database. Several database functions have been included which enable the selection and combination of data. USAGE provides the biologist increased functionality and flexibility for analysing SAGE data. AVAILABILITY: USAGE is freely accessible for academic institutions at http://www.cmbi.kun.nl/usage/. The source code of USAGE is freely available for academic institutions on request from the first author.

Databases, Factual↗
PubMed2006

An XML-based system for synthesis of data from disparate databases.

Diverse data sets have become key building blocks of translational biomedical research. Data types captured and referenced by sophisticated research studies include high throughput genomic and proteomic data, laboratory data, data from imagery, and outcome data. In this paper, the authors present the application of an XML-based data management system to support integration of data from disparate data sources and large data sets. This system facilitates management of XML schemas and on-demand creation and management of XML databases that conform to these schemas. They illustrate the use of this system in an application for genotype-phenotype correlation analyses. This application implements a method of phenotype-genotype correlation based on phylogenetic optimization of large data sets of mouse SNPs and phenotypic data. The application workflow requires the management and integration of genomic information and phenotypic data from external data repositories and from the results of phenotype-genotype correlation analyses. Our implementation supports the process of carrying out a complex workflow that includes large-scale phylogenetic tree optimizations and application of Maddison's concentrated changes test to large phylogenetic tree data sets. The data management system also allows collaborators to share data in a uniform way and supports complex queries that target data sets.

Animals↗
PubMed1998

NCCN Internet-based data system for the conduct of outcomes research.

The National Comprehensive Cancer Network (NCCN), an alliance of 17 of the world's leading cancer centers, is currently conducting its first shared outcomes project in breast cancer. City of Hope National Medical Center serves as the data coordinating center for the project. A database system has been designed and deployed which allows project staff located all over the United States to submit data to the central repository at City of Hope via the Internet. The database application consists of a series of webenabled front-end screens linked to a Microsoft SQL Server database. The NCCN system incorporates high levels of data security, confidentiality, and integrity via data encryption, password and ID protection, submission of anonymous data, and quality-control processing on several levels. The application also provides the flexibility of entering the data via the web-based screens, or transferring electronic files of data from existing database systems. Recently released SAS statistical software tools have been integrated into the system to allow for a seamless interface for analysis and web-enabled output of reports. The goals and strategies in designing the NCCN system are described and sample screens are shown. Our experience to date indicates that this system is highly effective in providing the ability to perform nationwide retrieval and analysis of outcomes data.

Breast Neoplasms↗
PubMedDate not supplied

Integration of multidisciplinary sensory data: a pilot model of the human brain project approach.

The paper provides an overview of neuroinformatics research at Yale University being performed as part of the national Human Brain Project. This research is exploring the integration of multidisciplinary sensory data, using the olfactory system as a model domain. The neuroinformatics activities fall into three main areas: 1) building databases and related tools that support experimental olfactory research at Yale and can also serve as resources for the field as a whole, 2) using computer models (molecular models and neuronal models) to help understand data being collected experimentally and to help guide further laboratory experiments, 3) performing basic neuroinformatics research to develop new informatics technologies, including a flexible data model (EAV/CR, entity-attribute-value with classes and relationships) designed to facilitate the integration of diverse heterogeneous data within a single unifying framework.

Amino Acid Sequence↗
PubMed1991

A computer-assisted health care cost management system.

To our knowledge, First Chicago has developed and implemented the first operational integrated health data computer system that includes the traditional occupational medicine data base together with medical claims and health risk appraisal data. OMNIS has combined medical claims, personnel, disability, employee assistance program, wellness program participation, administrative functions, laboratory, periodic health evaluation data, and health risk appraisal data in a single system. OMNIS provides data that are being used to more accurately predict health care and disability costs and design intervention strategies. Clearly, the integrated health data computer system provides information to manage increasingly complex issues of health care quality and cost. For companies concerned about the quality as well as the cost of health care, an integrated health data computer system (OMNIS) may be a valuable tool to objectively assess quality of care. For example, a company could evaluate how effectively various providers (eg, health maintenance organizations, preferred provider organizations, indemnity plan) control medical conditions such as hypertension. Integrated health data management systems have the potential to assist in the selection of the highest quality and most cost-effective health care plans.

Chicago↗