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At least 1,747 records · Page 97Linked to original sources
PubMed2003

Similar cases retrieval from the database of laboratory test results.

We proposed a suitable method to search similar cases from the laboratory test results database, whose data are basically numerical and ordinal data. We transformed raw data into ordinal ranks and into new scores lying between 0 and 1, then calculated the Mahalanobis distances as a similarity measure. We used 3000 cases of blood count data. In 100 sample cases, 95% of the most similar 20 cases obtained by our method were included in those by the criterion (Mahalanobis distances calculated from raw data). Next, we applied our method to the data relevant to thyroid diseases. In 96 sample cases, the most similar 10 cases were retrieved from 1655 cases. The diagnoses were consistent with that of the sample cases in 32.4%. When we used Euclidean distance, the result worsened to 27.7%. Our method proved to be suitable in our attempt to identify similar cases in complicated laboratory test data.

Biomarkers↗
PubMed2026

PheBee: A Graph-Aware System for Scalable, Traceable, and Semantic Phenotyping.

OBJECTIVES: Phenotype-driven workflows in clinical and translational research require standardized ontology-based representation, ontology-aware cohort discovery, and provenance inspection for each assertion. Existing approaches optimize either for semantic traversal or scalable batch analytics, but not both. We describe PheBee, a hybrid system that links semantic assertions to scalable evidence storage via a deterministic identifier, preserving provenance while supporting ontology-aware discovery at cohort scale. MATERIALS AND METHODS: PheBee represents phenotype assertions in a knowledge graph as ontology-linked nodes with clinical modifier context (e.g., negated, family history), and stores supporting evidence records in a scalable row-oriented evidence table for cohort-scale access. The two layers are connected by a deterministic identifier enabling stable joins across repeated ingestions without duplicating high-volume evidence in the graph. We evaluated PheBee using synthetic datasets designed to exercise end-to-end ingestion and query workflows. RESULTS: Functional evaluation validated hierarchical term expansion, qualifier-aware retrieval, duplicate-free assertion handling under re-ingestion, and privacy-conscious management of subjects shared across multiple research projects. At scale (10,000 subjects producing 12M evidence records) PheBee completed ingestion in ~30 minutes and responded to interactive queries within 6 seconds under concurrent load. DISCUSSION: PheBee exposes a unified API for ontology-aware cohort discovery with hierarchical term expansion, subject-centric retrieval of phenotypes and clinical modifiers, and evidence and provenance queries. Its data model aligns with GA4GH Phenopackets, facilitating interoperability with phenotype exchange standards. CONCLUSION: By combining ontology-aware semantics with scalable, provenance-bearing evidence storage, PheBee provides a practical open-source foundation for phenotype-driven research workflows that demand both semantic precision and cohort-scale traceability.

cohort studies↗
PubMed2002

Data quality probes-exploiting and improving the quality of electronic patient record data and patient care.

Increasing reliance is being placed on electronic medical records to support clinical care and achieve improved quality standards. In order for clinical information systems (CIS) to deliver excellence the data within it needs to be complete, consistent and accurate. This capture of data is critical but forms only part of the procedure in delivering quality health care during the clinician-patient encounter. A number of processes are involved in this encounter, each of which has to be performed flawlessly to deliver a perfect outcome. This paper outlines a method of assessing the quality of these processes involved in healthcare provision and data quality within a CIS. It proposes the principle of Data Quality Probes (DQP) to assess the performance of the whole encounter system. The main feature of this is the generation of a query which clinical knowledge predicts should not retrieve any cases in a system performing flawlessly. Any cases retrieved (which fail the DQP) indicate an error in either data quality or clinical judgment. This approach is applied practically within the paradigm of a UK family practice testing the hypothesis that a series DQPs can provide a valuable method for monitoring both the data accuracy of a CIS and the provision of quality patient care.

Delivery of Health Care↗
PubMed2004

IntAct: an open source molecular interaction database.

IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains approximately 2200 binary and complex interactions imported from the literature and curated in collaboration with the Swiss-Prot team, making intensive use of controlled vocabularies to ensure data consistency. All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.

Animals↗
PubMedDate not supplied

DICOM structured reporting: Part 2. Problems and challenges in implementation for PACS workstations.

Structured reporting (SR) was recently added to the Digital Imaging and Communications in Medicine (DICOM) standard to provide an efficient mechanism for the generation, distribution, and management of clinical reports. The main advantage of SR is the ability to link clinical documents with the referenced images for simultaneous retrieval and display. A generic SR toolkit that covers the different clinical reports used in today's healthcare enterprises was developed for picture archiving and communication system (PACS) workstations. The modules of the SR toolkit collaborate to automatically construct the DICOM SR files from the free-text input presented in hypertext markup language (HTML) by using the associated SR trees. The DICOM toolkit is reused for SR encoding and DICOM services. A setup module was required for creating both the standard and private SR templates used in different healthcare specialties. The SR manager transparently converts between the different SR document presentations, that is, DICOM SR files and HTML documents, to provide the end users with an easy-to-use toolkit. To evaluate and demonstrate the effectiveness of the SR toolkit in a pragmatic setting, the toolkit was integrated into PACS workstations.

Data Display↗
PubMed2004

The ASTRAL Compendium in 2004.

The ASTRAL Compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. Partially derived from the SCOP database of protein structure domains, it includes sequences for each domain and other resources useful for studying these sequences and domain structures. The current release of ASTRAL contains 54,745 domains, more than three times as many as the initial release 4 years ago. ASTRAL has undergone major transformations in the past 2 years. In addition to several complete updates each year, ASTRAL is now updated on a weekly basis with preliminary classifications of domains from newly released PDB structures. These classifications are available as a stand-alone database, as well as integrated into other ASTRAL databases such as representative subsets. To enhance the utility of ASTRAL to structural biologists, all SCOP domains are now made available as PDB-style coordinate files as well as sequences. In addition to sequences and representative subsets based on SCOP domains, sequences and subsets based on PDB chains are newly included in ASTRAL. Several search tools have been added to ASTRAL to facilitate retrieval of data by individual users and automated methods. ASTRAL may be accessed at http://astral.stanford. edu/.

Animals↗
PubMed2004

PaVESy: Pathway Visualization and Editing System.

UNLABELLED: A data managing system for editing and visualization of biological pathways is presented. The main component of PaVESy (Pathway Visualization and Editing System) is a relational SQL database system. The database design allows storage of biological objects, such as metabolites, proteins, genes and respective relations, which are required to assemble metabolic and regulatory biological interactions. The database model accommodates highly flexible annotation of biological objects by user-defined attributes. In addition, specific roles of objects are derived from these attributes in the context of user-defined interactions, e.g. in the course of pathway generation or during editing of the database content. Furthermore, the user may organize and arrange the database content within a folder structure and is free to group and annotate database objects of interest within customizable subsets. Thus, we allow an individualized view on the database content and facilitate user customization. A JAVA-based class library was developed, which serves as the database programming interface to PaVESy. This API provides classes, which implement the concepts of object persistence in SQL databases, such as entries, interactions, annotations, folders and subsets. We created editing and visualization tools for navigation in and visualization of the database content. User approved pathway assemblies are stored and may be retrieved for continued modification, annotation and export. Data export is interfaced with a range of network visualization programs, such as Pajek or other software allowing import of SBML or GML data format. AVAILABILITY: http://pavsey.mpimp-golm.mpg.de

Database Management Systems↗
PubMed2005

A multi-resolution approach for content-based image retrieval on the Grid--application to breast cancer detection.

OBJECTIVES: Hospitals and medical centers are producing more and more data that need to be processed. Those data are confidential, heterogeneous, and limited to the geographic site where they have been produced. Unless properly anonymized, they cannot be distributed on wide area networks. METHODS: Grid technologies allow the globalization of storage and processing resources, and enable large-scale experimentations on distributed data. They constitute a promising tool to treat the different data and analyze the knowledge they contain, while offering secured access and high-performance computing capacities to the different users. Our aim is to evaluate the possibilities of grid technologies for handling medical data. RESULTS AND CONCLUSIONS: In this paper, we focus on a breast cancer diagnosis assistance tool, based on distributed and incremental knowledge construction and a content-based image retrieval system. We analyze the different scenarios of uses of such a tool. We further propose an algorithm that indexes mammographic images for content-based query purposes. This algorithm is tested on images of different resolutions in order to reduce the indexation time and we analyze its performance with experiments on the grid.

Algorithms↗
PubMed2004

DDBJ in the stream of various biological data.

In the past year we at DDBJ (http://www.ddbj.nig. ac.jp) have made a steady increase in the number of data submissions with a 50.6% increment in the number of bases or 46.5% increment in the number of entries. Among them the genome data of man, ascidian and rice hold the top three. Our activity has extended to providing a tool that enables sequence retrieval using regular expressions, and to launching our SOAP server and web services to facilitate the acquisition of proper data and tools from a huge number of biological data resources on websites worldwide. We have also opened our public gene expression database, CIBEX.

Animals↗
PubMed2006

Biomedical knowledge navigation by literature clustering.

There is an urgent need for a system that facilitates surveys by biomedical researchers and the subsequent formulation of hypotheses based on the knowledge stored in literature. One approach is to cluster papers discussing a topic of interest and reveal its sub-topics that allow researchers to acquire an overview of the topic. We developed such a system called McSyBi. It accepts a set of citation data retrieved with PubMed and hierarchically and non-hierarchically clusters them based on the titles and the abstracts using statistical and natural language processing methods. A novel point is that McSyBi allows its users to change the clustering by entering a MeSH term or UMLS Semantic Type, and therefore they can see a set of citation data from multiple aspects. We evaluated McSyBi quantitatively and qualitatively: clustering of 27 sets of citation data (40643 different papers) and scrutiny of several resultant clusters. While non-hierarchical clustering provides us with an overview of the target topic, hierarchical clustering allows us to see more details and relationships among citation data. McSyBi is freely available at http://textlens.hgc.jp/McSyBi/.

Artificial Intelligence↗
PubMed1997

Data collection and retrieval to document the outcomes of cardiopulmonary resuscitation.

In this presentation from the Wolf Creek IV Conference, the panel reviewed data requirements for documenting the processes and outcomes associated with the treatment of out-of-hospital cardiac arrest. It was recognized that this was a multifaceted task and that at least three areas warrant consideration: a) emergency medical services system management, b) monitoring and improving the quality of care, and c) the establishment of databases for research. There was complete agreement that the desired outcome is the victim's survival with intact neurologic function. However, the means of improving outcome, short of speedy initiation of treatment, were less clear. It was suggested that the Utstein guidelines, modified for practicability, can serve as a framework to characterize the arrest and to describe the temporal aspect of interventions. However, it was recognized that there were major deficits in understanding the importance of specific interventions, including their timing. Additionally, means to evaluate the quality of care delivered on the scene are usually wanting. The availability of recording electrocardiograms with accompanying voice was regarded as a major opportunity to better monitor the care that was delivered at the scene. Some of the problems incurred with cardiopulmonary resuscitation research in animals were discussed.

Animals↗
PubMed1999

Vitamin E and EDTA Improve the Efficacy of Hypothermosol-Implication of Apoptosis.

The emergence of engineered tissues and new cell strains has called for the need to explore solutions that can be used to store these cells and tissues in a state of near suspended animation without using cryopreservation. The ability of the hypothermic solutions ViaSpan (DuPont Merck Pharmaceutical Company, Wilmington, DE), HypoThermosol (Cryomedical Sciences, Rockville, MD), HypoThermosol supplemented with either ethylenediaminetetraacetic acid (EDTA) or Vitamin E and HypoThermosol supplemented with apoptosis protease inhibitors were tested for their abilities to cold-protect Madin Darby Canine Kidney (MDCK) cells at 4 degrees C. Alamar Blue, a nontoxic metabolic indicator was used to measure cell viability. The order of cold protection was HypoThermosol with Vitamin E and EDTA > HypoThermosol with Vitamin E > HypoThermosol with EDTA > HypoThermosol > ViaSpan > Dulbecco's Modified Eagle's Medium (DMEM). Membrane integrity tests supported the Alamar Blue data that EDTA and Vitamin E conferred a benefit to the cold-storage capabilities of HypoThermosol. MDCK cells that died subsequent to 1 to 6 days cold-storage detached from the substratum and their DNA was harvested after being placed at 37 degrees C. This DNA was compared to DNA retrieved from adherent cells in the same cultures that survived the cold-storage regime. Gel electrophoresis of cells dying due to 1 to 4 days of cold-storage showed a DNA ladder indicating that cells died through apoptosis, programmed cell death. Dead cells harvested at 5 to 6 days of cold storage, however, had randomly cleaved DNA indicative of necrotic cell death. HypoThermosol supplemented with apoptosis protease inhibitors was better able to cold-protect cells than the base HypoThermosol. These data suggest that the inhibition of apoptosis should be considered in the future cold-storage formulations.

Journal Article↗