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PubMed2004

BioRAT: extracting biological information from full-length papers.

MOTIVATION: Converting the vast quantity of free-format text found in journals into a concise, structured format makes the researcher's quest for information easier. Recently, several information extraction systems have been developed that attempt to simplify the retrieval and analysis of biological and medical data. Most of this work has used the abstract alone, owing to the convenience of access and the quality of data. Abstracts are generally available through central collections with easy direct access (e.g. PubMed). The full-text papers contain more information, but are distributed across many locations (e.g. publishers' web sites, journal web sites and local repositories), making access more difficult. In this paper, we present BioRAT, a new information extraction (IE) tool, specifically designed to perform biomedical IE, and which is able to locate and analyse both abstracts and full-length papers. BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE. RESULTS: We show first, that BioRAT performs as well as existing systems, when applied to abstracts; and second, that significantly more information is available to BioRAT through the full-length papers than via the abstracts alone. Typically, less than half of the available information is extracted from the abstract, with the majority coming from the body of each paper. Overall, BioRAT recalled 20.31% of the target facts from the abstracts with 55.07% precision, and achieved 43.6% recall with 51.25% precision on full-length papers.

Abstracting and Indexing↗
PubMed2004

Patient data security in the DICOM standard.

The DICOM committee added the section "Security Profiles" to the DICOM standard, in order to provide the opportunity of safe communication between health care system partners. Data complying with the DICOM standard--e.g. pictures, signals or reports of examinations can be provided with one or more digital signatures. Attention should be paid to the fact that these possibilities of the DICOM standard are available or can be supplied subsequently by new acquisitions of radiological modalities. The required information to check these prerequisites are given.

Algorithms↗
PubMed2005

[Current developments in DICOM and IHE].

The broadening use of imaging management systems in radiology and other disciplines is due in large part to the success of the DICOM standard (Digital Imaging and Communications in Medicine), which has been accepted worldwide for more than 10 years and meanwhile represents one of the most successful standards in medicine. The central intent of establishing the initiative "Integrating the Healthcare Enterprise" (IHE) was to ensure interoperability of different IT systems in medical processes. IHE is essentially based on widespread standards such as DICOM or HL7. This overview article briefly addresses the principles and organization of DICOM and IHE and describes the current developments in both domains.

Database Management Systems↗
PubMedDate not supplied

Visual fusion.

Explore the source record for details and available documents.

Climate↗
PubMedDate not supplied

Metadata-driven ad hoc query of patient data: meeting the needs of clinical studies.

Clinical study data management systems (CSDMSs) have many similarities to clinical patient record systems (CPRSs) in their focus on recording clinical parameters. Requirements for ad hoc query interfaces for both systems would therefore appear to be highly similar. However, a clinical study is concerned primarily with collective responses of groups of subjects to standardized therapeutic interventions for the same underlying clinical condition. The parameters that are recorded in CSDMSs tend to be more diverse than those required for patient management in non-research settings, because of the greater emphasis on questionnaires for which responses to each question are recorded separately. The differences between CSDMSs and CPRSs are reflected in the metadata that support the respective systems' operation, and need to be reflected in the query interfaces. The authors describe major revisions of their previously described CSDMS ad hoc query interface to meet CSDMS needs more fully, as well as its porting to a Web-based platform.

Computer Security↗
PubMed2006

Medical Imaging Resource Center (MIRC) for veterinary medicine: a digital image teaching file.

RATIONALE FOR THE STUDY: Veterinary radiology has a need for software to facilitate the creation of digital image teaching files. The Medical Imaging Resource Center (MIRC) is widely used in medicine to create teaching cases and store data from clinical trials. This open-source software was identified as a solution for use in veterinary medicine. METHODOLOGY: The additional fields needed to adapt the system for veterinary use were identified as sex, species, and breed. Breed and species codes from the Matthew J. Ryan Veterinary Hospital of the University of Pennsylvania and from the Standard Nomenclature of Veterinary Diseases and Operations (SNVDO) were gathered and correlated. RESULTS: The sex fields added were male, male neutered, female, and female neutered. The breed and species codes were combined into a single term. These were coded in eXtensible Markup Language (XML) and added to the software's veterinary document template and search capabilities. CONCLUSIONS: MIRC was successfully adapted for use in creating digital teaching files for veterinary medicine.

Computer Graphics↗
PubMed1997

Healthcare information system approaches based on middleware concepts.

To meet the challenges for efficient and high-level quality, health care systems must implement the "Shared Care" paradigm of distributed co-operating systems. To this end, both the newly developed and legacy applications must be fully integrated into the care process. These requirements can be fulfilled by information systems based on middleware concepts. In the paper, the middleware approaches HL7, DHE, and CORBA are described. The relevance of those approaches to the healthcare domain is documented. The description presented here is complemented through two other papers in this volume, concentrating on the evaluation of the approaches, and on their security threats and solutions.

Computer Communication Networks↗
PubMed1998

Implementation of a low-cost PACS/CR for clinical use in Yonsei Cardiovascular Center.

The PACS/CR for clinical use in Yonsei Cardiovascular Center has been designed and implemented. Our system is open architecture to comply with emerging standards such as DICOM. database SQL, TCP/IP and to reduce operational and maintenance costs, PC-based low cost workstations running Microsoft Windows, database as Microsoft SQL based on Client/Server, Long-term storage using CD-ROM Jukebox are developed. Also, auto routing and image pre-fetching are implemented.

Ambulatory Care Facilities↗
PubMed2000

[Past, present and future of optical cards for medical use].

In the hospital, the chart is an important medical information record. However, it is not easy to refer to chart records. Although a computer is useful in referring to the chart, the most critical defect is the lack of exchangeability between hospitals. An optical card is a new medium for medical use. It has a large capacity for electronic storage, low price and high security. Therefore, the author considers this card a second medical chart. As another card, there is the IC card, which has some limitations in medical use. Although both systems are being examined experimentally, there is no actual practice in the medical field. The reason for this lack of wide use, it is thought that these systems are not yet supported by national health insurance.

Computer Communication Networks↗
PubMed2003

Automated discovery of patient-specific clinician information needs using clinical information system log files.

Knowledge about users and their information needs can contribute to better user interface design and organization of information in clinical information systems. This can lead to quicker access to desired information, which may facilitate the decision-making process. Qualitative methods such as interviews, observations and surveys have been commonly used to gain an understanding of clinician information needs. We introduce clinical information system (CIS) log analysis as a method for identifying patient-specific information needs and CIS log mining as an automated technique for discovering such needs in CIS log files. We have applied this method to WebCIS (Web-based Clinical Information System) log files to discover patterns of usage. The results can be used to guide design and development of relevant clinical information systems. This paper discusses the motivation behind the development of this method, describes CIS log analysis and mining, presents preliminary results and summarizes how the results can be applied.

Critical Pathways↗
PubMed2003

Use of online resources while using a clinical information system.

BACKGROUND: Clinical information system (CIS) use is likely to evoke information needs, yet information resources use during CIS use has not been studied. METHODS: We used CIS log files and a survey to characterize clinicians' use of resources and infobuttons (context-sensitive links from a CIS to specific resources) while using a CIS. RESULTS: We examined 38,763 uses of resources and infobuttons by 2,607 users to identify specific sources and contexts (CIS functions) in which they used them. Laboratory results review was the most frequent context and Micromedex was the most popular resource. Differences in resource use were related to context and user type. The survey confirmed that resources and infobuttons were perceived as useful for patient-specific questions while using a CIS. CONCLUSIONS: Understanding context- and user-type-specific information needs can guide the development of infobuttons for use in a CIS.

Clinical Laboratory Techniques↗
PubMed2004

Implementation and evaluation of a negation tagger in a pipeline-based system for information extract from pathology reports.

We have developed a pipeline-based system for automated annotation of Surgical Pathology Reports with UMLS terms that builds on GATE--an open-source architecture for language engineering. The system includes a module for detecting and annotating negated concepts, which implements the NegEx algorithm--an algorithm originally described for use in discharge summaries and radiology reports. We describe the implementation of the system, and early evaluation of the Negation Tagger. Our results are encouraging. In the key Final Diagnosis section, with almost no modification of the algorithm or phrase lists, the system performs with precision of 0.84 and recall of 0.80 against a gold-standard corpus of negation annotations, created by modified Delphi technique by a panel of pathologists. Further work will focus on refining the Negation Tagger and UMLS Tagger and adding additional processing resources for annotating free-text pathology reports.

Algorithms↗