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252 records · Page 14Linked to original sources

Contextualizing heterogeneous data for integration and inference.

Systems that attempt to integrate and analyze data from multiple data sources are greatly aided by the addition of specific semantic and metadata "context" that explicitly describes what a data value means. In this paper, we describe a systematic approach to constructing models of data and their context. Our approach provides a generic "template" for constructing such models. For each data source, a developer creates a customized model by filling in the tem-plate with predefined attributes and value. This approach facilitates model construction and provides consistent syntax and semantics among models created with the template. Systems that can process the template structure and attribute values can reason about any model so described. We used the template to create a detailed knowledge base for syndromic surveillance data integration and analysis. The knowledge base provided support for data integration, translation, and analysis methods.

Database Management Systems↗

TrialDB: A web-based Clinical Study Data Management System.

Clinical Study Data Management Systems (CSDMSs) are a class of software that support centralized management of data generated during the conduct of clinical studies. Commercial CSDMSs include Oracle Clinical, ClinTrial and MetaTrial. Such systems, which are typically deployed at an institutional or organizational level, must accommodate diverse types of data from different clinical domains that is generated by different groups of clinical investigators. Large-scale CSDMSs typically employ a high-end database engine that is usually accessed over an intranet or the Internet using Web-based technologies. CSDMSs in institution-wide use for a variety of clinical domains are best served by entity-attribute-value (EAV) modeling for the clinical data: all the commercial CSDMSs that we are aware of use EAV design. However, de novo development of EAV databases for data management is a challenging task. A large body of generic metadata-driven code must be developed before a basic EAV application can be written. Clearly, the availability of pre-existing software with the requisite functionality would be very valuable. We will discuss the benefits of such software being in open-source form.

Clinical Trials as Topic↗

Common data element (CDE) management and deployment in clinical trials.

The NCI provides the cancer Data Standards Repository (caDSR) to support development and deployment of CDEs in cancer research. The caDSR, part of the NCI caCORE infrastructure, supports data management workflow requirements and adherence to ISO/IEC 11179 metadata standards. CDEs are developed using standard terminology from caCORE vocabulary services, and are then deployed to multi-site clinical trials data management systems. Here we describe the caDSR and how CDEs are managed and deployed in clinical research.

Biomedical Research↗

E-oncology and health portals: instructions and standards for the evaluation, production organisation and use.

In 2002 the Italian Ministry of Health promoted the institution of a network and a web portal, E-oncology (2), for the seven NHS research institutions specialising in oncology (Istituti di Ricovero e Cura a Carattere Scientifico-IRCCS). One of the aims was to gather and provide information on tumoral pathologies to operators and the public. For an optimum organisation of a health web site it is necessary to comply with the standards internationally used. The World Wide Web Consortium (W3C) has developed guidelines for accessibility and usability of the sites, implemented in Italy through governmental issues. Many international organisations adopt rules and codes of conduct to validate biomedical information and have organised quality portals such as NLM, OMNI, MEDCIRCLE, HON etc. Some terminological standards, such as the MESH thesaurus and UMLS, have been produced by the libraries for a correct management and an effective information retrieval, and are currently used by the most important biomedical web sites. The Dublin Core, metadata standard for the integration of information deriving from heterogeneous archives, has also been developed by the libraries. The easy access to information dims the complex architecture necessary for the construction of a web site. The contribution of different professionals is necessary to guarantee the production of quality medical/health web sites, among them librarians have always been involved with the management of knowledge and their skills are extremely valuable. Furthermore, the libraries' network is essential in order to guarantee universal access to health information, mostly still against payment, and to contribute to overcoming the 'digital divide' and 'second-level digital divide'.

Evaluation Studies as Topic↗

Integration of Web-based and PC-based clinical research databases.

UNLABELLED: We have created a Web-based repository or data library of information about measurement instruments used in studies of multi-factorial geriatric health conditions (the Geriatrics Research Instrument Library - GRIL) based upon existing features of two separate clinical study data management systems. GRIL allows browsing, searching, and selecting measurement instruments based upon criteria such as keywords and areas of applicability. Measurement instruments selected can be printed and/or included in an automatically generated standalone microcomputer database application, which can be downloaded by investigators for use in data collection and data management. METHODS: Integration of database applications requires the creation of a common semantic model, and mapping from each system to this model. Various database schema conflicts at the table and attribute level must be identified and resolved prior to integration. Using a conflict taxonomy and a mapping schema facilitates this process. RESULTS: Critical conflicts at the table level that required resolution included name and relationship differences. CONCLUSIONS: A major benefit of integration efforts is the sharing of features and cross-fertilization of applications created for similar purposes in different operating environments. Integration of applications mandates some degree of metadata model unification.

Aged↗

Detection of gaps in the spatial coverage of coral reef monitoring projects in the US Caribbean and Gulf of Mexico.

As part of the US Coral Reef Task Force's National Program to Map, Assess, Inventory, and Monitor US Coral Reef Ecosystems, a comprehensive survey of projects/programs monitoring coral reef ecosystems and related habitats (i.e., seagrass beds and mangroves) in the US Caribbean and Pacific was undertaken. Information was gathered on a total of 296 monitoring and assessment projects conducted since 1990 in the US Caribbean and the Gulf of Mexico. Substantial gaps in monitoring coverage of US coral reef ecosystems were revealed through geographic information system (GIS) analysis of survey metadata. Although southern Florida contains approximately two-thirds of all marine monitoring projects found in the US Caribbean and Gulf of Mexico, we were unable to identify any ongoing projects that monitor coral reefs along Florida's western coast and off of the Florida Middle Grounds. Additionally, Florida is covered by approximately 1 900 km2 of mangroves, yet there were only four ongoing projects that monitor this ecosystem, leaving gaps in coverage in the Lower and Middle Keys and along the eastern and western coasts. The Flower Garden Banks National Marine Sanctuary, located offshore of the Texas/Louisiana border, has an integral long-term monitoring program, but lacks a monitoring project that gathers long-term, quantitative data on reef lish abundance and certain water quality parameters. Numerous coral reef monitoring projects in Puerto Rico are concentrated on the island's southwestern coast surrounding La Parguera, while far fewer monitoring projects are conducted along the northern and southeastern coasts and around Vieques Island. In the US Virgin Islands, the paucity of monitoring projects in large areas of St. Croix and St. Thomas contrasts with monitoring activity in three marine protected areas (MPAs), where 66% of the US Virgin Islands' coral reef monitoring sites were found. Only a series of assessments have been conducted at Navassa, a small, uninhabited island located 55 km west of Haiti and 137 km northeast of Jamaica. In order to better understand changes in coral reef communities and to produce a series of biennial reports on the status of US coral reef ecosystems, the National Oceanic and Atmospheric Administration (NOAA) is developing a national coral reef monitoring network. This network has already begun to fill some of these gaps in monitoring coverage through issuing cooperative grants to states and territories to build long-term monitoring capacity.

Animals↗

Models and inference methods for clinical systems: a principled approach.

Previous papers have argued for the existence of three different models in many clinical information systems--for the medical record, for inference in guidelines, and for concepts and re-usable facts. This paper presents a principled approach to deciding which information belongs in each model based on the nature of the queries or inference to be performed: necessary or contingent, open or closed world, algorithmic vs heuristic. It then discusses an important class of systems--"ontologically indexed knowledge bases"--and issues of metadata within this framework.

Abstracting and Indexing↗

Application of a Medical Text Indexer to an online dermatology atlas.

Clinical dermatology cases are presented as images and semi-structured text describing skin lesions and their relationships to disease. Metadata assignment to such cases is hampered by lack of a standardized dermatology vocabulary and facilitated methods for indexing legacy collections. In this pilot study descriptive clinical text from Dermatlas, a Web-based repository of dermatology cases, was indexed to Medical Subject Heading (MeSH) terms using the National Library of Medicine's Medical Text Indexer (MTI). The MTI is an automated text processing system that derives ranked lists of MeSH terms to describe the content of medical journal citations using knowledge from the Unified Medical Language System (UMLS) and from MEDLINE. For a representative, random sample of 50 Dermatlas cases, the MTI frequently derived MeSH indexing terms that matched expert-assigned terms for Diagnoses (88%), Lesion Types (72%), and Patient Characteristics (Gender and Age Groups, 62% and 84% respectively). This pilot demonstrates the potential for extending the MTI to automate indexing of clinical case presentations and for using MeSH to describe aspects of clinical dermatology.

Abstracting and Indexing↗

Relationships between healthcare and research records.

The ultimate end-point of healthcare and health-related life sciences, more or less as regulatory idea, is the prevention and cure of diseases, considering the fate of individual patients as well as the challenge of providing sufficient care for all. However, all undertakings stand under the "proviso of rightness of action". The movement of evidence-based medicine has triggered a renaissance of systematic self-assurance of best practise. The systematic utilization of healthcare records and research study recordings in an inter-linked manner provides a better enabling environment to improve evidence. Good e-health must contribute to accumulate inter-generation clinical experience. Qualified research should ensure methodological strictness via gold standards like controlled, randomised and masked trials. Building information systems for e-health as well as for e-science bears as a special focus the mutual cross-fertilization of these application domains. Analysing a variety of building blocks shows that both areas can benefit from generic solution pattern, keeping in mind that each domain has distinguished knowledge realms. Generic patterns as well as distinguished special features are illustrated by analysing state of the art solutions plus some experimental approaches, as there are: the generic part of the HL7 V3 RIM, the RCRIM work, laboratory information handling, vital sign standardization efforts, like ECG information models.Finally, the precision of the usage of the ubiquitous term "metadata" is taken as example of an open issue.

Data Collection↗

"What does this mean?" How Web-based consumer health information fails to support information seeking in the pursuit of informed consent for screening test decisions.

PURPOSE: The authors analyzed online consumer health information related to screening tests to see how well this information meets known standards for supporting the understanding of test uncertainty. SETTING/SUBJECTS: MedlinePlus documents regarding maternal serum screening (6), prostate-specific antigen testing (6), and screening mammography (6) were analyzed. METHODOLOGY: The content of the documents was analyzed. RESULTS: This study showed that most sites conscientiously report that tests are less than 100% accurate, but few provide important details about the level of uncertainty associated with test results. In particular, few resources give information about the predictive value of screening tests and have little mention of the fact that predictive value is influenced by the a priori likelihood of having the condition. DISCUSSION/CONCLUSION: These results suggest that online consumer health information does not adequately support decisions about medical screening. We suggest a potential solution to the problem: metadata harvesting coupled with optimized presentation techniques to format personalized information about screening tests. Using these techniques, the empowerment of personal choice in matters of health decisions could become the de facto standard.

Canada↗

Trends in free WWW-based E-learning Modules seen from the Learning Resource Server Medicine (LRSMed).

Despite the lost enthusiasm concerning E-learning a lot of material is available on the World Wide Web (WWW) free of charge. This material is collected and systematically described by services like the Learning Resource Server Medicine (LRSMed) at http://mmedia.medizin.uni-essen.de/portal/. With the LRSMed E-learning modules are made available for medical students by means of a metadata description that can be used for a catalogue search. The number of resources included has risen enormously from 100 in 1999 up to 805 today. Especially in 2004 there was an exponential increase in the LRSMed's content. Anatomy is still the field with the highest amount of available material, but general medicine has improved its position over the years and is now the second one. Technically and didactically simple material as scripts, textbooks, and link lists (called info services) is still dominating. Similar to 1999, there is not one module which could be truly referred to as tutorial dialogue. Simple material can not replace face-to-face-teaching. But it could be combined with conventional courses to establish some kind of blending learning. The scene of free E-learning modules on the WWW is ready to meet current challenges for efficient training of students and continuing education in medicine.

Computer-Assisted Instruction↗

Modeling public health interventions for improved access to the gray literature.

OBJECTIVE: Much of the useful information in public health (PH) is considered gray literature, literature that is not available through traditional, commercial pathways. The diversity and nontraditional format of this information makes it difficult to locate. The aim of this Robert Wood Johnson Foundation-funded project is to improve access to PH gray literature reports through established natural language processing (NLP) techniques. This paper summarizes the development of a model for representing gray literature documents concerning PH interventions. METHODS: The authors established a model-based approach for automatically analyzing and representing the PH gray literature through the evaluation of a corpus of PH gray literature from seven PH Websites. Input from fifteen PH professionals assisted in the development of the model and prioritization of elements for NLP extraction. RESULTS: Of 365 documents collected, 320 documents were used for analysis to develop a model of key text elements of gray literature documents relating to PH interventions. Survey input from a group of potential users directed the selection of key elements to include in the document summaries. CONCLUSIONS: A model of key elements relating to PH interventions in the gray literature can be developed from the ground up through document analysis and input from members of the PH workforce. The model provides a framework for developing a method to identify and store key elements from documents (metadata) as document surrogates that can be used for indexing, abstracting, and determining the shape of the PH gray literature.

Access to Information↗

[caCORE: core architecture of bioinformation on cancer research in America].

A critical factor in the advancement of biomedical research is the ease with which data can be integrated, redistributed and analyzed both within and across domains. This paper summarizes the Biomedical Information Core Infrastructure built by National Cancer Institute Center for Bioinformatics in America (NCICB). The main product from the Core Infrastructure is caCORE--cancer Common Ontologic Reference Environment, which is the infrastructure backbone supporting data management and application development at NCICB. The paper explains the structure and function of caCORE: (1) Enterprise Vocabulary Services (EVS). They provide controlled vocabulary, dictionary and thesaurus services, and EVS produces the NCI Thesaurus and the NCI Metathesaurus; (2) The Cancer Data Standards Repository (caDSR). It provides a metadata registry for common data elements. (3) Cancer Bioinformatics Infrastructure Objects (caBIO). They provide Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. The vision for caCORE is to provide a common data management framework that will support the consistency, clarity, and comparability of biomedical research data and information. In addition to providing facilities for data management and redistribution, caCORE helps solve problems of data integration. All NCICB-developed caCORE components are distributed under open-source licenses that support unrestricted usage by both non-profit and commercial entities, and caCORE has laid the foundation for a number of scientific and clinical applications. Based on it, the paper expounds caCORE-base applications simply in several NCI projects, of which one is CMAP (Cancer Molecular Analysis Project), and the other is caBIG (Cancer Biomedical Informatics Grid). In the end, the paper also gives good prospects of caCORE, and while caCORE was born out of the needs of the cancer research community, it is intended to serve as a general resource. Cancer research has historically contributed to many areas beyond tumor biology. At the same time, the paper makes some suggestions about the study at the present time on biomedical informatics in China.

Computational Biology↗

A standards-based approach for facilitating discovery of learning objects at the point of care.

Recent concerns about the quality and safety of healthcare practice provide an imperative for discovering and accessing learning resources. The growing ubiquity of the Internet, World Wide Web, and on-line educational content provide opportunity for healthcare practitioners to identify and master learning in a granular and rapid fashion. The e-learning community at large has developed a number of standards to facilitate interoperability of learner competencies, metadata describing on-line content, and packaging and navigation of such content. The overall goal of our project is to enable healthcare professionals to easily and rapidly discover learning content at the point of care. This discovery and access of learning content will be based on healthcare-specific extensions of existing e-learning standards, which are themselves based on other Web standards, such as Web Services.

Curriculum↗

Promoting the usability of online AMIA Symposium Proceedings.

A semi-automatic procedure that extracts metadata from MEDLINE was used to develop a search tool that facilitates online location and (free) access to full-text electronic documents from the Proceedings of the American Medical Informatics Association (AMIA) Annual Symposia (1997-2003). Log file analysis for six months showed steady use of the tool, with most queries originating from hosts in the US (60%), Canada (15.3%), Argentina (10.2%) and Australia (9.6%) for common informatics topics.

Congresses as Topic↗

Advancing of Russian ChemBioGrid by bringing Data Management tools into collaborative environment.

Virtual organizations of researchers need effective tools to work collaboratively with huge sets of heterogeneous data distributed over HealthGrid. This paper describes a mechanism of supporting Digital Libraries in High-Performance Computing environment based on Grid technology. The proposed approach provides abilities to assemble heterogeneous data from distributed sources into integrated virtual collections by using OGSA-DAI. The core of the conception is a Repository of Meta-Descriptions that are sets of metadata which define personal and collaborative virtual collections on base of virtualized information resources. The Repository is kept in a native XML-database Sedna and is maintained by Grid Data Services.

Cooperative Behavior↗

Privacy and security requirements of distributed computer based patient records.

Privacy and security issues increase in complexity as we move from the conventional patient record to the computer based patient record (CPR) supporting patient care and to cross-institutional networked CPRs. The privacy and security issues surrounding the CPR are outlined. Measures for privacy and security protection are summarized. It is suggested that we lack a key component of an information sharing culture. We need means for semantic indexing in the form of a metadata base at the level of the instantiation of a data base rather than at the level of its schemas.

Computer Communication Networks↗

Designing HeartCare: custom computerized home care for patients recovering from CABG surgery.

With the current trend toward discharge of cardiac artery bypass graft (CABG) patients from the hospital after 5 days, clinicians must make effective use of existing computer technology to provide more efficiently the services once available during the patient's lengthier hospital stay. This paper describes the design of the HeartCare initiative, a computerized cardiac recovery service designed to provide home-care support for patients in the first three months following CABG surgery. Capitalizing on the expansion in health resources on the Internet, and building on the lessons from the ComputerLink projects, HeartCare will employ the World Wide Web platform in the generation of personalized in-home computerized access to recovery resources. Key implementation decisions include selection of WebTV/ as the home-based device, and application of Metadata to organizing health-related knowledge resources on the WWW.

Computers↗