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Data storage for managing the health enterprise and achieving business continuity.
As organizations move away from a silo mentality to a vision of enterprise-level information, more healthcare IT departments are rejecting the idea of information storage as an isolated, system-by-system solution. IT executives want storage solutions that act as a strategic element of an IT infrastructure, centralizing storage management activities to effectively reduce operational overhead and costs. This article focuses on three areas of enterprise storage: tape, disk, and disaster avoidance.
A Taxonomic Search Engine: federating taxonomic databases using web services.
BACKGROUND: The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. RESULTS: The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. CONCLUSION: The Taxonomic Search Engine is available at http://darwin.zoology.gla.ac.uk/~rpage/portal/ and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names.
GAS CHROMATOGRAPHIC INFORMATION STORAGE AND RETRIEVAL BY THE UNITERM SYSTEM.
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International Joint Meeting EuroMISE 2004 satellite workshop on "RTD Potential in Central and Eastern Europe for Building Information Society in Healthcare".
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"Just-in-time" clinical information.
The just-in-time (JIT) model originated in the manufacturing industry as a way to manage parts inventories process so that specific components could be made available at the appropriate times (that is, "just in time"). This JIT model can be applied to the management of clinical information inventories, so that clinicians can have more immediate access to the most current and relevant information at the time they most need it--when making clinical care decisions. The authors discuss traditional modes of managing clinical information, and then describe how a new, JIT model may be developed and implemented. They describe three modes of clinician-information interactions that a JIT model might employ, the scope of information that may be made available in a JIT model (global information or local, case-specific information), and the challenges posed by the implementation of such an information-access model. Finally, they discuss how JIT information access may change how physicians practice medicine, various ways JIT information may be delivered, and concerns about the trustworthiness of electronically published and accessed information resources.
Extracting data from a DICOM file.
DICOM v3.0 is a vendor-independent standard for digital medical images that describes a file format and network protocol for the exchange of images between computer systems. When simply viewing a DICOM file, it is not necessary for the user to understand the details of the entire DICOM standard. However, understanding parts of the standard is essential when DICOM files are read and processed by a user-generated program. This paper offers an overview of information a user needs to write a program for extracting the image and acquisition parameters from a DICOM file.
Florida physicians' guide to on-line information and the Internet.
The combination of new computing technology with progress in data communications over wide geographic areas offers computer users the opportunity to publish information to each other rapidly across wide geographic expanses. The concept of networking computers to gain access to the most recent and widest range of available information is consistent with the aims and methods of quality health care. The Internet is the ultimate extension to the computer network concept- an unlimited link of digital servers and users world-wide, united by common protocols for purposes of information exchange, self-policed and without central controls. Although the concept is attractive, on-line servers and the Internet are sophisticated information tools whose most effective use requires that users be oriented to basic concepts and conventions. This article summarizes the basic conventions in computer networking and data security; the differences in concept and use between bulletin board systems (BBSes), online systems, and the Internet for information access; the various classes of Internet information resources and their uses; the basic use of search engines to expedite information retrieval in the Internet; and offers practical advice in choosing methods of Internet access.
Epidemiology of foot and ankle injuries in the workplace.
Injuries to the ankle, foot, and toes of injured workers are common. Although the workers' compensation system attempts to collect information about these injuries and report them in a meaningful way, the process is somewhat inconsistent, inaccurate, and provides information relevant to government agencies but not to physician organizations seeking to improve the prevention and treatment of work-related injuries. Several improvements in data collection could greatly increase the system's efficiency and usefulness. The first is to establish a national system of uniform data collection from each State. The second improvement involves standardization of the forms and means that the data are collected from the worker including a system to retrieve information that has been omitted during the initial encounter. The third, and most important, refinement is to change the reporting of the illness to match currently accepted medical diagnosis codes (ICD-9). Using the current system and making these improvements, the United States would be able to collect more meaningful data on work injuries in this country. From that point forward medical interventions could then be created and their effects more meaningfully analyzed. All those involved in the care and treatment of the injured worker must recognize not only the limitations of the collected data but also how this information can be manipulated. For example, whereas the total cost of benefits paid by employers increased during one decade the average cost per covered employee decreased. Employers and insurers can argue that their total costs have consistently risen but only by knowing that the cost per covered employee had decreased during that same time period can that argument be countered. Similarly, implementation of certain safety practices during a given time period may be accompanied by a reduction in the number of injuries. Changes in the laws that altered injury reporting and reduced the coverage for certain injuries, however, may have created a situation where the reported injury rates were reduced by accounting practice, not medical practice. It is also well established that insurance company profits may be linked as much to the general economy and stock market as they are to premiums and claims. It is hoped that this article begins an understanding of the extent of the problem of foot and ankle injuries in the working population. Additional statistical information on specific topics is presented elsewhere in this issue.
A comparison of the temporal expressiveness of three database query methods.
Time is a multifaceted phenomenon that developers of clinical decision-support systems can model at various levels of complexity. An unresolved issue for the design of clinical databases is whether the underlying data model should support interval semantics. In this paper, we examine whether interval-based operations are required for querying protocol-based conditions. We report on an analysis of a set of 256 eligibility criteria that the T-HELPER system uses to screen patients for enrollment in eight clinical-trial protocols for HIV disease. We consider three data-manipulation methods for temporal querying: the consensus query representation Arden Syntax, the commercial standard query language SQL, and the temporal query language TimeLineSQL (TLSQL). We compare the ability of these three query methods to express the eligibility criteria. Seventy nine percent of the 256 criteria require operations on time stamps. These temporal conditions comprise four distinct patterns, two of which use interval-based data. Our analysis indicates that the Arden Syntax can query the two non-interval patterns, which represent 54% of the temporal conditions. Timepoint comparisons formulated in SQL can instantiate the two non-interval patterns and one interval pattern, which encompass 96% of the temporal conditions. TLSQL, which supports an interval-based model of time, can express all four types of temporal patterns. Our results demonstrate that the T-HELPER system requires simple temporal operations for most protocol-based queries. Of the three approaches tested, TLSQL is the only query method that is sufficiently expressive for the temporal conditions in this system.
Setting the informatics standards: an overview of NIDSEC's information systems evaluation criteria.
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PhenoDB: an integrated client/server database for linkage and population genetics.
In this paper we describe PhenoDB, an Internet-accessible client/server database application for population and linkage genetics. PhenoDB stores genetic marker data on pedigrees and populations. A database for population and linkage genetics requires two core functions: data management tasks, such as interactive validation during data entry and editing, and data analysis tasks, such as generating summary population statistics and performing linkage analyses. In PhenoDB we attempt to make these tasks as easy as possible. The client/server architecture allows efficient management and manipulation of large datasets via an easy-to-use graphical interface. PhenoDB data (73 populations, 34 pedigrees, approximately 4200 individuals, and close to 80,000 typings) are stored in a generic format that can be readily exported to (or imported from) the file formats required by various existing analysis programs such as LIPED and Lathrop and Lalouel's Multipoint Linkage. PhenoDB allows performance of complex ad-hoc queries and can generate reports for use in project management. Finally, PhenoDB can produce statistical summaries such as allele frequencies, phenotype frequencies, and Chi-square tests of Hardy-Weinberg ratios of population/pedigree data.
GenXref. VI: Automatic generation of links between two heterogeneous databases.
MOTIVATION: A large proportion of the information found in public databases is not sufficiently cross-referenced. We developed genXref, an automated system for link inference, because embarking on a manual cross-referencing of genome data would require too much expensive human expertise. It uses information retrieval technology to generate links between objects of heterogeneous databases. RESULTS: GenXref was used to generate links between GDB genes and Genbank human sequences. It resulted in > 10,000 links with a precision of 83% and a recall of approximately 32%.
Reaching beyond the health care organization for expertise and a new perspective.
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Exposing the myths of high-tech dentistry: roadblocks in technology, techniques, and teamwork.
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Theoretical models in dentistry.
For the exchange between science and practice, a language that is as precise as possible is also required in dentisty. This language is necessarily based on our ideas about the relationships in reality. Since standardization is unavoidable, various methods have been developed in informatics as to how these models can be represented and made more precise. On this basis, it is possible to neutrally discuss the situations in which a given form of treatment is expedient or not. A step-by-step approach to standardization of dental language with the aid of meta models is shown by reference to examples. The medrapid.info service is presented as on approach to making medical and dental language more precise.
Identifying important concepts from medical documents.
Automated medical concept recognition is important for medical informatics such as medical document retrieval and text mining research. In this paper, we present a software tool called keyphrase identification program (KIP) for identifying topical concepts from medical documents. KIP combines two functions: noun phrase extraction and keyphrase identification. The former automatically extracts noun phrases from medical literature as keyphrase candidates. The latter assigns weights to extracted noun phrases for a medical document based on how important they are to that document and how domain specific they are in the medical domain. The experimental results show that our noun phrase extractor is effective in identifying noun phrases from medical documents, so is the keyphrase extractor in identifying important medical conceptual terms. They both performed better than the systems they were compared to.
Ranking the whole MEDLINE database according to a large training set using text indexing.
BACKGROUND: The MEDLINE database contains over 12 million references to scientific literature, with about 3/4 of recent articles including an abstract of the publication. Retrieval of entries using queries with keywords is useful for human users that need to obtain small selections. However, particular analyses of the literature or database developments may need the complete ranking of all the references in the MEDLINE database as to their relevance to a topic of interest. This report describes a method that does this ranking using the differences in word content between MEDLINE entries related to a topic and the whole of MEDLINE, in a computational time appropriate for an article search query engine. RESULTS: We tested the capabilities of our system to retrieve MEDLINE references which are relevant to the subject of stem cells. We took advantage of the existing annotation of references with terms from the MeSH hierarchical vocabulary (Medical Subject Headings, developed at the National Library of Medicine). A training set of 81,416 references was constructed by selecting entries annotated with the MeSH term stem cells or some child in its sub tree. Frequencies of all nouns, verbs, and adjectives in the training set were computed and the ratios of word frequencies in the training set to those in the entire MEDLINE were used to score references. Self-consistency of the algorithm, benchmarked with a test set containing the training set and an equal number of references randomly selected from MEDLINE was better using nouns (79%) than adjectives (73%) or verbs (70%). The evaluation of the system with 6,923 references not used for training, containing 204 articles relevant to stem cells according to a human expert, indicated a recall of 65% for a precision of 65%. CONCLUSION: This strategy appears to be useful for predicting the relevance of MEDLINE references to a given concept. The method is simple and can be used with any user-defined training set. Choice of the part of speech of the words used for classification has important effects on performance. Lists of words, scripts, and additional information are available from the web address http://www.ogic.ca/projects/ks2004/.