Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Data Storage And Retrieval”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,117 records · Page 62Linked to original sources

Automatic SNOMED classification--a corpus-based method.

This paper presents a method of automatic classification of clinical narrative through text comparison. A diagnosis report can be classified by searching archive texts that show a high textual similarity, and the 'nearest neighbor classifies the case. This paper describes the method's theoretical background and gives implementation details. Large scale simulation experiments were run with a wide range of histology reports. Results showed that for 80-84% of the trials, relevant classification lines were included among the first five alternatives. In 5% of the cases, retrieval was unsuccessful due to the absence of relevant archive reports. From the results it is concluded that the method is a versatile approach for finding potentially good classifications.

Algorithms↗

A prototype system for retrieval of gene functional information.

Microarrays allow researchers to gather data about the expression patterns of thousands of genes simultaneously. Statistical analysis can reveal which genes show statistically significant results. Making biological sense of those results requires the retrieval of functional information about the genes thus identified, typically a manual gene-by-gene retrieval of information from various on-line databases. For experiments generating thousands of genes of interest, retrieval of functional information can become a significant bottleneck. To address this issue, we are currently developing a prototype system to automate the process of retrieval of functional information from multiple on-line sources.

Animals↗

Reconsidering complete search algorithms for protein backbone NMR assignment.

MOTIVATION: Nuclear magnetic resonance (NMR) spectroscopy is widely used to determine and analyze protein structures. An essential step in NMR studies is determining the backbone resonance assignment, which maps individual atoms to experimentally measured resonance frequencies. Performing assignment is challenging owing to the noise and ambiguity in NMR spectra. Although automated procedures have been investigated, by-and-large they are still struggling to gain acceptance because of inherent limits in scalability and/or unacceptable levels of assignment error. To have confidence in the results, an algorithm should be complete, i.e. able to identify all solutions consistent with the data, including all arbitrary configurations of extra and missing peaks. The ensuing combinatorial explosion in the space of possible assignments has led to the perception that complete search is hopelessly inefficient and cannot scale to realistic datasets. RESULTS: This paper presents a complete branch-contract-and-bound search algorithm for backbone resonance assignment. The algorithm controls the search space by hierarchically agglomerating partial assignments and employing statistically sound pruning criteria. It considers all solutions consistent with the data, and uniformly treats all combinations of extra and missing data. We demonstrate our approach on experimental data from five proteins ranging in size from 70 to 154 residues. The algorithm assigns >95% of the positions with >98% accuracy. We also present results on simulated data from 259 proteins from the RefDB database, ranging in size from 25 to 257 residues. The median computation time for these cases is 1 min, and the assignment accuracy is >99%. These results demonstrate that complete search not only has the advantage of guaranteeing fair treatment of all feasible solutions, but is efficient enough to be employed effectively inpractice. AVAILABILITY: The MBA(2) software package is made available under an open-source software license. The datasets featured in the Results section can also be obtained from the contact author.

Algorithms↗

Digital echocardiographic communication using multivendor networked DICOM devices.

Digital acquisition, storage, and review of echocardiographic data are feasible in a multivendor networked DICOM environment. The authors' echocardiographic laboratory currently stores 120 studies per day using the ProSolv Echo Management System. Storage and retrieval is realized on standard computer hardware without the necessity for proprietary hardware solutions. DICOM storage has become more efficient as vendor solutions improve. Transmission rates over a 10/100 BT switched network are approximately 0.40 MB/s allowing a complete echo study (~40 MB) to be transferred to the server in approximately 1.5 minutes, however the ability to send data during a study has also been realized by one vendor.

Computer Communication Networks↗

DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams.

We at DDBJ (http://www.ddbj.nig.ac.jp) process and publicise the massive amounts of data submitted mainly by Japanese genome projects and sequencing teams. It is emphasised that the collaboration between data producing teams and the data bank is crucial in carrying out these processes smoothly. The amount of data submitted in 1999 is so large that it alone exceeds the total amount submitted in the preceding 10 years. To cope with this situation, we have developed tools not only for processing such massive amounts of data but also for efficiently retrieving data on demand.

Animals↗

The impact on database searching arising from inconsistency in the nomenclature of parasitic diseases.

The existing usage of disease names formed from the name of the parasite taxon is characterised by marked heterogeneity. This is largely due to the fact that, for coining disease names, four different suffixes, '-osis', '-iosis', '-asis' and '-iasis', are being used inconsistently. The result is that alternative terms are in use for naming the same disease, e.g. trypanosomosis and trypanosomiasis, fasciolosis and fascioliasis, ascariosis and ascariasis. Inspite of the SNOAPAD/SNOPAD guideline (1988) which proposed the principles of a uniform and standard disease nomenclature, the actual usage depends largely on tradition, educational imprinting and personal preferences, showing great variation. By using alternative disease names as search terms the author investigates in four databases the impact of nomenclatural heterogeneity on information storage and retrieval. It is evident that the existence of alternative disease names in parasitology markedly interferes with the efficacy of online data retrieval. The value of a disease name as a search term was shown to be greatly different in various databases. Until we have to coexist with an inconsistent disease terminology we need to adopt specially structured database-search techniques to ensure a proper level of precision in searching. Such possible techniques are considered.

Animals↗

A high-level object-oriented model for representing relationships in an electronic medical record.

The importance of electronic medical records to improve the quality and cost-effectiveness of medical care continues to be realized. This growing importance has spawned efforts at defining the structure and content of medical data, which is heterogeneous, highly inter-related, and complex. Computer-assisted data modeling tools have greatly facilitated the process of representing medical data, however the complex inter-relationships of medical information can result in data models that are large and cumbersome to manipulate and view. This report presents a high-level object-oriented model for representing the relationships between objects or entities that might exist in an electronic medical record. By defining the relationship between objects at a high level and providing for inheritance, this model enables relating any medical entity to any other medical entity, even though the relationships were not directly specified or known during data model design.

Databases, Factual↗

Intelligent processing of loosely structured documents as a strategy for organizing electronic health care records.

Loosely structured documents can capture more relevant information about medical events than is possible using today's popular databases. In order to realize the full potential of this increased information content, techniques will be required that go beyond the static mapping of stored data into a single, rigid data model. Through intelligent processing, loosely structured documents can become a rich source of detailed data about actual events that can support the wide variety of applications needed to run a health-care organization, document medical care or conduct research. Abstraction and indirection are the means by which dynamic data models and intelligent processing are introduced into database systems. A system designed around loosely structured documents can evolve gracefully while preserving the integrity of the stored data. The ability to identify and locate the information contained within documents offers new opportunities to exchange data that can replace more rigid standards of data interchange.

Database Management Systems↗

Using agent-based technology to create a cost effective, integrated, multimedia view of the electronic medical record.

Image Engine is multi-user, client-server database for the storage, retrieval and sharing of a wide range of digitized biomedical images under development at the University of Pittsburgh. This paper provides an overview of the system and describes the use of agent-based technology to integrate clinical information from the Image Engine database and the MARS clinical information system at the University of Pittsburgh Medical Center. Agent-mediated links provide a mechanism for combining clinical data from multiple databases to create a unified, multimedia view of the electronic medical record.

Computer Communication Networks↗

Incompleteness and retrieval of case notes in a case note audit of colorectal cancer.

Hospital case notes are a crucial source of data but are subject to two major biases: incompleteness of data and non-retrieval. To assess these biases in relation to colorectal cancer a study was performed of all cases of colorectal cancer listed in the Thames cancer registry in patients resident in one of four districts in South Thames regions with a diagnosis in 1988. Five medical record sites were involved. Retrieval rate for all case notes for districts combined was 80%. In two districts the rates were too high for further investigation; in the other two respectively patient survival and whether treatment was given were positively associated with retrieval. Among the four districts incompleteness of notes ranged from 38% to 62% for staging, 8% to 40% for treatment, and 70% to 25% for diagnostic tests. Information about treatment was missing in 3% to 20%; survival data were omitted in less than 5%. In all districts completeness of case notes was inadequate and in some non-retrieval compounded the problem. Missing data reduce the quality of cancer registry data and potentially undermine interpretation of epidemiological studies and evaluation of care. Further research is warranted into the standards and resourcing of medical records departments and their effects on retrieval and data quality. Structured proformas could be applied across specialties to identify missing items in case notes, to identify areas where standards are required, or to audit notes where standards have already been agreed. A staging protocol to set standards for colorectal cancer has been adopted in one district, and a prospective audit is being established.

Colorectal Neoplasms↗

Storing, linking, and mining microarray databases using SRS.

BACKGROUND: SRS (Sequence Retrieval System) has proven to be a valuable platform for storing, linking, and querying biological databases. Due to the availability of a broad range of different scientific databases in SRS, it has become a useful platform to incorporate and mine microarray data to facilitate the analyses of biological questions and non-hypothesis driven quests. Here we report various solutions and tools for integrating and mining annotated expression data in SRS. RESULTS: We devised an Auto-Upload Tool by which microarray data can be automatically imported into SRS. The dataset can be linked to other databases and user access can be set. The linkage comprehensiveness of microarray platforms to other platforms and biological databases was examined in a network of scientific databases. The stored microarray data can also be made accessible to external programs for further processing. For example, we built an interface to a program called Venn Mapper, which collects its microarray data from SRS, processes the data by creating Venn diagrams, and saves the data for interpretation. CONCLUSION: SRS is a useful database system to store, link and query various scientific datasets, including microarray data. The user-friendly Auto-Upload Tool makes SRS accessible to biologists for linking and mining user-owned databases.

Computational Biology↗

SeqHound: biological sequence and structure database as a platform for bioinformatics research.

BACKGROUND: SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. RESULTS: SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. CONCLUSIONS: The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit.

Amino Acid Sequence↗

Reversal of a trimethyltin-induced learning deficit by desglycinamide-8-arginine vasopressin.

Trimethyltin (TMT) is an organometal neurotoxin which produces lesions primarily in the limbic system. Selectivity seems to depend upon the dose, but the hippocampus and related entorhinal cortical structures, of importance for learning and memory, are most often described as target sites. We have previously demonstrated that subjects treated with a moderate dose of TMT prior to acquisition sessions, are unable to learn a forward autoshaping task with a 6 sec delay of reinforcement, but are capable of acquiring the same task when no delay of reinforcement is used. These data suggested that the performance deficit is one of learning (i.e. consolidation) rather than of memory (i.e. storage), retrieval, or sensorimotor impairment. To more rigorously test this hypothesis, we determined if performance of a task already learned would be impaired by the neurotoxin. Adult male Long Evans rats were given 10 acquisition sessions of 24 trials, following which TMT (6.0 mg/kg, p.o.) was administered. One month later, these rats performed the lever-touching behavior as well as controls, despite the fact that the same dose of TMT interfered with learning if given one month prior to acquisition sessions, thus confirming our hypothesis. In a second experiment we determined if the peptide analog of vasopressin, desglycinamide-8-arginine vasopressin (DGAVP), could reverse a learning deficit in a population of non-learners. Rats were treated with TMT or water vehicle one month prior to autoshaping. TMT significantly retarded acquisition. After 10 sessions of 12 trials each, non-learners (i.e. rats treated with TMT that failed to associate the lever with delivery of a reinforcer) were administered saline or DGAVP (7.5 micrograms/kg, s.c.) 1 hr before sessions 11-13; treatment was discontinued prior to sessions 14 and 15. Peptide treated subjects showed evidence of acquisition and exhibited higher levels of lever-directed behavior than saline treated nonlearners. Performance was maintained after DGAVP treatment was discontinued, indicating that the learning-enhancing action of DGAVP was not transient or state-dependent.

Animals↗

Computerized meiotic mapping in Aspergillus nidulans.

A computer system for the storage and processing of microbial meiotic data has been developed. Based on the language Fortran 4, the program retrieves relevant data and determines the order, map distances, and coefficient of coincidence for any three-gene group. Meiotic data from Aspergillus nidulans were used to test the program. A total of 61 three-gene sequences were processed, and the results were found to be compatible with the published values. The advantages and disadvantages of computer analysis for genetic analysis are discussed.

Aspergillus↗

Neuropsychological correlates of a right unilateral lacunar thalamic infarction.

OBJECTIVES: To report on a patient with a lacunar infarction in the right intralaminar nuclei of the thalamus. The role of the thalamic intralaminar nuclei in cognitive function is as yet insufficiently known. The patient described has shown signs of apathy and loss of initiative, in combination with cognitive deficits, which have persisted essentially unaltered up to the present day since an abrupt onset 17 years ago. METHODS: High resolution MRI was performed to show the extent of the lesion; a combination of published and experimental neuropsychological techniques was administered to show the nature of the cognitive defects; Single photon emission computed tomography (SPECT) was employed to obtain a measure of cortical perfusion. RESULTS: Brain MRI disclosed an isolated lacunar infarction in the dorsal caudal intralaminar nuclei of the thalamus. Neuropsychological evaluation indicated problems with attention and concentration, executive disturbances, and memory deficits both in the visual and verbal domains. The memory deficits could not be attributed to problems in the early stages of information processing, and are hence regarded as resulting from a failure of retrieval rather than encoding or storage. Brain SPECT disclosed a hypoperfusion of the right frontal cortex. CONCLUSION: The data indicate that the cognitive profile is the result of a dysfunction of executive functions. This is corroborated by the finding of decreased blood flow in the right frontal cortex, and by evidence from the neuroanatomical literature. Thus the dysexecutive symptoms are thought to be caused by disconnection of the prefrontal cortex from the brainstem activating nuclei through the strategic localisation of the right thalamic infarction.

Adult↗

MEDLARS AND THE LIBRARY COMMUNITY.

The intention of the National Library of Medicine is to share with other libraries the products and the capabilities developed by the MEDLARS system. MEDLARS will provide bibliographic services of use to other libraries from the central system. The decentralization of the central system to permit libraries with access to computers to establish local machine retrieval systems is also indicated. The implications of such decentralization for the American medical library network and its effect on library evolution are suggested, as are the implications for international development of mechanized storage and retrieval systems.

Abstracting and Indexing↗

Query by pictionary: an alternative to medical image retrieval.

This paper focuses on the visual interface for image retrieval from radiology image database and describes a Radiologic Pictionary. A Radiologic Pictionary is a picture-based controlled vocabulary that allows visual query formulation by providing the user with images (samplers) that are linked to the hierarchical index of radiological findings and mapped into image data within the database. Samplers selected during query formulation point to image records that share their characteristics; all matching images are returned to the user.

Abstracting and Indexing↗