Consultation-Liaison Psychiatry Literature Database (2003 update). Part II: topics, contributors, and database.
Explore the source record for details and available documents.
Databases, Bibliographic↗
SEARCH · Search PubMed
Results for “Databases as Topic”
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.
Bioinformatics in protein analysis.
The chapter gives an overview of bioinformatic techniques of importance in protein analysis. These include database searches, sequence comparisons and structural predictions. Links to useful World Wide Web (WWW) pages are given in relation to each topic. Databases with biological information are reviewed with emphasis on databases for nucleotide sequences (EMBL, GenBank, DDBJ), genomes, amino acid sequences (Swissprot, PIR, TrEMBL, GenePept), and three-dimensional structures (PDB). Integrated user interfaces for databases (SRS and Entrez) are described. An introduction to databases of sequence patterns and protein families is also given (Prosite, Pfam, Blocks). Furthermore, the chapter describes the widespread methods for sequence comparisons, FASTA and BLAST, and the corresponding WWW services. The techniques involving multiple sequence alignments are also reviewed: alignment creation with the Clustal programs, phylogenetic tree calculation with the Clustal or Phylip packages and tree display using Drawtree, njplot or phylo_win. Finally, the chapter also treats the issue of structural prediction. Different methods for secondary structure predictions are described (Chou-Fasman, Garnier-Osguthorpe-Robson, Predator, PHD). Techniques for predicting membrane proteins, antigenic sites and postranslational modifications are also reviewed.
Computational Biology↗
[Selection of annotated web sites devoted to documentation-health (updated as for July 2001)].
The author presents an annotated selection of web sites devoted to documentation and health. This directory may be used as bookmarks especially by the researchers who work in health, HIV/AIDS infection, and development fields.
Catalogs as Topic↗
Topics, contributors, and database. Consultation-Liaison Psychiatry Database (2000 update).
Explore the source record for details and available documents.
Databases, Bibliographic↗
ADAM: another database of abbreviations in MEDLINE.
MOTIVATION: Abbreviations are an important type of terminology in the biomedical domain. Although several groups have already created databases of biomedical abbreviations, these are either not public, or are not comprehensive, or focus exclusively on acronym-type abbreviations. We have created another abbreviation database, ADAM, which covers commonly used abbreviations and their definitions (or long-forms) within MEDLINE titles and abstracts, including both acronym and non-acronym abbreviations. RESULTS: A model of recognizing abbreviations and their long-forms from titles and abstracts of MEDLINE (2006 baseline) was employed. After grouping morphological variants, 59 405 abbreviation/long-form pairs were identified. ADAM shows high precision (97.4%) and includes most of the frequently used abbreviations contained in the Unified Medical Language System (UMLS) Lexicon and the Stanford Abbreviation Database. Conversely, one-third of abbreviations in ADAM are novel insofar as they are not included in either database. About 19% of the novel abbreviations are non-acronym-type and these cover at least seven different types of short-form/long-form pairs. AVAILABILITY: A free, public query interface to ADAM is available at http://arrowsmith.psych.uic.edu, and the entire database can be downloaded as a text file.
Animals↗
Databases, websites, and the Internet.
By the end of the year 2000, an estimated 100 to 500 million computers may be linked to the Internet, representing an enormous level of information exchange. Even today, a broad Internet search of a term such as "breast cancer" can produce an overwhelming list of web pages, most of which will not be of interest to the typical Internet user. A more sophisticated user such as the oncology professional will more likely refine the search by adding other terms, producing a more manageable and useful list of websites. Information on cancer can be readily accessed from thousands of websites developed by the government, medical organizations, other institutions, medical journals, patient support groups, and pharmaceutical companies, as well as through medical web directories. The Cancer Information Network (CIN), an independent website geared to the oncology community, provides access to Medline, PDQ, and hundreds of cancer-related resources on the World Wide Web. CIN also offers the complete NCCN conference proceedings and practice guidelines; full text of several medical journals, textbooks, and handbooks; a daily oncology news service; a clinically oriented drug reference guide; and an extensive calendar of medical meetings and CME courses.
Databases as Topic↗
A literature network of human genes for high-throughput analysis of gene expression.
We have carried out automated extraction of explicit and implicit biomedical knowledge from publicly available gene and text databases to create a gene-to-gene co-citation network for 13,712 named human genes by automated analysis of titles and abstracts in over 10 million MEDLINE records. The associations between genes have been annotated by linking genes to terms from the medical subject heading (MeSH) index and terms from the gene ontology (GO) database. The extracted database and accompanying web tools for gene-expression analysis have collectively been named 'PubGene'. We validated the extracted networks by three large-scale experiments showing that co-occurrence reflects biologically meaningful relationships, thus providing an approach to extract and structure known biology. We validated the applicability of the tools by analyzing two publicly available microarray data sets.
Computer Communication Networks↗
Phase4: automatic evaluation of database search methods.
It has become standard to evaluate newly devised database search methods in terms of sensitivity and selectivity and to compare them with existing methods. This involves the construction of a suitable evaluation scenario, the execution of the methods, the assessment of their performances, and the presentation of the results. Each of these four phases and their smooth connection usually imposes formidable work. To relieve the evaluator of this burden, a system has been designed with which evaluations can be effected rapidly. It is implemented in the programming language Python whose object-oriented features are used to offer a great flexibility in changing the evaluation design. A graphical user interface is provided which offers the usual amenities such as radio- and checkbuttons or file browsing facilities.
Data Interpretation, Statistical↗
Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases.
BACKGROUND: Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software configurations and are also often made available to users via the Internet. We have used the Java Data Object (JDO) persistence technology to develop the database layer of such a system known as the SigPath information management system. SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships. RESULTS: Using this system as an example, we perform a critical evaluation of current JDO technology; discuss the suitability of the JDO standard to achieve portability, scalability and performance. We show that JDO supports portability of the SigPath system from a relational database backend to an object database backend and achieves acceptable scalability. To answer the performance question, we have created the SigPath JDO application benchmark that we distribute under the Gnu General Public License. This benchmark can be used as an example of using JDO technology to create a complex biological database and makes it possible for vendors and users of the technology to evaluate the performance of other JDO implementations for similar applications. CONCLUSIONS: The SigPath JDO benchmark and our discussion of JDO technology in the context of biological databases will be useful to bioinformaticians who design new complex biological databases and aim to create systems that can be ported easily to a variety of database backends.
Computational Biology↗
[The role of electronic databases in practical decision making in the care of patients with cerebrovascular diseases].
The information revolution of recent years, the general accessibility of computers and especially the Internet, provided the possibility of immediate access to the newest and most reliable results of clinical research in everyday medical practice. When a question arises regarding the care of a certain patient, we can have answers within minutes. Summaries of systematic reviews of the Cochrane Library and abstracts of papers of several thousand journals indexed on MEDLINE are available free of charge. In addition, over 70,000 Internet home pages provide some sort of health care information. The fast accessibility of information made it possible to apply a new method, called evidence-based medicine, in everyday practice. This method implies the effective search of an answer to a well formed question, and the critical evaluation of the results found during the search. This paper summarises the most important electronic databases that can be used in the care of patients with cerebrovascular diseases. The paper emphasises the advantages and dangers of the use of the Internet. Enlisted are the most important English- and Hungarian-language home pages with information on cerebrovascular diseases. Internet addresses of home pages providing methodological help in critically evaluating the literature are also given. The paper summarises the most important questions to consider when we want to evaluate the validity and importance of papers on diagnostic methods, on prognosis, on treatment effect, when we read systematic reviews, economic evaluations, clinical decision analyses and guidelines.
Cerebrovascular Disorders↗
Biomedical named entity recognition using two-phase model based on SVMs.
Named entity (NE) recognition has become one of the most fundamental tasks in biomedical knowledge acquisition. In this paper, we present a two-phase named entity recognizer based on SVMs, which consists of a boundary identification phase and a semantic classification phase of named entities. When adapting SVMs to named entity recognition, the multi-class problem and the unbalanced class distribution problem become very serious in terms of training cost and performance. We try to solve these problems by separating the NE recognition task into two subtasks, where we use appropriate SVM classifiers and relevant features for each subtask. In addition, by employing a hierarchical classification method based on ontology, we effectively solve the multi-class problem concerning semantic classification. The experimental results on the GENIA corpus show that the proposed method is effective not only in reducing computational cost but also in improving performance. The F-score (beta=1) for the boundary identification is 74.8 and the F-score for the semantic classification is 66.7.
Abstracting and Indexing↗
Mining literature for systems biology.
Currently, literature is integrated in systems biology studies in three ways. Hand-curated pathways have been sufficient for assembling models in numerous studies. Second, literature is frequently accessed in a derived form, such as the concepts represented by the Medical Subject Headings (MeSH) and Gene Ontologies (GO), or functional relationships captured in protein-protein interaction (PPI) databases; both of these are convenient, consistent reductions of more complex concepts expressed as free text in the literature. Moreover, their contents are easily integrated into computational processes required for dealing with large data sets. Last, mining text directly for specific types of information is on the rise as text analytics methods become more accurate and accessible. These uses of literature, specifically manual curation, derived concepts captured in ontologies and databases, and indirect and direct application of text mining, will be discussed as they pertain to systems biology.
Animals↗
Measuring use patterns of online journals and databases.
PURPOSE: This research sought to determine use of online biomedical journals and databases and to assess current user characteristics associated with the use of online resources in an academic health sciences center. SETTING: The Library of the Health Sciences-Peoria is a regional site of the University of Illinois at Chicago (UIC) Library with 350 print journals, more than 4,000 online journals, and multiple online databases. METHODOLOGY: A survey was designed to assess online journal use, print journal use, database use, computer literacy levels, and other library user characteristics. A survey was sent through campus mail to all (471) UIC Peoria faculty, residents, and students. RESULTS: Forty-one percent (188) of the surveys were returned. Ninety-eight percent of the students, faculty, and residents reported having convenient access to a computer connected to the Internet. While 53% of the users indicated they searched MEDLINE at least once a week, other databases showed much lower usage. Overall, 71% of respondents indicated a preference for online over print journals when possible. CONCLUSIONS: Users prefer online resources to print, and many choose to access these online resources remotely. Convenience and full-text availability appear to play roles in selecting online resources. The findings of this study suggest that databases without links to full text and online journal collections without links from bibliographic databases will have lower use. These findings have implications for collection development, promotion of library resources, and end-user training.
Computer Literacy↗
Biosamples, genomics, and human rights: context and content of Iceland's Biobanks Act.
In recent years, human DNA sampling and collection has accelerated without the development of enforceable rules protecting the human rights of donors. The need for regulation of biobanking is especially acute in Iceland, whose parliament has granted a for-profit corporation, deCODE Genetics, an exclusive license to create a centralized database of health records for studies on human genetic variation. Until recently, how deCODE Genetics would get genetic material for its genotypic-phenotypic database remained unclear. However, in May 2000, the Icelandic Parliament passed the Icelandic Biobanks Act, the world's earliest attempt to construct binding rules for the use of biobanks in scientific research. Unfortunately, Iceland has lost an opportunity for bringing clear and ethically sound standards to the use of human biological samples in deCODE's database and in other projects: the Biobanks Act has extended a notion of "presumed consent" from the use of medical records to the use of patients' biological samples; worse, the act has made it possible--perhaps likely--that a donor's wish to withdraw his/her sample will be ignored. Inadequacies in the Act's legislative process help account for these deficiencies in the protection of donor autonomy.
Blood Specimen Collection↗
YeastHub: a semantic web use case for integrating data in the life sciences domain.
MOTIVATION: As the semantic web technology is maturing and the need for life sciences data integration over the web is growing, it is important to explore how data integration needs can be addressed by the semantic web. The main problem that we face in data integration is a lack of widely-accepted standards for expressing the syntax and semantics of the data. We address this problem by exploring the use of semantic web technologies-including resource description framework (RDF), RDF site summary (RSS), relational-database-to-RDF mapping (D2RQ) and native RDF data repository-to represent, store and query both metadata and data across life sciences datasets. RESULTS: As many biological datasets are presently available in tabular format, we introduce an RDF structure into which they can be converted. Also, we develop a prototype web-based application called YeastHub that demonstrates how a life sciences data warehouse can be built using a native RDF data store (Sesame). This data warehouse allows integration of different types of yeast genome data provided by different resources in different formats including the tabular and RDF formats. Once the data are loaded into the data warehouse, RDF-based queries can be formulated to retrieve and query the data in an integrated fashion. AVAILABILITY: The YeastHub website is accessible via the following URL: http://yeasthub.gersteinlab.org.
Biology↗
Utilisation of proteomics datasets generated via multidimensional protein identification technology (MudPIT).
Technological developments in proteomics have had a dramatic impact on biology in recent years. One of these developments--named multidimensional protein identification technology (MudPIT)--couples two-dimensional chromatography of peptides in mass spectrometry-compatible solutions directly to tandem mass spectrometry, allowing for the identification of proteins from highly complex mixtures. Since the initial descriptions of MudPIT, this approach has been implemented in the analysis of whole proteomes, organelles and protein complexes. Key aspects of many of the analyses are the validation of MudPIT datasets with alternate strategies and the integration of MudPIT datasets with other biochemical, cell biology or molecular biology approaches. This paper presents strategies for validating MudPIT datasets and incorporating these datasets into biologically driven experimental design.
Automation↗
M-study; arguments for regional trauma databases.
BACKGROUND: The TRISS methodology, in combination with coefficients derived from the Major Trauma Outcome Study (MTOS), is the most widely used outcome prediction model for the care of trauma patients. Utilizing the M-statistic, different populations of trauma patients can be compared with the population originally enrolled in the MTOS. PURPOSE: We hypothesized that databases outside of North-America would not be well matched to the MTOS study and thus the TRISS methodology would not accurately predict outcome in these different populations. METHODS: All trauma studies utilizing TRISS methodology that were published between 1990-2003 were reviewed and M-statistics calculated based on the population described in the study. The populations were grouped by the following geographic locations: Europe, Asia/Africa and North-America. RESULTS: The median M-statistic for Europe was 0.65, compared with 0.88 for Asian/African databases, and 0.90 for North-American studies. There was a significant difference between European and North-American studies (p < 0.05). CONCLUSION: The trauma populations described in European studies differ significantly from the MTOS with respect to injury severity match, indicating the need for the development of regional trauma databases and modified TRISS coefficients based on the geographic location of the injured population included.
Calibration↗
Searching biomedical databases on complementary medicine: the use of controlled vocabulary among authors, indexers and investigators.
BACKGROUND: The optimal retrieval of a literature search in biomedicine depends on the appropriate use of Medical Subject Headings (MeSH), descriptors and keywords among authors and indexers. We hypothesized that authors, investigators and indexers in four biomedical databases are not consistent in their use of terminology in Complementary and Alternative Medicine (CAM). METHODS: Based on a research question addressing the validity of spinal palpation for the diagnosis of neuromuscular dysfunction, we developed four search concepts with their respective controlled vocabulary and key terms. We calculated the frequency of MeSH, descriptors, and keywords used by authors in titles and abstracts in comparison to standard practices in semantic and analytic indexing in MEDLINE, MANTIS, CINAHL, and Web of Science. RESULTS: Multiple searches resulted in the final selection of 38 relevant studies that were indexed at least in one of the four selected databases. Of the four search concepts, validity showed the greatest inconsistency in terminology among authors, indexers and investigators. The use of spinal terms showed the greatest consistency. Of the 22 neuromuscular dysfunction terms provided by the investigators, 11 were not contained in the controlled vocabulary and six were never used by authors or indexers. Most authors did not seem familiar with the controlled vocabulary for validity in the area of neuromuscular dysfunction. Recently, standard glossaries have been developed to assist in the research development of manual medicine. CONCLUSIONS: Searching biomedical databases for CAM is challenging due to inconsistent use of controlled vocabulary and indexing procedures in different databases. A standard terminology should be used by investigators in conducting their search strategies and authors when writing titles, abstracts and submitting keywords for publications.
Abstracting and Indexing↗