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At least 487 records · Page 27Linked to original sources

CVD: the intestinal crypt/villus in situ hybridization database.

UNLABELLED: The intestinal crypt/villus in situ hybridization database (CVD) query interface is a web-based tool to search for genes with similar relative expression patterns along the crypt/villus axis of the mammalian intestine. The CVD is an online database holding information for relative gene expression patterns in the mammalian intestine and is based on the scoring of in situ hybridization experiments reported in the literature. CVD contains expression data for 88 different genes collected from 156 different in situ hybridization profiles. The web-based query interface allows execution of both single gene queries and pattern searches. The query results provide links to the most relevant public gene databases. AVAILABILITY: http://pc113.imbg.ku.dk/ps/

Animals↗

Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach.

MOTIVATION: Sequence annotations, functional and structural data on snake venom neurotoxins (svNTXs) are scattered across multiple databases and literature sources. Sequence annotations and structural data are available in the public molecular databases, while functional data are almost exclusively available in the published articles. There is a need for a specialized svNTXs database that contains NTX entries, which are organized, well annotated and classified in a systematic manner. RESULTS: We have systematically analyzed svNTXs and classified them using structure-function groups based on their structural, functional and phylogenetic properties. Using conserved motifs in each phylogenetic group, we built an intelligent module for the prediction of structural and functional properties of unknown NTXs. We also developed an annotation tool to aid the functional prediction of newly identified NTXs as an additional resource for the venom research community. AVAILABILITY: We created a searchable online database of NTX proteins sequences (http://research.i2r.a-star.edu.sg/Templar/DB/snake_neurotoxin). This database can also be found under Swiss-Prot Toxin Annotation Project website (http://www.expasy.org/sprot/).

Animals↗

Automatic extraction of gene/protein biological functions from biomedical text.

MOTIVATION: With the rapid advancement of biomedical science and the development of high-throughput analysis methods, the extraction of various types of information from biomedical text has become critical. Since automatic functional annotations of genes are quite useful for interpreting large amounts of high-throughput data efficiently, the demand for automatic extraction of information related to gene functions from text has been increasing. RESULTS: We have developed a method for automatically extracting the biological process functions of genes/protein/families based on Gene Ontology (GO) from text using a shallow parser and sentence structure analysis techniques. When the gene/protein/family names and their functions are described in ACTOR (doer of action) and OBJECT (receiver of action) relationships, the corresponding GO-IDs are assigned to the genes/proteins/families. The gene/protein/family names are recognized using the gene/protein/family name dictionaries developed by our group. To achieve wide recognition of the gene/protein/family functions, we semi-automatically gather functional terms based on GO using co-occurrence, collocation similarities and rule-based techniques. A preliminary experiment demonstrated that our method has an estimated recall of 54-64% with a precision of 91-94% for actually described functions in abstracts. When applied to the PUBMED, it extracted over 190 000 gene-GO relationships and 150 000 family-GO relationships for major eukaryotes.

Abstracting and Indexing↗

PatGen--a consolidated resource for searching genetic patent sequences.

UNLABELLED: Compared to the wealth of online resources covering genomic, proteomic and derived data the Bioinformatics community is rather underserved when it comes to patent information related to biological sequences. The current online resources are either incomplete or rather expensive. This paper describes, PatGen, an integrated database containing data from bioinformatic and patent resources. This effort addresses the inconsistency of publicly available genetic patent data coverage by providing access to a consolidated dataset. AVAILABILITY: PatGen can be searched at http://www.patgendb.com CONTACT: rjdrouse@patentinformatics.com.

Abstracting and Indexing↗

Visualizing information across multidimensional post-genomic structured and textual databases.

MOTIVATION: Visualizing relationships among biological information to facilitate understanding is crucial to biological research during the post-genomic era. Although different systems have been developed to view gene-phenotype relationships for specific databases, very few have been designed specifically as a general flexible tool for visualizing multidimensional genotypic and phenotypic information together. Our goal is to develop a method for visualizing multidimensional genotypic and phenotypic information and a model that unifies different biological databases in order to present the integrated knowledge using a uniform interface. RESULTS: We developed a novel, flexible and generalizable visualization tool, called PhenoGenesviewer (PGviewer), which in this paper was used to display gene-phenotype relationships from a human-curated database (OMIM) and from an automatic method using a Natural Language Processing tool called BioMedLEE. Data obtained from multiple databases were first integrated into a uniform structure and then organized by PGviewer. PGviewer provides a flexible query interface that allows dynamic selection and ordering of any desired dimension in the databases. Based on users' queries, results can be visualized using hierarchical expandable trees that present views specified by users according to their research interests. We believe that this method, which allows users to dynamically organize and visualize multiple dimensions, is a potentially powerful and promising tool that should substantially facilitate biological research. AVAILABILITY: PhenogenesViewer as well as its support and tutorial are available at http://www.dbmi.columbia.edu/pgviewer/ CONTACT: Lussier@dbmi.columbia.edu.

Computer Graphics↗

Applying GIFT, a Gene Interactions Finder in Text, to fly literature.

UNLABELLED: A number of freely available text mining tools have been put together to extract highly reliable Drosophila gene interaction data from text. The system has been tested with The Interactive Fly, showing low recall (27-34%), but very high precision (93-97%). AVAILABILITY: The extracted data and a web interface for submission of texts to GIFT analysis are available at http://gift.cryst.bbk.ac.uk/gift CONTACT: n.domedel_puig@cryst.bbk.ac.uk SUPPLEMENTARY INFORMATION: Additional documentation, such as the dictionaries and the reference sets, are available at the GIFT website.

Artificial Intelligence↗

Markov model recognition and classification of DNA/protein sequences within large text databases.

MOTIVATION: Short sequence patterns frequently define regions of biological interest (binding sites, immune epitopes, primers, etc.), yet a large fraction of this information exists only within the scientific literature and is thus difficult to locate via conventional means (e.g. keyword queries or manual searches). We describe herein a system to accurately identify and classify sequence patterns from within large corpora using an n-gram Markov model (MM). RESULTS: As expected, on test sets we found that identification of sequences with limited alphabets and/or regular structures such as nucleic acids (non-ambiguous) and peptide abbreviations (3-letter) was highly accurate, whereas classification of symbolic (1-letter) peptide strings with more complex alphabets was more problematic. The MM was used to analyze two very large, sequence-containing corpora: over 7.75 million Medline abstracts and 9000 full-text articles from Journal of Virology. Performance was benchmarked by comparing the results with Journal of Virology entries in two existing manually curated databases: VirOligo and the HLA Ligand Database. Performance estimates were 98 +/- 2% precision/84% recall for primer identification and classification and 67 +/- 6% precision/85% recall for peptide epitopes. We also find a dramatic difference between the amounts of sequence-related data reported in abstracts versus full text. Our results suggest that automated extraction and classification of sequence elements is a promising, low-cost means of sequence database curation and annotation. AVAILABILITY: MM routine and datasets are available upon request.

Abstracting and Indexing↗

An online literature mining tool for protein phosphorylation.

A web-based version of the RLIMS-P literature mining system was developed for online mining of protein phosphorylation information from MEDLINE abstracts. The online tool presents extracted phosphorylation objects (phosphorylated proteins, phosphorylation sites and protein kinases) in summary tables and full reports with evidence-tagged abstracts. The tool further allows mapping of phosphorylated proteins to protein entries in the UniProt Knowledgebase based on PubMed ID and/or protein name. The literature mining, coupled with database association, allows retrieval of rich biological information for the phosphorylated proteins and facilitates database annotation of phosphorylation features.

Animals↗

PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature.

SUMMARY: PDQ Wizard automates the process of interrogating biomedical references using large lists of genes, proteins or free text. Using the principle of linkage through co-citation biologists can mine PubMed with these proteins or genes to identify relationships within a biological field of interest. In addition, PDQ Wizard provides novel features to define more specific relationships, highlight key publications describing those activities and relationships, and enhance protein queries. PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research. AVAILABILITY: PDQ Wizard is freely available from http://www.gti.ed.ac.uk/pdqwizard/.

Abstracting and Indexing↗

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↗

Variation in GP referral rates: what can we learn from the literature?

BACKGROUND: Variations in referral rates exist, at GP and practice level. Although the National Institute for Clinical Excellence is to produce referral guidelines, it is unclear if this variation requires regulation. A critical review of the literature on variation in referral rates was undertaken to see if existing evidence could inform the debate. OBJECTIVES: The aim of this study was to describe the variation in referral rates; to identify likely explanatory variables; and to describe the effect of GPs' decision making on the referral process. METHODS: Six bibliographic databases, the Cochrane Library, the NHS Centre for Reviews and Dissemination, and the National Research Register were searched. RESULTS: Patient characteristics explain <40% of the observed variation; practice and GP characteristics <10%. The availability of specialist care does affect referral rates, but its influence on the observed variation of referral rates is not known. Intrinsic psychological variables are important. GPs who are less tolerant of uncertainty or who perceive serious disease to be a more frequent event may refer more patients. There is a lack of consensus about what constitutes an appropriate referral, and the use of guidelines has had only limited success in altering referral behaviour. CONCLUSIONS: Variation in referral rates remains largely unexplained. Targeting high or low referrers through clinical guidelines may not be the issue. Rather, activity should concentrate on increasing the number of appropriate referrals, regardless of the referral rate. Pressure on GPs to review their referral behaviour through the use of guidelines may reduce their willingness to tolerate uncertainty and manage problems in primary care, resulting in an increase in referrals to secondary care. The use of referral rates to stimulate dialogue and joint working between primary and secondary care may be more appropriate.

Decision Making↗

Work-related disease in general practice: a systematic review.

OBJECTIVES: The objective was to answer the following questions: What is the prevalence of potentially work-related diseases in the general practice population? What is the incidence of consulting a GP for a potentially work-related disease? What is the relationship between diseases seen in general practice and work ability? METHODS: Cochrane standards and QUOROM principals were used. For this systematic review the available literature was identified in a computerized search of the bibliographical databases Medline, Embase and Osh-rom. A total of 22 publications (24 studies) met the inclusion criteria. RESULTS: In the general practice population high prevalence rates of potentially work-related diseases were found for low back pain, neck pain and shoulder pain. Incidence rates of consulting a GP for a potentially work-related disease were high also. Musculoskeletal disorders were the main reasons for work-related consultations in general practice. Work-related diseases can affect work ability. CONCLUSIONS: Work-related diseases are common, given the high incidence and prevalence of potentially work-related diseases found in the general practice population and seen by the GP. This review underlines the important role of GPs in identifying and managing work-related diseases. GPs should consider the work factor and pay special attention to the effects of work on health, because patients often link their work with their illness.

Epidemiologic Methods↗

Effectiveness of continuing education in long-term care: a literature review.

PURPOSE: This review of the literature examines the effectiveness of continuing education programs in long-term care facilities. DESIGN AND METHODS: A comprehensive literature search was made for evaluation studies and included computerized bibliographic databases, manual searches of journals, the bibliographies of retrieved articles, and information from key informants. RESULTS: Forty-eight studies met our selection criteria. Rigorous research in this area has been limited. Because of the lack of follow-up evaluation, there is minimal evidence that knowledge gained from training programs is sustained in the long term. Most studies do not consider organizational and system factors when planning and implementing training initiatives. This may account for difficulties encountered in the sustained transfer of knowledge to practice. IMPLICATIONS: There is a need for further rigorous research on the effectiveness of continuing education in long-term care, with systematic attention to the role of organizational and system factors.

Education, Continuing↗

Dementia care mapping: a review of the research literature.

PURPOSE: The published literature on dementia care mapping (DCM) in improving quality of life and quality of care through practice development and research dates back to 1993. The purpose of this review of the research literature is to answer some key questions about the nature of the tool and its efficacy, to inform the ongoing revision of the tool, and to set an agenda for future research. DESIGN AND METHODS: The DCM bibliographic database at the University of Bradford in the United Kingdom contains all publications known on DCM (http://www.bradford.ac.uk/acad/health/dcm). This formed the basis of the review. Texts that specifically examined the efficacy of DCM or in which DCM was used as a main measure in the evaluation or research were reviewed. RESULTS: Thirty-four papers were categorized into five main types: (a) cross-sectional surveys, (b) evaluations of interventions, (c) practice development evaluations, (d) multimethod evaluations, and (e) papers investigating the psychometric properties of DCM. IMPLICATIONS: These publications provide some evidence regarding the efficacy of DCM, issues of validity and reliability, and its use in practice and research. The need for further development and research in a number of key areas is highlighted.

Dementia↗

Insulin-sensitizing agents as primary therapy for patients with polycystic ovarian syndrome.

BACKGROUND: This paper is a systematic review of metformin versus clomiphene citrate (CC) in women with polycystic ovary syndrome (PCOS). METHODS: Meta-analysis Of Observational Studies in Epidemiology (MOOSE) and QUality Of Reporting Of Meta-analyses (QUOROM) guidelines were followed. A systematic computerized literature search was done of seven bibliographic databases. Inclusion criteria included cohort and randomized controlled trials (RCT) of women with PCOS and the following medications: metformin versus placebo; metformin versus CC; metformin plus CC versus placebo plus CC. Rev-man 4.1 and Metaview 4.0 were used to analyse data. Relative risk (RR) estimates were presented. A chi2-test determined the significance of the association. Heterogeneity was determined by the Cochran Q-test. RESULTS: Metformin was 50% better than placebo for ovulation induction in infertile PCOS patients [RR 1.50; 95% confidence interval (CI) 1.13, 1.99]. Metformin was also of benefit in non-infertile (i.e. patients with PCOS who were not complaining of infertility) PCOS patients for cycle regulation compared to placebo (RR 1.45; CI 1.11, 1.90). Metformin was not of confirmed benefit versus placebo for achievement of pregnancy (RR 1.07; CI 0.20, 5.74). Metformin plus CC may be 3-4-fold superior to CC alone for ovulation induction (RR 3.04; CI 1.77, 5.24) and pregnancy (RR 3.65; CI 1.11, 11.99) in women with PCOS. CONCLUSIONS: Metformin is effective for ovulation induction and cycle regulation in this group of patients. Metformin plus CC appears to be very effective for achievement of pregnancy compared to CC alone. No RCTs directly compare metformin to CC but the need for such a trial exists.

Clomiphene↗

A systematic review and meta-analysis of randomized controlled trials on metformin co-administration during gonadotrophin ovulation induction or IVF in women with polycystic ovary syndrome.

BACKGROUND: A systematic review of randomized controlled trials (RCTs) comparing whether metformin co-administration with gonadotrophins for ovulation induction (OI) with timed intercourse or IVF improves outcome in women with polycystic ovary syndrome (PCOS). METHODS: The quality of reporting of meta-analyses (QUOROM) guidelines were followed. A systematic computerized literature search of three bibliographic databases was performed. RESULTS: Eight RCTs were included in the overall review. Meta-analysis demonstrated that the co-administration of metformin to gonadotrophin OI does not significantly improve ovulation [odds ratio (OR) = 3.27; 95% confidence interval (95% CI) = 0.31-34.72] or pregnancy (OR = 3.46; 95% CI = 0.98-12.2) rates. Metformin co-administration to IVF treatment does not improve pregnancy (OR = 1.29; 95% CI = 0.84-1.98) or live birth (OR = 2.02, 95% CI = 0.98-4.14) rates but reduces the risk of ovarian hyperstimulation syndrome (OHSS) (OR = 0.21; 95% CI = 0.11-0.41, P < 0.00001). CONCLUSIONS: Current data on the use of metformin in the gonadotrophin OI or IVF treatment settings are inconclusive because of the review's failure to exclude an important clinical treatment effect. Further RCTs are necessary to definitively clarify whether metformin co-administration during gonadotrophin OI or IVF will improve the efficacy of these treatments in PCOS women.

Adult↗

A structured review of studies on health-related quality of life and economic evaluation in pediatric acute lymphoblastic leukemia.

BACKGROUND: A comprehensive review was made of the literature on the health-related quality of life (HRQL) and economic outcomes of children with acute lymphoblastic leukemia (ALL), the most common of all cancers in childhood. OBJECTIVES: The primary objectives of the review were to locate and describe measures of HRQL used in pediatrics and in pediatric oncology that might be applicable to ALL, to summarize studies that have applied HRQL measures to ALL, to identify and summarize economic evaluations of the costs and consequences of care for pediatric ALL, and to identify areas requiring further research. DATA SOURCES: To identify the HRQL literature in pediatric ALL, searches were run on the major biomedical and social science bibliographic databases. Search terms included a variety of MeSH and other thesaurus terms, text words, names of HRQL instruments, and the names of key authors in the field. The economic literature searches included most of the same databases, with the addition of the National Health Service Economic Evaluation Database and EconLit. Searches on specific authors and instruments and hand searches were also conducted. STUDY SELECTION: Only English language studies published from 1975 through 2000 were included. DATA EXTRACTION: Standardized data extraction forms were used to abstract information from HRQL and economic evaluation studies. Two reviewers independently screened the search results, and differences were resolved by consensus. DATA SYNTHESIS: A number of generic HRQL measures, both adult and pediatric, have been applied in pediatric ALL. In addition, a number of pediatric oncology-specific instruments and pediatric oncology disease-specific instruments have been developed. Most of these instruments have been used to measure the health status of patients undergoing therapy. Despite the limited numbers of patients and resources available to assess HRQL measures in children with cancer, a fairly substantial body of literature has been published. Economic studies of pediatric ALL have only recently been undertaken. Most studies focus on a particular, narrow aspect of costs associated with the disease. There are relatively few cost-effectiveness studies that compare the costs and consequences of two or more treatment options. There are no published, comprehensive economic evaluations of pediatric ALL. CONCLUSIONS: HRQL measures provide not only important information on the improvements offered by new therapies but also an outcome measure for economic evaluations. Recently developed HRQL measures and applications that include the direct assessments of children are important contributions. By the age of 7 or 8 years, children can generally provide reliable responses. Furthermore, children often provide information that is not available from parental reports (e.g., in the more subjective areas of pain and emotion). However, the use of multiple viewpoints, such as the patient, parent, and health professional perspectives, can provide valid and important complementary information. Expertise in HRQL measurement should be included in the design of most future trials. Funds for HRQL research should be made available to enhance the scope of HRQL activities by organizations such as the Children's Oncology Group. In the near future, further work to generate evidence of validity for available HRQL measures for use in children with ALL will be a high priority. Continuation of inquiries into the methods for HRQL assessment of younger children (i.e., preschoolers) is also a priority.

Child↗