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PubMed1990

On dividing reference data into subgroups to produce separate reference ranges.

We consider statistical criteria for partitioning a reference database to obtain separate reference ranges for different subpopulations. Using general formulas relating population variances, sample sizes, and the normal deviate test for the significance of the difference between two subgroup means, we show that partitioning into separate ranges produces little reduction in between-person variability, even when the differences between means are highly significant statistically. However, when there is a clear physiological basis for distinguishing between certain subgroups, simulation studies show that partitioning may be necessary to obtain reference limits that cut off the desired proportions of low and high values in each subgroup. Guidelines based on these results are provided to help decide whether separate ranges should be obtained for a given analyte.

Analysis of Variance↗
PubMed1994

A portable search engine and browser for the Entrez database.

Entrez is a molecular sequence and reference database. We present a tool called CLEVER which permits flexible access to the Entrez database by other applications and interactively by users. In this way, CLEVER is both a search engine and a command-line browser of the Entrez database.

Computer Communication Networks↗
PubMedDate not supplied

Approaching the millennium: perinatal problems and software solutions.

Strategic planning for rational development of perinatal computing capabilities for the year 2000 should be driven by anticipated trends in (1) the health care business, (2) computer technology and (3) medicine, as well as (4) the needs of perinatal practitioners. In the USA, health care is the fastest growing segment of the economy. This will produce increasing attention from hardware and software developers, and vendors, and will lead to a proliferation of computing platforms, operating systems and specific medical application software. Desktop computers, already capable of 20 million instructions per second (MIPS) with massive storage capacities, will continue to evolve and fall in price. Increasingly, perinatologists will develop software packages to facilitate patient care in their own environments. All of these trends will lead to severe fragmentation in medical computing. Simultaneously, however, the need for integrated institutional computer-based data access for quality assurance and fiscal and operations management will increase. Perinatal care will be more regionalized, complex and rigorous with new clinical trial- and effectiveness research-based interventions, as well as molecular diagnosis and therapy. To practice appropriately, clinicians will need to be familiar with computer capabilities. Having been exposed to computer-aided instruction (CAI) at the undergraduate and postgraduate levels, they will except on-line access to detailed and accurate patient information with linkage to laboratory, radiology and other medical databases, as well as to reference databases, such as Medlines and the Oxford Database of Perinatal Trials. Artificial intelligence (AI) software may support perinatal decision making; computerized professional and facility billing will be available.

Forecasting↗
PubMed2006

Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes.

Most common genetic disorders have a complex inheritance and may result from variants in many genes, each contributing only weak effects to the disease. Pinpointing these disease genes within the myriad of susceptibility loci identified in linkage studies is difficult because these loci may contain hundreds of genes. However, in any disorder, most of the disease genes will be involved in only a few different molecular pathways. If we know something about the relationships between the genes, we can assess whether some genes (which may reside in different loci) functionally interact with each other, indicating a joint basis for the disease etiology. There are various repositories of information on pathway relationships. To consolidate this information, we developed a functional human gene network that integrates information on genes and the functional relationships between genes, based on data from the Kyoto Encyclopedia of Genes and Genomes, the Biomolecular Interaction Network Database, Reactome, the Human Protein Reference Database, the Gene Ontology database, predicted protein-protein interactions, human yeast two-hybrid interactions, and microarray co-expressions. We applied this network to interrelate positional candidate genes from different disease loci and then tested 96 heritable disorders for which the Online Mendelian Inheritance in Man database reported at least three disease genes. Artificial susceptibility loci, each containing 100 genes, were constructed around each disease gene, and we used the network to rank these genes on the basis of their functional interactions. By following up the top five genes per artificial locus, we were able to detect at least one known disease gene in 54% of the loci studied, representing a 2.8-fold increase over random selection. This suggests that our method can significantly reduce the cost and effort of pinpointing true disease genes in analyses of disorders for which numerous loci have been reported but for which most of the genes are unknown.

Computational Biology↗
PubMed2006

methBLAST and methPrimerDB: web-tools for PCR based methylation analysis.

BACKGROUND: DNA methylation plays an important role in development and tumorigenesis by epigenetic modification and silencing of critical genes. The development of PCR-based methylation assays on bisulphite modified DNA heralded a breakthrough in speed and sensitivity for gene methylation analysis. Despite this technological advancement, these approaches require a cumbersome gene by gene primer design and experimental validation. Bisulphite DNA modification results in sequence alterations (all unmethylated cytosines are converted into uracils) and a general sequence complexity reduction as cytosines become underrepresented. Consequently, standard BLAST sequence homology searches cannot be applied to search for specific methylation primers. RESULTS: To address this problem we developed methBLAST, a sequence similarity search program, based on the original BLAST algorithm but querying in silico bisulphite modified genome sequences to evaluate oligonucleotide sequence similarities. Apart from the primer specificity analysis tool, we have also developed a public database termed methPrimerDB for the storage and retrieval of validated PCR based methylation assays. The web interface allows free public access to perform methBLAST searches or database queries and to submit user based information. Database records can be searched by gene symbol, nucleotide sequence, analytical method used, Entrez Gene or methPrimerDB identifier, and submitter's name. Each record contains a link to Entrez Gene and PubMed to retrieve additional information on the gene, its genomic context and the article in which the methylation assay was described. To assure and maintain data integrity and accuracy, the database is linked to other reference databases. Currently, the database contains primer records for the most popular PCR-based methylation analysis methods to study human, mouse and rat epigenetic modifications. methPrimerDB and methBLAST are available at http://medgen.ugent.be/methprimerdb and http://medgen.ugent.be/methblast. CONCLUSION: We have developed two integrated and freely available web-tools for PCR based methylation analysis. methBLAST allows in silico assessment of primer specificity in PCR based methylation assays that can be stored in the methPrimerDB database, which provides a search portal for validated methylation assays.

Algorithms↗
PubMed2005

Y chromosome STR typing.

Because of their unique transmission properties and male specificity, markers located on the nonrecombining region of the Y chromosome (NRY) have become an important tool in forensic investigation. In the past few years, more than 50 polymorphic Y chromosome-specific short tandem repeats (STRs) have been described and a set of 9 loci were selected, considered as the minimal haplotype included in the forensic databases, Y-STR Haplotype Reference Databases, the largest now available online (http://www.yhrd.org). Here, we describe a multiplex amplification strategy developed for ABI platforms to amplify the nine loci included in the minimal haplotype (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) as well as a second set of markers (DYS437, DYS438, DYS439, DYS460, DYS461, GATA A10, GATA C4, and GATA H4) used to improve the minimal haplotype diversity and, hence, the discrimination power. Together, these 17 Y-STRs can be used to define highly discriminative haplotypes, providing a powerful tool in male lineage identification.

Base Sequence↗
PubMed2002

Densitometric diagnosis of osteoporosis in men: effect of measurement site and normative database.

Controversy exists regarding which sites to measure, and the appropriate reference database to use, for densitometric diagnosis of osteoporosis in men. While hip and spine bone mineral density (BMD) measurement is routine, spinal osteoarthritis often elevates measured BMD in older men. Additionally, the use of male reference data is standard practice; however, recent reports suggest that a female database may be more appropriate. This study evaluated the effect of sites measured, and normative database utilized, on the densitometric diagnosis of osteoporosis in men. Spine, femur, and ultradistal radial BMD T-scores were determined in 595 male veterans using the GE Lunar male normative database. Subsequently, World Health Organization diagnostic criteria were applied, identifying 282 men with osteoporosis (T-score </= 2.5). The combination of femoral (lowest of neck or total) with the ultradistal radius site was more sensitive (p < 0.0001) for diagnosing osteoporosis than femur plus lumbar spine. When scans from 129 subjects with documented fractures were analyzed using female normative data, fewer (p < 0.0001) met an arbitrary threshold for receiving pharmacologic osteoporosis therapy. In conclusion, BMD measurement at only the spine and hip leads to underdiagnosis of osteoporosis in men. This situation will be exacerbated by utilization of a female normative database; more men with prior fracture may be categorized as not meeting a pharmaceutical intervention threshold.

Absorptiometry, Photon↗
PubMed2004

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database.

Large forensic mtDNA databases which adhere to strict guidelines for generation and maintenance, are not available for many populations outside of the United States and western Europe. We have established a high quality mtDNA control region sequence database for urban Nairobi as both a reference database for forensic investigations, and as a tool to examine the genetic variation of Kenyan sequences in the context of known African variation. The Nairobi sequences exhibited high variation and a low random match probability, indicating utility for forensic testing. Haplogroup identification and frequencies were compared with those reported from other published studies on African, or African-origin populations from Mozambique, Sierra Leone, and the United States, and suggest significant differences in the mtDNA compositions of the various populations. The quality of the sequence data in our study was investigated and supported using phylogenetic measures. Our data demonstrate the diversity and distinctiveness of African populations, and underline the importance of establishing additional forensic mtDNA databases of indigenous African populations.

Black People↗
PubMed1992

A profile for molecular biology databases and information resources.

This paper examines the requirements for building database management systems and multi-database information resources to support molecular biology research. The paper profiles the most important features of 16 integrated resources and 102 databases related to molecular biology research. The aspects surveyed in this paper include the nature of information in these databases, their sizes, update properties, cross-references, database management system heterogeneity, geographical distribution, data quality, use of temporal information and level of interpretation. The paper also comments on the access patterns to these databases. Since not all these aspects were available for all databases, specific comparisons sometimes compare fewer than the full 102 databases. Consequently, the same set of databases is not necessarily always being compared with respect to every aspect. The paper is organized primarily according to these comparison aspects and ends with some concluding remarks.

Databases, Bibliographic↗
PubMed2006

Bone mineral density of the spine and femur in healthy Chinese men.

AIM: To establish bone mineral density (BMD) reference database in healthy Chinese men of Han ethnicity, and to estimate the prevalence of osteoporosis in the population. METHODS: The BMD in the lumbar spine 1-4 (L1-4) and proximal femur was measured using dual energy X-ray absorptiometry in a total of 1 385 healthy Chinese men of Han ethnicity aged 20-89 years old in Shanghai. RESULTS: The highly significant negative correlation between age and BMD at any sites of proximal femur was found in the studied population, wheras no correlation between age and BMD at lumbar spine was observed. The peak BMD of the lumbar spine and any sites of hip in Chinese men was defined as the mean BMD for the subjects aged 20-89 years. According to World Health Organization (WHO) criteria, the BMD cut-off values for osteoporosis of the L1-4, total hip, femoral neck, trochanter and intertrochanter in Chinese men are 0.719, 0.638, 0.575, 0.437 and 0.725 g/cm(2), respectively. Using the current Chinese reference data, the prevalence of osteoporosis at the L1-4, total hip, femoral neck, trochanter and intertrochanter is 5.4%, 3.8%, 6.3%, 1.8% and 2.8% in 1 084 men aged 50 years or older, respectively. However, using a database for US non-Hispanic white men (NHANES III), the prevalence of osteoporosis or osteopenia at any sites of the hip was significantly higher than that while using the current Chinese reference data. CONCLUSION: The BMD reference database was established in healthy Chinese men of Han ethnicity, and will facilitate more accurate diagnosis of osteoporosis in Chinese men.

Absorptiometry, Photon↗
PubMed2004

DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics.

DBTBS (http://dbtbs.hgc.jp) was originally released in 1999 as a reference database of published transcriptional regulation events in Bacillus subtilis, one of the best studied bacteria. It is essentially a compilation of transcription factors with their regulated genes as well as their recognition sequences, which were experimentally characterized and reported in the literature. Here we report its major update, which contains information on 114 transcription factors, including sigma factors, and 633 promoters of 525 genes. The number of references cited in the database has increased from 291 to 378. It also supports a function to find putative transcription factor binding sites within input sequences by using our collection of weight matrices and consensus patterns. Furthermore, though preliminarily, DBTBS now aims to contribute to comparative genomics by showing the presence or absence of potentially orthologous transcription factors and their corresponding cis-elements on the promoters of their potentially orthologously regulated genes in 50 eubacterial genomes.

Bacillus subtilis↗
PubMed2004

Casimage project: a digital teaching files authoring environment.

The goal of the Casimage project is to offer an authoring and editing environment integrated with the Picture Archiving and Communication Systems (PACS) for creating image-based electronic teaching files. This software is based on a client/server architecture allowing remote access of users to a central database. This authoring environment allows radiologists to create reference databases and collection of digital images for teaching and research directly from clinical cases being reviewed on PACS diagnostic workstations. The environment includes all tools to create teaching files, including textual description, annotations, and image manipulation. The software also allows users to generate stand-alone CD-ROMs and web-based teaching files to easily share their collections. The system includes a web server compatible with the Medical Imaging Resource Center standard (MIRC, http://mirc.rsna.org) to easily integrate collections in the RSNA web network dedicated to teaching files. This software could be installed on any PACS workstation to allow users to add new cases at any time and anywhere during clinical operations. Several images collections were created with this tool, including thoracic imaging that was subsequently made available on a CD-Rom and on our web site and through the MIRC network for public access.

CD-ROM↗
PubMed2003

The clinical and cost-effectiveness of patient education models for diabetes: a systematic review and economic evaluation.

OBJECTIVES: To assess the clinical effectiveness and cost-effectiveness of educational interventions for patients with diabetes, compared with usual care or other educational interventions. DATA SOURCES: Electronic databases, reference lists and experts were all consulted in this study. Sponsor submissions to the National Institute of Clinical Excellence were also reviewed. REVIEW METHODS: Electronic databases were searched, references of all retrieved articles were checked for relevant studies, and experts were contacted for advice and peer review and to identify additional published and unpublished references. Randomised clinical trials (RCTs) and controlled clinical trials (CCTs) were included if they fulfilled pre-specified criteria, among which was follow-up from inception for 12 months or longer. Data were synthesised through a narrative review because the diversity of studies prevented a meta-analysis. RESULTS: Twenty-four studies (18 RCTs and six CCTs) that compared education with either a control group or with another educational intervention were included. The quality of reporting and methodology was generally found to be poor by today's standards. As part of treatment intensification, education in Type 1 diabetes (four studies) resulted in significant and long-lasting improvements in metabolic control and reductions in complications. In Type 2 diabetes (16 studies) a diversity of educational programmes did not yield consistent results on measures of metabolic control. Inconsistent results on metabolic control were also found in studies of diabetes of either type (four studies), with studies of lower quality producing significant effects. Few studies evaluated quality of life. Economic evaluations comparing education with usual care or other educational interventions were not identified. CONCLUSIONS: Education as part of intensification of treatment produces improvement in diabetic control in Type 1 diabetes. Mixed results in Type 2 diabetes mean that no clear characterisation is possible as to what features of education may be beneficial. Cost analysis and information from sponsor submissions indicated that where costs associated with patient education were in the region of 500-600 pounds sterling per patients, the benefits over time would have to be very modest to offer an attractive cost-effectiveness profile. Further research should focus on RCTs with clear designs based on explicit hypotheses and with a range of outcomes evaluated after long follow-up intervals.

Cost-Benefit Analysis↗
PubMed2002

A systematic compilation and classification of the literature on lameness in cattle.

This paper presents the first systematic review of the literature on lameness in cattle. It identifies, tabulates and classifies relevant published work and was conducted using electronic reference databases (BIDS ISI, BIOSIS, MEDLINE and the CAB Abstracts CD-ROM). A total of 1373 unique references were obtained from 1981 to 2000, of which 914 were written in the English language. A written search protocol was designed to ensure transparency and repeatability. Pilot studies were undertaken to create search terms that minimised bias and ensured relevance. Electronic files of the search terms allow the database to be updated in future. A further 93 references were included from the most recent international conference on lameness giving a total of 1007 English language references. The systematic review process is described, including a method of classifying papers according to their study design and statistical analysis, and it is hoped that other veterinary researchers will conduct similar reviews in their fields. The compiled and classified references are available as a searchable database through the web-sitehttp://cattle-lameness.dhs.org/. The review may be used in several ways; to identify practical interventions to reduce lameness in dairy cows and to use the resultant web-site as the basis of a decision support system for farmers, veterinarians and advisors.

Animals↗
PubMed2005

Use of normative databases and statistical methods in demonstrating clinical utility of QEEG: importance and cautions.

The clinical utility of the EEG, especially in psychiatric, learning and cognitive disorders, has been greatly enhanced by the use of quantitative analysis (QEEG) and comparisons to a normative database. Of primary importance in the use of such a reference database are the following considerations and cautions: adequate sampling across a broad age range; consideration of inclusion/exclusion criteria; adequate sample of artifact-free data to demonstrate reliability and replicability of norms; demonstration of specificity and sensitivity. A normative database meeting these criteria allows the multivariate description of patterns of QEEG abnormalities in patients as compared to age appropriate normative values, and the exploration of neurophysiological heterogeneity within populations. Demonstrations of the clinical significance of this approach exist in the scientific literature and demonstrate that QEEG provides high sensitivity and specificity to abnormalities in brain function seen in psychiatric populations.

Algorithms↗
PubMed2005

MetaCyc and AraCyc. Metabolic pathway databases for plant research.

MetaCyc (http://metacyc.org) contains experimentally determined biochemical pathways to be used as a reference database for metabolism. In conjunction with the Pathway Tools software, MetaCyc can be used to computationally predict the metabolic pathway complement of an annotated genome. To increase the breadth of pathways and enzymes, more than 60 plant-specific pathways have been added or updated in MetaCyc recently. In contrast to MetaCyc, which contains metabolic data for a wide range of organisms, AraCyc is a species-specific database containing only enzymes and pathways found in the model plant Arabidopsis (Arabidopsis thaliana). AraCyc (http://arabidopsis.org/tools/aracyc/) was the first computationally predicted plant metabolism database derived from MetaCyc. Since its initial computational build, AraCyc has been under continued curation to enhance data quality and to increase breadth of pathway coverage. Twenty-eight pathways have been manually curated from the literature recently. Pathway predictions in AraCyc have also been recently updated with the latest functional annotations of Arabidopsis genes that use controlled vocabulary and literature evidence. AraCyc currently features 1,418 unique genes mapped onto 204 pathways with 1,156 literature citations. The Omics Viewer, a user data visualization and analysis tool, allows a list of genes, enzymes, or metabolites with experimental values to be painted on a diagram of the full pathway map of AraCyc. Other recent enhancements to both MetaCyc and AraCyc include implementation of an evidence ontology, which has been used to provide information on data quality, expansion of the secondary metabolism node of the pathway ontology to accommodate curation of secondary metabolic pathways, and enhancement of the cellular component ontology for storing and displaying enzyme and pathway locations within subcellular compartments.

4-Hydroxyphenylpyruvate Dioxygenase↗
PubMed2026

CamK-DB: A k-mer MinHash fingerprint database for reference-free genotyping of Camellia accessions.

Tea (Camellia sinensis L.), a major global economic crop in Asia, poses challenges for genetic identification because its highly heterozygous, repetitive genome reduces the efficacy of conventional single-nucleotide polymorphism (SNP) and microsatellite markers, and interspecific hybridization further complicates the situation. To address these issues, CamK-DB was developed as a reference-free Camellia fingerprinting database built on MIKE MinHash sketches. We curated 418 candidate resequencing datasets, and built a database using standardized 5&#xd7; genome-coverage fingerprints. Each accession is stored as a MIKE. jac fingerprint generated with k = 21 and recommended sketch/pre_cnt = 2000. CamK-DB provides a command-line interface for data management and a custom C++ query engine that computes top-10 matches using Jaccard similarity, complemented by a QT-based graphical interface for interactive analysis. This resource offers a robust and scalable framework for precise and routine germplasm identification, genomic phylogenetic inference, and strategic breeding program design. CamK-DB (database and code) is publicly available at&#xa0;https://github.com/sc-zhang/CamK-DB. CamK-DB binaries are provided for Windows 10/11 and Linux (x86_64, glibc &#x2265; 2.27).

Databases, Genetic↗
PubMed2006

Estimating probabilities of peptide database identifications to LC-FTICR-MS observations.

BACKGROUND: The field of proteomics involves the characterization of the peptides and proteins expressed in a cell under specific conditions. Proteomics has made rapid advances in recent years following the sequencing of the genomes of an increasing number of organisms. A prominent technology for high throughput proteomics analysis is the use of liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS). Meaningful biological conclusions can best be made when the peptide identities returned by this technique are accompanied by measures of accuracy and confidence. METHODS: After a tryptically digested protein mixture is analyzed by LC-FTICR-MS, the observed masses and normalized elution times of the detected features are statistically matched to the theoretical masses and elution times of known peptides listed in a large database. The probability of matching is estimated for each peptide in the reference database using statistical classification methods assuming bivariate Gaussian probability distributions on the uncertainties in the masses and the normalized elution times. RESULTS: A database of 69,220 features from 32 LC-FTICR-MS analyses of a tryptically digested bovine serum albumin (BSA) sample was matched to a database populated with 97% false positive peptides. The percentage of high confidence identifications was found to be consistent with other database search procedures. BSA database peptides were identified with high confidence on average in 14.1 of the 32 analyses. False positives were identified on average in just 2.7 analyses. CONCLUSION: Using a priori probabilities that contrast peptides from expected and unexpected proteins was shown to perform better in identifying target peptides than using equally likely a priori probabilities. This is because a large percentage of the target peptides were similar to unexpected peptides which were included to be false positives. The use of triplicate analyses with a "2 out of 3" reporting rule was shown to have excellent rejection of false positives.

Journal Article↗