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PubMedDate not supplied

The Blue Obelisk-interoperability in chemical informatics.

The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group: a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.

Algorithms↗
PubMed1996

Utility of the National Cooperative Growth Study database for safety reporting.

The National Cooperative Growth Study (NCGS) maintains the largest database in the world, collecting information on patients with growth disorders treated with growth hormone (GH). More than 24,000 children have been monitored during its first decade (1985 through 1995). The database provides unique opportunities to learn about effectiveness of GH therapy in a real-world context. Its size also makes it possible to investigate rare adverse reactions, which is not reasonable in a randomized controlled trial (RCT). The frequency of adverse experiences reported in an observational study like the NCGS is lower than in an RCT, because the investigators in an observational study typically do not report events that they believe are clearly unrelated to the study drug. Nevertheless the NCGS has greatly facilitated collecting adverse-event data; approximately 75% of all adverse-event reports for GH received by the manufacturer are through NCGS data-collection forms. The NCGS has thus amassed a repository of GH safety data that is unparalleled. Furthermore, in contrast to an RCT, the NCGS database reflects real-world experience with long-term GH therapy in North America. Although the advantages of an observational study such as the NCGS must be recognized, such a study does differ from an RCT in important ways. For example, because the NCGS protocol allows customized patient treatment and individualization of GH therapy, it may be difficult to use the database to address questions (e. g., estimation of dose-response relationships, true incidence of adverse events) that require RCT designs.

Adverse Drug Reaction Reporting Systems↗
PubMed1999

IXDB, an X chromosome integrated database (update).

Chromosome specific databases are an important research tool as they integrate data from different directions, such as genetic and physical mapping data, expression data, sequences etc. They supplement the genome-wide repositories in molecular biology, such as GenBank, Swiss-Prot or OMIM, which usually concentrate on one type of information. The Integrated X Chromosome Database (IXDB, http://ixdb.mpimg-berlin-dahlem.mpg.de/) is a repository for physical mapping data of the human X chromosome and aims at providing a global view of genomic data at a chromosomal level. We present here an update of IXDB which includes schema extensions for storing submaps and sequence information, additional links to external databases, and the integration of an increasing number of physical and transcript mapping data. The gene data was completely updated according to the approved gene symbols of the HUGO Nomenclature Committee. IXDB receives over 1000 queries per month, an indication that its content is valuable to researchers seeking mapping data of the human X chromosome.

Chromosome Mapping↗
PubMed2026

Integrative analysis of single-cell sequencing identifies CD8+ TIM3+ CD101+ T cell-associated genes as prognostic biomarkers in breast cancer.

BACKGROUND: Breast cancer is a prevalent and deadly malignancy that significantly impacts women's quality of life and imposes financial burdens. Despite therapeutic advancements, tumour heterogeneity and frequent relapses remain major challenges. Accordingly, this study aimed to characterize immune features associated with CD8+ TIM3+ CD101+ T cells and develop a prognostic signature for breast cancer. METHODS: This study integrated single-cell and bulk transcriptomic datasets to characterize CD8+ TIM3+ CD101+ T cell (CCT)-related immune features and construct a prognostic signature in breast cancer. Single-cell RNA-seq data were sourced from the Gene Expression Omnibus (GEO) repository, and bulk transcriptomic data were from The Cancer Genome Atlas (TCGA) and GEO databases. Analytical methods included pseudo-time trajectory reconstruction (Monocle2), intercellular signalling analysis (CellChat), functional enrichment (ClusterProfiler), and immune profiling (ssGSEA). Prognostic modeling was conducted using least absolute shrinkage and selection operator (LASSO) Cox regression, with validation via Kaplan-Meier and time-dependent receiver operating characteristic (ROC) analyses. RESULTS: Single-cell analysis identified 17 clusters spanning seven cell types, including T cells, myeloid cells, and epithelial cells. T-cell sub-clustering revealed four subtypes. Pseudotime analysis suggested a potential state-transition relationship between CD8+ CD101- TIM3+ and CD8+ CD101+ TIM3+ T-cell states. A total of 121 differentially expressed genes were enriched in vital biological processes. An 11-gene prognostic model showed strong predictive power across cohorts. Single-cell T-cell reclustering identified a CD8+ CD101+ TIM3+ T-cell subpopulation, which was primarily characterized by the expression of markers such as CD101 and HAVCR2/TIM3. CONCLUSIONS: This study maps cellular heterogeneity and molecular networks in breast cancer, offering insights for targeted therapy and improved prognosis.

Breast invasive carcinoma↗
PubMed2003

A human tissue and data resource: an overview of opportunities, challenges, and development of a provider/researcher partnership model.

As we continue to strive to apply the findings of in vitro and animal studies to human disease and transition from genomics to proteomics, we will experience an ever-increasing need for human tissues. A web based system that provides access to tissues repositories and associated data will best facilitate the access to these vital resources and the application of research information to human disease treatment. There are organizational and design requirements that must be addressed in the implementation of the infrastructures that are needed to implement such a system, with special attention paid to the protection of patient anonymity. This report describes the implementation of a prototype human tissue network in the hope of encouraging implementation of similar systems among other consortia of providers and researchers.

Animals↗
PubMedDate not supplied

Organizing the present, looking to the future: an online knowledge repository to facilitate collaboration.

BACKGROUND: Comprehensive data available in the Canadian province of Manitoba since 1970 have aided study of the interaction between population health, health care utilization, and structural features of the health care system. Given a complex linked database and many ongoing projects, better organization of available epidemiological, institutional, and technical information was needed. OBJECTIVE: The Manitoba Centre for Health Policy and Evaluation wished to develop a knowledge repository to handle data, document research Methods, and facilitate both internal communication and collaboration with other sites. METHODS: This evolving knowledge repository consists of both public and internal (restricted access) pages on the World Wide Web (WWW). Information can be accessed using an indexed logical format or queried to allow entry at user-defined points. The main topics are: Concept Dictionary, Research Definitions, Meta-Index, and Glossary. The Concept Dictionary operationalizes concepts used in health research using administrative data, outlining the creation of complex variables. Research Definitions specify the codes for common surgical procedures, tests, and diagnoses. The Meta-Index organizes concepts and definitions according to the Medical Sub-Heading (MeSH) system developed by the National Library of Medicine. The Glossary facilitates navigation through the research terms and abbreviations in the knowledge repository. An Education Resources heading presents a web-based graduate course using substantial amounts of material in the Concept Dictionary, a lecture in the Epidemiology Supercourse, and material for Manitoba's Regional Health Authorities. Confidential information (including Data Dictionaries) is available on the Centre's internal website. RESULTS: Use of the public pages has increased dramatically since January 1998, with almost 6,000 page hits from 250 different hosts in May 1999. More recently, the number of page hits has averaged around 4,000 per month, while the number of unique hosts has climbed to around 400. CONCLUSIONS: This knowledge repository promotes standardization and increases efficiency by placing concepts and associated programming in the Centre's collective memory. Collaboration and project management are facilitated.

Databases as Topic↗
PubMed2007

Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.

Defining protein complexes is critical to virtually all aspects of cell biology. Two recent affinity purification/mass spectrometry studies in Saccharomyces cerevisiae have vastly increased the available protein interaction data. The practical utility of such high throughput interaction sets, however, is substantially decreased by the presence of false positives. Here we created a novel probabilistic metric that takes advantage of the high density of these data, including both the presence and absence of individual associations, to provide a measure of the relative confidence of each potential protein-protein interaction. This analysis largely overcomes the noise inherent in high throughput immunoprecipitation experiments. For example, of the 12,122 binary interactions in the general repository of interaction data (BioGRID) derived from these two studies, we marked 7504 as being of substantially lower confidence. Additionally, applying our metric and a stringent cutoff we identified a set of 9074 interactions (including 4456 that were not among the 12,122 interactions) with accuracy comparable to that of conventional small scale methodologies. Finally we organized proteins into coherent multisubunit complexes using hierarchical clustering. This work thus provides a highly accurate physical interaction map of yeast in a format that is readily accessible to the biological community.

Cluster Analysis↗
PubMed2002

Data collection in clinical toxicology: are there too many variables?

The evidence base of clinical toxicology suffers in comparison to other clinical disciplines. There is an excess of case reports and case series with little in the way of case control or cohort studies, and very few randomized controlled trials. While randomized controlled trials are rightly regarded as the gold standard for interventional studies, they have limitations that are particularly evident in the practice of clinical toxicology. Properly conducted observational studies using quantitative, epidemiological methods [nonrandomized trials, cohort studies (prospective and retrospective), case control methods] can provide answers that may be impossible to obtain from randomized controlled trials. Development of a strong evidence base is essential for progress in clinical toxicology. Whether that evidence base is derived from randomized controlled trials or observational studies, it is essential to collect data. Important observations can be made from basic clinical data and systematic collection of those data into some form of electronic database has siginificant advantages. A clinical database provides accurate information in the areas of clinical practice, quality assurance (audit), and research. In the area of research, an appropriately designed database can be both a source of hypotheses as well as a vehicle to test them. It can also serve as a repository of research data in subsequent randomized controlled trials.

Confounding Factors, Epidemiologic↗
PubMed2000

BALL--rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library.

MOTIVATION: Rapid software prototyping can significantly reduce development times in the field of computational molecular biology and molecular modeling. Biochemical Algorithms Library (BALL) is an application framework in C++ that has been specifically designed for this purpose. RESULTS: BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization. BALL has been carefully designed to be robust, easy to use, and open to extensions. Especially its extensibility which results from an object-oriented and generic programming approach distinguishes it from other software packages. BALL is well suited to serve as a public repository for reliable data structures and algorithms. We show in an example that the implementation of complex methods is greatly simplified when using the data structures and functionality provided by BALL.

Algorithms↗
PubMed2003

Proteomic informatics: in silico methods lead to data management challenges.

Proteomics, which identifies proteins and analyzes their function in cells, is foreseen as the next challenge in biomedicine as diseases in the body are most easily recognized through the function of their proteins. Achieving this recognition is more difficult than pure gene analysis: it is estimated that 35,000 genes are present in human DNA, encoding more than 1 million proteins. A myriad of in vitro and in silico technologies now exist for studying proteins and their biological function. This review focuses on the vast array of in silico proteomic analysis methods, highlights public and commercial repositories for this data, and discusses the challenges associated with resolving and integrating the knowledge originating from this data.

Amino Acid Sequence↗
PubMedDate not supplied

ArrayExpress: a public database of gene expression data at EBI.

ArrayExpress is a public repository for microarray-based gene expression data, resulting from the implementation of the MAGE object model to ensure accurate data structuring and the MIAME standard, which defines the annotation requirements. ArrayExpress accepts data as MAGE-ML files for direct submissions or data from MIAMExpress, the MIAME compliant web-based annotation and submission tool of EBI. A team of curators supports the submission process, providing assistance in data annotation. Data retrieval is performed through a dedicated web interface. Relevant results may be exported to ExpressionProfiler, the EBI based expression analysis tool available online (http://www.ebi.ac.uk/arrayexpress).

Computational Biology↗
PubMed1998

Six opinions on IT security. Panel discussion.

Physicians consult over the Internet. Diagnoses are delivered via E-mail. Data is kept in multimedia repositories. Health care IT is filled with data security challenges. Here's what six experts think about the possibilities and vulnerabilities.

Chronology as Topic↗
PubMed1981

Left ventriculometry: the Minnesota experience with a bioengineering approach.

Left ventriculography is used by cardiologists, surgeons, and pharmacologists. Cardiologists use it to assess ventricular function and to scan the results of longitudinal studies to follow the course of the patient. Surgeons employ the results to appreciate changes following surgery, as improvement postbypass, and to compare the effectiveness of alternative procedures or maneuvers. Pharmacologists examine the results to assess the consequences of drug administration. In patients with ischemic heart disease, left ventriculography is an indispensable adjunct to selective coronary arteriography, and it provides anatomic and functional information important for diagnosis and for predicting the outcome of the patient. Using the results from cine left ventriculography, it is possible to calculate the EDV, ESV, SV, and EF and thus to evaluate the pump function of the left ventricle objectively, quantitatively, and reproducibly. However, these measures indicate total left ventricular function. A more detailed analysis of the cine left ventriculogram can provide specific information about the impaired segments. Methods for measuring and calculating the volume changes of the entire left ventricle were described and illustrated with their clinical implementation. Five methods of determining regional myocardial wall motion were applied to a population of subjects with normal wall motion and to patients with abnormal wall motion. The method was chosen which agreed best with the visual assessment of the cine by experienced cardiovascular radiologists. Clinical applications of regional wall motion assessment were described. A computer-compatible data base was created for roentgen images of a normally and of an abnormally contracting left ventricle, and this data base was contributed to a national repository for computer-compatible data bases. An automatic pattern recognition method was used to determine whether regional wall motion was normal or abnormal, and it was able to distinguish between these two groups satisfactorily. Current trends in ventriculography were described. A bioengineering approach has been used to solve the problem of measuring and describing the wall motion of the left ventricle of the human heart. The approach has been applied to the analysis of the contraction of the whole ventricle, regional wall motion, and the temporal pattern of wall motion. The mathematical equations underlying the analysis have been given, explained, and illustrated with examples. The implementation of the analyses using computers was discussed. The assumptions and sources of error have received particular attention.

Angiocardiography↗
PubMed2004

A catalog of dermatology utilities: a measure of the burden of skin diseases.

Utilities are measures of quality of life that reflect the strength of individuals' preferences or values for a particular health outcome. As such, utilities represent a measure of disease burden. The aim of this article is to introduce the concept of utilities to the dermatology community and to present a catalog of dermatology utilities obtained from direct patient interviews. Our data are based on 236 total subjects from Grady Hospital (Atlanta, GA), Stanford Medical Center (Palo Alto, CA), and Parkland Hospital (Dallas, TX). The mean time trade-off utilities ranged from 0.640 for blistering disorders to 1.000 for alopecia, cosmetic, and urticaria. The mean utility across all diagnoses was 0.943. We present utilities for 17 diagnostic categories and discuss the underlying reasons for the significant disease burden that these utilities represent. We also present these dermatology categories relative to noncutaneous diseases to place the cutaneous utilities in perspective and to compare the burden of disease. We have demonstrated that skin diseases have considerable burden of disease and provided a preliminary repository of utility data for future researchers and policy makers.

Cost of Illness↗
PubMed2026

Freely available genomic datasets for atrial fibrillation research: current resources and analytical pipeline.

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, characterized by clinical and genetic heterogeneity. Increasing use of genomics and other omics approaches has driven reliance on publicly available AF datasets to advance biological discovery. Thus, this systematic review aimed to identify freely available genomic AF datasets through Mendeley Data and its interconnected repositories, and to characterize the most common analyses performed on these data. The search was conducted in adherence to the PRISMA 2020 guideline. Nineteen freely available genomic AF datasets were identified: Summary statistics for 'Biobank-driven genomic discovery yields new insight into atrial fibrillation biology', hum0014.v8.58qt.v1, AF GWAS in UK Biobank, UK Biobank (Publication 9659), GWAS summary statistics from a 2025 multi-ancestry AF meta-analysis, GSE115574, GSE128188, GSE14975, GSE2240, GSE238242, GSE254133, GSE261170, GSE271748, GSE271839, GSE293813, GSE294456, GSE31821, GSE41177, and GSE79768. The GEO datasets were further examined using differential gene expression, functional enrichment, protein-protein interaction networks, hub gene analysis, microRNA target prediction, and gene clustering, as well as, for the more recently deposited datasets, eQTL colocalization, single-cell/single-nucleus clustering, cell-cell communication analysis, and gene-dosage-dependent transcriptional and electrophysiological profiling. These analyses show some consistency but also considerable heterogeneity in initial conditions, data normalization, and analytical methodological settings. In conclusion, only a limited number of datasets are freely available, so additional, well-characterized and standardized datasets are needed to provide a complete picture of the AF pathology.

Mendeley Data↗