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PubMed2002

Building a genome database using an object-oriented approach.

GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.

Databases, Genetic↗
PubMed2002

Prediction of food protein allergenicity: a bioinformatic learning systems approach.

Food hypersensitivity is constantly increasing in Western societies with a prevalence of about 1-2% in Europe and in the USA. Among children, the incidence is even higher. Because of the introduction of foods derived from genetically modified crops on the marketplace, the scientific community, regulatory bodies and international associations have intensified discussions on risk assessment procedures to identify potential food allergenicity of the newly introduced proteins. In this work, we present a novel biocomputational methodology for the classification of amino acid sequences with regard to food allergenicity and non-allergenicity. This method relies on a computerised learning system trained using selected excerpts of amino acid sequences. One example of such a successful learning system is presented which consists of feature extraction from sequence alignments performed with the FASTA3 algorithm (employing the BLOSUM50 substitution matrix) combined with the k-Nearest-Neighbour (kNN) classification algorithm. Briefly, the two features extracted are the alignment score and the alignment length and the kNN algorithm assigns the pair of extracted features from an unknown sequence to the prevalent class among its k nearest neighbours in the training (prototype) set available. 91 food allergens from several specialised public repositories of food allergy and the SWALL database were identified, pre-processed, and stored, yielding one of the most extensively characterised repositories of allergenic sequences known today. All allergenic sequences were classified using a standard one-leave-out cross validation procedure yielding about 81% correctly classified allergens and the classification of 367 non-allergens in an independent test set resulted in about 98% correct classifications. The biocomputational approach presented should be regarded as a significant extension and refinement of earlier attempts suggested for in silico food safety assessment. Our results show that the framework described here is powerful enough to become useful as part of a multiple-procedure test scheme that also depicts other evaluation approaches such as solid phase immunoassay and tests for stability to digestions.

Algorithms↗
PubMed1958

Clinical problems in the antibiotic treatment of gonorrhoea.

After briefly reviewing the history of penicillin therapy in gonorrhoea, the author shows that the number of cures effected with the repository penicillins, although originally very high, has diminished considerably in recent years, despite a general tendency to increase the dosage. The reduced efficacy of PAM and benzathine penicillin is demonstrated by an exposition of the current results obtained with these two preparations in the treatment of gonorrhoea patients in London. Some of the difficulties involved in distinguishing between treatment failures and reinfections are discussed.The paper continues with an examination of the possible alternatives to repository penicillin in the treatment of gonorrhoea. Data are given on the comparative efficacy of a number of prepations, including mixed penicillins, phenoxymethyl penicillin and various other antibiotics, such as streptomycin and the tetracycline group.The problem of re-examination of treated gonorrhoea cases is also dealt with, practical reasons being given for restricting the period of follow-up to three weeks.Finally, in a discussion of possible future developments, the author suggests a number of measures designed to prevent a further loss of sensitivity to penicillin in the gonococcus.

Anti-Bacterial Agents↗
PubMed1965

MEDICAL ARTICLES IN EIGHTEENTH CENTURY AMERICAN MAGAZINES.

Formal medical publication began in the United States with The Medical Repository in 1797. Between 1741, the date of the first American magazine, and 1797 medical articles were included in general magazines. This study deals with ten representative magazines and reviews their general content. The varying content of the medical articles is analyzed into broad categories, and several important physicians, contributors to the magazines, are discussed. The Medical Repository is treated as a culmination of eighteenth century medical publication.

Ethnicity↗
PubMed2002

Intelligent healthcare information assistant: towards agent-based healthcare knowledge management.

Initiatives in healthcare knowledge management have provided some interesting solutions for the implementation of large-scale information repositories vis-à-vis the implementation of Healthcare Enterprise Memories (HEM). In this paper, we present an agent-based Intelligent Healthcare Information Assistant (IHIA) for dynamic information gathering, filtering and adaptation from a HEM comprising an amalgamation of (i) databases storing empirical knowledge, (ii) case-bases storing experiential knowledge, (iii) scenario-bases storing tacit knowledge and (iv) document-bases storing explicit knowledge. The featured work leverages intelligent agents and medical ontologies for autonomous HEM-wide navigation, approximate content matching, inter- and intra-repositories content correlation and information adaptation to meet the user's information request. We anticipate that the use of IHIA will empower healthcare stakeholders to actively communicate with an 'information/knowledge-rich' HEM and will be able to retrieve with ease 'useful' task-specific information via the presentation of cognitively intuitive queries.

Internet↗
PubMed2005

The Community Physicians' Network (CPN): an academic-community partnership to eliminate healthcare disparities.

INTRODUCTION: Disparities in health care are maintained by three primary factors: 1) patient factors which include multiple risk factors and comorbidities; 2) healthcare practitioner factors comprising inconsistent application of practice guidelines due to a limited database of clinical trials of effective therapies in African Americans and other underrepresented minorities; and 3) barriers in the healthcare delivery system resulting in poor access to care. The Morehouse School of Medicine Community Physicians' Network (CPN) was established to address disparities in health care by focusing on provider-specific strategies. OBJECTIVES: To: 1) use disease-specific registries to identify treatment gaps and facilitate quality improvement processes among CPN practices; 2) develop practice-specific and guideline-based educational messages to promote quality care; 3) engage and train CPN-physicians for participation in approved NIH, other government, and industry-supported clinical protocols; and 4) develop a data repository of all CPN-sponsored clinical trials that include significant numbers of African Americans and other underrepresented minorities. METHODS: The disease-specific outpatient registries will have the following features: 1) data structures and data elements will use standard database codes and a data dictionary; 2) HIPPA-compliant data abstraction and data transfer tool; 3) baseline chart review to establish practice patterns and provide practice-specific feedback; 4) annual update of registry; 5) data registry and repository maintained on Morehouse School of Medicine's secure servers; 6) registry publications will include only aggregate data, without identification of contributing practices; 7) an electronic medical records platform will be encouraged as the ultimate data management tool for CPN practices. In addition, up to three continuing medical education (CME) programs each year will feature national speakers and promote evidence-based practice guidelines. RESULTS: Eighty-five primary care and subspecialty practices are actively enrolled in CPN with a total of 385,000 annual outpatient visits. The makeup of insurance status is: HMO/PPO (45%); Medicare only (19%); Medicare HMO (11%); Medicare plus (8%); Medicaid (6%); Uninsured (11%). CONCLUSIONS: The Community Physicians' Network will address specific gaps in the health care of African-American and other minority patients by promoting quality care among its members and by facilitating participation in approved clinical trial protocols. The unique academic community partnership is consistent with the NIH roadmap goal of eliminating healthcare disparities.

Black or African American↗
PubMed2006

Designing new methodologies for integrating biomedical information in clinical trials.

OBJECTIVES: To propose a modification to current methodologies for clinical trials, improving data collection and cost-efficiency. To describe a system to integrate distributed and heterogeneous medical and genetic databases for improving information access, retrieval and analysis of biomedical information. METHODS: Data for clinical trials can be collected from remote, distributed and heterogeneous data sources. In this distributed scenario, we propose an ontologybased approach, with two basic operations: mapping and unification. Mapping outputs the semantic model of a virtual repository with the information model of a specific database. Unification provides a single schema for two or more previously available virtual repositories. In both processes, domain ontologies can improve other traditional approaches. RESULTS: Private clinical databases and public genomic and disease databases (e.g., OMIM, Prosite and others) were integrated. We successfully tested the system using thirteen databases containing clinical and biological information and biomedical vocabularies. CONCLUSIONS: We present a domain-independent approach to biomedical database integration, used in this paper as a reference for the design of future models of clinico-genomic trials where information will be integrated, retrieved and analyzed. Such an approach to biomedical data integration has been one of the goals of the IST INFOBIOMED Network of Excellence in Biomedical Informatics, funded by the European Commission, and the new ACGT (Advanced Clinico-Genomic Trials on Cancer) project, where the authors will apply these methods to research experiments.

Clinical Trials as Topic↗
PubMed2005

Medical facts to support inferencing in natural language processing.

We report on the use of medical facts to support the enhancement of natural language processing of biomedical text. Inferencing in semantic interpretation depends on a fact repository as well as an ontology. We used statistical methods to construct a repository of drug-disorder co-occurrences from a large collection of clinical notes, and this resource is used to validate inferences automatically drawn during semantic interpretation of Medline citations about pharmacologic interventions for disease. We evaluated the results against a published reference standard for treatment of diseases.

Disease↗
PubMed2006

Advancing of Russian ChemBioGrid by bringing Data Management tools into collaborative environment.

Virtual organizations of researchers need effective tools to work collaboratively with huge sets of heterogeneous data distributed over HealthGrid. This paper describes a mechanism of supporting Digital Libraries in High-Performance Computing environment based on Grid technology. The proposed approach provides abilities to assemble heterogeneous data from distributed sources into integrated virtual collections by using OGSA-DAI. The core of the conception is a Repository of Meta-Descriptions that are sets of metadata which define personal and collaborative virtual collections on base of virtualized information resources. The Repository is kept in a native XML-database Sedna and is maintained by Grid Data Services.

Cooperative Behavior↗
PubMed2006

An XML-based framework for personalized health management.

This paper proposes a framework for personalized health management. In this framework, XML technology is used for representing and managing the health information and knowledge. Major components of the framework are Health Management Prescription (HMP) Expert System and Health Information Repository. The HMP Expert System generates a HMP efficiently by using XML-based templates. Health Information Repository provides integrated health information and knowledge for personalized health management by using XML and relational database together.

Humans↗
PubMed1991

Using comparative clinical information to understand practice patterns and affect organizational change.

The University Hospital Consortium is collecting clinical, administrative and financial data from its members to develop a Clinical Information Network. The value of this collective data lies in how comparative information about peer hospitals and physicians in the same specialty can be used to influence practice. The raw data from each hospital is analyzed, classified, normalized and stored in a data repository which is easily accessible. This data becomes information when it is presented in a variety of ways, and is supported by a knowledge-base of health care rules. The "drilling down" technique to progressive levels of detail serves the needs of all levels in the organization--executives, managers, and analysts. The system combines the power of a mainframe for the data repository with the ease of use of a PC-based workstation. With an open-ended approach, the users can ask a variety of questions of the data, as well as perform statistical analysis, create graphical presentations and generate explanations of the analysis techniques.

Artificial Intelligence↗
PubMed1991

A variant database.

Variant biomacromolecules, either natural or artificially created, are proving to be useful in determining structure-function relationships. Research in this field would be facilitated by the compilation of data of variants into a central and widely available repository. The Variant Database acts as a repository for data concerning variant molecules. It complements the Biological Activity and the Physicochemical Property Databases as well as provides variant sequences.

Amino Acid Sequence↗
PubMedDate not supplied

Screening of Morinda lucida leaf extract for antimalarial action on Plasmodium berghei berghei in mice.

The leaf extract of Morinda lucida collected in August was administered subcutaneously to albino Swiss mice infected with P. berghei berghei. The schizontocidal activity on early infection was assessed by administering chloroquine (standard) distilled water or Morinda lucida as single daily dose on day 0-3 to infected mice. On day 4 the degree of parasitaemia and percentage was determined in relation to control. Its schizontocidal activity was also observed on an established infection by administering the drugs 72 h after infecting the mice and the degree of parasitaemia was determined daily. The repository action of pyrimethamine was also compared with Morinda lucida. On the early infection, the chloroquine equivalent of Morinda lucida was found to be 1.0 mg/kg. In established infection a daily increase in parasitaemia was observed in control group while the animals that received chloroquine (5 mg/kg) and 1/6 dilution of the stock of Morinda lucida extract showed a sharp fall in parasitaemia from the second day of treatment. For the prophylactic test, 1.2 mg/kg of pyrimethamine and 1/6 dilution of stock of extract produced 80.5% and 70% chemosuppression respectively. It is interesting to note that Morinda lucida leaves extract appears to have schizontocidal and repository effects in mice infected with P. berghei berghei.

Animals↗
PubMed1987

Echographic localization of corticosteroids after periocular injection.

The location of repository corticosteroid after subtenon injection was determined in 24 patients with macular edema associated with uveitis or anterior segment surgery. Standardized A-scan and B-scan echography were performed immediately before and after each injection. Localization was compared after subtenon injection in either the superior or inferior temporal quadrants. Echography showed that corticosteroid was deposited within the subtenon space over the macula in 11 of 24 cases. The therapeutic response manifested by improvement in macular function may be related to the proximity of the corticosteroid to the macular area. Lack of therapeutic response to repository corticosteroids may be because of placement at a site relatively far from the target zone.

Adrenal Cortex Hormones↗
PubMed1985

Characterization of Brucella abortus strain 19 isolated from human and bovine tissues and fluids.

One hundred isolates of Brucella abortus, which were recovered from bovine and human tissues or fluids, were identified as strain 19 by conventional bacteriologic methods. Each isolate was examined using a Warburg respirometer to determine oxidative rates on substrates of D- and L-alanine, L-glutamic acid, d(+)-galactose, D-ribose, and i-erythritol. These results were compared with those of repository (seed) cultures of strain 19 used for making antigens and vaccines. Except on the substrate of i-erythritol, each of the 100 isolates oxidized these substrates with rates different from the repository cultures and indistinguishable from those of field strains of B abortus. Thus, oxidatively, i-erythritol was the only substrate useful to help distinguish between strain 19 and virulent strains of B abortus biotype 1.

Amino Acids↗
PubMed2025

A decentralized future for the open-science databases.

The continuous and reliable open access to curated biological data repositories is indispensable for accelerating rigorous scientific inquiry and fostering reproducible research outcomes. However, the current paradigm, which relies heavily on centralized infrastructure for the storage and distribution of foundational biomedical datasets, inherently introduces significant vulnerabilities. This centralized model is susceptible to single points of failure, including cyberattacks, technical malfunctions, natural disasters, and even political or funding uncertainties. Such disruptions can lead to widespread data unavailability, data loss, integrity compromises, and substantial delays in critical research, ultimately impeding scientific progress. The downstream effect of such interruptions can be the widespread paralysis of diverse research activities, including computational, clinical, molecular, and climate studies. This scenario vividly illustrates the inherent dangers of consolidating essential scientific resources within a single geopolitical or institutional locus. As data generation is accelerating and the global landscape continues to fluctuate, the sustainability of centralized models must be critically re-evaluated. A shift toward federated and decentralized architectures may offer a robust and forward-looking approach to enhancing the resilience of scientific data infrastructures by reducing exposure to governance instability, infrastructural fragility, and funding volatility, while also promoting equity and global accessibility. Inspired by established models such as ELIXIR's federated infrastructure and the policy and funding frameworks developed by CODATA and the Global Biodata Coalition (GBC), emerging Decentralized Science (DeSci) initiatives can contribute to building more resilient, fair, and incentive-aligned data ecosystems. The future of open science depends on integrating these complementary approaches to establish a globally distributed, economically sustainable, and institutionally robust infrastructure that safeguards scientific data as a public good, further ensuring continued accessibility, interoperability, and preservation for generations to come. Here, we examine the structural limitations of centralized repositories, evaluate federated and decentralized models, and propose a hybrid framework for resilient, fair, and sustainable scientific data stewardship.

data accessibility↗
PubMed1970

Manuscripts and oral history: common interests and problems in the history of medicine.

The acceptance of the tape-recorded interview as a research tool and historical record in the history of medicine suggests some problems both for the researcher with respect to resource materials and for the repository. A direct relationship exists between manuscript collections and the oral history product, and it would be in the interest of the oral historian, the curator of manuscripts, and the repository if a unified conceptual approach were taken in the acquisition and preservation of manuscript records and oral history interviews.

History, Modern 1601-↗
PubMed1983

Malignant lymphoma, mixed cell type, diffuse.

This retrospective study of diffuse mixed (DM) cell lymphoma was undertaken as a collaborative study between the Repository Center for Lymphoma Clinical Studies and four cooperative oncology groups (CALGB, ECOG, SECSG, SWOG), and was based on 62 patients from the files of the Repository Center. We wanted to ascertain whether there were any significant clinical differences among the various morphological subtypes of this lymphoma. All patients were treated according to different protocols of the Cooperative Oncology Groups sponsored by the National Cancer Institute. In 16 patients (26%), the malignant lymphoma (ML) had morphological features consistent with follicular center cell origin (FCC); in 34 patients (55%), the ML did not have features of follicular center cell type (non-FCC), but had morphology described for peripheral T-cell-derived ML. In 8 of the patients (13%), no agreement could be reached by the 7 histopathologists who participated in the study, and these were classified as unresolved; the remaining 4 (6%) were unclassifiable. We compared the survival times of the 16 patients having the morphological features of the FCC subtype with the survival times of the 34 patients with the non-FCC subtype and found that patients with FCC lived longer (p = 0.07 Cox's regression). In the FCC group, all patients who had complete remissions (CR) were alive; however, their survival times were similar to those who had a partial or no response (p = 0.32). In contrast, in the non-FCC group, the median survival was 20 mo, and patients with a CR had a significantly longer survival than did incomplete responders (p = 0.003). According to these results the non-FCC diffuse mixed cell lymphoma appears to be a high-grade malignant lymphoma, whereas the FCC type is not.

B-Lymphocytes↗