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PubMed2001

ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources.

MOTIVATION: Heterogeneity of databases and software resources continues to hamper the integration of biological information. Top-down solutions are not feasible for the full-scale problem of integration across biological species and data types. Bottom-up solutions so far have not integrated, in a maximally flexible way, dynamic and interactive graphical-user-interface components with data repositories and analysis tools. RESULTS: We present a component-based approach that relies on a generalized platform for component integration. The platform enables independently-developed components to synchronize their behavior and exchange services, without direct knowledge of one another. An interface-based data model allows the exchange of information with minimal component interdependency. From these interactions an integrated system results, which we call ISYSf1.gif" BORDER="0">. By allowing services to be discovered dynamically based on selected objects, ISYS encourages a kind of exploratory navigation that we believe to be well-suited for applications in genomic research.

Arabidopsis↗

PubMed2001

Challenges in using the Arden Syntax for computer-based nosocomial infection surveillance.

CONTEXT: Detection of outbreaks of infection in the hospital typically requires daily manual review of microbiology laboratory test results. This process is time-consuming, tedious, prone to error and may miss trends in infection. A standard formalism for procedural knowledge representation, the Arden Syntax, provides a vehicle for implementing algorithms for detecting such infections. OBJECTIVE: To design and implement a computer-based system for detection of concerning patterns of infection or antibiotic resistance. SETTING: Computer-based event monitor and central patient data repository at the Columbia-Presbyterian Medical Center (CPMC). RESULTS: We designed a two-phase system, including initial filtering of individual patient laboratory results by Arden Syntax Medical Logic Modules (MLMs) and subsequent aggregation and analysis across patients and locations using a statistical monitor. Preliminary data for the filtration phase demonstrate a 94.8% reduction in the volume of messages that must be considered in surveillance. CONCLUSIONS: Filtering raw laboratory results using a standard formalism eases the process of aggregating data across patients and sites as well as detecting trends in infection. There is a need for augmenting such formalisms in order to enable population-based decision support.

Algorithms↗

PubMed2006

Ethical issues arising from the participation of children in genetic research.

With new tools derived from the Human Genome Project, genetic research is expanding from the study of rare, single gene disorders to the evaluation of genetic contributors to common, complex diseases. Many genetic studies include pediatric participants. The ethical concerns related to pediatric participation in genetic research derive from the study designs commonly employed in gene discovery and from the power accorded to genetic prediction in our society. In both family-based studies and large studies combining genetic and other health-related data, special attention should be placed on recruitment procedures, informed consent, and confidentiality protections. If data repositories are created for long-term use, we recommend re-consent of pediatric participants when they reach adulthood. In addition, the potential for disclosure of individual results should be considered as part of the institutional review of genetic studies, taking into account the validity of research data and the potential that such data could be used in health care. The potential for genetic results to pose harms of personal and group stigma is also a consideration. Because genetic information is often accorded special power in our society, careful attention should be paid to how genetic information is collected and used in research involving pediatric participants.

Child↗

PubMed2001

Information technology tools for efficient SNP studies.

We are currently facing a new era of studies involving single nucleotide polymorphisms (SNPs). This increased attention is stimulated by interest in individual differences in disease susceptibility as well as individual responses to drug treatment and the falling cost of genotyping. This review is a guide to the numerous public data repositories and Information Technology (IT) tools that may aid planning, preparation, running and analysis of studies involving SNPs. I will also highlight areas where researchers will have to resort to home-made IT solutions. Unfortunately, both information and IT tools are scattered throughout the internet and a lack of data exchange conventions can hamper the efficient use of these existing resources. This can lead to situations where the planning, preparation and analysis of a SNP study can actually cost more than the actual genotyping. We propose that only a customizable backbone IT infrastructure for SNP studies can help reduce costs associated with SNP data handling and tool launching.

Genetic Diseases, Inborn↗

PubMed1999

A strategy for statistical Master Person Index linking.

A linking program used by Connecticut Healthcare Information Management and Exchange to maintain the Master Person Index for its large, state-wide patient data repository is being stretched beyond its limits by the growing size and complexity of the database. This paper presents the early work into developing a second-generation linking program. Like the original program, the new linker will use a unique multi-step process to allow effective linking of data from a large number of dissimilar data sources. The new linker will use parallel multi-processing to allow improved performance and scalability. These changes will also make possible more sophisticated statistical methods of defining link confidence. The system is implemented using a scalable collection of inexpensive, PC based systems running the Linux operating system, a freely available database engine, and the Java programming language.

Abstracting and Indexing↗

PubMed2004

WormBase: a multi-species resource for nematode biology and genomics.

WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system.

Animals↗

PubMed2005

METLIN: a metabolite mass spectral database.

Endogenous metabolites have gained increasing interest over the past 5 years largely for their implications in diagnostic and pharmaceutical biomarker discovery. METLIN (http://metlin.scripps.edu), a freely accessible web-based data repository, has been developed to assist in a broad array of metabolite research and to facilitate metabolite identification through mass analysis. METLINincludes an annotated list of known metabolite structural information that is easily cross-correlated with its catalogue of high-resolution Fourier transform mass spectrometry (FTMS) spectra, tandem mass spectrometry (MS/MS) spectra, and LC/MS data.

Biomarkers↗

PubMed1995

A standards-based clinical information system for HIV/AIDS.

OBJECTIVE: To create a clinical data repository to interface the Veteran's Administration (VA) Decentralized Hospital Computer Program (DHCP) and a departmental clinical information system for the management of HIV patients. This system supports record-keeping, decision-making, reporting, and analysis. The database development was designed to overcome two impediments to successful implementations of clinical databases: (i) lack of a standard reference data model, and; (ii) lack of a universal standard for medical concept representation. BACKGROUND: Health Level Seven (HL7) is a standard protocol that specifies the implementation of interfaces between two computer applications (sender and receiver) from different vendors or sources of electronic data exchange in the health care environment. This eliminates or substantially reduces the custom interface programming and program maintenance that would otherwise be required. HL7 defines the data to be exchanged, the timing of the interchange, and the communication of errors to the application. The formats are generic in nature and must be configured to meet the needs of the two applications involved. The standard conceptually operates at the seventh level of the ISO model for Open Systems Interconnection (OSI). The OSI simply defines the data elements that are exchanged as abstract messages, and does not prescribe the exact bit stream of the messages that flow over the network. Lower level network software developed according to the OSI model may be used to encode and decode the actual bit stream. The OSI protocols are not universally implemented and, therefore, a set of encoding rules for defining the exact representation of a message must be specified. The VA has created an HL7 module to assist DHCP applications in exchanging health care information with other applications using the HL7 protocol. The DHCP HL7 module consists of a set of utility routines and files that provide a generic interface to the HL7 protocol for all DHCP applications. SETTING: The VA's DHCP core modules are in standard use at 169 hospitals, and the role of the VA system in health care delivery has been discussed elsewhere. This development was performed at the Miami VA Medical Center Special Immunology Unit, where a database was created for an HIV patient registry in 1987. Over 2,300 patient have been entered into a database that supports a problem-oriented summary of the patient's clinical record. The interface to the VA DHCP was designed and implemented to capture information from the patient treatment file, pharmacy, laboratory, radiology, and other modules. RESULTS: We obtained a suite of programs for implementing the HL7 encoding rules from Columbia-Presbyterian Medical Center in New York, written in ANSI C. This toolkit isolates our application programs from the details of the HL7 encoding rules, and allows them to deal with abstract messages and the programming level. While HL7 has become a standard for healthcare message exchange, SQL (Structured Query Language) is the standard for database definition, data manipulation, and query. The target database (Stitt F.W. The Problem-Oriented Medical Synopsis: a patient-centered clinical information system. Proc 17 SCAMC. 1993:88-93) provides clinical workstation functionality. Medical concepts are encoded using a preferred terminology derived from over 15 sources that include the Unified Medical Language System and SNOMed International ( Stitt F.W. The Problem-Oriented Medical Synopsis: coding, indexing, and classification sub-model. Proc 18 SCAMC, 1994: in press). The databases were modeled using the Information Engineering CASE tools, and were written using relational database utilities, including embedded SQL in C (ESQL/C). We linked ESQL/C programs to the HL7 toolkit to allow data to be inserted, deleted, or updated, under transaction control. A graphical format will be used to display the entity-rel

Acquired Immunodeficiency Syndrome↗

PubMed2006

Incorporating carer effects into economic evaluation.

BACKGROUND: Despite great interest in the development of methods used in the economic evaluation of health technologies, the effects of carer costs and quality of life (QOL) on the cost effectiveness of treatments has not been widely explored. Yet carer effects are clearly evident in the literature and relevant to the perspective of many published economic evaluations. OBJECTIVE: To examine whether patient QOL is associated with carer time and carer QOL. METHODS: We used two datasets to investigate carer effects. Firstly, we used 40,312 cases from the Health Outcomes Data Repository (HODaR) to assess the relationship between patient utility, using the EuroQoL (EQ)-5D, and the number of days care needed from friends and relatives. The stability of the relationship across patient subgroups was assessed by replicating the analysis in ten disease groups. Secondly, we used 64 cases from a study of patients with Alzheimer's disease and their primary carer. These data allowed us to estimate the relationships between patient and carer utility, using the EQ-5D, and patient utility and carer burden using the Community Dementia Quality of Life Profile (CDQLP). RESULTS: For carer time, a linear model showed that each 0.1-point reduction in patient utility was associated with a 2.5-day increase in carer time over a 6-week period. A more general model, based on EQ-5D domain scores, was better specified and showed that decreased functioning within each domain is associated with increased carer time. Problems with self-care and usual activities have the greatest impact on carer time. These models do not appear to be stable across different disease groups. For carer utility, the relationships between carer and patient utility have low explanatory power and are poorly specified. A clearer relationship is shown between carer burden and utility, such that when sociodemographic covariates are introduced, the relationship reaches conventional levels of statistical significance (p < 0.05). CONCLUSIONS: The preliminary work described here shows that improving patient QOL may reduce the need for carer time and improve carer QOL. Incorporating such effects into economic evaluations will change cost-per-QALY estimates, with the size of reduction dependent on the domains of health affected by treatment. Clinical studies need to capture carer data so that we can better understand these effects, and how they impact on economic evaluation.

Activities of Daily Living↗

PubMed1998

Waiting on clinicians to catch up.

Outcomes assessment tools like data repositories and benchmarking databases can help cut the cost of care. More tools are on the way. But clinicians who can't catch up may be the biggest barrier to more widespread use.

Artificial Intelligence↗

PubMed2006

SPLASH: systematic proteomics laboratory analysis and storage hub.

In the field of proteomics, the increasing difficulty to unify the data format, due to the different platforms/instrumentation and laboratory documentation systems, greatly hinders experimental data verification, exchange, and comparison. Therefore, it is essential to establish standard formats for every necessary aspect of proteomics data. One of the recently published data models is the proteomics experiment data repository [Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D. et al., Nat. Biotechnol. 2003, 21, 247-254]. Compliant with this format, we developed the systematic proteomics laboratory analysis and storage hub (SPLASH) database system as an informatics infrastructure to support proteomics studies. It consists of three modules and provides proteomics researchers a common platform to store, manage, search, analyze, and exchange their data. (i) Data maintenance includes experimental data entry and update, uploading of experimental results in batch mode, and data exchange in the original PEDRo format. (ii) The data search module provides several means to search the database, to view either the protein information or the differential expression display by clicking on a gel image. (iii) The data mining module contains tools that perform biochemical pathway, statistics-associated gene ontology, and other comparative analyses for all the sample sets to interpret its biological meaning. These features make SPLASH a practical and powerful tool for the proteomics community.

Database Management Systems↗

PubMed2005

Discrimination and calibration of mortality risk prediction models in interventional cardiology.

OBJECTIVES: Using a local percutaneous coronary intervention (PCI) data repository, we sought to compare the performance of a number of local and well-known mortality models with respect to discrimination and calibration. BACKGROUND: Accurate risk prediction is important for a number of reasons including physician decision support, quality of care assessment, and patient education. Current evidence on the value of applying PCI risk models to individual cases drawn from a different population is controversial. METHODS: Data were collected from January 01, 2002 to September 30, 2004 on 5216 consecutive percutaneous coronary interventions at Brigham and Women's Hospital (Boston, MA). Logistic regression was used to create a local risk model for in-hospital mortality in these procedures, and a number of statistical methods were used to compare the discrimination and calibration of this new and old local risk models, as well as the Northern New England Cooperative Group, New York State (1992 and 1997), University of Michigan consortium, American College of Cardiology-National Cardiovascular Data Registry, and The Cleveland Clinic Foundation risk prediction models. Areas under the ROC (AUC) curves were used to evaluate discrimination, and the Hosmer-Lemeshow (HL) goodness-of-fit test and calibration curves assessed applicability of the models to individual cases. RESULTS: Multivariate risk factors included in the newly constructed local model were: age, prior intervention, diabetes, unstable angina, salvage versus elective procedure, cardiogenic shock, acute myocardial infarction (AMI), and left anterior descending artery intervention. The area under the ROC curve (AUC) was 0.929 (SE=0.017), and the p value for the Hosmer-Lemeshow (HL) goodness-of-fit was 0.473. This indicates good discrimination and calibration. Bootstrap re-sampling indicated AUC stability. Evaluation of the external models showed an AUC range from 0.82 to 0.90 indicating good discrimination across all models, but poor calibration (HL p value < or = 0.0001). CONCLUSIONS: Validation of AUC values across all models suggests that certain risk factors have remained important over the last decade. However, the lack of calibration suggests that small changes in patient populations and data collection methods quickly reduce the accuracy of patient level estimations over time. Possible solutions to this problem involve either recalibration of models using local data or development of new local models.

Angioplasty, Balloon, Coronary↗

PubMed2003

WorfDB: the Caenorhabditis elegans ORFeome Database.

WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of approximately 19 000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans (also referred to as the 'worm ORFeome'). WorfDB serves as a central data repository enabling the scientific community to search for availability and quality of cloned ORFs. So far, ORF sequence tags (OSTs) obtained for all individual clones have allowed exon structure corrections for approximately 3400 ORFs originally predicted by the C. elegans sequencing consortium. In addition, we now have OSTs for approximately 4300 predicted genes for which no ESTs were available. The database contains this OST information along with data pertinent to the cloning process. WorfDB could serve as a model database for other metazoan ORFeome cloning projects.

Animals↗

PubMed2026

Development of a Blockchain-Based Platform to Enable Indigenous Data Sovereignty and Shared Research Participation With Indigenous Communities: Technology Prototyping and Community Engagement Study.

BACKGROUND: Historic and ongoing problematic practices regarding the collection, storage, and use of Indigenous health data have led to the need to ensure principles of Indigenous Data Sovereignty (IDS) are followed in research practices and technology development. OBJECTIVE: This project, a partnership between UC San Diego and the Native BioData Consortium (NativeBio), sought to explore the practical application of blockchain technology and its potential to facilitate Indigenous-led research collaboration. METHODS: This project first undertook purposeful relationship building with NativeBio to form a Community Advisory Board (CAB) for identifying community and technology needs for a blockchain research collaboration platform with an initial focus on genomic data. Over a 2-year project period, a series of public meetings and presentations at Indigenous-led conferences introduced the concept of exploring compatibility between blockchain and IDS principles, followed by iterative prototyping and co-design of a blockchain platform with NativeBio, using Ethereum as the underlying protocol. RESULTS: Direct engagement with NativeBio and the CAB informed the initial design and development of a "b-IDS" proof-of-concept (POC) blockchain platform. The POC consists of three main components: (1) the web front-end layer, (2) the Ethereum network that executes the smart contract and blockchain storage aspects of the framework, and (3) the back-end database that stores off-chain interactions and data for future use with external genomic data repositories. After refinement of the POC, a community-based participatory research (CBPR) use case aligned with IDS principles was identified as a practical workflow and incorporated into the design of the POC for implementation. CONCLUSIONS: The findings from this project demonstrated the potential use of operationalizing IDS through blockchain technology with proactive and sustained engagement with Indigenous partners. Blockchain technology may have certain advantages over other data governance approaches and systems, facilitating timely oversight, shared decision-making and consent structures, and direct involvement of Indigenous communities in technology design, respecting the core principles of IDS and CBPR. Future development of the blockchain-IDS POC will need to incorporate other research practices and ethics frameworks to expand its use to other public health and biomedical research use cases.

Blockchain↗

PubMed2006

Web-based analysis of the mouse transcriptome using Genevestigator.

BACKGROUND: Gene function analysis often requires a complex and laborious sequence of laboratory and computer-based experiments. Choosing an effective experimental design generally results from hypotheses derived from prior knowledge or experimentation. Knowledge obtained from meta-analyzing compendia of expression data with annotation libraries can provide significant clues in understanding gene and network function, resulting in better hypotheses that can be tested in the laboratory. DESCRIPTION: Genevestigator is a microarray database and analysis system allowing context-driven queries. Simple but powerful tools allow biologists with little computational background to retrieve information about when, where and how genes are expressed. We manually curated and quality-controlled 3110 mouse Affymetrix arrays from public repositories. Data queries can be run against an annotation library comprising 160 anatomy categories, 12 developmental stage groups, 80 stimuli, and 182 genetic backgrounds or modifications. The quality of results obtained through Genevestigator is illustrated by a number of biological scenarios that are substantiated by other types of experimentation in the literature. CONCLUSION: The Genevestigator-Mouse database effectively provides biologically meaningful results and can be accessed at https://www.genevestigator.ethz.ch.

Animals↗

PubMed2000

C3: A comprehensive physician activity and billing tool

Purpose: The Clinical Charge Capture system (C3) was developed at the University of Michigan to increase the efficiency and accuracy with which information about physician activity and billing is tracked in academic medical centers. Description: This Oracle-based, Visual Basic system integrates the operating room scheduling system, transcription database, clinical data repository, referring physician database, and IDX to allow physicians and staff to perform paperless and on-line standard tasks such as preauthorizing procedures; creating a bill which describes the charges for procedures performed along with their supporting diagnoses; identifying inpatient daily care and consult charges; dictating, editing, signing, and providing attestations for procedural and inpatient notes (menu-driven boilerplate notes are used for common procedures); submitting of charges on-line to IDX; and downloading of payment data from IDX. A messaging system between physicians and billing specialists allows questions to be posed regarding coding issues and options. Summary information about charges is presented and the status of the bill as it progresses through the internal review and billing process is demonstrated. Any missing data are flagged such that delivery of a bill is accurate, timely, and complete. Outpatient clinic visit charges are acquired on line using bar code technology with direct download of clinic charges to IDX. Generation of charges and referral letters may be performed immediately following the performance of a procedure or patient encounter or subsequently in the office. Resident activity is also tracked. Finally, search functions are provided which allow the program to serve as a clinical information research database. Results: The time to bill submission for operative procedures in fiscal year 1996 (Pre-C3) when compared to 1999 (Post-C3) decreased in each individual surgical division (See figure)as well as for the overall Department (Total: mean Pre-C3=40 days, mean Post-C3=8 days). The average bill was increased by 9% for each primary charge submitted. Conclusions: We conclude that this system has the potential to enhance the efficiency, accuracy, and organization of routine physician documentation, billing, and data collection activities.

Journal Article↗

PubMed2006

Comparative microarray analysis.

Microarrays enable high-throughput parallel gene expression analysis, and their use has grown exponentially during the past decade. We are now in a position where individual experiments could benefit from using the swelling public data repositories to allow microarrays to progress from being a hypothesis-generating tool to a powerful resource that can be used to test hypothesis about biology. Comparative microarray analysis could better distinguish phenotypes from associated phenotypes; identify valid differentially expressed genes by combining many studies; test new hypothesis; and discover fundamental patterns of gene regulation. This review aims to describe the additional methodology needed for such comparative microarray analysis, and we identify and discuss a number of problems such as loss of published data, lack of annotations, and variable array quality, which need to be solved before comparative microarray analysis can be used in a more systematic and powerful manner.

Animals↗

PubMed2000

Can radiologic images be incorporated into the electronic patient record?

As radiology makes advances toward filmlessness, all of medicine is headed, just as rapidly, toward paperless transmission of patient information. While there are obvious advantages to this electronic approach, and several standards to conform to for the transmission of textual (Health Level 7 [HL-7]) and image (Digital Imaging and Communications in Medicine [DICOM]) data, it is the integration of these two data sets that is clinically essential and yet poorly defined. This report defines an approach for, and the successful implementation of, the integration of radiologic image data with textual data contained within the electronic patient record (EPR) through the use of standard internet protocols. Incorporation of medical images in the EPR has proven to be critical to the successful deployment of picture archiving and communications systems (PACS) and the reduction of film consumption at Massachusetts General Hospital (MGH). Since the installation of the first internet-based Image Data Repository (IDR) at MGH in 1995, the system has adequately served to meet the needs of clinical requests by both radiology-only browser users and users of the EPR. It has drastically reduced the need for film and provided concurrent display of images and text throughout the institution and beyond.

Computer Systems↗