Dataset Information

The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers.

ABSTRACT: This paper describes the NIF LinkOut Broker (NLB) that has been built as part of the Neuroscience Information Framework (NIF) project. The NLB is designed to coordinate the assembly of links to neuroscience information items (e.g., experimental data, knowledge bases, and software tools) that are (1) accessible via the Web, and (2) related to entries in the National Center for Biotechnology Information's (NCBI's) Entrez system. The NLB collects these links from each resource and passes them to the NCBI which incorporates them into its Entrez LinkOut service. In this way, an Entrez user looking at a specific Entrez entry can LinkOut directly to related neuroscience information. The information stored in the NLB can also be utilized in other ways. A second approach, which is operational on a pilot basis, is for the NLB Web server to create dynamically its own Web page of LinkOut links for each NCBI identifier in the NLB database. This approach can allow other resources (in addition to the NCBI Entrez) to LinkOut to related neuroscience information. The paper describes the current NLB system and discusses certain design issues that arose during its implementation.

SUBMITTER: Marenco L

PROVIDER: S-EPMC2704600 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature

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The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers.

Marenco Luis L Ascoli Giorgio A GA Martone Maryann E ME Shepherd Gordon M GM Miller Perry L PL

Neuroinformatics 20080901 3

This paper describes the NIF LinkOut Broker (NLB) that has been built as part of the Neuroscience Information Framework (NIF) project. The NLB is designed to coordinate the assembly of links to neuroscience information items (e.g., experimental data, knowledge bases, and software tools) that are (1) accessible via the Web, and (2) related to entries in the National Center for Biotechnology Information's (NCBI's) Entrez system. The NLB collects these links from each resource and passes them to th ...[more]

PMID: 18975149

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Project description:BackgroundThe Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the supported species. In addition to providing a robust means of identifier conversion, BRM also incorporates a suite of microRNA (miRNA)-target databases upon which to query target genes or to perform reverse target lookups using gene identifiers.ResultsBRM has the capability to perform cross-species identifier lookups across common identifier types, directly integrate datasets across platform or species by performing identifier retrievals in the background, and retrieve miRNA targets from multiple databases simultaneously and integrate the resulting gene targets with experimental mRNA data. Here we use workflows provided in BRM to integrate RNA sequencing data across species to identify common biomarkers of exposure after treatment of human lung cells and zebrafish to benzo[a]pyrene (BAP). We further use the miRNA Target workflow to experimentally determine the role of miRNAs as regulators of BAP toxicity and identify the predicted functional consequences of miRNA-target regulation in our system. The output from BRM can easily and directly be uploaded to freely available visualization tools for further analysis. From these examples, we were able to identify an important role for several miRNAs as potential regulators of BAP toxicity in human lung cells associated with cell migration, cell communication, cell junction assembly and regulation of cell death.ConclusionsOverall, BRM provides bioinformatics tools to assist biologists having minimal programming skills with analysis and integration of high-content omics' data from various transcriptomic and proteomic platforms. BRM workflows were developed in Java and other open-source technologies and are served publicly using Apache Tomcat at https://cbb.pnnl.gov/brm/ .

Project description:BackgroundFederated digital identifiers (FDIs) have been cited to improve the interoperability of data and information management while enhancing the privacy of individuals verifying their identity on the web. Many countries around the world have implemented FDIs in various sectors, such as banking and government. Similarly, FDIs could improve the experience for those wanting to access their health care information; however, they have only been introduced in a few jurisdictions around the world, and their impact remains unclear.ObjectiveThe main objective of this environmental scan was to describe how FDIs have been established and implemented to enable patients' access to health care.MethodsWe conducted this study in 2 stages, with the primary stage being a rapid review, which was supplemented by a targeted gray literature search. Specifically, the rapid review was conducted through a database search of MEDLINE and Embase, which generated a list of countries and their services that use FDIs in health care. This list was then used to conduct a targeted gray literature search using the Google search engine.ResultsA total of 93 references from the database and targeted Google searches were included in this rapid review. FDIs were implemented in health care in 11 countries (Australia, Belgium, Canada, Denmark, Estonia, Finland, Iceland, Norway, Singapore, Sweden, and Taiwan) and exclusively used with a patient-accessible electronic health record system through a single sign-on interface. The most common FDIs were implemented nationally or provincially, and establishing them usually required individuals to visit a bank or government office in person. In contrast, some countries, such as Australia, allow individuals to verify their identities entirely on the web. We found that despite the potential of FDIs for use in health care to facilitate the amalgamation of health information from different data sources into one platform, the adoption of most health care services that use FDIs remained below 30%. The exception to this was Australia, which had an adoption rate of 90%, which could be correlated with the fact that it leveraged an opt-out consent model.ConclusionsThis rapid review highlights key features of FDIs across regions and elements associated with higher adoption of the patient-accessible electronic health record systems that use them, like opt-out registration. Although FDIs have been reported to facilitate the collation of data from multiple sources through a single sign-on interface, there is little information on their impact on care or patient experience. If FDIs are used to their fullest potential and implemented across sectors, adoption rates within health care may also improve.

Dataset Information

The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers.

Publications

The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers.

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