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The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.

ABSTRACT: Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services.Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications.By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at http://www.bridgedb.org.

SUBMITTER: van Iersel MP

PROVIDER: S-EPMC2824678 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

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The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.

van Iersel Martijn P MP Pico Alexander R AR Kelder Thomas T Gao Jianjiong J Ho Isaac I Hanspers Kristina K Conklin Bruce R BR Evelo Chris T CT

BMC bioinformatics 20100104

<h4>Background</h4>Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services.<h4>Results</h4>Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework pro ...[more]

PMID: 20047655

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Project description:BackgroundPopulation groups experience differential access to timely and high-quality mental healthcare. Despite efforts of recent UK policies to improve the accessibility of mental health services, there remains a lack of comprehensive understanding of inequalities in access to services needed to do this. This systematic mapping review aimed to address this gap by identifying which population groups continue to be poorly served by access to adult mental health services in the UK, how access has been measured, and what research methods have been applied.MethodsSeven electronic databases were searched from January 2014 up to May 2022. Primary research studies of any design were included if they examined access to adult NHS mental health services in the UK by population groups at risk of experiencing inequalities. Study characteristics, measures of access, inequalities studied, and key findings were extracted. A best-fit framework approach was used, applying Levesque's Conceptual Framework for Healthcare Access to synthesise measures of access, and applying a template derived from Cochrane Progress-Plus and NHS Long Term Plan equality characteristics to synthesise key findings associated with inequalities.ResultsOf 1,929 publications retrieved, 152 studies of various types were included. The most frequently considered dimensions of inequality were gender, age, and ethnicity, whilst social capital, religion, and sexual orientation were least frequently considered. Most studies researched access by measuring "healthcare utilisation", followed by studies that measured "healthcare seeking". Key barriers to access were associated with individuals' "ability to seek" (e.g. stigma and discrimination) and "ability to reach" (e.g. availability of services). Almost half of the studies used routinely collected patient data, and only 16% of studies reported patient and public involvement.ConclusionsLittle appears to have changed in the nature and extent of inequalities, suggesting that mental health services have not become more accessible. Actions to reduce inequalities should address barriers to population groups' abilities to seek and reach services such as stigma-reducing interventions, and re-designing services and pathways. Significant benefits exist in using routinely collected patient data, but its limitations should not be ignored. More theoretically informed research, using a holistic measurement of access, is needed in this area.Review registrationhttps://doi.org/10.17605/OSF.IO/RQ5U7 .

Dataset Information

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.

Publications

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services.

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