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How FAIR can you get? Image Retrieval as a Use Case to calculate FAIR Metrics

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      Abstract

      A large number of services for research data management strive to adhere to the FAIR guiding principles for scientific data management and stewardship. To evaluate these services and to indicate possible improvements, use-case-centric metrics are needed as an addendum to existing metric frameworks. The retrieval of spatially and temporally annotated images can exemplify such a use case. The prototypical implementation indicates that currently no research data repository achieves the full score. Suggestions on how to increase the score include automatic annotation based on the metadata inside the image file and support for content negotiation to retrieve the images. These and other insights can lead to an improvement of data integration workflows, resulting in a better and more FAIR approach to manage research data.

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      caCORE: a common infrastructure for cancer informatics.

      Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications. We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP-XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources. caCORE downloads and web interfaces can be accessed from links on the caCORE web site (http://ncicb.nci.nih.gov/core). caBIO software is distributed under an open source license that permits unrestricted academic and commercial use. Vocabulary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads. http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide, which provide detailed information on the present caCORE architecture, data sources and APIs. Updated information appears on a regular basis on the caCORE web site (http://ncicb.nci.nih.gov/core).
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        Image processing for artist identification

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          Making Research Data Repositories Visible: The re3data.org Registry

          Researchers require infrastructures that ensure a maximum of accessibility, stability and reliability to facilitate working with and sharing of research data. Such infrastructures are being increasingly summarized under the term Research Data Repositories (RDR). The project re3data.org–Registry of Research Data Repositories–has begun to index research data repositories in 2012 and offers researchers, funding organizations, libraries and publishers an overview of the heterogeneous research data repository landscape. In July 2013 re3data.org lists 400 research data repositories and counting. 288 of these are described in detail using the re3data.org vocabulary. Information icons help researchers to easily identify an adequate repository for the storage and reuse of their data. This article describes the heterogeneous RDR landscape and presents a typology of institutional, disciplinary, multidisciplinary and project-specific RDR. Further the article outlines the features of re3data.org, and shows how this registry helps to identify appropriate repositories for storage and search of research data.
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            Author and article information

            Journal
            09 October 2018
            1810.03824

            http://creativecommons.org/licenses/by/4.0/

            Custom metadata
            This is a preprint for a paper accepted for the 2018 IEEE conference
            cs.CY

            Applied computer science

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