Dataset Information

The Data Use Ontology to streamline responsible access to human biomedical datasets.

ABSTRACT: Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Identities (DURI) work stream developed and approved the Data Use Ontology (DUO) standard. DUO is a hierarchical vocabulary of human and machine-readable data use terms that consistently and unambiguously represents a dataset's allowable data uses. DUO has been implemented by major international stakeholders such as the Broad and Sanger Institutes and is currently used in annotation of over 200,000 datasets worldwide. Using DUO in data management and access facilitates researchers' discovery and access of relevant datasets. DUO annotations increase the FAIRness of datasets and support data linkages using common data use profiles when integrating the data for secondary analyses. DUO is implemented in the Web Ontology Language (OWL) and, to increase community awareness and engagement, hosted in an open, centralized GitHub repository. DUO, together with the GA4GH Passport standard, offers a new, efficient, and streamlined data authorization and access framework that has enabled increased sharing of biomedical datasets worldwide.

SUBMITTER: Lawson J

PROVIDER: S-EPMC8591903 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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The Data Use Ontology to streamline responsible access to human biomedical datasets.

Lawson Jonathan J Cabili Moran N MN Kerry Giselle G Boughtwood Tiffany T Thorogood Adrian A Alper Pinar P Bowers Sarion R SR Boyles Rebecca R RR Brookes Anthony J AJ Brush Matthew M Burdett Tony T Clissold Hayley H Donnelly Stacey S Dyke Stephanie O M SOM Freeberg Mallory A MA Haendel Melissa A MA Hata Chihiro C Holub Petr P Jeanson Francis F Jene Aina A Kawashima Minae M Kawashima Shuichi S Konopko Melissa M Kyomugisha Irene I Li Haoyuan H Linden Mikael M Rodriguez Laura Lyman LL Morita Mizuki M Mulder Nicola N Muller Jean J Nagaie Satoshi S Nasir Jamal J Ogishima Soichi S Ota Wang Vivian V Paglione Laura D LD Pandya Ravi N RN Parkinson Helen H Philippakis Anthony A AA Prasser Fabian F Rambla Jordi J Reinold Kathy K Rushton Gregory A GA Saltzman Andrea A Saunders Gary G Sofia Heidi J HJ Spalding John D JD Swertz Morris A MA Tulchinsky Ilia I van Enckevort Esther J EJ Varma Susheel S Voisin Craig C Yamamoto Natsuko N Yamasaki Chisato C Zass Lyndon L Guidry Auvil Jaime M JM Nyrönen Tommi H TH Courtot Mélanie M

Cell genomics 20211110 2

Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they are processed and made available to comply with ethical and regulatory frameworks and informed consent data conditions. To enable and streamline data access for these biomedical datasets, the Global Alliance for Genomics and Health (GA4GH) Data Use and Researcher Ide ...[more]

PMID: 34820659

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Project description:The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

Project description:BackgroundOntologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms.MethodsWe developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data.ResultsOur evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios.ConclusionsOntology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available (both via the user interface at http://bioportal.bioontology.org/recommender , and via a Web service API).

Dataset Information

The Data Use Ontology to streamline responsible access to human biomedical datasets.

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The Data Use Ontology to streamline responsible access to human biomedical datasets.

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