title: The center for expanded data annotation and retrieval.
abstract: The Center for Expanded Data Annotation and Retrieval is studying the creation of comprehensive and expressive metadata for biomedical datasets to facilitate data discovery, data interpretation, and data reuse. We take advantage of emerging community-based standard templates for describing different kinds of biomedical datasets, and we investigate the use of computational techniques to help investigators to assemble templates and to fill in their values. We are creating a repository of metadata from which we plan to identify metadata patterns that will drive predictive data entry when filling in metadata templates. The metadata repository not only will capture annotations specified when experimental datasets are initially created, but also will incorporate links to the published literature, including secondary analyses and possible refinements or retractions of experimental interpretations. By working initially with the Human Immunology Project Consortium and the developers of the ImmPort data repository, we are developing and evaluating an end-to-end solution to the problems of metadata authoring and management that will generalize to other data-management environments.
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA USA musen@stanford.edu.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Musen
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA USA.
authors.forename: Carol A
authors.initials: CA
authors.lastname: Bean
authors.affiliation: Interdepartmental Program in Computational Biology and Bioinformatics, Department of Emergency Medicine, Yale University School of Medicine, New Haven, CT USA.
authors.forename: Kei-Hoi
authors.initials: KH
authors.lastname: Cheung
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA USA.
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
authors.affiliation: Stanford University Libraries, Stanford University, Stanford, CA USA.
authors.forename: Kim A
authors.initials: KA
authors.lastname: Durante
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA USA.
authors.forename: Olivier
authors.initials: O
authors.lastname: Gevaert
authors.affiliation: Oxford e-Research Centre, University of Oxford, Oxford, UK.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Gonzalez-Beltran
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA USA Stanford Institute for Immunity, Transplantation, and Infection, Stanford, CA USA.
authors.forename: Purvesh
authors.initials: P
authors.lastname: Khatri
authors.affiliation: Interdepartmental Program in Computational Biology and Bioinformatics, Departments of Pathology and Immunobiology, Yale University School of Medicine, New Haven, CT USA.
authors.forename: Steven H
authors.initials: SH
authors.lastname: Kleinstein
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA USA.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: O'Connor
authors.affiliation: Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA USA.
authors.forename: Yannick
authors.initials: Y
authors.lastname: Pouliot
authors.affiliation: Oxford e-Research Centre, University of Oxford, Oxford, UK.
authors.forename: Philippe
authors.initials: P
authors.lastname: Rocca-Serra
authors.affiliation: Oxford e-Research Centre, University of Oxford, Oxford, UK.
authors.forename: Susanna-Assunta
authors.initials: SA
authors.lastname: Sansone
authors.affiliation: Northrop Grumman Corporation, West Falls Church, VA USA.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Wiser
mesh_terms: D064229:Biological Ontologies; D035843:Biomedical Research; D057225:Data Mining; D066264:Datasets as Topic; D006801:Humans; D016247:Information Storage and Retrieval; D014481:United States
keywords: biological ontologies; data collection; data curation; datasets as topic; standards