Literature DB >> 32219223

The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments.

Rafael S Gonçalves1, Martin J O'Connor1, Marcos Martínez-Romero1, Attila L Egyedi1, Debra Willrett1, John Graybeal1, Mark A Musen1.   

Abstract

The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have developed-the CEDAR Workbench-is a suite of Web-based tools and REST APIs that allows users to construct metadata templates, to fill in templates to generate high-quality metadata, and to share and manage these resources. The CEDAR Workbench provides a versatile, REST-based environment for authoring metadata that are enriched with terms from ontologies. The metadata are available as JSON, JSON-LD, or RDF for easy integration in scientific applications and reusability on the Web. Users can leverage our APIs for validating and submitting metadata to external repositories. The CEDAR Workbench is freely available and open-source.

Entities:  

Keywords:  Metadata; Metadata authoring; Metadata repository; Ontologies

Year:  2017        PMID： 32219223      PMCID： PMC7098808          DOI： 10.1007/978-3-319-68204-4_10

Source DB:  PubMed          Journal:  Semant Web ISWC


  8 in total

1.  Unleashing the value of Common Data Elements through the CEDAR Workbench.

Authors:  Martin J O'Connor; Denise B Warzel; Marcos Martínez-Romero; Josef Hardi; Debra Willrett; Attila L Egyedi; Aras Eftekhari; John Graybeal; Mark A Musen
Journal:  AMIA Annu Symp Proc       Date:  2020-03-04

2.  CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis.

Authors:  Pavel S Novichkov; John-Marc Chandonia; Adam P Arkin
Journal:  Gigascience       Date:  2022-10-17       Impact factor: 7.658

3.  Towards FAIR protocols and workflows: the OpenPREDICT use case.

Authors:  Remzi Celebi; Joao Rebelo Moreira; Ahmed A Hassan; Sandeep Ayyar; Lars Ridder; Tobias Kuhn; Michel Dumontier
Journal:  PeerJ Comput Sci       Date:  2020-09-21

4.  From Reductionism to Reintegration: Solving society's most pressing problems requires building bridges between data types across the life sciences.

Authors:  Anne E Thessen; Paul Bogdan; David J Patterson; Theresa M Casey; César Hinojo-Hinojo; Orlando de Lange; Melissa A Haendel
Journal:  PLoS Biol       Date:  2021-03-26       Impact factor: 8.029

5.  Categorizing metadata to help mobilize computable biomedical knowledge.

Authors:  Brian S Alper; Allen Flynn; Bruce E Bray; Marisa L Conte; Christina Eldredge; Sigfried Gold; Robert A Greenes; Peter Haug; Kim Jacoby; Gunes Koru; James McClay; Marc L Sainvil; Davide Sottara; Mark Tuttle; Shyam Visweswaran; Robin Ann Yurk
Journal:  Learn Health Syst       Date:  2021-05-09

6.  FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research.

Authors:  Jeroen A M Beliën; Mariëlle E van Gijn; Morris A Swertz; K Joeri van der Velde; Gurnoor Singh; Rajaram Kaliyaperumal; XiaoFeng Liao; Sander de Ridder; Susanne Rebers; Hindrik H D Kerstens; Fernanda de Andrade; Jeroen van Reeuwijk; Fini E De Gruyter; Saskia Hiltemann; Maarten Ligtvoet; Marjan M Weiss; Hanneke W M van Deutekom; Anne M L Jansen; Andrew P Stubbs; Lisenka E L M Vissers; Jeroen F J Laros; Esther van Enckevort; Daphne Stemkens; Peter A C 't Hoen
Journal:  Sci Data       Date:  2022-04-13       Impact factor: 8.501

7.  A collaborative semantic-based provenance management platform for reproducibility.

Authors:  Sheeba Samuel; Birgitta König-Ries
Journal:  PeerJ Comput Sci       Date:  2022-03-10

8.  Ten simple rules for annotating sequencing experiments.

Authors:  Irene Stevens; Abdul Kadir Mukarram; Matthias Hörtenhuber; Terrence F Meehan; Johan Rung; Carsten O Daub
Journal:  PLoS Comput Biol       Date:  2020-10-05       Impact factor: 4.475
  8 in total

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