The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments.
Rafael S. Gonçalves,Martin J. O'Connor,Marcos Martínez-Romero,Attila L. Egyedi,Debra Willrett,John Graybeal,Mark A. Musen +6 more
- Vol. 10588, pp 103-110
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TLDR
The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored as discussed by the authors, and the CEDAR Workbench is a suite of Web-based tools and REST APIs that allows users to construct metadata templates, fill in templates to generate high-quality metadata, and to share and manage these resources.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.read more
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Journal ArticleDOI
FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.
Damion M. Dooley,Emma Griffiths,Emma Griffiths,Gurinder Gosal,Pier Luigi Buttigieg,Robert Hoehndorf,Matthew Lange,Lynn M. Schriml,Fiona S. L. Brinkman,William W. L. Hsiao,William W. L. Hsiao +10 more
TL;DR: A group of international scientists give a detailed description of FoodOn, a-consortium-driven project to build a comprehensive food ontology that covers vocabulary from farm to fork, and addresses current gaps in food terminology and focuses on human and domesticated animal food description.
Journal ArticleDOI
The variable quality of metadata about biological samples used in biomedical experiments.
TL;DR: Overall, the metadata the authors analyzed reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements, and significant aberrancies that are likely to impede search and secondary use of the associated datasets.
Journal ArticleDOI
COPO: a metadata platform for brokering FAIR data in the life sciences
Felix Shaw,Anthony Etuk,Alice Minotto,Alejandra Gonzalez-Beltran,Alejandra Gonzalez-Beltran,David Johnson,David Johnson,Philippe Rocca-Serra,Marie-Angélique Laporte,Elizabeth Arnaud,Medha Devare,Paul J. Kersey,Susanna-Assunta Sansone,Robert P. Davey +13 more
TL;DR: COPO is a computational system that attempts to address some of these challenges by enabling scientists to describe their research objects using community-sanctioned metadata sets and vocabularies, and then use public or institutional repositories to share them with the wider scientific community.
Journal ArticleDOI
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language
Charles Tapley Hoyt,Charles Tapley Hoyt,Daniel Domingo-Fernández,Daniel Domingo-Fernández,Rana Aldisi,Rana Aldisi,Lingling Xu,Lingling Xu,Kristian Kolpeja,Sandra Spalek,Esther Wollert,John A. Bachman,Benjamin M. Gyori,Patrick Greene,Martin Hofmann-Apitius,Martin Hofmann-Apitius +15 more
TL;DR: Two workflows are developed: one for re-curating a given KG to assure its syntactic and semantic quality and another for rationally enriching it by manually revising automatically extracted relations for nodes with low information density.
Journal ArticleDOI
The variable quality of metadata about biological samples used in biomedical experiments
TL;DR: In this paper, the authors present an analytical study of the quality of metadata about samples used in biomedical experiments and reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements.
References
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TL;DR: The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data and provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-power gene expression and genomic hybridization experiments.
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The FAIR Guiding Principles for scientific data management and stewardship
Mark Wilkinson,Michel Dumontier,IJsbrand Jan Aalbersberg,Gabrielle Appleton,Myles Axton,Arie Baak,Niklas Blomberg,Jan-Willem Boiten,Luiz Olavo Bonino da Silva Santos,Philip E. Bourne,Jildau Bouwman,Anthony J. Brookes,Timothy Clark,Mercè Crosas,Ingrid Dillo,Olivier G. Dumon,Scott C. Edmunds,Chris T. Evelo,Richard Finkers,Alejandra Gonzalez-Beltran,Alasdair J. G. Gray,Paul Groth,Carole Goble,Jeffrey S. Grethe,Jaap Heringa,Peter A C 't Hoen,Rob Hooft,Tobias Kuhn,Ruben Kok,Joost N. Kok,Scott J. Lusher,Maryann E. Martone,Albert Mons,Abel L. Packer,Bengt Persson,Philippe Rocca-Serra,Marco Roos,Rene van Schaik,Susanna-Assunta Sansone,Erik Anthony Schultes,Thierry Sengstag,Ted Slater,George Strawn,Morris A. Swertz,Mark Thompson,Johan van der Lei,Erik M. van Mulligen,Jan Velterop,Andra Waagmeester,Peter Wittenburg,Katherine Wolstencroft,Jun Zhao,Barend Mons,Barend Mons +53 more
TL;DR: The FAIR Data Principles as mentioned in this paper are a set of data reuse principles that focus on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals.
Journal ArticleDOI
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Alvis Brazma,Pascal Hingamp,John Quackenbush,Gavin Sherlock,Paul T. Spellman,Chris Stoeckert,John Aach,Wilhelm Ansorge,Catherine A. Ball,Helen C. Causton,Terry Gaasterland,Patrick Glenisson,Frank C. P. Holstege,Irene F. Kim,Victor Markowitz,John C. Matese,Helen Parkinson,Alan J. Robinson,Ugis Sarkans,Steffen Schulze-Kremer,Jason E. Stewart,Ronald C. Taylor,Jaak Vilo,Martin Vingron +23 more
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Journal ArticleDOI
From core referencing to data re-use: two French national initiatives to reinforce paleodata stewardship (National Cyber Core Repository and LTER France Retro-Observatory)
Fabien Arnaud,Cécile Pignol,Pierre Stéphan,Anne-Lise Develle,Pierre Sabatier,Olivier Evrard,Brice Mourier,Maxime Debret,Cécile Grobois,Laurent Millet,Damien Rius,Dominique Marguerie,Mathias Rouan,Elodie Godinho,Bruno Galabertier,Arnaud Caillo +15 more
TL;DR: ROZA was developed under the umbrella of LTER-France (Long Term Ecological Research) in order to facilitate the re-use of data and samples and will favor to use of paleodata by non-paleodata scientists, in particular ecologists.
Journal ArticleDOI
BioPortal: ontologies and integrated data resources at the click of a mouse
Natalya F. Noy,Nigam H. Shah,Patricia L. Whetzel,Benjamin Dai,Michael Dorf,Nicholas Griffith,Clement Jonquet,Daniel L. Rubin,Margaret-Anne Storey,Christopher G. Chute,Mark A. Musen +10 more
TL;DR: BioPortal not only provides investigators, clinicians, and developers ‘one-stop shopping’ to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.
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