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

Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez-Romero, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen
2017 Lecture Notes in Computer Science  
The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored.  ...  The CEDAR Workbench provides a versatile, REST-based environment for authoring metadata that are enriched with terms from ontologies.  ...  Acknowledgements CEDAR is supported by grant U54 AI117925 awarded by the National Institute of Allergy and Infectious Diseases through funds provided by the trans-NIH Big Data to Knowledge (BD2K) initiative  ... 
doi:10.1007/978-3-319-68204-4_10 pmid:32219223 pmcid:PMC7098808 fatcat:u5k5w4ts5nc7jenqzfzxgcltom

Embracing Semantic Technology for Better Metadata Authoring in Biomedicine

Attila L. Egyedi, Martin J. O'Connor, Marcos Martínez Romero, Debra Willrett, Josef Hardi, John Graybeal, Mark A. Musen
2017 Workshop on Semantic Web Applications and Tools for Life Sciences  
The Center for Expanded Data Annotation and Retrieval (CEDAR) has developed a suite of tools and services that allow scientists to create and publish metadata describing scientific experiments.  ...  This paper presents the architecture of the CEDAR Workbench and focuses on the technology choices made to construct an easily usable, open system that allows users to create and publish semantically enriched  ...  Acknowledgments CEDAR is supported by the National Institutes of Health through the NIH Big Data to Knowledge program under grant 1U54AI117925.  ... 
dblp:conf/swat4ls/EgyediORWHGM17 fatcat:66cpustwhfbjle4yj2pqplpgbm

Modeling community standards for metadata as templates makes data FAIR [article]

Mark A. Musen, Martin J. O'Connor, Erik Schultes, Marcos Martinez Romero, Josef Hardi, John Graybeal
2022 arXiv   pre-print
We have explored this approach in the context of two software systems that use such metadata templates. One is the CEDAR Workbench, which is used to author both metadata templates and new metadata.  ...  The other is the FAIRware Workbench, which evaluates the metadata of archived datasets for their adherence to community standards.  ...  We are grateful to Stephen Fisher for providing us with legacy HuBMAP datasets, to Sunteasja Billings for creating the initial templates for HuBMAP metadata, and to Michelle Barker for helpful discussions  ... 
arXiv:2208.02836v1 fatcat:ze7m5kebtbgkliclybbl6vw4xi

Using Semantic Technologies to Enhance Metadata Submissions to Public Repositories in Biomedicine

Attila L. Egyedi, Martin J. O'Connor, Marcos Martínez-Romero, Debra Willrett, Josef Hardi, John Graybeal, Mark A. Musen
2018 Figshare  
There is a lack of tools for integrating metadata support when building these pipelines. In this paper we describe a system called CEDAR that aims to address this challenge.  ...  The emergence of the FAIR principles is driving renewed efforts in the biomedical community to produce high-quality metadata that describe da- tasets submitted to public repositories.  ...  Acknowledgments CEDAR is supported by the National Institutes of Health through the NIH Big Data to Knowledge program under grant 1U54AI117925.  ... 
doi:10.6084/m9.figshare.7324175.v1 fatcat:d6lidvqqqvdrpokun2vevrrk54

Ten simple rules for annotating sequencing experiments

Irene Stevens, Abdul Kadir Mukarram, Matthias Hörtenhuber, Terrence F. Meehan, Johan Rung, Carsten O. Daub, Scott Markel
2020 PLoS Computational Biology  
Several empirical studies have shown the need for better practices in curating scientific data [2] [3] [4] [5] .  ...  Accompanying information describing data, known as metadata, is important for fueling artificial intelligence and ensuring data longevity as technologies evolve.  ...  Acknowledgments We thank the members and contributors of the DANIO-CODE consortium and Dog Genome Annotation (DoGA) consortium.  ... 
doi:10.1371/journal.pcbi.1008260 pmid:33017400 fatcat:cibocj4fgzay5ogc6m6t5tpyay

A Practical Approach of Actions for FAIRification Workflows [article]

Natalia Queiroz de Oliveira, Vânia Borges, Henrique F. Rodrigues, Maria Luiza Machado Campos, Giseli Rabello Lopes
2022 arXiv   pre-print
Although defined for a particular use case, it is expected that this workflow can be applied for other epidemical research and in other domains, benefiting the entire scientific community.  ...  This paper presents a workflow of actions that is being adopted in the VODAN BR pilot for generating FAIR (meta)data for COVID-19 research.  ...  ETL4LinkedProv approach representing the provenance metadata in steps 5a, 5b and 6. 4.3 Center for Expanded Data Annotation and Retrieval (CEDAR) Workbench CEDAR Workbench 19 provides a suite of Web-based  ... 
arXiv:2201.07866v1 fatcat:5bfrhbd27jcxbnwiyziujdrxzq

BY-COVID- D2.1 - Initial data and metadata harmonisation at domain level to enable fast responses to COVID-19

Tom Giles, Phil Quinlan, Jeroen Belien, Julia Lischke, Laura Portell-Silva, Salvador Capella-Gutierrez, Reagon Karki, Vasso Kalaitzi, Enrique Bernal-Delgado, Antje Keppler
2022 Zenodo  
Interaction with WP4 will enable the development of tools for processing and harmonising metadata across data sources within the same domain.  ...  It also explores the initial infrastructure set-up activities undertaken to provide the capability for the rapid onboarding of resources in the future.  ...  The metadata is collected using the CEDAR Workbench utilising the CEDAR metadata templates and thus is machine readable and will be automatically harvested by the COVID-19 Data portals Mendix platform.  ... 
doi:10.5281/zenodo.7017728 fatcat:3vooduemvzbwxiacgpavusox7q

D5.1 Interoperability Implementation Regulations

Carol Goble, Chris Evelo, Helen Parkinson, ELIXIR Interoperability Community
2018 Zenodo  
APIs for the data repositories and biological knowledge bases agreed and implemented in the field with WP6 to 9 (Use Cases), and WP3 (Data)", as well has ensuring that resources were registered in appropriate  ...  The main aim of this deliverable is to present our progress for the implementation of our interoperability framework for EXCELERATE Use Cases WP6-9 and the ELIXIR Data Platform (WP3).  ...  Plant Ontology, Crop Ontology, Plant Trait Ontology) with sample environment descriptors drawn from the Environment Ontology (EnvO) and the eXtensible Experiment Markup Language (XEML) (WP7); Marine metagenomics  ... 
doi:10.5281/zenodo.1452414 fatcat:j6bod5nlinadhl623uez7x46m4

D2.1 Report on FAIR requirements for persistence and interoperability 2019

Heikki Lehväslaiho, Jessica Parland-von Essen, Claudia Behnke, Heidi Laine, Leah Riungu-Kalliosaari, Yann Le Franc, Christine Staiger
2019 Zenodo  
This document is the first iteration of three annual reports on the state of FAIR in European scientific data by the FAIRsFAIR project.  ...  The details of the FAIR principles for data, the implementation and implications for services are neither defined nor settled yet.  ...  (Assistant Professor from a higher education institution in Finland) Environment The research in domains relevant for understanding the environment are gaining in societal and political importance as  ... 
doi:10.5281/zenodo.3557380 fatcat:mtfhacbtxjd6hl7ltfbzafyodq

CAPABLE D3.1: Information Architecture

Ronald Cornet, Francesca Polce, Rowdy de Groot
2021 Zenodo  
Relevant data models, terminologies, and metadata models are introduced, which will form the basis for the representation of data and metadata that are exposed to researchers external to CAPABLE.  ...  This deliverable addresses the relevant aspects of such FAIR data, including what data the project will generate, what metadata adequately describes the data, and which standards are used so that data  ...  for Scientific Data Management and Stewardship A1.1 The protocol is open, free, and universally implementable A1.2 The protocol allows for an authentication and authorization procedure, where necessary  ... 
doi:10.5281/zenodo.5159072 fatcat:xaf27hdzhrbevmj3cez5dr33we

OASIcs-OpenAccess Series in Informatics

José Leal, Ricardo Rocha, Alberto Simões, Paulo Leal, Ricardo Rocha, Alberto Simões, Daniel Cremers, Barbara Hammer, Marc Langheinrich, Dorothea Wagner
nd Symposium on Languages, Applications and Technologies SLATE'13   unpublished
Acknowledgements The authors are in debt to the anonymous Referees for their valuable comments that have clearly contribute for the progress of our proposal as well as for the improvement of the paper.  ...  We also acknowledge the numerous fruitful discussions with Nuno Oliveira and Ismael Vilas Boas -Quimera's co-author and a permanent project contributor. Acknowledgements  ...  According to that proposal, the students develop their own grammar and test their project using the tool XMLlint. The authors also describe their experience following that approach.  ...