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Examining data sharing and data reuse in the dataone environment

Angela P. Murillo
2014 Proceedings of the American Society for Information Science and Technology  
The research presented in this poster-paper reports on two studies examining data sharing and reuse in the DataONE environment.  ...  The two studies include 1) a profiling data assessment that examines the data and metadata being deposited into the DataONE system for data sharing, and 2) a pilot think-aloud study that examines what  ...  To address the above, in 2007 the U.S. National Science Foundation announced a request for proposals for Sustainable Digital Data Preservation and Access Network Partners (DataNet).  ... 
doi:10.1002/meet.2014.14505101155 fatcat:32cpogmlvbfwtbxjzv3zcyfpdq

Quality evaluation of data management plans at a research university

James E. Van Loon, Katherine G. Akers, Cole Hudson, Alexandra Sarkozy
2017 IFLA Journal  
With the emergence of the National Science Foundation (NSF) requirement for data management plans (DMPs), academic librarians have increasingly aided researchers in developing DMPs and disseminating research  ...  during the project, or how data will be preserved and shared after the completion of the project.  ...  Acknowledgement The authors wish to thank Gail Ryan and Tim Foley of the Wayne State University Office of Sponsored Programs Administration for their support and guidance in this work.  ... 
doi:10.1177/0340035216682041 fatcat:6xl6yn5y6nbarorxv5lifwkjpq

Knowledge Representation and Management. From Ontology to Annotation

J. Charlet, S. J. Darmoni
2015 IMIA Yearbook of Medical Informatics  
Objective: To summarize the best papers in the field of Knowledge Representation and Management (KRM).  ...  Methods: A comprehensive review of medical informatics literature was performed to select some of the most interesting papers of KRM published in 2014.  ...  Acknowledgements We would like to thank Martina Hutter for her support and the reviewers for their participation in the selection process of the IMIA Yearbook.  ... 
doi:10.15265/iy-2015-038 pmid:26293860 pmcid:PMC4587031 fatcat:bveni7udunem7el2oy6mz3dv4m

Imaging Biomarker Ontology (IBO): A Biomedical Ontology to Annotate and Share Imaging Biomarker Data

Emna Amdouni, Bernard Gibaud
2018 Journal on Data Semantics  
The use of semantic technologies will enable to efficiently retrieve imaging related data and to enhance the interoperability in the biomedical field.  ...  In this paper, we introduce our motivation for semantically describing this concept and we outline shortcomings of the state-of-the art methods.  ...  Conclusion The importance of imaging biomarkers in biomedical research and drug design is well acknowledged in the literature, calling for appropriate standards and guidelines for biomarker development  ... 
doi:10.1007/s13740-018-0093-3 fatcat:bjo2nfelnjcqtfgyii6bc3h4hu

Implementation of FAIR Principles for Ontologies in the Disaster Domain: A Systematic Literature Review

Allan Mazimwe, Imed Hammouda, Anthony Gidudu
2021 ISPRS International Journal of Geo-Information  
However, the difficulty in finding, accessing and reusing interoperable vocabularies to organise disaster management data creates a challenge for collaboration among stakeholders in the disaster management  ...  By using FAIR indicators to evaluate the maturity in sharing, discovery and integration of disaster management ontologies, we reveal potential research opportunities for managing reusable and evolving  ...  In the FAIR ecosystem, novel literature exists on FAIR metrics and evaluation criteria for digital objects [8, 11, 16] .  ... 
doi:10.3390/ijgi10050324 fatcat:4fzkuxe55zdwpbujesy3cafpci

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability

Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton, Edison Ong
2018 Journal of Biomedical Semantics  
With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation  ...  Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis.  ...  Acknowledgements We acknowledge the OBO Foundry consortium and OBO ontology developers for their support and collaborations.  ... 
doi:10.1186/s13326-017-0169-2 pmid:29329592 pmcid:PMC5765662 fatcat:5w3acqcqd5hnxphdq76ruqlrja

Cardiac Tissue Engineering as Use Case to Connect Biomedical Research Laboratories to an Emerging Global Data Infrastructure

Markus Suhr, Nadine Umbach, Tim Meyer, Wolfram-Hubertus Zimmermann, Ulrich Sax
2019 Studies in Health Technology and Informatics  
Methods for cardiac tissue engineering and application in experiments are core technologies developed at the Institute of Pharmacology and Toxicology in Göttingen.  ...  The architecture concept and developed integration tools explore connection of routine experimental work in a biomedical research lab to a universal infrastructure of data.  ...  Ideally, the concept should be flexible enough to be reused for different experimental scenarios in biomedical research laboratories.  ... 
doi:10.3233/shti190244 pmid:31437946 fatcat:wcjtvn2l3vhnpibi3itvwmock4

DiiS: A Biomedical Data Access Framework for Aiding Data Driven Research Supporting FAIR Principles

Priya Deshpande, Alexander Rasin, Jacob Furst, Daniela Raicu, Sameer Antani
2019 Data  
Our research work describes the challenges inhibiting data producers, data stewards, and data brokers in achieving FAIR goals for sharing biomedical data.  ...  We evaluated our framework using the software architecture testing technique and also looked at how different challenges in data integration are addressed by our system.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/data4020054 fatcat:qnx7ahj2yvbc5ccuu66asiko54

Biomedical Scholarly Article Editing and Sharing using Holistic Semantic Uplifting Approach

Asim Abbas, Steve Fonin Mbouadeu, Fazel Keshtkar, Joan DeBello, Syed Ahmad Chan Bukhari
2022 Proceedings of the ... International Florida Artificial Intelligence Research Society Conference  
., GoogleScholar, require machine-interpretable metadata to correctly index items in a context-aware manner for accurate biomedical literature searches.  ...  It further utilizes the meta tags and provides an intuitive interface for users to associate the semantics tags at the document level.  ...  Acknowledgments This work is supported by the National Science Foundation grant ID: 2101350.  ... 
doi:10.32473/flairs.v35i.130695 fatcat:m2xnm74vv5dg7jb4m4tus64z6u

Celebrating parasites

Casey S Greene, Lana X Garmire, Jack A Gilbert, Marylyn D Ritchie, Lawrence E Hunter
2017 Nature Genetics  
At the Pacific Symposium on Biocomputing (PSB) 2017, we presented the inaugural Research Parasite Awards to researchers selected for their rigorous analysis of publicly accessible data.  ...  We opened a call for nominations and applications in April 2016 and received 41 completed applications. From these, we selected an exemplar of Junior Research Parasitism and a Sustained Parasite.  ...  The authors were supported in part by grants from the Gordon and Betty Moore Foundation (GBMF 4552 to C.S.G.) and the US National Institutes of Health (R01LM012373 and K01ES025434 to L.X.G. and R01LM008111  ... 
doi:10.1038/ng.3830 pmid:28358134 pmcid:PMC5710834 fatcat:4nvkepyat5fw5d6nuujebdzkgu

Clinical Research Informatics: Contributions from 2017

Dipak Kalra, Christel Daniel
2018 IMIA Yearbook of Medical Informatics  
The last best paper proposes a new method for bias reduction in association studies using electronic health records data.  ...  Beyond securing these new platforms for exploiting large-scale health data, another major challenge is the limitation of biases related to the use of "real-world" data.  ...  Acknowledgement We would like to acknowledge the support of Martina Hutter and the reviewers in the selection process of the IMIA Yearbook.  ... 
doi:10.1055/s-0038-1641220 pmid:30157521 fatcat:hmpia6aobrczdp6lfahlm2viu4

Developing an ontology for representing the domain knowledge specific to non‐pharmacological treatment for agitation in dementia

Zhenyu Zhang, Ping Yu, Hui Chen (Rita) Chang, Sim Kim Lau, Cui Tao, Ning Wang, Mengyang Yin, Chao Deng
2020 Alzheimer s & Dementia Translational Research & Clinical Interventions  
DRANPTO consisted of 569 concepts and 48 object properties. It meets the standards for biomedical ontology.  ...  However, the valuable information in these data has not been used effectively to generate insights for improving the quality of care.  ...  For example, Malhotra et al. 72 applied both CQ evaluation and domain expert evaluation to assess the quality of their proposed ADO for AD. In addition, Berges et al. 44 used OOPS!  ... 
doi:10.1002/trc2.12061 pmid:32995470 pmcid:PMC7507392 fatcat:szh5geegfrarpeg3ez7qg6y5ty

Minimum Information about a Genotyping Experiment (MIGEN)

Jie Huang, Daniel Mirel, Elizabeth Pugh, Chao Xing, Peter N. Robinson, Alexander Pertsemlidis, LiangHao Ding, Julia Kozlitina, Joseph Maher, Jonathan Rios, Michael Story, Nishanth Marthandan (+1 others)
2011 Standards in Genomic Sciences  
To accommodate the wide variety of techniques and methodologies applied in current and future genotyping experiment, MIGen leverages foundational concepts from the Ontology for Biomedical Investigations  ...  MIGen can also serve as a framework for the development of data models for capturing and storing genotyping results and experiment metadata in a structured way, to facilitate the exchange of metadata.  ...  interpretation, reproduction and reuse of the data.  ... 
doi:10.4056/sigs.1994602 pmid:22180825 pmcid:PMC3235517 fatcat:eimzzyng6zgy5haev3ybvtkvtu

Data Communities: Empowering Researcher-Driven Data Sharing in the Sciences

Rebecca Springer, Danielle Cooper
1970 International Journal of Digital Curation  
In this paper, we propose a new mechanism for conceptualizing and supporting STEM research data sharing..  ...  However many scientists are not engaging in data sharing and remain skeptical of its relevance to their work.  ...  Acknowledgements The authors are deeply grateful to Sayeed Choudhury, Alastair Dunning, Themba Flowers, Maggie Levenstein, Cameron Neylon, Oya Rieger, and Elizabeth Yakel for their comments on a draft  ... 
doi:10.2218/ijdc.v15i1.695 fatcat:2opmmagtqjbtxdrfmlnhujgp2e

BioC: a minimalist approach to interoperability for biomedical text processing

D. C. Comeau, R. Islamaj Dogan, P. Ciccarese, K. B. Cohen, M. Krallinger, F. Leitner, Z. Lu, Y. Peng, F. Rinaldi, M. Torii, A. Valencia, K. Verspoor (+3 others)
2013 Database: The Journal of Biological Databases and Curation  
Acknowledgement The authors thank the anonymous reviewers for their useful suggestions in improving this manuscript. .................................................................................  ...  information extraction and text mining for biomedical literature.  ...  Concept, design, data, code and documentation were shared from the early stages of the initiative. In this section, we provide our views on the utility of the BioC proposal and where to go next.  ... 
doi:10.1093/database/bat064 pmid:24048470 pmcid:PMC3889917 fatcat:m5q3ltrfobg4fgkash3katpkia
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