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AgroPortal: A vocabulary and ontology repository for agronomy

Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo, Vincent Emonet, John Graybeal, Marie-Angélique Laporte, Mark A. Musen, Valeria Pesce, Pierre Larmande
2018 Computers and Electronics in Agriculture  
By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology repository for the agronomy domain.  ...  Therefore, there is need for a common platform to receive and host them, align them, and enabling their use in agro-informatics applications.  ...  We also thank the National Center for Biomedical Ontologies for their help and time spent with us in deploying the AgroPortal.  ... 
doi:10.1016/j.compag.2017.10.012 fatcat:tsvou7l42bg5hn6cw43ogtj2je

Harnessing the Power of Unified Metadata in an Ontology Repository: The Case of AgroPortal

Clement Jonquet, Anne Toulet, Biswanath Dutta, Vincent Emonet
2018 Journal on Data Semantics  
We have then built a new metadata model for our AgroPortal vocabulary and ontology repository, a platform dedicated to agronomy based on the NCBO BioPortal technology.  ...  Ontology libraries and repositories also have to play an important role.  ...  AgroPortal's main objective is to be a reference ontology repository for agronomy, plant sciences, biodiversity, and nutrition.  ... 
doi:10.1007/s13740-018-0091-5 fatcat:jzj4ndutzbfulkq7p3ecxkky4e

Ontology Service Center: a datahub for ontology application [article]

CHEN Tao, SU Rina, ZHANG Yongjuan, YIN Xin, ZHU Rui
2021 arXiv   pre-print
Ontology is the soul between series digital humanities resources, which provides a good way for people to discover and understand these datasets.  ...  However, how to discover, integrate and reuse these distributed heterogeneous research datasets is a challenging task.  ...  By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, Jonquet C. et al. (2018) have designed AgroPortal, a vocabulary and ontology repository for agronomy, food, plant sciences  ... 
arXiv:2108.05639v1 fatcat:63gx5pya25blthe5zwtbecdf5e

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E. Lewis, Mark P. Schildhauer, Ramona L. Walls, Christopher J. Mungall
2016 Journal of Biomedical Semantics  
We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications.  ...  Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy.  ...  We are also grateful to the CGIAR and Bioversity International, in particular Medha Devare, Elizabeth Arnaud, Marie-Angelique Laporte, and Céline Audebert for work and meetings associated with the Agronomy  ... 
doi:10.1186/s13326-016-0097-6 pmid:27664130 pmcid:PMC5035502 fatcat:4gznhpc35nashnqdtvpovs4xza

SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes

Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Stella Zevio, Clement Jonquet
2018 BMC Bioinformatics  
and ontologies and 333 K concepts.  ...  However, semantic resources are required to design semantic indexes and transform biomedical (text)data into knowledge for better information mining and retrieval.  ...  Acknowledgements We would like to thank the US National Center for Biomedical Ontology at Stanford University, for their assistance with the NCBO Annotator, the CépiDC and CLEF eHealth organizers (Aurélie  ... 
doi:10.1186/s12859-018-2429-2 pmid:30400805 pmcid:PMC6218966 fatcat:dmwmnr4qs5fbfgcz2obqualfpq

OntoCommons D3.2 - Report on existing domain ontologies in

Yann Le Franc
2022 Zenodo  
This first analysis highlighted the strong heterogeneities within and among the different domains and the low level of compliance to FAIR principles for each community.  ...  Using this dataset, we collected information both manually and automatically to better describe the landscape (number of ontologies by domains, usage of Top-Level Ontologies, serialisation, complexity,  ...  It is implemented for several domains: biomedicine (BioPortal26 located in the USA), agronomy (AgroPortal27 located in France), environment (EcoPortal28 located in Italy).  ... 
doi:10.5281/zenodo.6504552 fatcat:nvbn37rbdvhjtlxu2rvkjaun4q

Data management challenges for artificial intelligence in plant and agricultural research

Hugh F. Williamson, Julia Brettschneider, Mario Caccamo, Robert P. Davey, Carole Goble, Paul J. Kersey, Sean May, Richard J. Morris, Richard Ostler, Tony Pridmore, Chris Rawlings, David Studholme (+2 others)
2021 F1000Research  
After a brief summary of the reasons for the interest in data science and AI within plant science, the paper identifies and discusses eight key challenges in data management that must be addressed to further  ...  unlock the potential of AI in crop and agronomic research, and particularly the application of Machine Learning (AI) which holds much promise for this domain.  ...  This fragmented data landscape limits the opportunities for the application of AI to plant research and agronomy.  ... 
doi:10.12688/f1000research.52204.1 fatcat:rgd2m3ospvbknhwhljehmyybnu

European Landscape Of Tdm Applications Report

Stelios Piperidis, Kanella Pouli, Maria Gavriilidou, Dimitris Galanis, Juli Bakagianni
2016 Zenodo  
and applications in a number of areas.  ...  Due to the fact that TDM is currently a very hot field in terms of research, development and business applications, highly convoluted with the big data hype, and as a result constantly changing, the present  ...  AgroPortal 172 repository AgroPortal is a repository which provides access and sharing for ontologies on the environment, agriculture and agronomy.  ... 
doi:10.5281/zenodo.1240758 fatcat:ie25jfzuqne3bc37dc5qotcyyi

Research data management in academic institutions: A scoping review

Laure Perrier, Erik Blondal, A. Patricia Ayala, Dylanne Dearborn, Tim Kenny, David Lightfoot, Roger Reka, Mindy Thuna, Leanne Trimble, Heather MacDonald, Sanjay B Jadhao
2017 PLoS ONE  
Materials and methods We conducted a scoping review by searching forty literature databases encompassing a broad range of disciplines from inception to April 2016.  ...  Objective The purpose of this study is to describe the volume, topics, and methodological nature of the existing research literature on research data management in academic institutions.  ...  Acknowledgments We thank Mikaela Gray for retrieving articles, tracking papers back to their original literature databases, and assisting with references.  ... 
doi:10.1371/journal.pone.0178261 pmid:28542450 pmcid:PMC5441653 fatcat:kwky7jhca5gs7ayhysgcw72xqe

Mining information for functional genomics

L. Bernardi, E. Ratsch, R. Kania, J. Saric, I. Rojas, J.H. Park, B.R. Schatz, C. Blaschke, A. Valencia, C. Nedellec
2002 IEEE Intelligent Systems  
In this installation, contributors describe some of the principal challenges in this area and pathways to approaching them.  ...  Advanced natural language processing (NLP) and data mining methods, enriched by ontologies that specify the domain's semantics, seem to be a promising approach.  ...  Acknowledgments I thank MRC, UK, for funding, and Maryana Huston, Dan Bosler, Michael Lappe, and Amalia Teichmann for collaboration.  ... 
doi:10.1109/mis.2002.1005634 fatcat:bpvtgxfojre5xc2ndy62ho5df4

Rapport d'activités IFB 2019-2020 [article]

Claudine Médigue, Suzanne Lauriou, Angela Saenz, Jacques Van Helden, IFB Teams
2021 Zenodo  
challenges. 2019 paved the way to consolidate IFB sustainability, with a very positive evaluation of our 2018-2021 roadmap, a validation of the IFB renewal through funding by the Ministry of Science and  ...  , applications of IA to life sciences, deployment of certified Health Data Storage (HDS) digital spaces. 2020 was definitely marked by the worldwide sanitary crisis with the COVID-19 pandemic.  ...  , agronomy and health. .  ... 
doi:10.5281/zenodo.5324333 fatcat:py5xp6q7ungkdevdqx25zxfwmq

Understanding Data Search as a Socio-technical Practice [article]

Kathleen Gregory, Helena Cousijn, Paul Groth, Andrea Scharnhorst, Sally Wyatt
2019 arXiv   pre-print
The socio-technical problem of locating data for reuse is often reduced to the technological dimension of designing data search systems.  ...  In this article, we explore how adopting a contextual, socio-technical perspective can help to understand user practices and behavior and ultimately help to improve the design of data discovery systems  ...  Acknowledgements KG developed the conceptual frameworks, collected and analyzed the data, and wrote the manuscript. HC, PG, AS, and SW contributed to theory development and editing.  ... 
arXiv:1801.04971v3 fatcat:fncql4gqcffnjj2457r7enocpe

The role of software in science: a knowledge graph-based analysis of software mentions in PubMed Central

David Schindler, Felix Bensmann, Stefan Dietze, Frank Krüger
2022 PeerJ Computer Science  
Science across all disciplines has become increasingly data-driven, leading to additional needs with respect to software for collecting, processing and analysing data.  ...  Thus, transparency about software used as part of the scientific process is crucial to understand provenance of individual research data and insights, is a prerequisite for reproducibility and can enable  ...  ) for deep learning models, Huggingface transformers 4.9.1 (Wolf et al., 2020) to load and fine-tune pre-trained BERT models, Gensim 4.0.1 (Řehůřek & Sojka, 2010) for pre-training word embeddings,  ... 
doi:10.7717/peerj-cs.835 pmid:35111920 pmcid:PMC8771769 fatcat:nivowrjq7fbnrprbsrhg62lmam

Biological and Medical Sciences

Detlev W. Bronk, Carl-Goran Heden, C. H. Waddington
1971 Annals of the New York Academy of Sciences  
Figure 31 illustrates an estimate of the contribution of each individual BMS RI to research activities across this spectrum, from basic medical/ biological research and innovation activities to activities  ...  dedicated to health care.  ...  Translation of basic research discoveries into clinical application has turned out to be a major challenge for the European Research Area.  ... 
doi:10.1111/j.1749-6632.1971.tb41309.x fatcat:6zdkjtuojrdwhib3lpdzoq7i3u

Biological and Medical Sciences

G. J. Kennedy
1989 The gerontologist  
Figure 31 illustrates an estimate of the contribution of each individual BMS RI to research activities across this spectrum, from basic medical/ biological research and innovation activities to activities  ...  dedicated to health care.  ...  Translation of basic research discoveries into clinical application has turned out to be a major challenge for the European Research Area.  ... 
doi:10.1093/geront/29.1.137a fatcat:32k4evfphzhdddo3ikpfvbwcgi
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