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AgroPortal: A vocabulary and ontology repository for agronomy
2018
Computers and Electronics in Agriculture
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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
2018
Journal on Data Semantics
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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]
2021
arXiv
pre-print
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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
2016
Journal of Biomedical Semantics
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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
2018
BMC Bioinformatics
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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
2022
Zenodo
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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
2021
F1000Research
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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
2016
Zenodo
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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
2017
PLoS ONE
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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
2002
IEEE Intelligent Systems
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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]
2021
Zenodo
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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]
2019
arXiv
pre-print
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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
2022
PeerJ Computer Science
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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
1971
Annals of the New York Academy of Sciences
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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
1989
The gerontologist
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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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