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COPO: a metadata platform for brokering FAIR data in the life sciences

Felix Shaw, Anthony Etuk, Alice Minotto, Alejandra Gonzalez-Beltran, David Johnson, Phillipe Rocca-Serra, Marie-Angélique Laporte, Elizabeth Arnaud, Medha Devare, Paul Kersey, Susanna-Assunta Sansone, Robert P. Davey
2020 F1000Research  
That said, we have come a long way in the last decade, with funders, publishers, and researchers themselves making the case for open, interoperable data as a key component of an open science philosophy  ...  Demand for technical experts (data scientists and bioinformaticians) to process these data is at an all-time high, but these are not typically trained in good data management practices.  ...  Unclear why this aspect of python is needed for a data annotation platform, which is usually hosted on platforms not suited for heavy computation.  ... 
doi:10.12688/f1000research.23889.1 fatcat:5jstsv7mbveudfaz2uq3hhzcpm

COPO: a metadata platform for brokering FAIR data in the life sciences [article]

Anthony Etuk, Felix Shaw, Alejandra Gonzalez-Beltran, David Johnson, Marie-Angelique Laporte, Philippe Rocca-Serra, Elizabeth Arnaud, Medha Devare, Paul J Kersey, Susanna-Assunta Sansone, Robert P Davey
2019 bioRxiv   pre-print
Availability: COPO is entirely open source and freely available on GitHub at https://github.com/collaborative-open-plant-omics.  ...  That said, we have come a long way in the last decade, with funders, publishers, and researchers themselves making the case for open, interoperable data as a key component of an open science philosophy  ...  Conclusions COPO is a semantic metadata annotation and data brokering platform, initially designed to ease data curation and submission to public repositories for plant scientists.  ... 
doi:10.1101/782771 fatcat:valzo7wtzffbrlmruhlwqwrthy

Data management and best practice for plant science

Sabina Leonelli, Robert P. Davey, Elizabeth Arnaud, Geraint Parry, Ruth Bastow
2017 Nature Plants  
One such projects is the Collaborative Open Plant Omics (COPO), devoted to the development of web-based interfaces for plant scientists to describe multi-omics datasets according to relevant domain metadata  ...  Projects such as the Collaborative Open Plant Omics (COPO) [23], GnpIS [24] and the Agroportal project [22] are developing useroriented services to simplify annotations of plant data using ontologies  ... 
doi:10.1038/nplants.2017.86 pmid:28585570 fatcat:5r4ymlczc5bq5mrnqgdkrgsb4u

D7.2 Phenotypic Data Exposed Through Integrating Api By All Participants

Célia Miguel, Cyril Pommier, Richard Finkers, Frederik Coppens, Dan Bolser
2018 Zenodo  
This architecture uses the Breeding API (BrAPI, www.brapi.org ), an API for accessing data relevant for plant breeding developed by the international plant community.  ...  Hence, several standards have been built these past years for the annotation of data sets, and the Elixir plant community is coautoring most of them.  ...  It is an open API based on the principles of open linked data and a web-based architecture that has been driven by a collaborative community-based global effort.  ... 
doi:10.5281/zenodo.1452451 fatcat:oycqplrtlrborjkoaiakrvw544

ISA API: An open platform for interoperable life science experimental metadata

David Johnson, Dominique Batista, Keeva Cochrane, Robert P Davey, Anthony Etuk, Alejandra Gonzalez-Beltran, Kenneth Haug, Massimiliano Izzo, Martin Larralde, Thomas N Lawson, Alice Minotto, Pablo Moreno (+9 others)
2021 GigaScience  
formats required for depositing data in public databases.  ...  Background The Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open source community specifications and software tools for enabling discovery, exchange, and  ...  by the Oxford e-Research Centre, UK, attendees of the 2016 "China-UK Data Dissemination in Metabolomics (CUD-DEL)" workshop hosted by GigaScience, Hong Kong, and the EMBL-EBI MetaboLights team for guidance  ... 
doi:10.1093/gigascience/giab060 pmid:34528664 pmcid:PMC8444265 fatcat:emisaswturffta4b6bv7rlu5by

ISA API: An open platform for interoperable life science experimental metadata [article]

David Johnson, Keeva Cochrane, Robert P Davey, Anthony Etuk, Alejandra Gonzalez-Beltran, Kenneth Haug, Massimiliano Izzo, Martin Larralde, Thomas N Lawson, Alice Minotto, Pablo Moreno, Venkata Chandrasekhar Nainala (+8 others)
2020 bioRxiv   pre-print
formats required for depositing data in public databases.  ...  The Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open-source community specifications and software tools for enabling discovery, exchange and publication  ...  The copyright holder for this this version posted November 16, 2020.  ... 
doi:10.1101/2020.11.13.382119 fatcat:d6dyr4b67ndz3fm6lrg5btpn2m

CORBEL Delivery of Toolkit supporting community ontology mapping and development

Simon Jupp, Helen Parkinson, Carol Goble, Nick Juty, Jan-Willem Boiten, Morris Swertz
2019 Zenodo  
This deliverable reports on the services that were developed for CORBEL to support access to ontologies and ontology mapping services.  ...  This was undertaken within OLS, a recognised 'Recommended Interoperability Resource' in ELIXIR Extending and improving the Zooma repository of data to ontology mappings that can be used to predict ontology  ...  /The-EBI-RDF-platform-linked-open-data-for-the-life 5 https://www.scibite.com/exploring-ontology-visualisation-techniques-for-biological-data/ 6 http://environmentontology.org/Browse-EnvO 7 http://www.hipsci.org  ... 
doi:10.5281/zenodo.2559159 fatcat:kkijrl2ncfe6le4joduvb47icm

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems

Elizabeth Arnaud, Marie-Angélique Laporte, Soonho Kim, Céline Aubert, Sabina Leonelli, Berta Miro, Laurel Cooper, Pankaj Jaiswal, Gideon Kruseman, Rosemary Shrestha, Pier Luigi Buttigieg, Christopher J. Mungall (+26 others)
2020 Patterns  
In this paper, we discuss the added value of the Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture for harnessing relevant expertise in ontology development and identifying  ...  Despite the existence of robust ontologies in the Life Sciences, there is currently no comprehensive full set of ontologies recommended for data annotation across agricultural research disciplines.  ...  Ontologies for Plant Traits and Agronomy Data Crop breeding relies on collecting data on the desired traits for a new crop variety by testing it in multiple locations and diverse environments, linking  ... 
doi:10.1016/j.patter.2020.100105 pmid:33205138 pmcid:PMC7660444 fatcat:6efus64zwzgldov6gy5y2motyi

Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Donat Agosti, Petr Baldrian, Bachir Balech, Erwan Corre, Robert P. Davey, Henrik Lantz, Graziano Pesole, Christian Quast, Frank Oliver Glöckner, Niels Raes (+7 others)
2021 F1000Research  
For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global  ...  to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures  ...  Across the board, tools that make metadata management easier, such as the COPO platform for brokering collaborative open omics data (Shaw et al. 2020) , are helping to ensure that data are increasingly  ... 
doi:10.12688/f1000research.73825.1 fatcat:wphybjxe4bd3dgdewjqobb2hfe

How to build an effective research network: lessons from two decades of the GARNet plant science community

Geraint Parry, Yoselin Benitez-Alfonso, Daniel J Gibbs, Murray Grant, Andrea Harper, C Jill Harrison, Eirini Kaiserli, Sabina Leonelli, Sean May, Sarah McKim, Steven Spoel, Colin Turnbull (+2 others)
2020 Journal of Experimental Botany  
Collaboration requires venues, infrastructures, training facilities and, perhaps most importantly, a sustained commitment to working together as a community.  ...  Over the past twenty years, this is a role that the UKRI-BBSRC funded GARNet network has played in the support of the UK curiosity-driven, discovery-led plant science research community.  ...  Data availability The data on the number of UK-based plant science principal investigators ( Fig. 1) are available from Geraint Parry upon request.  ... 
doi:10.1093/jxb/eraa397 pmid:32898228 pmcid:PMC7906777 fatcat:mvdd6zpuz5ctxigip35r2yulfe

Harnessing diversity from ecosystems to crops to genes

Vicky Buchanan-Wollaston, Zoe Wilson, François Tardieu, Jim Beynon, Katherine Denby
2017 Food and Energy Security  
These data and alleles are useful globally to speed progress in breeding for similar environments while not wasting time on ineffective genotypes.  ...  To feed humanity, while maintaining a stable and diverse biosphere, crop science needs to adapt to an open research environment where genetic resources and the data demonstrating the environments in which  ...  Acknowledgements This paper is based on outcomes from a Stress Resilience Symposium held in Brazil in October 2015 organized by the Global Plant Council and Society for Experimental Biology.  ... 
doi:10.1002/fes3.106 fatcat:dmhctjziqjhhfjnm4nqgp63afi

Cyberinfrastructure and resources to enable an integrative approach to studying forest trees

Jill L Wegrzyn, Taylor Falk, Emily Grau, Sean Buehler, Risharde Ramnath, Nic Herndon
2019 Evolutionary Applications  
Successful implementation of life science cyberinfrastructure is improving data standards, ontologies, analytic workflows, and integrated database platforms for both model and non-model plant species.  ...  Genomic data from these projects generates sequences that represent intermediate assemblies for transcriptomes and genomes.  ...  In non-model species, the For plant biologists, the ELIXIR UK-supported Collaborative Open Plant Omics (COPO) initiative is improving the situation for plant genomic and phenomic data with standards-based  ... 
doi:10.1111/eva.12860 pmid:31892954 pmcid:PMC6935593 fatcat:r2zcwfc7irdgdln4faunycp3ui

Sequence locally, think globally: The Darwin Tree of Life Project

2022 Proceedings of the National Academy of Sciences of the United States of America  
The Darwin Tree of Life Project was founded to demonstrate the credibility of these goals and to deliver at-scale genome sequences of unprecedented quality for a biogeographic region: the archipelago of  ...  Together, we have built a workflow that collects specimens from the field, robustly identifies them, performs sequencing, generates high-quality, curated assemblies, and releases these openly for the global  ...  For the purpose of Open Access, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission.  ... 
doi:10.1073/pnas.2115642118 pmid:35042805 pmcid:PMC8797607 fatcat:xlkzf6fw6jdufdcllprknfxldi

Identifier Services: Modeling and Implementing Distributed Data Management in Cyberinfrastructure

Maria Esteva, Ramona L. Walls, Andrew B. Magill, Weijia Xu, Ruizhu Huang, James Carson, Jawon Song
2019 Data and Information Management  
The prototype implementation is based on a three-step data modeling process involving: a) understanding and recording of different researcher workflows, b) mapping the workflows and data to a generic data  ...  Identity functions are operationalized as continuous tracking of authenticity attributes including data location, differences between seemingly identical datasets, metadata, data integrity, and the roles  ...  Infrastructure for Distributed Data Several pieces of infrastructure exist to manage the lifecycle of life sciences data.  ... 
doi:10.2478/dim-2019-0002 fatcat:hmmq6kchw5guhoe66w3dbfp5eq

Can the periphery achieve core? The case of the automobile components industry in Spain

Jesús F. Lampón, Santiago Lago-Peñas, Pablo Cabanelas
2014 Papers in Regional Science  
The analysis of plants set up (investments) and relocated (divestments) by multinationals (MNEs) between 2001 and 2010 show that Spain is no longer a place for labour-intensive activities and standardized  ...  However, the continuing majority presence of foreign-owned companies is limiting decision power for generating and transferring technology, concentrating it mainly in those which Spanish MNEs have specialised  ...  For collecting data we combine different sources of information, field research and in-depth interviews 3 with managers who participated in these processes of investment and production mobility, also data  ... 
doi:10.1111/pirs.12146 fatcat:cjlwajrj55he5mq63piafdqu34
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