agINFRA: a research data hub for agriculture, food and the environment
Identifieur interne : 000000 ( Pmc/Curation ); suivant : 000001agINFRA: a research data hub for agriculture, food and the environment
Auteurs : Andreas Drakos [Espagne] ; Vassilis Protonotarios [Espagne] ; Nikos Manouselis [Grèce]Source :
- F1000Research [ 2046-1402 ] ; 2015.
Abstract
The agINFRA project (www.aginfra.eu) was a European Commission funded project under the 7th Framework Programme that aimed to introduce agricultural scientific communities to the vision of open and participatory data-intensive science. agINFRA has now evolved into the European hub for data-powered research on agriculture, food and the environment, serving the research community through multiple roles.
Working on enhancing the interoperability between heterogeneous data sources, the agINFRA project has left a set of grid- and cloud- based services that can be reused by future initiatives and adopted by existing ones, in order to facilitate the dissemination of agricultural research, educational and other types of data. On top of that, agINFRA provided a set of domain-specific recommendations for the publication of agri-food research outcomes. This paper discusses the concept of the agINFRA project and presents its major outcomes, as adopted by existing initiatives activated in the context of agricultural research and education.
Url:
DOI: 10.12688/f1000research.6349.2
PubMed: 26339472
PubMed Central: 4544381
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">agINFRA: a research data hub for agriculture, food and the environment</title><author><name sortKey="Drakos, Andreas" sort="Drakos, Andreas" uniqKey="Drakos A" first="Andreas" last="Drakos">Andreas Drakos</name><affiliation wicri:level="1"><nlm:aff id="a1">Polytechnic Building, University of Alcala, Barcelona, 28871, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Polytechnic Building, University of Alcala, Barcelona, 28871</wicri:regionArea></affiliation></author><author><name sortKey="Protonotarios, Vassilis" sort="Protonotarios, Vassilis" uniqKey="Protonotarios V" first="Vassilis" last="Protonotarios">Vassilis Protonotarios</name><affiliation wicri:level="1"><nlm:aff id="a1">Polytechnic Building, University of Alcala, Barcelona, 28871, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Polytechnic Building, University of Alcala, Barcelona, 28871</wicri:regionArea></affiliation></author><author><name sortKey="Manouselis, Nikos" sort="Manouselis, Nikos" uniqKey="Manouselis N" first="Nikos" last="Manouselis">Nikos Manouselis</name><affiliation wicri:level="1"><nlm:aff id="a2">Agro-Know, 152 35 Vrilissia, Greece</nlm:aff><country xml:lang="fr">Grèce</country><wicri:regionArea>Agro-Know, 152 35 Vrilissia</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26339472</idno><idno type="pmc">4544381</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544381</idno><idno type="RBID">PMC:4544381</idno><idno type="doi">10.12688/f1000research.6349.2</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000000</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000000</idno><idno type="wicri:Area/Pmc/Curation">000000</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000000</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">agINFRA: a research data hub for agriculture, food and the environment</title><author><name sortKey="Drakos, Andreas" sort="Drakos, Andreas" uniqKey="Drakos A" first="Andreas" last="Drakos">Andreas Drakos</name><affiliation wicri:level="1"><nlm:aff id="a1">Polytechnic Building, University of Alcala, Barcelona, 28871, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Polytechnic Building, University of Alcala, Barcelona, 28871</wicri:regionArea></affiliation></author><author><name sortKey="Protonotarios, Vassilis" sort="Protonotarios, Vassilis" uniqKey="Protonotarios V" first="Vassilis" last="Protonotarios">Vassilis Protonotarios</name><affiliation wicri:level="1"><nlm:aff id="a1">Polytechnic Building, University of Alcala, Barcelona, 28871, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Polytechnic Building, University of Alcala, Barcelona, 28871</wicri:regionArea></affiliation></author><author><name sortKey="Manouselis, Nikos" sort="Manouselis, Nikos" uniqKey="Manouselis N" first="Nikos" last="Manouselis">Nikos Manouselis</name><affiliation wicri:level="1"><nlm:aff id="a2">Agro-Know, 152 35 Vrilissia, Greece</nlm:aff><country xml:lang="fr">Grèce</country><wicri:regionArea>Agro-Know, 152 35 Vrilissia</wicri:regionArea></affiliation></author></analytic><series><title level="j">F1000Research</title><idno type="eISSN">2046-1402</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The agINFRA project (www.aginfra.eu) was a European Commission funded project under the 7th Framework Programme that aimed to introduce agricultural scientific communities to the vision of open and participatory data-intensive science. agINFRA has now evolved into the European hub for data-powered research on agriculture, food and the environment, serving the research community through multiple roles.</p><p>Working on enhancing the interoperability between heterogeneous data sources, the agINFRA project has left a set of grid- and cloud- based services that can be reused by future initiatives and adopted by existing ones, in order to facilitate the dissemination of agricultural research, educational and other types of data. On top of that, agINFRA provided a set of domain-specific recommendations for the publication of agri-food research outcomes. This paper discusses the concept of the agINFRA project and presents its major outcomes, as adopted by existing initiatives activated in the context of agricultural research and education.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Gavrilut, L" uniqKey="Gavrilut L">L Gavrilut</name></author><author><name sortKey="Thanopoulos, C" uniqKey="Thanopoulos C">C Thanopoulos</name></author><author><name sortKey="Drakos, A" uniqKey="Drakos A">A Drakos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Manouselis, N" uniqKey="Manouselis N">N Manouselis</name></author><author><name sortKey="Drakos, A" uniqKey="Drakos A">A Drakos</name></author><author><name sortKey="Sicilia, Ma" uniqKey="Sicilia M">MA Sicilia</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cave, B" uniqKey="Cave B">B Cave</name></author><author><name sortKey="Pesce, V" uniqKey="Pesce V">V Pesce</name></author><author><name sortKey="Geser, G" uniqKey="Geser G">G Geser</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="discussion"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">F1000Res</journal-id><journal-id journal-id-type="iso-abbrev">F1000Res</journal-id><journal-id journal-id-type="pmc">F1000Research</journal-id><journal-title-group><journal-title>F1000Research</journal-title></journal-title-group><issn pub-type="epub">2046-1402</issn><publisher><publisher-name>F1000Research</publisher-name><publisher-loc>London, UK</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26339472</article-id><article-id pub-id-type="pmc">4544381</article-id><article-id pub-id-type="doi">10.12688/f1000research.6349.2</article-id><article-categories><subj-group subj-group-type="heading"><subject>Opinion Article</subject></subj-group><subj-group><subject>Articles</subject><subj-group><subject>Agriculture & Biotechnology</subject></subj-group><subj-group><subject>Data Sharing</subject></subj-group></subj-group></article-categories><title-group><article-title>agINFRA: a research data hub for agriculture, food and the environment</article-title><fn-group content-type="pub-status"><fn><p>v2; ref status: indexed</p></fn></fn-group></title-group><contrib-group><contrib contrib-type="author"><name><surname>Drakos</surname><given-names>Andreas</given-names></name><xref ref-type="corresp" rid="c1">a</xref><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Protonotarios</surname><given-names>Vassilis</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Manouselis</surname><given-names>Nikos</given-names></name><xref ref-type="aff" rid="a2">2</xref></contrib><aff id="a1"><label>1</label>Polytechnic Building, University of Alcala, Barcelona, 28871, Spain</aff><aff id="a2"><label>2</label>Agro-Know, 152 35 Vrilissia, Greece</aff></contrib-group><author-notes><corresp id="c1"><label>a</label><email xlink:href="mailto:andr.drakos@gmail.com">andr.drakos@gmail.com</email></corresp><fn fn-type="con"><p>AD authored the first draft of the paper, VP critically revised it for content and NM was the main contributor to the vision of the project. All authors approved the final manuscript for publication.</p></fn><fn fn-type="conflict"><p><bold>Competing interests: </bold>Andreas Drakos is a consulting project manager responsible for the coordination of the agINFRA project. Vassilis Protonotarios is a consulting researcher, one of the main contributors in the agINFRA project work on data interoperability. Nikos Manouselis is the CEO of Agro-Know and technical leader of the agINFRA project.</p></fn></author-notes><pub-date pub-type="epub"><day>15</day><month>6</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>4</volume><elocation-id>127</elocation-id><history><date date-type="accepted"><day>11</day><month>6</month><year>2015</year></date></history><permissions><copyright-statement>Copyright: © 2015 Drakos A et al.</copyright-statement><copyright-year>2015</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri content-type="pdf" xlink:type="simple" xlink:href="f1000research-4-7112.pdf"></self-uri><abstract><p>The agINFRA project (www.aginfra.eu) was a European Commission funded project under the 7th Framework Programme that aimed to introduce agricultural scientific communities to the vision of open and participatory data-intensive science. agINFRA has now evolved into the European hub for data-powered research on agriculture, food and the environment, serving the research community through multiple roles.</p><p>Working on enhancing the interoperability between heterogeneous data sources, the agINFRA project has left a set of grid- and cloud- based services that can be reused by future initiatives and adopted by existing ones, in order to facilitate the dissemination of agricultural research, educational and other types of data. On top of that, agINFRA provided a set of domain-specific recommendations for the publication of agri-food research outcomes. This paper discusses the concept of the agINFRA project and presents its major outcomes, as adopted by existing initiatives activated in the context of agricultural research and education.</p></abstract><kwd-group kwd-group-type="author"><kwd>agri-food</kwd><kwd>cloud-based</kwd><kwd>grid-based</kwd></kwd-group><funding-group><award-group id="fund-1"><funding-source>Combination of Collaborative Project and Coordination and Support Action: Integrated Infrastructure Initiative</funding-source><award-id>INFRA-2011-1.2.2</award-id></award-group><funding-statement>This work is funded with the support by European Commission and more specifically the FP7 project agINFRA “A data infrastructure to support agricultural scientific communities” (
<ext-link ext-link-type="uri" xlink:href="http://aginfra.eu">http://aginfra.eu</ext-link>), which is funded by the schema “Combination of Collaborative Project and Coordination and Support Action: Integrated Infrastructure Initiative (I3)” under the work programme topic “INFRA-2011-1.2.2: data infrastructures for e-Science”. This publication reflects the views only of the authors, and the Commission cannot be held responsible for any use which may be made of the information contained therein.</funding-statement><funding-statement><italic>I confirm that the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</italic></funding-statement></funding-group></article-meta><notes notes-type="version-changes"><sec><label>Updated</label><title>Changes from Version 1</title><p>The agINFRA project is now successfully over and revisions reflecting its new role as a research data hub have been introduced to the manuscript.</p></sec></notes></front><sub-article id="report8761" article-type="peer-review"><front-stub><article-id pub-id-type="doi">10.5256/f1000research.7112.r8761</article-id><title-group><article-title>Referee response for version 2</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Brewster</surname><given-names>Christopher</given-names></name><xref ref-type="aff" rid="r8761a1">1</xref><role>Referee</role></contrib><aff id="r8761a1"><label>1</label>Aston Business School, Aston University, Birmingham, UK</aff></contrib-group><author-notes><fn fn-type="conflict"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>18</day><month>8</month><year>2015</year></pub-date><related-article id="d35e636" related-article-type="peer-reviewed-article" ext-link-type="doi" xlink:href="10.12688/f1000research.6349.2">Version </related-article><custom-meta-group><custom-meta><meta-name>recommendation</meta-name><meta-value>approve</meta-value></custom-meta></custom-meta-group></front-stub><body><p>This paper is a good summary of the objectives and achievements of the AgInfra project,</p><p>and as such provides an good introduction for researchers wishing to use the AgInfra tools and services.</p><p>The paper could be strengthened by:
<list list-type="order"><list-item><p>The description of 1-2 tools developed within the project so that the reader can understand what was possible after the project that was not before.</p></list-item><list-item><p>The "conclusion" section should be left with the title "Creating new products and opportunities" and a separate conclusion added which could a. reflect on where the data infrastructure for agrifood research is heading now, and/or b. identify directions for future research/development project.</p></list-item></list><underline>Specific Comments</underline></p><p>Frequent infelicities in the use of English:
<list list-type="bullet"><list-item><p>In several places the language is a little too telegraphic, appropriate for a bullet point list but not very readable for a journal paper.</p></list-item><list-item><p>What do you mean by "Provide mediating capabilities ..." p2 ?</p></list-item><list-item><p>"took upon" --> "undertook" p3</p></list-item><list-item><p>vo.aginfra.eu does not respond</p></list-item><list-item><p>voms.ipb.ac.rs does not respond</p></list-item><list-item><p>p3 "and on user membership" --> "and for ..."</p></list-item><list-item><p>p3 "Both of the generic versions of the SG have been customized to support the needs of the agricultural research data community." -- in what way?</p></list-item><list-item><p>p3 "allows the easy of new resources to be committed to the project" --> "allows new resources to be easily committed ..."</p></list-item><list-item><p>p5 "As it has been show cased" --> "As has been ..."</p></list-item><list-item><p>p5 "The usage of such format" --> "The use of such a format ..."</p></list-item><list-item><p>p5 "a lot of effort was made on" --> "a lot of effort was devoted to ..."</p></list-item><list-item><p>p5 "OpenAIRE (https:// www.openaire.eu), a three-year project, establish" --> "established/establishes (?)"</p></list-item><list-item><p>p5 "European Resuscitation Council Guidelines on Open Access" -- are you sure it is "resuscitation"? Repositories? Resuscitation does not make sense.</p></list-item><list-item><p>p5 "dissemination aiming among others to provide" --> "dissemination, with the aim to provide"</p></list-item><list-item><p>p5 "These recommendations are: ..." --- there are no verbs in the recommendations which follow so it is unclear what the recommendations are. I suggest the use of modal verbs such as "should/ought/might/may ... do XYZ"</p></list-item><list-item><p>p5 concerning the recommendations - should the recommendations give *examples* or should they be more categorical?</p></list-item><list-item><p>p5 "After the kick-off meeting of the agINFRA project, it was obvious that the expectations were set very high. " -- irrelevant/inappropriate</p></list-item><list-item><p>p6 - all the material explaining what GODAN is feels extraneous to the project. A short reference should suffice.</p></list-item><list-item><p>p6 "This effort was realized with a European approach ..." -- what does this mean?</p></list-item><list-item><p>p6 "Towards this end, two different aspects of agINFRA work implemented this strategy" --> "In order to implement this strategy, agINRA undertook two types of actions:"</p></list-item></list></p><p>I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.</p></body></sub-article><sub-article id="report8763" article-type="peer-review"><front-stub><article-id pub-id-type="doi">10.5256/f1000research.6807.r8763</article-id><title-group><article-title>Referee response for version 1</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Adamides</surname><given-names>George</given-names></name><xref ref-type="aff" rid="r8763a1">1</xref><role>Referee</role></contrib><aff id="r8763a1"><label>1</label>Agricultural Research Institute, Nicosia, Cyprus</aff></contrib-group><author-notes><fn fn-type="conflict"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>3</day><month>6</month><year>2015</year></pub-date><related-article id="d35e764" related-article-type="peer-reviewed-article" ext-link-type="doi" xlink:href="10.12688/f1000research.6349.1">Version </related-article><custom-meta-group><custom-meta><meta-name>recommendation</meta-name><meta-value>approve</meta-value></custom-meta></custom-meta-group></front-stub><body><p>In general I find the article very interesting and its tackling a very interesting topic sharing open scientific data.The article is well organized and provides sufficient information on the goals and outcomes of the agInfra project. I would expect to see more on related work and other background information related to the sharing of agricultural information among scientist. For example what other practices exist and how the agINFRA project outcomes complement or differ from other sharing tools for scientific research (not necessarily only in agriculture).</p><p>I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.</p></body><sub-article id="comment1419" article-type="response"><front-stub><contrib-group><contrib contrib-type="author"><name><surname>Drakos</surname><given-names>Andreas</given-names></name><aff></aff></contrib></contrib-group><author-notes><fn fn-type="conflict"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>9</day><month>6</month><year>2015</year></pub-date></front-stub><body><p>Dear George,</p><p>thank you very much for your comments. The main concept of the agINFRA project was to re-use main infrastructure elements, connect with existing generic solutions and create something specified for the agricultural research domain. While in this article we tried to summarize the work of agINFRA,the specific aspects of each element has been presented in the numerous publications made from the partners (they can all be found at
<ext-link ext-link-type="uri" xlink:href="http://publications.aginfra.eu/">http://publications.aginfra.eu/</ext-link> ).</p><p>The agINFRA vision was to improve research collaboration and data exchange, but during the lifetime of the project, this had to be limited in creating the necessary building blocks (e-infrastructure) for services to built upon (as for example the new AGRIS). Hopefully this effort will continue and in the future we will be able to present a number of different end-user services specialized for the agricultural research community.</p></body></sub-article><sub-article id="comment1420" article-type="response"><front-stub><contrib-group><contrib contrib-type="author"><name><surname>Protonotarios</surname><given-names>Vassilis</given-names></name><aff>Agro-Know, Greece</aff></contrib></contrib-group><author-notes><fn fn-type="conflict"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>9</day><month>6</month><year>2015</year></pub-date></front-stub><body><p>Dear George,</p><p>We would like to thank you for your comments. As Andreas mentioned earlier, the agINFRA project aimed at reusing existing components and provide the necessary interconnections or missing links in order to provide meaningful services that would facilitate agricultural researchers in conducting, publishing and disseminating their research.</p><p>Despite the fact that we could indeed elaborate on the existing similar efforts, previous experiences and use cases, we decided to focus on the agINFRA approach and how potential end-users could benefit from that. However, based on your idea, we could work on an additional article that will focus on the background of the agINFRA project and the services that the project made use of.</p></body></sub-article></sub-article></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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