A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing
Identifieur interne : 000457 ( Main/Exploration ); précédent : 000456; suivant : 000458A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing
Auteurs : Dagmar Triebel [Allemagne] ; Wolfgang Reichert [Allemagne] ; Simone Bosert [Allemagne] ; Martin Feulner [Allemagne] ; Daniel Osieko Okach [Kenya] ; Abderachid Slimani [Algérie] ; Gerhard Rambold [Allemagne]Source :
- Database: The Journal of Biological Databases and Curation [ 1758-0463 ] ; 2018.
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English descriptors
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Abstract
Sampling of biological and environmental vouchers in the field is rather challenging, particularly under adverse habitat conditions and when various activities need to be handled simultaneously. The workflow described here includes five procedural steps, which result in professional sampling and the generation of universally identifiable data. In preparation for the field campaign, sample containers need to be labelled with universally unique identifier (UUID)-QR-codes. At the collection site, labelled containers, sampled material and attached supplementary information are imaged using a GNSS- respectively GPS-enabled smartphone or camera. Image processing, tagging and data storage as CSV text file is subsequently achieved in a field station or laboratory. For this purposes, the newly implemented tool
Url:
DOI: 10.1093/database/bax096
PubMed: 29688348
PubMed Central: 7206647
Affiliations:
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Le document en format XML
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xml:lang="fr">Allemagne</country><wicri:regionArea>Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80638 München</wicri:regionArea></affiliation></author><author><name sortKey="Reichert, Wolfgang" sort="Reichert, Wolfgang" uniqKey="Reichert W" first="Wolfgang" last="Reichert">Wolfgang Reichert</name><affiliation wicri:level="1"><nlm:aff id="bax096-aff1">Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80638 München, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80638 München</wicri:regionArea></affiliation></author><author><name sortKey="Bosert, Simone" sort="Bosert, Simone" uniqKey="Bosert S" first="Simone" last="Bosert">Simone Bosert</name><affiliation wicri:level="1"><nlm:aff id="bax096-aff2">University of Bayreuth, 95440 Bayreuth, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>University of Bayreuth, 95440 Bayreuth</wicri:regionArea></affiliation></author><author><name sortKey="Feulner, Martin" sort="Feulner, Martin" uniqKey="Feulner M" first="Martin" last="Feulner">Martin Feulner</name><affiliation wicri:level="1"><nlm:aff id="bax096-aff2">University of Bayreuth, 95440 Bayreuth, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>University of Bayreuth, 95440 Bayreuth</wicri:regionArea></affiliation></author><author><name sortKey="Okach, Daniel Osieko" sort="Okach, Daniel Osieko" uniqKey="Okach D" first="Daniel Osieko" last="Okach">Daniel Osieko Okach</name><affiliation wicri:level="1"><nlm:aff id="bax096-aff3">JOOUST, 40601 Bondo, Kenya</nlm:aff><country xml:lang="fr">Kenya</country><wicri:regionArea>JOOUST, 40601 Bondo</wicri:regionArea></affiliation></author><author><name sortKey="Slimani, Abderachid" sort="Slimani, Abderachid" uniqKey="Slimani A" first="Abderachid" last="Slimani">Abderachid Slimani</name><affiliation wicri:level="1"><nlm:aff id="bax096-aff4">BADJI Mokhtar University, 23000 Annaba, Algeria</nlm:aff><country xml:lang="fr">Algérie</country><wicri:regionArea>BADJI Mokhtar University, 23000 Annaba</wicri:regionArea></affiliation></author><author><name sortKey="Rambold, Gerhard" sort="Rambold, Gerhard" uniqKey="Rambold G" first="Gerhard" last="Rambold">Gerhard Rambold</name><affiliation wicri:level="1"><nlm:aff id="bax096-aff2">University of Bayreuth, 95440 Bayreuth, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>University of Bayreuth, 95440 Bayreuth</wicri:regionArea></affiliation></author></analytic><series><title level="j">Database: The Journal of Biological Databases and Curation</title><idno type="eISSN">1758-0463</idno><imprint><date when="2018">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Factual (MeSH)</term><term>Electronic Data Processing (methods)</term><term>Image Processing, Computer-Assisted (methods)</term><term>Workflow (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données factuelles (MeSH)</term><term>Flux de travaux (MeSH)</term><term>Traitement automatique des données (méthodes)</term><term>Traitement d'image par ordinateur (méthodes)</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Electronic Data Processing</term><term>Image Processing, Computer-Assisted</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Traitement automatique des données</term><term>Traitement d'image par ordinateur</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Factual</term><term>Workflow</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données factuelles</term><term>Flux de travaux</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>Sampling of biological and environmental vouchers in the field is rather challenging, particularly under adverse habitat conditions and when various activities need to be handled simultaneously. The workflow described here includes five procedural steps, which result in professional sampling and the generation of universally identifiable data. In preparation for the field campaign, sample containers need to be labelled with universally unique identifier (UUID)-QR-codes. At the collection site, labelled containers, sampled material and attached supplementary information are imaged using a GNSS- respectively GPS-enabled smartphone or camera. Image processing, tagging and data storage as CSV text file is subsequently achieved in a field station or laboratory. For this purposes, the newly implemented tool <italic>DiversityImageInspector</italic> (URL: <ext-link ext-link-type="uri" xlink:href="http://diversityworkbench.net/Portal/DiversityImageInspector">http://diversityworkbench.net/Portal/DiversityImageInspector</ext-link>) is used<italic>.</italic> It addresses combined image and data processing in such a context including the extraction of the QR-coded UUID from the image content and the extraction of geodata and time information from the Exif image header. The import of the resulting data files into a relational database or other kind of data management systems is optional but recommended. If applied, the import might be guided by a data transformation tool with compliant schema as described here. The new approach is discussed also with regard to implications for virtual research environments and data publication networks.</p><p><bold>Database URL</bold>: <ext-link ext-link-type="uri" xlink:href="http://diversityworkbench.net/Portal/DiversityImageInspector">http://diversityworkbench.net/Portal/DiversityImageInspector</ext-link></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Diepenbroek, M" uniqKey="Diepenbroek M">M. Diepenbroek</name></author><author><name sortKey="Glockner, F" uniqKey="Glockner F">F. Glöckner</name></author><author><name sortKey="Grobe, P" uniqKey="Grobe P">P. Grobe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guralnick, R P" uniqKey="Guralnick R">R.P. Guralnick</name></author><author><name sortKey="Cellinese, N" uniqKey="Cellinese N">N. Cellinese</name></author><author><name sortKey="Deck, J" uniqKey="Deck J">J. 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Mealling</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Algérie</li><li>Allemagne</li><li>Kenya</li></country></list><tree><country name="Allemagne"><noRegion><name sortKey="Triebel, Dagmar" sort="Triebel, Dagmar" uniqKey="Triebel D" first="Dagmar" last="Triebel">Dagmar Triebel</name></noRegion><name sortKey="Bosert, Simone" sort="Bosert, Simone" uniqKey="Bosert S" first="Simone" last="Bosert">Simone Bosert</name><name sortKey="Feulner, Martin" sort="Feulner, Martin" uniqKey="Feulner M" first="Martin" last="Feulner">Martin Feulner</name><name sortKey="Rambold, Gerhard" sort="Rambold, Gerhard" uniqKey="Rambold G" first="Gerhard" last="Rambold">Gerhard Rambold</name><name sortKey="Reichert, Wolfgang" sort="Reichert, Wolfgang" uniqKey="Reichert W" first="Wolfgang" last="Reichert">Wolfgang Reichert</name></country><country name="Kenya"><noRegion><name sortKey="Okach, Daniel Osieko" sort="Okach, Daniel Osieko" uniqKey="Okach D" first="Daniel Osieko" last="Okach">Daniel Osieko Okach</name></noRegion></country><country name="Algérie"><noRegion><name sortKey="Slimani, Abderachid" sort="Slimani, Abderachid" uniqKey="Slimani A" first="Abderachid" last="Slimani">Abderachid Slimani</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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