A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devices
Identifieur interne : 000149 ( Main/Merge ); précédent : 000148; suivant : 000150A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devices
Auteurs : Karin Köhl [Allemagne] ; Jürgen Gremmels [Allemagne]Source :
- Plant Methods [ 1746-4811 ] ; 2015.
Abstract
Plant breeding and genetics demand fast, exact and reproducible phenotyping. Efficient statistical evaluation of phenotyping data requires standardised data storage ensuring long-term data availability while maintaining intellectual property rights. This is state of the art at phenomics centres, which, however, are unavailable for most scientists. For them we developed a simple and cost-efficient system, the Phenotyper, which employs mobile devices or personal digital assistants (PDA) for on-site data entry and open-source software for data management.
A graphical user interface (GUI) on a PDA replaces paper-based form sheet and data entry on a desktop. The user can define his phenotyping schemes in a web tool without in-depth knowledge of the system and thus adjust it more easily to new research aspects than in a classical laboratory information management system (LIMS). In the Phenotyper, schemes are built from controlled vocabulary gained from published ontologies. Vocabulary and schemes are stored in a database that also manages the user access. From the web page, schemes are downloaded as extended markup language (XML) files for the transfer to the PDA and the exchange between users. On the PDA, the GUI displays the schemes and stores data in comma separated value format and XML format. After manual quality control, data are uploaded via a web page to an independently hosted results database, in which data are stored in an entity-attribute-value structure to provide maximum flexibility. Datasets are linked to the original and curated data files stored on a file server. The ownership stamp, project affiliation and date stamp of a dataset are used to regulate data access, which is restricted to data belonging to the user or to his projects and data, for which the embargo period has ended. By export of standardised ASCII reports to long-term data storage facility, long-term accessibility allows searching, citing and use of raw data beyond the lifetime of the database. The Phenotyper is available to the scientific community for use and further development.
The Phenotyper provides a well-structured, but flexible data acquisition and management structure for mobile on-site measurements for efficient evaluation and shared use of data.
The online version of this article (doi:10.1186/s13007-015-0069-3) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13007-015-0069-3
PubMed: 25866550
PubMed Central: 4393613
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devices</title><author><name sortKey="Kohl, Karin" sort="Kohl, Karin" uniqKey="Kohl K" first="Karin" last="Köhl">Karin Köhl</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm</wicri:regionArea><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion></affiliation></author><author><name sortKey="Gremmels, Jurgen" sort="Gremmels, Jurgen" uniqKey="Gremmels J" first="Jürgen" last="Gremmels">Jürgen Gremmels</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm</wicri:regionArea><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25866550</idno><idno type="pmc">4393613</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393613</idno><idno type="RBID">PMC:4393613</idno><idno type="doi">10.1186/s13007-015-0069-3</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000188</idno><idno type="wicri:Area/Pmc/Curation">000188</idno><idno type="wicri:Area/Pmc/Checkpoint">000139</idno><idno type="wicri:Area/Ncbi/Merge">000620</idno><idno type="wicri:Area/Ncbi/Curation">000620</idno><idno type="wicri:Area/Ncbi/Checkpoint">000620</idno><idno type="wicri:Area/Main/Merge">000149</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devices</title><author><name sortKey="Kohl, Karin" sort="Kohl, Karin" uniqKey="Kohl K" first="Karin" last="Köhl">Karin Köhl</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm</wicri:regionArea><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion></affiliation></author><author><name sortKey="Gremmels, Jurgen" sort="Gremmels, Jurgen" uniqKey="Gremmels J" first="Jürgen" last="Gremmels">Jürgen Gremmels</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm</wicri:regionArea><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14424 Potsdam-Golm</wicri:noRegion></affiliation></author></analytic><series><title level="j">Plant Methods</title><idno type="eISSN">1746-4811</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Plant breeding and genetics demand fast, exact and reproducible phenotyping. Efficient statistical evaluation of phenotyping data requires standardised data storage ensuring long-term data availability while maintaining intellectual property rights. This is state of the art at phenomics centres, which, however, are unavailable for most scientists. For them we developed a simple and cost-efficient system, the Phenotyper, which employs mobile devices or personal digital assistants (PDA) for on-site data entry and open-source software for data management.</p></sec><sec><title>Results</title><p>A graphical user interface (GUI) on a PDA replaces paper-based form sheet and data entry on a desktop. The user can define his phenotyping schemes in a web tool without in-depth knowledge of the system and thus adjust it more easily to new research aspects than in a classical laboratory information management system (LIMS). In the Phenotyper, schemes are built from controlled vocabulary gained from published ontologies. Vocabulary and schemes are stored in a database that also manages the user access. From the web page, schemes are downloaded as extended markup language (XML) files for the transfer to the PDA and the exchange between users. On the PDA, the GUI displays the schemes and stores data in comma separated value format and XML format. After manual quality control, data are uploaded via a web page to an independently hosted results database, in which data are stored in an entity-attribute-value structure to provide maximum flexibility. Datasets are linked to the original and curated data files stored on a file server. The ownership stamp, project affiliation and date stamp of a dataset are used to regulate data access, which is restricted to data belonging to the user or to his projects and data, for which the embargo period has ended. By export of standardised ASCII reports to long-term data storage facility, long-term accessibility allows searching, citing and use of raw data beyond the lifetime of the database. The Phenotyper is available to the scientific community for use and further development.</p></sec><sec><title>Conclusions</title><p>The Phenotyper provides a well-structured, but flexible data acquisition and management structure for mobile on-site measurements for efficient evaluation and shared use of data.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13007-015-0069-3) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Tester, M" uniqKey="Tester M">M Tester</name></author><author><name sortKey="Langridge, P" uniqKey="Langridge P">P Langridge</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Finkel, E" uniqKey="Finkel E">E Finkel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Furbank, Rt" uniqKey="Furbank R">RT 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Murray</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Exner, V" uniqKey="Exner V">V Exner</name></author><author><name sortKey="Hirsch Hoffmann, M" uniqKey="Hirsch Hoffmann M">M Hirsch-Hoffmann</name></author><author><name sortKey="Gruissem, W" uniqKey="Gruissem W">W Gruissem</name></author><author><name sortKey="Hennig, L" uniqKey="Hennig L">L Hennig</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Dinu, V" uniqKey="Dinu V">V Dinu</name></author><author><name sortKey="Nadkarni, P" uniqKey="Nadkarni P">P Nadkarni</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mabee, P" uniqKey="Mabee P">P Mabee</name></author><author><name sortKey="Balhoff, J" uniqKey="Balhoff J">J Balhoff</name></author><author><name sortKey="Dahdul, W" uniqKey="Dahdul W">W Dahdul</name></author><author><name sortKey="Lapp, H" uniqKey="Lapp H">H Lapp</name></author><author><name sortKey="Midford, P" uniqKey="Midford P">P Midford</name></author><author><name sortKey="Vision, T" uniqKey="Vision T">T Vision</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Klukas, C" uniqKey="Klukas C">C Klukas</name></author><author><name sortKey="Schreiber, F" uniqKey="Schreiber F">F Schreiber</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chern, C G" uniqKey="Chern C">C-G Chern</name></author><author><name sortKey="Fan, M J" uniqKey="Fan M">M-J Fan</name></author><author><name sortKey="Yu, S M" uniqKey="Yu S">S-M Yu</name></author><author><name sortKey="Hour, A L" uniqKey="Hour A">A-L Hour</name></author><author><name sortKey="Lu, P C" uniqKey="Lu P">P-C Lu</name></author><author><name sortKey="Lin, Y C" uniqKey="Lin Y">Y-C 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