PMID- 25866550
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20150413
LR  - 20240322
IS  - 1746-4811 (Print)
IS  - 1746-4811 (Electronic)
IS  - 1746-4811 (Linking)
VI  - 11
DP  - 2015
TI  - A software tool for the input and management of phenotypic data using personal 
      digital assistants and other mobile devices.
PG  - 25
LID - 10.1186/s13007-015-0069-3 [doi]
LID - 25
AB  - BACKGROUND: 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. RESULTS: 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. 
      CONCLUSIONS: 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.
FAU - Kohl, Karin
AU  - Kohl K
AD  - Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm, Germany.
FAU - Gremmels, Jurgen
AU  - Gremmels J
AD  - Max-Planck-Institute of Molecular Plant Physiology, 14424 Potsdam-Golm, Germany.
LA  - eng
PT  - Journal Article
DEP - 20150407
PL  - England
TA  - Plant Methods
JT  - Plant methods
JID - 101245798
PMC - PMC4393613
OTO - NOTNLM
OT  - Controlled vocabulary
OT  - Data management
OT  - Field research
OT  - Phenotyping
OT  - Relational database
EDAT- 2015/04/14 06:00
MHDA- 2015/04/14 06:01
PMCR- 2015/04/07
CRDT- 2015/04/14 06:00
PHST- 2015/01/12 00:00 [received]
PHST- 2015/03/19 00:00 [accepted]
PHST- 2015/04/14 06:00 [entrez]
PHST- 2015/04/14 06:00 [pubmed]
PHST- 2015/04/14 06:01 [medline]
PHST- 2015/04/07 00:00 [pmc-release]
AID - 69 [pii]
AID - 10.1186/s13007-015-0069-3 [doi]
PST - epublish
SO  - Plant Methods. 2015 Apr 7;11:25. doi: 10.1186/s13007-015-0069-3. eCollection 
      2015.