DataPLAN: A Web-Based Data Management Plan Generator for the Plant Sciences
Abstract
:1. Introduction
2. Materials and Methods
2.1. DMP Template and Questionnaire Design
2.2. Software Development
2.3. Testing
3. Results
3.1. DMP Content Generation and Modification Using DataPLAN
3.1.1. Incorporation of RDM Practices and Platforms for the Plant Sciences
Genomics | Transcriptomics | Proteomics | Metabolomics | Plant Phenotyping | |
---|---|---|---|---|---|
Minimum information standard | MinSEQe [86] | MIAME [45] MinSEQe [86] | MIAPE [44] | MSI [84] | MIAPPE [43] |
Endpoint repositories | ENA [87] EBI NCBI [88] DDBJ [89] SRA [90] GenBank [91] | GEO [88] SRA [90] | PRIDE ProteomeXchange [92] | Metabolights [93] | e!DAL-PGP [46] Gnpis [94] EURISCO [95] |
RDM platform | DataPLANT [59] |
3.1.2. Categories of Prewritten DMP Content
3.2. User Interface
3.2.1. Main Menu
3.2.2. Questionnaire (Right Panel)
3.2.3. Live Preview (Left Panel)
3.3. DataPLAN Workflow
3.3.1. Saving and Importing Data
3.3.2. Main Output (DMP-Related Documents)
3.3.3. Warnings
3.4. Testing and Validating DataPLAN According to FAIR Principles of Software
3.4.1. Findability of the Software
3.4.2. Accessibility of the Software
3.4.3. Interoperability of the Software
3.4.4. Reusability of the Software
4. Discussion
4.1. Comparison with Existing DMP Tools
Name | Programming Language | Funding Body Templates | Customizable | Templates | Content Preview | Open Source |
---|---|---|---|---|---|---|
Data Stewardship Wizard (DSW) [18] | Haskell ELM | 3 | Yes, with programming | Yes | Yes [107] | No |
DMP Canvas Generator [108] | JavaScript | 0 | No | No | No | No |
DMPonline [19] | Ruby JavaScript | 18 | Yes, with programming | No | Yes [29] | No |
DMP tools [2] | Ruby JavaScript | 19 | Yes, with programming | No | Yes [29] | No |
DMProadmap | Ruby JavaScript | 19 | Yes, with programming | No | Yes [29] | No |
RDMO [20] | Python (Django) and JavaScript (AngularJS) | 6 | Yes, with programming | No | Yes [30] | Yes |
Research Data Manager (UQRDM) [21] | Not available | 0 | Not available | No | No | No |
DataWiz [22] | JAVA | 0 | Not available | No | Yes [32] | No |
ezDMP [27] | Not available | 0 | No | No | No | No |
ARGOS [23] | JAVA and Typescript | 0 | Yes | No | Yes [29] | No |
UWADMP [26] | Not available | 0 | NA | No | No | No |
DMPTY [25] | JavaScript, HTML | 0 | No | Yes | No | No |
easyDMP [24] | Python (Django) | 1 | No | No | No | No |
DAMAP [39] | Typescript, Java | 1 | NA | NA | No | Yes |
DataPLAN (the tool in this paper) | Frontend: JavaScript No backend | 3 | Yes, no need for programming | Yes | Yes | Yes |
4.1.1. Technical Comparison
4.1.2. Content Comparison
4.2. Outlook
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ARC | annotated research context |
DDBJ | DNA Data Bank of Japan |
DFG | German Research Foundation (Deutsche Forschungsgemeinschaft) |
DMP | data management plan |
EBI | European Bioinformatics Institute |
ENA | European Nucleotide Archive |
EU | European Union |
FAIR | findable, accessible, interoperable and reusable |
GDPR | EU General Data Protection Regulation |
GEO | Gene Expression Omnibus |
MIAME | minimal information about a microarray experiment |
MIAPE | minimum information about a proteomics experiment |
MIAPPE | minimal information about plant phenotyping experiment |
MinSEQe | minimum information about a high-throughput sequencing experiment |
MSI | Metabolomics Standards Initiative |
NCBI | National Center for Biotechnology Information |
NFDI | National Research Data Infrastructure (of Germany) |
PRIDE | Proteomics Identification Database |
RDM | research data management |
RNA-Seq | RNA sequencing |
SRA | Sequence Read Archive |
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Zhou, X.-R.; Beier, S.; Brilhaus, D.; Martins Rodrigues, C.; Mühlhaus, T.; von Suchodoletz, D.; Twyman, R.M.; Usadel, B.; Kranz, A. DataPLAN: A Web-Based Data Management Plan Generator for the Plant Sciences. Data 2023, 8, 159. https://doi.org/10.3390/data8110159
Zhou X-R, Beier S, Brilhaus D, Martins Rodrigues C, Mühlhaus T, von Suchodoletz D, Twyman RM, Usadel B, Kranz A. DataPLAN: A Web-Based Data Management Plan Generator for the Plant Sciences. Data. 2023; 8(11):159. https://doi.org/10.3390/data8110159
Chicago/Turabian StyleZhou, Xiao-Ran, Sebastian Beier, Dominik Brilhaus, Cristina Martins Rodrigues, Timo Mühlhaus, Dirk von Suchodoletz, Richard M. Twyman, Björn Usadel, and Angela Kranz. 2023. "DataPLAN: A Web-Based Data Management Plan Generator for the Plant Sciences" Data 8, no. 11: 159. https://doi.org/10.3390/data8110159