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| NSF_dmp = {"NSF-dmp" : `<div id="NSF-dmp" class=""> | ||
| <div class="content-page" id="text_start"> | ||
| <span class="c2">Data management and sharing plan of $_PROJECTNAME for U.S. National Science Foundation (NSF)</span> | ||
| <ul class="c0 "> | ||
| <li class="c0 li-bullet-0"><span class="c0">Types of data, samples, physical collections, software, curriculum materials, and other materials. <br> – $_PROJECTNAME will collect | ||
| and/or generate the following types of raw data: #if$_GENETIC genetic data, #endif$_GENETIC | ||
| #if$_GENOMIC genomic data, | ||
| #if$_PANGENOMIC Pangenomic data, #endif$_PANGENOMIC | ||
| #endif$_GENOMIC | ||
| #if$_CLONED-DNA cloned DNA data, #endif$_CLONED-DNA | ||
| #if$_TRANSCRIPTOMIC transcriptomic data, | ||
| #if$_SPATIALTRANSCRIPTOMIC spatial transcriptomic data, #endif$_SPATIALTRANSCRIPTOMIC | ||
| #endif$_TRANSCRIPTOMIC | ||
| #if$_RNASEQ RNAseq data, | ||
| #if$_SCRNASEQ single cell RNAseq data, #endif$_SCRNASEQ | ||
| #endif$_RNASEQ | ||
| #if$_METABOLOMIC Metabolomic data, #endif$_METABOLOMIC | ||
| #if$_PROTEOMIC proteomic data, #endif$_PROTEOMIC | ||
| #if$_PHENOTYPIC phenotypic data, #endif$_PHENOTYPIC | ||
| #if$_TARGETED targeted assays (e.g. glucose and fructose content), #endif$_TARGETED | ||
| #if$_IMAGE image datasets, #endif$_IMAGE | ||
| #if$_MODELS modelling data, #endif$_MODELS | ||
| #if$_CODE computational code, #endif$_CODE | ||
| #if$_EXCEL excel files, #endif$_EXCEL | ||
| which are related to $_STUDYOBJECT. In addition, the raw data will also be processed and | ||
| modified using analytical pipelines, which may yield different results or include ad hoc data | ||
| analysis parts. #if$_DATAPLANT These pipelines will be tracked in the DataPLANT | ||
| ARC. #endif$_DATAPLANT Therefore, care will be taken to document and archive these resources | ||
| (including the analytical pipelines) as well#if$_DATAPLANT relying on the expertise in the | ||
| DataPLANT consortium #endif$_DATAPLANT. </span></li> | ||
| <span class="c0">We expect to generate raw data in the range of $_RAWDATA GB of data. The size of the | ||
| derived data will be about $_DERIVEDDATA GB.</span> | ||
| <p class="c0"><span class="c0"></span></p> | ||
| <li class="c0 li-bullet-0"><span class="c0">The standards to be used for data and metadata format and content<br> – <span class="c1"> | ||
| All datasets will be associated with unique identifiers and will be annotated with metadata. We will | ||
| use Investigation, Study, Assay (ISA) specification for metadata creation. $_PROJECTNAME will rely | ||
| on community standards plus additional recommendations applicable in the plant science, such as the | ||
| <span class="list-to-remove-comma"> | ||
| The following metadata/ minimum information standards will be used to collect metadata: | ||
| #if$_GENOMIC|$_GENETIC #if$_MIXS MIxS (Minimum Information about any (X) Sequence), #endif$_MIXS | ||
| #if$_MIGSEU MigsEu (Minimum Information about a Genome Sequence: Eucaryote), #endif$_MIGSEU | ||
| #if$_MIGSORG MigsOrg (Minimum Information about a Genome Sequence: Organelle), #endif$_MIGSORG | ||
| #if$_MIMS MIMS (Minimum Information about Metagenome or Environmental), #endif$_MIMS | ||
| #if$_MIMARKSSPECIMEN MIMARKSSpecimen (Minimal Information about a Marker Specimen: | ||
| Specimen), #endif$_MIMARKSSPECIMEN | ||
| #if$_MIMARKSSURVEY MIMARKSSurvey (Minimal Information about a Marker Specimen: | ||
| Survey), #endif$_MIMARKSSURVEY | ||
| #if$_MISAG MISAG (Minimum Information about a Single Amplified Genome), #endif$_MISAG | ||
| #if$_MIMAG MIMAG (Minimum Information about Metagenome-Assembled Genome), #endif$_MIMAG | ||
| #endif$_GENOMIC|$_GENETIC | ||
| #if$_TRANSCRIPTOMIC | ||
| #if$_MINSEQE MINSEQE (Minimum Information about a high-throughput SEQuencing | ||
| Experiment), #endif$_MINSEQE | ||
| #if$_MIAME MIAME (Minimum Information About a Microarray | ||
| Experiment), #endif$_MIAME #endif$_TRANSCRIPTOMIC | ||
| #if$_IMAGE | ||
| #if$_REMBI REMBI (Recommended Metadata for Biological Images), #endif$_REMBI | ||
| #endif$_IMAGE | ||
| #if$_RNASEQ|$_GENOMIC | ||
| #if$_MINSEQE | ||
| MinSEQe (Minimum Information about a high-throughput Sequencing Experiment), | ||
| #endif$_MINSEQE | ||
| #endif$_RNASEQ|$_GENOMIC | ||
| #if$_METABOLOMIC | ||
| #if$_MMIAMET | ||
| MIAMET (Minimum Information About a METabolomics experiment), | ||
| #endif$_MMIAMET | ||
| #endif$_METABOLOMIC | ||
| #if$_PROTEOMIC | ||
| #if$_MIAPE MIAPE (Minimum Information About a Proteomics Experiment), #endif$_MIAPE | ||
| #if$_MIMIX MIMix (The Minimum Information required for reporting a Molecular Interaction Experiment), #endif$_MIMIX | ||
| #endif$_PROTEOMIC | ||
| #if$_PHENOTYPIC #if$_MIAPPE MIAPPE (Minimum Information about Plant Phenotyping Experiment) #endif$_MIAPPE #endif$_PHENOTYPIC . | ||
| </span> | ||
| </span> | ||
| <span class="c1">#if$_METABOLOMIC #if$_METABOLIGHTS The Metabolights submission compliant standards are used for metabolomic data. #issuewarning Some metabolomics partners considers Metabolights | ||
| not an accepted standard. #endissuewarning #endif$_METABOLIGHTS #endif$_METABOLOMIC These specific standard unlike cross-domain minimal sets such as the Dublin core, which | ||
| mostly define the submitter and the general type of data, allow reusability by other researchers by | ||
| defining properties of the plant (see the preceding section). However, $_PROJECTNAME also implement minimal cross-domain annotations #if$_DUBLINCORE|$_DARWINCORE|$_BIOSCHEMAS|$_SCHEMAORG|$_MARC21 such as #endif$_DUBLINCORE|$_DARWINCORE|$_BIOSCHEMAS|$_SCHEMAORG|$_MARC21 <span class="list-to-remove-comma"> #if$_DUBLINCORE Dublin Core, #endif$_DUBLINCORE #if$_DARWINCORE Darwin Core, #endif$_DARWINCORE #if$_SCHEMAORG Schema.org, #endif$_SCHEMAORG #if$_BIOSCHEMAS BioSchemas, #endif$_BIOSCHEMAS #if$_MARC21 MARC 21 #endif$_MARC21 . </span> #if$_DATAPLANT The core integration with DataPLANT will also allow | ||
| individual releases to be tagged with a Digital Object Identifier (DOI). | ||
| #endif$_DATAPLANT #if$_OTHERSTANDARDS Other standards such as $_OTHERSTANDARDINPUT are also adhered | ||
| to. #endif$_OTHERSTANDARDS | ||
| </span> | ||
| </span> | ||
| </li> | ||
| <li class="c0 li-bullet-0"><span class="c0">Policies for data access and sharing <p class="c0"> | ||
| <span class="c1"> The data will not only initially benefit the | ||
| $_PROJECTNAME partners, but will also be made available to selected stakeholders closely involved in | ||
| the project, and then the scientific community working on $_STUDYOBJECT. $_DATAUTILITY In | ||
| addition, the general public interested in $_STUDYOBJECT can also use the data after | ||
| publication. The data will be disseminated according to $_PROJECTNAME's dissemination and | ||
| communication plan, #if$_DATAPLANT which aligns with DataPLANT platform or other means #endif$_DATAPLANT.</span> | ||
| <span class="c1"> | ||
| – Data will be made available via the $_PROJECTNAME platform or a public platform using a user-friendly frontend | ||
| that allows data visualization. | ||
| #if$_DATAPLANT DataPLANT offers opensource data curation tools such as the <a target="_blank" href="https://nfdi4plants.github.io/nfdi4plants.knowledgebase/arcitect/">ARC management tool ARCitect </a>, command line tool <a target="_blank" href="https://nfdi4plants.github.io/nfdi4plants.knowledgebase/arc-commander/">ARCcommander </a>, <a target="_blank" href="https://github.com/nfdi4plants/nfdi4plants_ontology"> DataPLANT Biological Ontology (DPBO)</a>, <a target="_blank" href="https://nfdi4plants.github.io/nfdi4plants.knowledgebase/swate/">metadata annotation tool swate</a>, <a target="_blank" href="https://nfdi4plants.github.io/nfdi4plants.knowledgebase/resources/metadata-quiz/">the Metadata Quiz</a> and <a target="_blank" href="https://nfdi4plants.github.io/nfdi4plants.knowledgebase/resources/dataplan/">DataPLAN DMP generator</a>. #endif$_DATAPLANT | ||
| </span> | ||
| – #if$_EARLY Some raw data is made public as soon as it is collected and processed. #endif$_EARLY | ||
| #if$_BEFOREPUBLICATION Relevant processed datasets are made public when the research findings | ||
| are published. #endif$_BEFOREPUBLICATION #if$_ENDOFPROJECT At the end of the project, all data | ||
| without embargo period will be published. #endif$_ENDOFPROJECT #if$_EMBARGO Data, which is | ||
| subject to an embargo period, is not publicly accessible until the end of embargo | ||
| period. #endif$_EMBARGO #if$_REQUEST Data is made available upon request, allowing controlled | ||
| sharing while ensuring responsible use. #endif$_REQUEST #if$_IPISSUE IP issues will be checked | ||
| before publication. #endif$_IPISSUE All consortium partners will be | ||
| encouraged to make data available before publication, openly and/or under pre-publication | ||
| agreements #if$_GENOMIC such as those started in Fort Lauderdale and set forth by the Toronto | ||
| International Data | ||
| Release Workshop #endif$_GENOMIC . This will be implemented as soon as IP-related checks are | ||
| complete. | ||
| </p></span></li> | ||
| <li class="c0 li-bullet-0"><span class="c0">Policies and provisions for data reuse, redistribution and the production of derivatives <br> – Open public | ||
| data will be used whenever possible. The project builds on | ||
| existing data sets and relies on them. #if$_RNASEQ For example, without a proper genomic | ||
| reference it is very difficult to analyze next-generation sequencing (NGS) data | ||
| sets. #endif$_RNASEQ It is also important to include existing data-sets on the expression and | ||
| metabolic behavior of the $_STUDYOBJECT, and on existing background knowledge. #if$_PARTNERS of | ||
| the partners: $_PARTNERS #endif$_PARTNERS Genomic references can be gathered from reference databases for | ||
| genomes/ and sequences, like the NCBI (US National Center for Biotechnology Information), | ||
| EBI (European Bioinformatics Institute) and DDBJ (DNA Data Bank of Japan). Furthermore, prior | ||
| 'unstructured' data in the form of publications and data contained therein will be used | ||
| for decision making.</span></li> | ||
| <li class="c0 li-bullet-0"><span class="c0">Plans for archiving data, samples and other research products, and for preserving access to them <br> | ||
| In addition to project related sharing platform, data will be stored in international discipline related repositories which use specialized technologies and preserve data for more than 10 years: | ||
| <p class="c0"> | ||
| <span class="c1 list-to-remove-comma"> #if$_GENETIC|$_GENOMIC|$_RNASEQ For genetic or genomic data: #if$_GENBANK NCBI-GenBank, #endif$_GENBANK #if$_ENA EBI-ENA, #endif$_ENA #endif$_GENETIC|$_GENOMIC|$_RNASEQ #if$_GENETIC #if$_SRA NCBI-SRA (Sequence Read Archive), #endif$_SRA #if$_ARRAYEXPRESS EBI-ArrayExpress, #endif$_ARRAYEXPRESS | ||
| #if$_GEO NCBI-GEO (Gene Expression Omnibus), #endif$_GEO #endif$_GENETIC #if$_GENETIC|$_GENOMIC|$_RNASEQ . #endif$_GENETIC|$_GENOMIC|$_RNASEQ </span> | ||
| </p> | ||
| <p class="c0"> | ||
| <span class="c1 list-to-remove-comma">#if$_TRANSCRIPTOMIC|$_SPATIALTRANSCRIPTOMIC For Transcriptomic data: #if$_SRA | ||
| NCBI-SRA (Sequence Read Archive), #endif$_SRA #if$_GEO NCBI-GEO (Gene Expression Omnibus), #endif$_GEO #if$_ARRAYEXPRESS | ||
| EBI-ArrayExpress, #endif$_ARRAYEXPRESS . #endif$_TRANSCRIPTOMIC|$_SPATIALTRANSCRIPTOMIC</span> | ||
| </p> | ||
| <p class="c0"> | ||
| <span class="c1 list-to-remove-comma">#if$_IMAGE For image data: #if$_BIOIMAGE EBI-BioImage | ||
| Archive, #endif$_BIOIMAGE #if$_IDR IDR (Image Data Resource), #endif$_IDR . | ||
| #endif$_IMAGE </span> | ||
| </p> | ||
| <p class="c0"> | ||
| <span class="c1 list-to-remove-comma">#if$_METABOLOMIC For metabolomic data: #if$_METABOLIGHTS | ||
| EBI-Metabolights, #endif$_METABOLIGHTS #if$_METAWORKBENCH Metabolomics | ||
| Workbench, #endif$_METAWORKBENCH #if$_INTACT IntAct (Molecular | ||
| interactions), #endif$_INTACT . #endif$_METABOLOMIC </span> | ||
| </p> | ||
| <p class="c0"> | ||
| <span class="c1 list-to-remove-comma">#if$_PROTEOMIC For proteomics data: #if$_PRIDE | ||
| EBI-PRIDE (PRoteomics IDEntifications Database), #endif$_PRIDE #if$_PDB PDB (Protein Data Bank), #endif$_PDB | ||
| #if$_CHEBI Chebi (Chemical Entities of Biological Interest), #endif$_CHEBI . | ||
| #endif$_PROTEOMIC </span> | ||
| </p> | ||
| <p class="c0"> | ||
| <span class="c1 list-to-remove-comma">#if$_PHENOTYPIC For phenotypic data: #if$_EDAL e!DAL-PGP (Plant | ||
| Genomics & Phenomics Research Data Repository), #endif$_EDAL . #endif$_PHENOTYPIC | ||
| </span> | ||
| </p> | ||
| #if$_OTHEREP $_OTHEREP will also be used to store data and the data will be | ||
| processed there as well. #endif$_OTHEREP | ||
| </span></li> | ||
| </div> | ||
| </div>`} |
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