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Standards #47

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Standards #47

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xiaoranzhou Sep 13, 2024
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xiaoranzhou Sep 13, 2024
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xiaoranzhou Sep 17, 2024
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174 changes: 174 additions & 0 deletions DMPDocs/BBSRC-dmp.js
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BBSRC_dmp = {"BBSRC-dmp" : `<div id="BBSRC-dmp" class="">
<div id="BBSRC-dmp1" class="content-page" id="text_start">
<span class="c2">Data management plan of $_PROJECTNAME for BBSRC</span>
<ul class="c0 ">

<li class="c0 li-bullet-0"><span class="c0">Data Areas and Data Types &ndash; $_PROJECTNAME will collect
and/or generate the following types of raw data: #if$_GENETIC genetic data, #endif$_GENETIC
#if$_GENOMIC genomic data, #endif$_GENOMIC
#if$_CLONED-DNA cloned DNA data, #endif$_CLONED-DNA
#if$_TRANSCRIPTOMIC transcriptomic data, #endif$_TRANSCRIPTOMIC
#if$_RNASEQ RNAseq data, #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">Standards and Metadata &ndash;&nbsp; <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. $_PROJECTNAME will rely
on community standards plus additional recommendations applicable in the plant science, such as the
<span class="list-to-remove-comma">
The following metadata/ minimum informatin standards will be used to collect metadata:
#if$_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 #endif$_TRANSCRIPTOMIC
#if$_TRANSCRIPTOMIC #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">Reuse of published data &ndash; 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
&#39;unstructured&#39; data in the form of publications and data contained therein will be used
for decision making.</span></li>
</ul>
<p class="c0 c0"><span class="c0"></span></p>
<ul class="c0 ">
<li class="c0 li-bullet-0"><span class="c0">Secondary Use &ndash; The data will 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 $_PROJECTNAME&#39;s dissemination and
communication plan, #if$_DATAPLANT which aligns with DataPLANT platform or other means #endif$_DATAPLANT.</span></li>

<li class="c0 li-bullet-0"><span class="c0">Methods for Data Sharing &ndash; <p class="c0">
<span class="c1">
Data will be made available via the $_PROJECTNAME platform using a user-friendly front end
that allows data visualization. Besides this it will be ensured that data which can be
stored in
international discipline related repositories which use specialized technologies:



<p class="c0">
<span class="c1 list-to-remove-comma"> #if$_GENETIC|$_GENOMIC For genetic or genomic data: #if$_GENBANK NCBI-GenBank, #endif$_GENBANK #if$_ENA EBI-ENA, #endif$_ENA #endif$_GENETIC|$_GENOMIC #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 . #endif$_GENETIC|$_GENOMIC </span>
</p>

<p class="c0">
<span class="c1 list-to-remove-comma">#if$_TRANSCRIPTOMIC For Transcriptomic data: #if$_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</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>
</p></span></li li class="c0 li-bullet-0"><span class="c0">Proprietary Data &ndash; Open public
data will be used whenever possible. </span></li>
<li class="c0 li-bullet-0"><span class="c0">Timeframes
#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.
</span></li>
<li class="c0 li-bullet-0"><span class="c0">Format of the Final Dataset &ndash; Whenever possible, data
will be stored in common and openly defined formats including all the necessary metadata. By
default, no proprietary formats will be used. However Microsoft Excel files (according to
ISO/IEC 29500-1:2016) might be used as intermediates by the consortium#if$_DATAPLANT and by some
Annotated Research Context (ARC) components#endif$_DATAPLANT. In addition, text files might be edited in text processor
files, but will be shared as pdf.</span>
</div>
</div>`}
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