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submission.html
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---
layout: idr
title: Submission
redirect_from:
- submission/
---
<!-- begin marketing header -->
<header class="marketing-hero">
<div class="row homepage text-center">
<div class="medium-12 columns">
<h1 class="hero-main-header">Submission of datasets to the IDR</h1>
<p class="hero-subheader small-10 medium-10 large-10 small-offset-1 medium-offset-1 large-offset-1">
The Image Data Resource (IDR) publishes “reference image” datasets supporting conventional peer-reviewed
publications and integrates them with other imaging datasets for cross-dataset querying of metadata
(e.g. genes, phenotypes, small molecules) and re-analysis.
<p style="font-size: 0.6em">
Submission Guidelines v1.0 - last modified: March 2017
</p>
</p>
</div>
</div>
</header>
<!-- begin guidelines section -->
<hr class="whitespace">
<div class="row column text-center">
<h2>What we are looking for</h2>
</div>
<hr>
<div class="row">
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>We aim to publish reference image datasets, which have value beyond simply
supporting an original publication according to the
<a href="https://www.eurobioimaging.eu/upload/document_gallery/euro-bioimaging_elixir_image_data_strategy.pdf">
Euro-BioImaging - Elixir Image Data Strategy</a>. This includes:<p>
<ul>
<li>Datasets <b>associated</b> with an existing or upcoming publication</li>
<li><b>Complete</b> datasets - not just images supporting one figure in the publication</li>
<li>Datasets whose metadata can be <b>integrated</b> with other datasets via identifiers
from well-known biomolecular resources (Ensembl, NCBI Entrez Gene, RefSeq, PubChem, ChEBI etc) </li>
<li>Datasets generated using new imaging <b>methods</b> or new analysis methods</li>
<li>Datasets that are likely to be <b>re-analysed or incorporated</b> into other studies
or integrated with other imaging datasets</li>
</ul>
</p>
<p>To make IDR datasets as widely re-usable as possible,
we strongly recommend that submitters make their datasets
available under <a href="https://creativecommons.org/licenses/by/4.0/">
CC-BY</a> license. The licensing information should
be included as part of the metadata .</p>
</div>
<p>Image datasets that don't meet the criteria for reference images may still be published on
<a href="https://www.ebi.ac.uk/biostudies/">BioStudies</a> or
<a href="https://datadryad.org/">Dryad</a>. Contact these projects for more information.
</p>
</div>
</div>
</div>
</div>
<!-- end guidelines section -->
<!-- begin size section -->
<hr class="whitespace">
<div class="row column text-center">
<h2>Dataset size</h2>
</div>
<hr>
<div class="row">
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>Dataset <b>size</b> is typically <i>not</i> an issue,
but for sizes significantly larger than 1000 GB special planning may be needed.</p>
</div>
</div>
</div>
</div>
<!-- end size section -->
<!-- begin prep section -->
<hr class="whitespace">
<div class="row column text-center">
<h2><a class="anchor" id="metadata"></a>Preparing the metadata</h2>
</div>
<hr>
<div class="row">
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>Metadata describing an imaging study is submitted using template files.
These are available for download from
<a href="https://github.com/IDR/idr0000-lastname-example/archive/master.zip">
https://github.com/IDR/idr0000-lastname-example/archive/master.zip</a>.</p>
<p>There are template files for two different use cases:</p>
<ol>
<li>Templates for <b>high content screens</b> (HCS),
or imaging studies performed in plates (e.g. 96 or 384 well plates)</li>
<li>Templates for <b>non-screen datasets</b>, or studies which group images
into a number of distinct experiments</li>
</ol>
<p>There are help pages to provide more information about filling out the
<a href="screens.html">high content screen</a> and
<a href="experiments.html">non-screen dataset</a> templates.</p>
<p>For both types of study three files should be submitted:
<ul>
<li><b>Study file</b> - describing the overall study and the screens or experiments that were performed</li>
<li><b>Library</b> (screens) or <b>assay</b> files (non-screens). For HCS the library file describes the
plate layout of each screen. If more than one screen is performed as part of the study there
should be a library file for each screen. For non-screen datasets, the assay file(s) describes
each imaging experiment included in the study.</li>
<li><b>Processed data</b> files - containing summary results and/or a ‘hit' list for each screen
or experiment. It may include phenotypes observed.</li>
</ul></p>
<p>Example files for HCS studies can be found here:
<ul>
<li><a href="https://github.com/IDR/idr-metadata/tree/master/idr0001-graml-sysgro">
idr0001 - gene deletion screen</a></li>
<li><a href="https://github.com/IDR/idr0002-heriche-condensation">
idr0002 - RNAi screen</a></li>
<li><a href="https://github.com/IDR/idr0006-fong-nuclearbodies">
idr0006 - protein localization screen</a></li>
<li><a href="https://github.com/IDR/idr-metadata/tree/master/idr0009-simpson-secretion">
idr0009 - primary and validation RNAi screens</a></li>
<li><a href="https://github.com/IDR/idr0017-breinig-drugscreen">
idr0017 - small molecule screen</a></li>
<li><a href="https://github.com/IDR/idr0019-sero-nfkappab">
idr0019 - imaging experiment performed in plates but not a screen</a></li>
</ul></p>
<p>Example files for non-screen studies can be found here:
<ul>
<li><a href="https://github.com/IDR/idr0018-neff-histopathology">
idr0018 - histopathology of gene knockouts</a></li>
<li><a href="https://github.com/IDR/idr0021-lawo-pericentriolarmaterial">
idr0021 - protein localization using 3D-SIM </a></li>
<li><a href="https://github.com/IDR/idr-metadata/tree/master/idr0023-szymborska-nuclearpore">
idr0023 - protein localization using dSTORM</a></li>
<li><a href="https://github.com/IDR/idr-metadata/tree/master/idr0027-dickerson-chromatin">
idr0027 - 3D-tracking of tagged chromatin loci</a></li>
<li><a href="https://github.com/IDR/idr-metadata/tree/master/idr0032-yang-meristem">
idr0032 - in situ hybridzation of RNA</a></li>
</ul></p>
<p>Each study is slightly different and advice on how to fill in the template can be given.
Questions should be sent to
<a href="mailto:idr@openmicroscopy.org">idr@openmicroscopy.org</a>.</p>
</div>
</div>
</div>
</div>
<!-- end prep section -->
<!-- begin opt section -->
<hr class="whitespace">
<div class="row column text-center">
<h2>Optional metadata</h2>
</div>
<hr>
<div class="row">
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>Imaging datasets can be remarkably complex. To the extent that it's well-structured
and reusable by the community, we are interested in enriching your online dataset with
your additional metadata, e.g.:
<ul>
<li>Rendering settings: if you have information on the channel intensities or
mappings that you would like to see displayed in the IDR, please let us know.</li>
<li>Regions of interest: if you have ROIs or masks, whether detected automatically
or hand-annotated, we'd like to make them available in the IDR.</li>
<li>Features: if you've calculated features for your dataset for machine learning,
we'd be interested in sharing those analysis results with others.</li>
<li>Pipelines and workflows: further, if you have a representation of how you ran
the analysis itself, we think that should be included with your features.</li>
</ul>
</p>
</div>
</div>
</div>
</div>
<!-- end opt section -->
<!-- begin transfer section -->
<hr class="whitespace">
<div class="row column text-center">
<h2>How to transfer images and metadata</h2>
</div>
<hr>
<div class="row">
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>There are several options for having your image data transferred to the IDR:
<ul>
<li><b>Provide a link</b>: if your data is already
available online (e.g. Dropbox, FTP, etc), a link to the location may be the
easiest option.</li>
<li><b>FTP</b>: data can be uploaded using our FTP
server. We will provide you with details via email.</li>
<li><b>Shipping disks</b>: Sending hard-drives by mail
remains a reliable way of transferring your data. We will provide you with
shipping details via email.</li>
<li><b>FTP / Aspera</b>: we are working on a link
between IDR and BioStudies (<a href="https://www.ebi.ac.uk/biostudies/submit">
https://www.ebi.ac.uk/biostudies/submit.html</a>). If
you can upload your image data to BioStudies via FTP or Aspera, IDR may be able
to access your data directly from there.</li>
</div>
</div>
</div>
</div>
<!-- end transfer section -->
<!-- begin timeline section -->
<hr class="whitespace">
<div class="row column text-center">
<h2>Publication timelines<h2>
</div>
<hr>
<div class="row">
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>
A submission is considered complete only after your uploaded metadata and image
data have been validated. Validation may itself take significant time depending
on, e.g., the size of the dataset, the file formats used and the consistency in
naming between files. During validation, frequent consultation with the author
and/or data producer may be necessary.
</p>
<p>
Once your data is validated and ready for import, you will be notified that the
publication pipeline can begin.
</p>
<ul>
<li>Allow <b>at least</b> 3 weeks before your dataset will be available online</li>
<li><b>No private access</b> is available for reviewers during this period</li>
<li>Minting a DOI requires approximately <b>1 additional week</b>
(Note: if you plan on incorporating a data DOI into
your publication, please allow time for adding this DOI into the final version
of your paper).</li>
</ul>
</div>
</div>
</div>
</div>
<!-- end timeline section -->
<!-- begin cite section -->
<hr class="whitespace">
<div class="row column text-center">
<h2>How to cite a dataset in the IDR</h2>
</div>
<hr>
<div class="row">
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>Your dataset in IDR will be given an accession number (e.g. “idr1234”) which you can use
for informally referring to your entry. For more formal uses such as citing the imaging dataset
in your publication, we suggest using a DOI:<p>
<p style="display:inline-block;margin-left:5em;">
<i>
Image files are available in the Image Data Resource (Williams et al 2017)
under DOI <a href="https://doi.org/10.17867/10000105">https://doi.org/10.17867/10000105</a> .
</i>
</p>
<p>DOIs can be made available upon request but require an additional depositor agreement and
license form on top of your completed submission.</p>
</div>
</div>
</div>
</div>
<!-- end cite section -->
<!-- begin paper section -->
<hr class="whitespace">
<div class="row column text-center">
<h2>How to cite the IDR</h2>
</div>
<hr>
<div class="row">
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>If you want to include a citation to the IDR in a paper or other publication, please use:</p>
<p style="display:inline-block;margin-left:5em;">
<i>
Williams et al (2017) Image Data Resource: a bioimage data integration and publication platform,
<a href="https://doi.org/10.1038/nmeth.4326">
https://doi.org/10.1038/nmeth.4326</a>.
</i>
</p>
</div>
</div>
</div>
</div>
<!-- end transfer section -->
<!-- begin contact section -->
<hr class="whitespace">
<div class="row column text-center">
<h2>Contact us if you would like to submit a dataset</h2>
</div>
<hr>
<div class="row">
<div class="small-10 small-centered medium-10 medium-centered columns">
<div class="row horizontal">
<div>
<p>Email
<a href="mailto:idr@openmicroscopy.org">idr@openmicroscopy.org</a>
with some information about your dataset and timeline for publication.</p>
</div>
</div>
</div>
</div>
<!-- end contact section -->