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surchs committed Nov 16, 2023
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<h1>
👋 Welcome to the neurobagel annotation tool
</h1>
<p>
This tool allows you to create a machine readable data dictionary
in .json format for a tabular phenotypic file in .tsv format (Data table).
If you already have a BIDS-like .json data dictionary, you can provide it here
and augment it with more detailed annotations.
in .json format for a tabular phenotypic file in .tsv format ("Data table").
If you already have a <a href="https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#phenotypic-and-assessment-data" target="_blank">BIDS-like .json data dictionary</a>, you can provide it here
(under "Data Dictionary") and augment it with more detailed annotations.
</p>
<p>
🏗️ This tool (like all of neuroabgel) is under active development and we are thankful
🏗️ This tool (like all of neurobagel) is under active development and we are thankful
for all feedback and suggestions you may have. You can either use our feedback widget
on the side of this window, or open an issue on <a href="https://github.com/neurobagel/annotation_tool" target="_blank">our GitHub repository</a>.
</p>
<p>
The process of annotations works like this:
</p>
<ol>
<li>Upload a .tsv tabular phenotypic file (<a href="https://neurobagel.org/annotation_tool/" target="_blank">see our docs for details</a>)</li>
<li>Upload a <a href="https://neurobagel.org/dictionaries/" target="_blank">BIDS-like .json data dictionary</a> (optional)</li>
<li>Annotate any or all "Columns" in your table by telling us what data they are "about"</li>
<li>Annotate the values in the "Columns" you have annotated, by mapping them to controlled terms from
<a href="https://neurobagel.org/term_naming_standards/#currently-used-namespaces" target="_blank">existing vocabularies</a>
</li>
<li>Download your augmented data dictionary in .json</li>
<li>Use the augmented data dictionary to <a href="https://neurobagel.org/cli/" target="_blank">create a harmonized view of your data</a> (optional, uses other neurobagel tools)</li>
</ol>
<p>
If you want to learn more about neurobagel, check out our website: <a href="https://neurobagel.org/" target="_blank">neurobagel.org</a>.
</p>
<b-button v-b-toggle.collapse-1 variant="primary">More details on the annotation process</b-button>
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<ol>
<li>Upload a .tsv tabular phenotypic file (<a href="https://neurobagel.org/annotation_tool/" target="_blank">see our docs for details</a>)</li>
<li>Upload a <a href="https://neurobagel.org/dictionaries/" target="_blank">BIDS-like .json data dictionary</a> (optional)</li>
<li>Annotate any or all "Columns" in your table by telling us what data they are "about"</li>
<li>Annotate the values in the "Columns" you have annotated, by mapping them to controlled terms from
<a href="https://neurobagel.org/term_naming_standards/#currently-used-namespaces" target="_blank">existing vocabularies</a>
</li>
<li>Download your augmented data dictionary in .json</li>
<li>Use the augmented data dictionary to <a href="https://neurobagel.org/cli/" target="_blank">create a harmonized view of your data</a> (optional, uses other neurobagel tools)</li>
</ol>
<p>
If you want to learn more about neurobagel, check out our website: <a href="https://neurobagel.org/" target="_blank">neurobagel.org</a>.
</p>
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