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lubianat committed Feb 14, 2022
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Expand Up @@ -77,11 +77,12 @@ <h2>Organizing the knowledge about cell types via Wikidata</h2>

</section>

<!------------------>
<!-- Introduction -->
<!------------------>
<!-------------------->
<!--- Introduction --->
<!-------------------->

<section class="center" data-transition="fade" data-name="Introduction">
<section>[present the HUMAN CELL ATLAS] </section>
<section>
<h2>How many cell types have been described?</h2>
</section>
Expand All @@ -105,19 +106,225 @@ <h2>How many cell types have been described?</h2>
</section>

<section>
[connecting knowledge is
important for data viz and data analysis;
and for integrating datasets]
[resources that use the cell ontology]
<p>Resources using the Cell Ontology:</p>

<div class="u-container u-mt-32 u-mb-32 u-clearfix" data-component="article-container"
data-track-component="table" style="font-size: small;">

<div class="c-article-table-container">
<div class="c-article-table-border c-table-scroll-wrapper">
<div class="c-table-scroll-wrapper__content c-table-scroll-wrapper__fade--transparent"
data-component-scroll-wrapper="">
<table class="data last-table">
<thead class="c-article-table-head">
<tr>
<th class="u-text-left ">
Project
</th>
<th class="u-text-left ">
Description
</th>
<th class="u-text-left ">
CL use
</th>
<th class="u-text-left ">
URL
</th>
</tr>
</thead>
<tbody>
<tr>
<td class="u-text-left ">
Cell Annotation Platform
</td>
<td class="u-text-left ">
An open annotation platform for scRNA-seq data
</td>
<td class="u-text-left ">
Uses CL and free text for cell-type annotation
</td>
<td class="u-text-left ">
<a href="http://celltype.info">http://celltype.info</a>
</td>
</tr>
<tr>
<td class="u-text-left ">
EBI Single Cell Expression Atlas and Cambridge Cell Atlas
</td>
<td class="u-text-left ">
Open public repository for the exploration of single-cell gene
expression data
</td>
<td class="u-text-left ">
Uses CL to annotate samples and cell types in tertiary analysis
</td>
<td class="u-text-left ">
<a
href="https://www.ebi.ac.uk/gxa/sc%20">https://www.ebi.ac.uk/gxa/sc</a>
and <a
href="https://www.cambridgecellatlas.org">https://www.cambridgecellatlas.org</a>
</td>
</tr>
<tr>
<td class="u-text-left ">
HCA Data Coordination Platform (DCP)
</td>
<td class="u-text-left ">
Community-generated, multi-omics, open data processed by
standardized pipelines
</td>
<td class="u-text-left ">
Uses CL to annotate samples and cell types in tertiary analysis
</td>
<td class="u-text-left ">
<a
href="https://data.humancellatlas.org">https://data.humancellatlas.org</a>
</td>
</tr>
<tr>
<td class="u-text-left ">
HuBMAP Common Coordinate Framework (CCF) ASCT+B tables
</td>
<td class="u-text-left ">
Expert-curated tables of human cell types, their markers and
anatomical context
</td>
<td class="u-text-left ">
Maps all cell types to CL
</td>
<td class="u-text-left ">
<a
href="https://hubmapconsortium.github.io/ccf-asct-reporter">https://hubmapconsortium.github.io/ccf-asct-reporter</a>
</td>
</tr>
<tr>
<td class="u-text-left ">
cellxgene
</td>
<td class="u-text-left ">
An open annotation platform requiring annotation with ontology terms
</td>
<td class="u-text-left ">
Uses CL to annotate samples and cell types in tertiary analysis
</td>
<td class="u-text-left ">
<a
href="https://chanzuckerberg.github.io/cellxgene">https://chanzuckerberg.github.io/cellxgene</a>
</td>
</tr>
<tr>
<td class="u-text-left ">
Tabula Muris
</td>
<td class="u-text-left ">
Curated whole mouse scRNA-seq atlas
</td>
<td class="u-text-left ">
Uses CL to annotate gross cell types, extending definitions with
free text and markers
</td>
<td class="u-text-left ">
<a
href="https://tabula-muris.ds.czbiohub.org">https://tabula-muris.ds.czbiohub.org</a>
</td>
</tr>
<tr>
<td class="u-text-left ">
Monarch Initiative
</td>
<td class="u-text-left ">
A resource building ontologies of phenotypes and disease and using
these to build an integrated collection of phenotype/disease to
gene/variant associations
</td>
<td class="u-text-left ">
Defines cellular phenotypes and diseases
</td>
<td class="u-text-left ">
<a
href="https://monarchinitiative.org">https://monarchinitiative.org</a>
</td>
</tr>
<tr>
<td class="u-text-left ">
Gene Ontology
</td>
<td class="u-text-left ">
The world’s largest source of information on the function and
location of gene products
</td>
<td class="u-text-left ">
Defines cell-type-specific organelles and biological processes
</td>
<td class="u-text-left ">
<a href="http://geneontology.org">http://geneontology.org</a>
</td>
</tr>
<tr>
<td class="u-text-left ">
CellTypist
</td>
<td class="u-text-left ">
An open-source tool for automated cell-type annotations as well as a
working group in charge of curating models and ontologies
</td>
<td class="u-text-left ">
Maps all cell types to CL
</td>
<td class="u-text-left ">
<a href="https://www.celltypist.org">https://www.celltypist.org</a>
</td>
</tr>
<tr>
<td class="u-text-left ">
Human Immunology Project Consortium (HIPC)
</td>
<td class="u-text-left ">
A comprehensive, centralized research resource with the goal of
facilitating a comprehensive understanding of the human immune
system and its regulation
</td>
<td class="u-text-left ">
Works with CL to improve the representation of human immune cell
types for use in data annotation
</td>
<td class="u-text-left ">
<a
href="https://www.immuneprofiling.org/hipc">https://www.immuneprofiling.org/hipc</a>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
<p class='ref'>
Table from <a href="https://doi.org/10.1038/S41556-021-00787-7">
David Osumi-Sutherland et al, Nat. Cell Biol., 2021
</a>
</p>
</section>


<section>
[OBO foundry and biomedical ontologies - a broader need for knowledge management]
<p>OBO foundry - over 150 active biomedical ontologies</p>
<img
src="https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/database/2021/10.1093_database_baab069/1/m_baab069f1.jpeg?Expires=1647415767&Signature=SJMnzas~yn~0RVPXDj6M-dA4b9mgUcocYdX10esl1JendkS9UuJNqFs1T0owaAuvIpvtTGMYCqX3z4BbNtxhb5I1O~qmRYglKEpn2DN2-Gr8mNt3bv8QO0SUNyZ4rBK5zr6Li~veZghSQBmrdcXITQHc~ORa7JhUXyAzMXW263xslgQSUIhz-BxFUaZRz4PwEc0JQVdK~MuJ4aNa-EuO3QyD8xoSq6wil-QKnvZNCEuQmhEor7HysJThZzztEiNBhNQq0W5z8bF4szJY3vw1s-xncH4NzCIt8icR9oTIs8QViTmWXRmpYJDp4T2AgHh6xzFMQuVJT7oYPnpS1jv4qA__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA">

<p class='ref'>
<a href="https://doi.org/10.1093/database/baab069">
Rebecca Jackson et al, Database, 2021
</a>
</p>
</section>

<section>
[OBO technology - RDF]
Resource Description Framework and OBO ontologies
<br />
<p style="font-size: medium; text-align: left;">mini_cl.ttl</p>
<script src="https://gist.github.com/lubianat/8cfb3a19732038c761370510c9f62071.js"></script>

</section>

<section> [protege, multiple namespaces, GitHub protocols etc] </section>
Expand All @@ -138,17 +345,41 @@ <h2>How many cell types have been described?</h2>
</section>
</section>

<!------------------>
<!-- Introduction -->
<!------------------>
<!------------------->
<!--- Methodology --->
<!------------------->

<section class=" center" data-transition="fade" data-name="Methodology">
<section>[Research action]</section>
<section>

3 pillars of the project:
<br />
<br />

<div class="row">
<div class="column">
<img src="https://obofoundry.org/images/CL-logo.jpg" width="200">
</div>
<div class="column">
<img src="https://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Wikidata-logo-en.svg/800px-Wikidata-logo-en.svg.png"
width="230">
</div>

<section class="center" data-transition="fade" data-name="Methodology">
<section>[3 pillars of the project]</section>
<div class="column">
<img src="img/tsunami.png" width="200">
</div>
</div>
</section>
<section>[Cell Ontology]</section>
<section>[Wikidata]</section>
<section>[Wikidata Bib + Biocuration]</section>
</section>

<!---------------------------->
<!--- Concept of Cell Type --->
<!---------------------------->

<section class="center" data-transition="fade" data-name="Concept of Cell Type">

<section>
Expand All @@ -167,6 +398,9 @@ <h2>How many cell types have been described?</h2>

</section>

<!----------------->
<!--- PanglaoDB --->
<!----------------->

<section class="center" data-transition="fade" data-name="PanglaoDB">
<section>adapt slides from <a
Expand All @@ -178,6 +412,9 @@ <h2>How many cell types have been described?</h2>
</section>
</section>

<!-------------------->
<!--- Wikidata Bib --->
<!-------------------->

<section class="center" data-transition="fade" data-name="Wikidata Bib">
<section>Wikidata Bib - Why</section>
Expand All @@ -194,15 +431,54 @@ <h2>How many cell types have been described?</h2>
<iframe width="100%" height="500" src="https://lubianat.github.io/wikidata_bib/"></iframe>
</section>

<section>
[Cell types are connected to Wikidata - summmary]
</section>

<section>
[Mix'n'match]
</section>

<section>
[Query cell types on Wikidata]
</section>

</section>

<!------------------>
<!--- Next steps --->
<!------------------>

<section class="center" data-transition="fade" data-name="Next steps">
<h3 class="left">Next steps</h3>
<ul>
<li>Test Wikidata Bib with more people</li>
<li>Connect better Cell Ontology and Wikidata</li>
<li>Gather more people to curate cell types</li>
<li>Connect Wikidata to R packages for scRNA-seq</li>

</ul>

</h2>
</section>

<section class="center" data-transition="fade" data-name="Conclusion">
<h2>DEMO</h2>
<!------------------>
<!--- Extra work --->
<!------------------>

<section class="center" data-transition="fade" data-name="Additional Work">
<section>[Complex portal]</section>
<section>[Review activity]</section>
<section>[Course work]</section>
</section>

<!------------------------>
<!--- Acknowledgements --->
<!------------------------>

<section class="center" data-transition="fade" data-name="Acknowledgements">
<section>
<h2>DEMO</h2>
DEMO
</section>

<section class="center" data-transition="fade">
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