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<!doctype html>
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<title>Organizing the knowledge about cell types via Wikidata</title>
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<div class="slides">
<!------------->
<!--- Title --->
<!------------->
<section class="center" data-transition="fade" data-name="Title">
<h3>Building a biological knowledge graph via Wikidata with a focus on the Human Cell Atlas.</h3>
<div align="left">
<p>Student: Tiago Lubiana</p>
<p>Advisor: Prof. Helder Nakaya</p>
</div>
<div class="row">
<div class="column2">
<img src="https://irp.cdn-website.com/683b19b1/dms3rep/multi/LOGO_CSBL.svg" height="100">
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height="100">
</div>
</div>
<div align="center">
<p>Feb 23rd 2022 - São Paulo - SP</p>
</div>
</section>
<!-------------------->
<!--- Introduction --->
<!-------------------->
<section class="center" data-transition="fade" data-name="Introduction">
<section>
<img
src="https://www.broadinstitute.org/files/styles/gsp_image__1112x410_/public/generic-page/images/2016/Banner_HCA_1112x410.jpg?itok=frtpi6B4"></img>
<div class="row">
<div class="column2">
<img src="https://irp-cdn.multiscreensite.com/683b19b1/HCB-BRAZIL-v4.jpg" width="400">
</div>
<div class="column2" style="align-content: right;">
<img src="img/jaguar.png" width="400">
</div>
</div>
</section>
<section>
<h2>How many cell types have been described?</h2>
</section>
<section>
<img width="90%" src="./img/how_many_cells_google.png">
</section>
<section>
<img width="90%" src="./img/how_many_cells_hca.png">
</section>
<section>
<img src="https://obofoundry.org/images/CL-logo.jpg">
<p>"2,311 terms covering all major cell types"</p>
<p class='ref'>
<a href="https://doi.org/10.1038/S41556-021-00787-7">
David Osumi-Sutherland et al, Nat. Cell Biol., 2021
</a>
</p>
</section>
<section>
<p>Goals of the PhD project</p>
<ul style="font-size: 40px;">
<li>1. Find all classes of cells relevant to the Human Cell Atlas</li>
<li style="visibility: hidden">2. Organize the knowledge using knowledge graphs</li>
<li style="visibility: hidden">3. Advance Wikidata as a tool for the life sciences</li>
</ul>
</section>
<section>
<p>To catalog and count cell types is fundamental</p>
<ul align="left">
<li>Mint unique IDs for data integration</li>
<li>Make gaps explicit </li>
<li>Disambiguate and merge common terms</li>
</ul>
</section>
<section>
<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>
<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>
Ontology: a specification of a conceptualization
<br />
<p>"All plasmacytoid dendritic cells are dendritic cells." </p>
<div width="400">
<script src="https://gist.github.com/lubianat/8cfb3a19732038c761370510c9f62071.js"></script>
</div>
</section>
<!--
<section> OBO: Knowledge Management via Protégé
<img height="400"
src="https://protege.stanford.edu/assets/img/screenshots/desktopprotege-screenshot-5.jpg">
<div class="ref">
<a href="https://protege.stanford.edu/">https://protege.stanford.edu/</a>
</div>
</section>
-->
<section> OBO: Ontology management via GitHub
<img height="300" src="img/cl_github.png">
<div class="ref">
<a
href="https://github.com/obophenotype/cell-ontology">https://github.com/obophenotype/cell-ontology</a>
</div>
</section>
<section>
<p>Goals of the PhD project</p>
<ul style="font-size: 40px;">
<li style="opacity: 0.5;">1. Find all classes of cells relevant to the Human Cell Atlas</li>
<li>2. Organize the knowledge using knowledge graphs</li>
<li style="visibility: hidden">3. Advance Wikidata as a tool for the life sciences</li>
</ul>
</section>
<section>
Wikidata: Item model
<img height="450"
src="https://upload.wikimedia.org/wikipedia/commons/a/ae/Datamodel_in_Wikidata.svg">
</section>
<section>
<p>Wikidata: GUI live editing</p>
<iframe width="120%" height="500" src="https://www.wikidata.org/wiki/Q67801129?safemode=1"></iframe>
</section>
<section>
<p>Wikidata is increasingly used by the life sciences community</p>
<img height="400"
src="https://iiif.elifesciences.org/lax/52614%2Felife-52614-fig1-v1.tif/full/1500,/0/default.jpg">
<div class="ref">
<a href="https://10.7554/eLife.52614">
Andra Waagmeester et al, eLife, 2020
</a>
</div>
</section>
<section>
<div class="row">
<div class="column2" style="align-content: right;font-size: 35px;">
<h4>OBO Foundry</h4>
<img height=100 src="https://obofoundry.org/images/foundrylogo.png">
<ul>
<li>Steep learning curve</li>
<li>Many namespaces (CL, GO ...)</li>
<li>Single language (English)</li>
<li>Built by experts (consistent)</li>
</ul>
</div>
<div class="column2" style="align-content: right;font-size: 35px;">
<h4>Wikidata</h4>
<img height=100
src="https://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Wikidata-logo-en.svg/800px-Wikidata-logo-en.svg.png">
<ul>
<li>Quick onboarding </li>
<li>Single namespace</li>
<li>Support for +200 languages</li>
<li>Built by everyone (diverse)</li>
</ul>
</div>
</div>
</section>
<section>
<p>Goals of the PhD project</p>
<ul style="font-size: 40px;">
<li style="opacity: 0.5;">1. Find all classes of cells relevant to the Human Cell Atlas</li>
<li style="opacity: 0.5;">2. Organize the knowledge using knowledge graphs</li>
<li>3. Advance Wikidata as a tool for the life sciences</li>
</ul>
</section>
</section>
<!------------------->
<!--- Methodology --->
<!------------------->
<section class=" center" data-transition="fade" data-name="Methodology">
<section>
<p>Action research</p>
<p style="font-size: 35px;">"transformative change through the simultaneous process of
taking action
and doing research, which are linked together by critical reflection."
</p>
<a class="ref"
href="https://en.wikipedia.org/wiki/Action_research">https://en.wikipedia.org/wiki/Action_research
</a>
</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>
<div class="column">
<img src="img/tsunami.png" width="200">
</div>
</div>
</section>
<section>
3 ways of action:
<br />
<ul>
<li> Theoretical work on the concept of cell type </li>
<li> Integration of canonical databases to Wikidata </li>
<li> Development of a Wikidata-based biocuration and literature management framework
</li>
</ul>
</section>
</section>
<!---------------------------->
<!--- Concept of Cell Type --->
<!---------------------------->
<section class="center" data-transition="fade" data-name="Concept of Cell Type">
<section>
<p>What do we mean by "cell type"?</p>
<img src="./img/conceptual_definition_cell_systems.png">
<p class='ref'>
<a href="https://doi.org/10.1016/J.CELS.2017.03.006">
Cell Systems, 2017
</a>
</p>
</section>
<section>
<p>Theoretical considerations on the concept of cell type </p>
<img
src="https://raw.githubusercontent.com/lubianat/fapesp_report_1/main/content/images/archetypes_hn.jpg">
</section>
<!--
<section>
<p>Practical considerations - Multi Level Theory </p>
<img
src="https://github.com/lubianat/multilevel_ontology_drawings/blob/master/human_gandhi.png?raw=true">
</section>
-->
<section>
<p>Practical considerations - Multi Level Theory </p>
<img
src="https://github.com/lubianat/multilevel_ontology_drawings/blob/master/cell_gandhi_zygote.png?raw=true">
</section>
<section>
<p>Our pragmatic definition </p>
<br />
<p style="font-size: 40px;">a cell type is any <strong>class</strong> of cells described by a
domain
expert
</p>
</section>
</section>
<!----------------->
<!--- PanglaoDB --->
<!----------------->
<section class="center" data-transition="fade" data-name="PanglaoDB">
<section>
<p>Introduction</p>
<img height="400" src="img/panglao_3_stars.png">
<p class='ref'>
<a href="https://doi.org/10.1093/database/baz046">
Oscar Franzen et al, Database, 2019
</a>
</p>
</section>
<section>
<p>Methods</p>
<img
src="https://github.com/lubianat/fapesp_report_1/blob/main/content/images/poster_ISCB_intro.png?raw=true">
</section>
<section>
Information on Wikidata
<iframe width="120%" height="400" src="https://www.wikidata.org/wiki/Q101404947"></iframe>
</section>
<section>
Query: diseases related to beta cells
<br />
<p>SPARQL code </p>
<div class="scrollable">
<script src="https://gist.github.com/lubianat/0d1afafff6e21e1af01e70b3b08911c1.js"></script>
</div>
</section>
<section>
Query: diseases related to beta cells
<br />
<iframe style="width: 80vw; height: 50vh; border: none;"
src="https://query.wikidata.org/embed.html#SELECT%20%3FcellTypeLabel%20%3FdiseaseLabel%20%0A%28COUNT%28DISTINCT%20%3FdiseaseGene%29%20AS%20%3Fcount%29%20%0A%28GROUP_CONCAT%28DISTINCT%20%3FgeneLabel%3B%20SEPARATOR%3D%22%2C%20%22%29%20AS%20%3Fgenes%29%0AWHERE%20%0A%7B%0A%20%20wd%3AQ101405087%20wdt%3AP8872%20%3FdiseaseGene%20.%20%20%20%20%23%20human%20pancreatic%20beta%20cell%20--%3E%20%20has%20marker%20--%3E%20%20gene%0A%20%20%3Fdisease%20wdt%3AP2293%20%3FdiseaseGene%20.%20%20%20%20%20%20%20%20%20%23%20disease%20--%3E%20genetic%20association%20--%3E%20gene%0A%20%20%0A%20%20wd%3AQ101405087%20rdfs%3Alabel%20%3FcellTypeLabel%20.%0A%20%20%3Fdisease%20rdfs%3Alabel%20%3FdiseaseLabel%20.%0A%20%20%3FdiseaseGene%20%20%20rdfs%3Alabel%20%3FgeneLabel%20.%0A%0A%20%20FILTER%28LANG%28%3FcellTypeLabel%29%20%3D%20%22en%22%29%0A%20%20FILTER%28LANG%28%3FdiseaseLabel%29%20%3D%20%22en%22%29%0A%20%20FILTER%28LANG%28%3FgeneLabel%29%20%3D%20%22en%22%29%0A%20%20%0A%20%7D%0A%0AGROUP%20BY%20%3FdiseaseLabel%20%3FcellTypeLabel%20%0AORDER%20BY%20DESC%28%3Fcount%29"
referrerpolicy="origin" sandbox="allow-scripts allow-same-origin allow-popups"></iframe>
</section>
</section>
<!-------------------->
<!--- Wikidata Bib --->
<!-------------------->
<section class="center" data-transition="fade" data-name="Wikidata Bib">
<section>
<img height="100"
src="https://raw.githubusercontent.com/wikidatabib/rootstock/main/images/logo.png">
<ul>
<li> Fully open-source system</li>
<li> Based on: Python, Wikidata, GitHub and Markdown</li>
<li> Increases throughput </li>
<li> Provide analytics on reading </li>
</ul>
</section>
<section>
<p>1. Obtain list of articles via Wikidata </p>
<br />
<iframe style="width: 80vw; height: 50vh; border: none;"
src="https://query.wikidata.org/embed.html#SELECT%20%3Fwork%20%3FworkLabel%20WHERE%20%7B%0A%20%20values%20%3Fjournal%20%7Bwd%3AQ180445%20wd%3AQ192864%20wd%3AQ2000008%20wd%3AQ655814%20wd%3AQ573880%7D.%0A%20%20%3Fwork%20%20wdt%3AP921%20wd%3AQ105406038.%0A%20%20%3Fwork%20%20wdt%3AP1433%20%3Fjournal.%0A%20%20SERVICE%20wikibase%3Alabel%20%7B%20bd%3AserviceParam%20wikibase%3Alanguage%20%22%5BAUTO_LANGUAGE%5D%2Cen%22.%20%7D%0A%7D%0A"
referrerpolicy="origin" sandbox="allow-scripts allow-same-origin allow-popups"></iframe>
</section>
<section>
<p>2. Generate annotation station on demand (2/day) </p>
<img height="400"
src="https://github.com/lubianat/quali_phd/blob/main/content/images/note_taking_station_annotated.png?raw=true">
</section>
<section>
<p>3. Add articles read to online dashboard (automatic)</p>
<iframe width="120%" height="500" src="https://lubianat.github.io/wikidata_bib/"></iframe>
</section>
<section>
<p>4. Screen articles for cell types </p>
<iframe width="120%" height="500"
src="https://docs.google.com/spreadsheets/d/1SPgKpMEwHJSD-7M9I2hyVLJo7dlNk8maiL4SQhBGtXs/edit#gid=0"></iframe>
</section>
</section>
<!------------------>
<!--- Next steps --->
<!------------------>
<section class="center" data-transition="fade" data-name="Conclusion">
<section>
<h3> Progress Overview</h3>
<ul style="font-size: 40px">
<li>Wikidata 08/2020: 264 organized cell classes</li>
<li>Wikidata 12/2021: 2940 organized cell classes</li>
<ul style="font-size: xx-large">
<li>2812 (95.6%) somehow modified by me</li>
<li>1668 (56.7%) created by me</li>
</ul>
<li>724 cross-references to Cell Ontology</li>
<li>(~2400 cell classes on Cell Ontology)</li>
</ul>
</section>
<section>
<h3 class="left">Next steps</h3>
<ul>
<li>Connect better Cell Ontology and Wikidata</li>
<li>Gather more people to curate cell types</li>
<li>Test Wikidata Bib with more people</li>
<li>Connect Wikidata to R packages for scRNA-seq</li>
</ul>
</h2>
</section>
</section>
<!------------------>
<!--- Extra work --->
<!------------------>
<section class="center" data-transition="fade" data-name="Extra">
<section>
<p>Course work</p>
<img
src="https://github.com/lubianat/quali_phd/blob/main/content/images/janus_courses_taken.png?raw=true">
</section>
</section>
<!------------------------>
<!--- Acknowledgements --->
<!------------------------>
<section class="center" data-transition="fade" data-name="End">
<section>
<p>Acknowledgements</p>
<div class="row">
<div class="column2">
<img src="/img/csbl_people.png" height="380">
</div>
<div class="column2">
<div class="column2">
<img src="https://imagens.usp.br/wp-content/uploads/USP-Bras%C3%A3o.jpg" height="200">
</div>
<div class="column2">
<img src="https://upload.wikimedia.org/wikipedia/commons/4/45/Wiki_Movimento_Brasil_logo.svg"
height="200">
</div>
<img src="https://fapesp.br/files/home/portalPT_60.jpg?1626980694">
</div>
</div>
</section>
<section class="center" data-transition="fade">
<h3>Building a biological knowledge graph via Wikidata with a focus on the Human Cell Atlas.
</h3>
<div align="left">
<p>Student: Tiago Lubiana</p>
<p>Advisor: Prof. Helder Nakaya</p>
</div>
<div class="row">
<div class="column2">
<img src="https://irp.cdn-website.com/683b19b1/dms3rep/multi/LOGO_CSBL.svg" height="100">
</div>
<div class="column2">
<img src="https://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Wikidata-logo-en.svg/800px-Wikidata-logo-en.svg.png"
height="100">
</div>
</div>
<div align="center">
<p>Feb 23rd 2022 - São Paulo - SP</p>
</div>
</section>
</section>
</div>
</div>
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