completed Metabolites sets

PWA-4_Metabolomics-Slides.html

@@ -448,9 +448,11 @@ <h2>An open problem: Metabolites IDs</h2>
 <ul>
 <li><p>To be able to do Pathway Analysis, metabolites need to be <em>mappable</em> to their sources of information.</p>
 <ul>
-<li>Must be uniquely identifiable through their names or IDs. -Must be possible to link/relate these names/IDs with the corresponding IDs in the source of information we wish to rely.</li>
+<li>Must be uniquely identifiable by names/IDs.</li>
+<li>Must be possible to link/relate these names/IDs with the corresponding IDs in the source of information we wish to rely.</li>
 </ul></li>
-<li><p>Nowadays, this is <em>far from possible</em> for all metabolites and the task of uniquely and ambiguosly naming the metabolites is a hard one.</p></li>
+<li><p>This is <em>far from possible</em> for all metabolites.</p></li>
+<li><p>Uniquely and unambiguosly naming all metabolites is, in the best of cases, “work in progress”.</p></li>
 </ul>
 </section>
 <section id="the-where-to-now-question" class="slide level2 smaller">
@@ -514,10 +516,20 @@ <h2>The elements of Pathways Analysis</h2>
 <li><p>In this section, we focus on <em>sources of information</em> and on <em>how to provide it to the algorithms</em>.</p></li>
 </ul>
 </section>
-<section id="metabolites-databases" class="slide level2">
-<h2>Metabolites Databases</h2>
+<section id="sources-of-information-for-pwa" class="slide level2">
+<h2>Sources of information for PWA</h2>
 
 <img data-src="images/PWA-4_Metabolomics-Slides_insertimage_14.png" class="r-stretch quarto-figure-center"><p class="caption">Some common databases in Metabolomics</p></section>
+<section id="ontologies-databases-et-alt." class="slide level2 smaller">
+<h2>Ontologies, Databases et alt.</h2>
+<p>Although incomplete s.o.i are multiple and diverse.</p>
+<ul>
+<li><strong>Ontologies:</strong> Structured vocabularies for categorizing and describing relationships within a domain. <a href="https://geneontology.org/">GO</a>, <a href="https://www.ebi.ac.uk/chebi/">ChEBI</a></li>
+<li><strong>Pathway Databases:</strong> Detailed information about biological pathways and their the biological context. <a href="https://www.genome.jp/kegg/">KEGG</a>, <a href="https://reactome.org/">Reactome</a>, <a href="https://www.smpdb.ca/">SMPDB</a>.</li>
+<li><strong>Compound Databases:</strong> Information on small molecules for identification and characterization of metabolites. <a href="https://hmdb.ca/">HMDB</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/">PubChem</a>, <a href="https://lipidmaps.org/">LipidMaps</a>, and <a href="https://massbank.eu/MassBank/">MassBank</a></li>
+<li>And many more: <strong>Networks DBs</strong>, <strong>Spectral DBs</strong>, …</li>
+</ul>
+</section>
 <section id="the-human-metabolome-db" class="slide level2 smaller">
 <h2>The Human Metabolome DB</h2>
 <div class="columns">
@@ -598,14 +610,34 @@ <h2>Small Molecule Pathway Database</h2>
 </div>
 </div>
 </section>
-<section id="from-databases-to-metabolite-sets" class="slide level2">
-<h2>From Databases to Metabolite Sets</h2>
-
-<img data-src="images/PWA-4_Metabolomics-Slides_insertimage_19.png" class="r-stretch quarto-figure-center"><p class="caption">MSEA Workflow</p></section>
+<section id="obtaining-metabolite-sets" class="slide level2">
+<h2>Obtaining Metabolite Sets</h2>
+<ul>
+<li><p>As described, PWA matches lists of metabolites with previously defined metabolite sets that characterize a process, a disease or a group.</p></li>
+<li><p>Some sources of information (Ontologies, Pathways DBs) directly provide metabolite sets.</p></li>
+<li><p>For compound DBs, Metabolite sets have to be built</p>
+<ul>
+<li>By manual curation</li>
+<li>Automatically (some type of clustering)</li>
+</ul></li>
+</ul>
+</section>
 <section id="metabolites-set-libraries" class="slide level2">
 <h2>Metabolites Set libraries</h2>
 
-<img data-src="images/PWA-4_Metabolomics-Slides_insertimage_20.png" class="r-stretch quarto-figure-center"><p class="caption">Overview of MSEA’s metabolite set libraries</p></section></section>
+<img data-src="images/PWA-4_Metabolomics-Slides_insertimage_20.png" class="r-stretch quarto-figure-center"><p class="caption">Overview of MSEA’s metabolite set libraries</p></section>
+<section id="metamap-clusters" class="slide level2">
+<h2>Metamap clusters</h2>
+
+<img data-src="PWA-4_Metabolomics-Slides_insertimage_4.png" class="r-stretch"></section>
+<section id="chemical-similarity-clusters" class="slide level2">
+<h2>Chemical similarity clusters</h2>
+
+<img data-src="PWA-4_Metabolomics-Slides_insertimage_5.png" class="r-stretch"></section>
+<section id="chemical-ontologies" class="slide level2">
+<h2>Chemical Ontologies</h2>
+
+<img data-src="PWA-4_Metabolomics-Slides_insertimage_3.png" class="r-stretch"></section></section>
 <section id="analysis-methods" class="title-slide slide level1 center">
 <h1>Analysis Methods</h1>
 

PWA-4_Metabolomics-Slides.qmd

@@ -145,10 +145,11 @@ editor_options:
 
 - To be able to do Pathway Analysis, metabolites need to be *mappable* to their sources of information.
 
-  - Must be uniquely identifiable through their names or IDs.
-  -Must be possible to link/relate these names/IDs with the corresponding IDs in the source of information we wish to rely.
+  - Must be uniquely identifiable by  names/IDs.
+  - Must be possible to link/relate these names/IDs with the corresponding IDs in the source of information we wish to rely.
 
-- Nowadays, this is *far from possible* for all metabolites and the task of uniquely and ambiguosly naming the metabolites is a hard one.
+- This is *far from possible* for all metabolites.
+- Uniquely and unambiguosly naming all metabolites is, in the best of cases, "work in progress".
 
 ## The *where to, now?* question {.smaller}
 
@@ -218,10 +219,18 @@ Once a list of feature is obtained it can be studied on a one-by-one basis
 - In this section, we focus on *sources of information* and on *how to provide it to the algorithms*.
 
 
-## Metabolites Databases
+## Sources of information for PWA
 
 ![Some common databases in Metabolomics ](images/PWA-4_Metabolomics-Slides_insertimage_14.png)
 
+## Ontologies, Databases et alt.{.smaller}
+
+Although incomplete s.o.i are multiple and diverse.
+
+- **Ontologies:** Structured vocabularies for categorizing and describing relationships within a domain. [GO](https://geneontology.org/), [ChEBI](https://www.ebi.ac.uk/chebi/)
+- **Pathway Databases:** Detailed information about biological pathways and their the biological context. [KEGG](https://www.genome.jp/kegg/), [Reactome](https://reactome.org/), [SMPDB](https://www.smpdb.ca/).
+- **Compound Databases:** Information on small molecules for identification and characterization of metabolites. [HMDB](https://hmdb.ca/), [PubChem](https://pubchem.ncbi.nlm.nih.gov/), [LipidMaps](https://lipidmaps.org/), and [MassBank](https://massbank.eu/MassBank/)
+- And many more: **Networks DBs**, **Spectral DBs**, ...
 
 ## The  Human Metabolome DB {.smaller}
 
@@ -334,14 +343,33 @@ process pathways (70)
 
 ::::
 
-## From Databases to Metabolite Sets
+## Obtaining Metabolite Sets
+
+- As described, PWA matches lists of metabolites with previously defined metabolite sets that characterize a process, a disease or a group.
+
+- Some sources of information (Ontologies, Pathways DBs) directly provide metabolite sets.
+
+- For compound DBs, Metabolite sets have to be built
+  - By manual curation
+  - Automatically (some type of clustering)
 
-![MSEA Workflow ](images/PWA-4_Metabolomics-Slides_insertimage_19.png)
 
 ## Metabolites Set libraries
 
 ![Overview of MSEA's metabolite set libraries ](images/PWA-4_Metabolomics-Slides_insertimage_20.png)
 
+## Metamap clusters
+
+![](PWA-4_Metabolomics-Slides_insertimage_4.png)
+
+## Chemical similarity clusters
+
+![](PWA-4_Metabolomics-Slides_insertimage_5.png)
+
+## Chemical Ontologies
+
+![](PWA-4_Metabolomics-Slides_insertimage_3.png)
+
 # Analysis Methods
 
 # Limitations and Recommendations