fix: update organism page

docs/advanced-guides/nmr-repositories/organism.md

@@ -4,17 +4,17 @@ title: Organism
 ---
 
 # Organism
-[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/organism.ipynb)
+[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/organism.ipynb) where you can find all the graphs.
 
-Data created at: 17.10.2022 at 19:32:45
+Data created on 17.10.2022 at 19:32:45
 
-Data updated at: 17.10.2022 at 19:32:45
+Data updated on 17.10.2022 at 19:32:45
 
 ## Support by Ontologies
-[NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy) provides an excelent source for organisms. 
+[NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy) provides an excellent source for organisms. 
 
 ## Data Sanitisation and Missing Values
-Organisms are found only in metabolomics related repositories, a.k.a., MTBLS and MW. 
+Organisms are found only in metabolomics-related repositories, i.e., MTBLS and MW. 
 
 <table>
   <tr>
@@ -43,3 +43,38 @@ Organisms are found only in metabolomics related repositories, a.k.a., MTBLS and
   </tr>
 </table>
 
+<table>
+  <tr>
+    <th></th>
+    <th>Input Examples</th>
+    <th>Output</th>
+  </tr>
+  <tr>
+    <td><b>MTBLS</b></td>
+    <td>["Homo sapiens", "Blank sample", "Lactobacillus sp. asf360;Parabacteroides sp. asf519",   "Sus scrofa domesticus", "NCBITAXON:Thalassiosira pseudonana;NCBITAXON:Ruegeria pomeroyi"]</td>
+    <td>["homo-sapiens", "mus-musculus", etc.]</td>
+  </tr>
+  <tr>
+    <td><b>MW</b></td>
+    <td>["Homo sapiens", "Sus scrofa", "Sus Scrofa", "C57BL/6J Mouse",  "Multi-species non-defined biofilm consortium", "Alexandrium catenella; Alexandrium tamarense"]</td>
+    <td>["homo-sapiens", "mus-musculus", etc.]</td>
+  </tr>
+</table>
+
+## Results
+Organism details are available in metabolomics repositories. The users usually use the scientific name that can be obtained from [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy). However, some inconsistencies were encountered such as with writing the scientific name (e.g.,  Mus Musculus instead of Mus musculus), providing a common name (Goat instead of Capra hircus), or providing the source along with the value (e.g., NCBITAXON:Homo sapiens), or even typos.
+
+Some values were ambiguous such as "Various", "Extract", "Multi-species non-defined biofilm consortium" or not even species, such as NMR buffer. Additionally, sometimes, more than one species was mentioned. The combination of species is usually standardized by putting ";" or "/" between the names, but still, the relation between the species is not clear (samples from multiple species vs one sample from a species tissue infected by another species). Lastly, the organism provided varys in rank. Mostly the species is provided, but sometimes it is the genus or strain.  
+
+However, even after taking all that was mentioned above, it is still clear that the most studied species are humans (Homo sapiens) and mice (Mus musculus)
+<div style={{textAlign: 'center'}}>
+<img src="/img/analysis/org/all.png" width="500"/>
+<figcaption>A rough estimate of the percentages of all studies in MTBLS and MW repositories based on the sample pH</figcaption>
+</div>
+<br></br>
+
+Here one can see the number of studies providing the organism and its value.
+<div style={{textAlign: 'center'}}>
+<img src="/img/analysis/org/h.png" width="1000"/>
+<figcaption>The number of studies in MTBLS and MW based on the organism</figcaption>
+</div>

docs/advanced-guides/nmr-repositories/ph.md

@@ -36,7 +36,6 @@ It was possible to get the pH details only from [MetaboLights](https://www.ebi.a
 
 ## Results
 
-### pH
 It was possible to obtain the pH only from MTBLS, even though most of the studies didn't provide this metadata. Most samples' pHs were leaning towards the neutral 7, while a small percentage was around 4.
 
 <div style={{textAlign: 'center'}}>