DO NOT MERGE: add notebook demonstrating proteomic aggregation and example analysis

.github/workflows/notebook_check_python.yml

@@ -46,4 +46,9 @@ jobs:
     - id: execute-NOM
       name: Execute NOM notebook
       run: |
-        jupyter nbconvert --execute --to notebook --inplace NOM_visualizations/python/nom_data.ipynb
+        jupyter nbconvert --execute --to notebook --inplace NOM_visualizations/python/nom_data.ipynb
+
+    - id: execute-aggregation
+      name: Execute proteomic aggregation notebook
+      run: |
+        jupyter nbconvert --execute --to notebook --inplace proteomic_aggregation/python/proteomic_aggregation.ipynb

README.md

@@ -7,7 +7,7 @@ Notebooks that are ready for use and exploration.
 - [Bio-Scales Biogeochemical MetaData](https://github.com/microbiomedata/nmdc_notebooks/tree/main/bioscales_biogeochemical_metadata)
 - [NEON Soil Microbial Community Composition](https://github.com/microbiomedata/nmdc_notebooks/tree/main/taxonomic_dist_by_soil_layer)
 - [Natural Organic Matter Composition by Sample Type](https://github.com/microbiomedata/nmdc_notebooks/tree/main/NOM_visualizations)
-
+- [Proteomic Data Aggregation and Visualization](https://github.com/microbiomedata/nmdc_notebooks/tree/main/proteomic_aggregation_and_visualization)
 
 ## Overview 
 

proteomic_aggregation/README.md

@@ -0,0 +1,10 @@
+# Proteomic Data Aggregation and Visualization
+
+This folder includes two notebooks (in R and Python) that demonstrate the aggregation of proteomic data via National Microbiome Data Collaborative's [Runtime API](https://api.microbiomedata.org/docs). They also provide an example proteomic analysis and a method of connecting the results to other datasets in NMDC. 
+
+## R
+Coming soon!
+
+## Python
+- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/main//proteomic_aggregation/python/proteomic_aggregation.ipynb). This is the recommended way to interact with the notebook. _Viewing only, not editable_
+- [![Open In Colab]((https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/main//proteomic_aggregation/python/proteomic_aggregation.ipynb). **Running this notebook in the colab interactive environment is not recommended due to long API calls** _You need a google account to use this option_