Add source files (csv) for figures

.gitignore

@@ -3,7 +3,6 @@
 **/*.conf
 **/*.cands*
 **/*.peaks
-**/*.csv*
 **/*.tar.gz
 __pycache__
 **/ISOTOPE.DAT
@@ -47,3 +46,5 @@ data/tools/
 data/massbank.sqlite.gz
 results_processed/publication/massbank/ssvm_lib=v2__exp_ver=4/massbank
 results_processed/publication/massbank/ssvm_lib=v2__exp_ver=4/massbank__with_stereo/
+data/PubChemLite_31Oct2020_exposomics.csv
+misc_scripts/massbank_groups__meta_data.csv

results_processed/publication/massbank/ssvm_lib=v2__exp_ver=4/README.md

@@ -3,12 +3,12 @@
 Here you can find the jupyter notebooks used to produce the figures in our manuscript. The relevant notebooks for 
 the latest version of our manuscript are:
 
-| **Notebook name**                                                           | **Content**                                                                                                                                                                                                                      |
-|-----------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| ```exp_01__comparison_of_different_score_integration_approaches_3D.ipynb``` | Here we compare the ranking performance of LC-MS²Struct with the different comparison methods.                                                                                                                                   |
-| ```exp_02__performance_analysis_using_molecule_classification_3D.ipynb```   | Here we analyze the performance improvements using LC-MS²Struct for different ClassyFire and PubChemLite molecular classes.                                                                                                      |
-| ```exp_03__stereochemistry.ipynb```                                         | Here we assess the performance of LC-MS²Struct in the ONLYSTEREO setting.                                                                                                                                                        |
-| ```exp_04__using_3D_features_for_inchikey1_aggregation.ipynb```             | Here we compare the ranking performance in the ALLDATA setting when using 2D and 3D FCFP fingerprints in combination with LC-MS²Struct. The generated figures can be also found in the supplementary material of the manuscript. |
+| **Notebook name**                                                           | **Content**                                                                                                                                                                                                                      | **Figure (in manuscript)**                        |
+|-----------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------|
+| ```exp_01__comparison_of_different_score_integration_approaches_3D.ipynb``` | Here we compare the ranking performance of LC-MS²Struct with the different comparison methods.                                                                                                                                   | - Figure 2 (a, b) <br/> - Extended Data Figure 4  | 
+| ```exp_02__performance_analysis_using_molecule_classification_3D.ipynb```   | Here we analyze the performance improvements using LC-MS²Struct for different ClassyFire and PubChemLite molecular classes.                                                                                                      | - Figure 3 (a, b) <br/> - Extended Data Figure 2  |
+| ```exp_03__stereochemistry.ipynb```                                         | Here we assess the performance of LC-MS²Struct in the ONLYSTEREO setting.                                                                                                                                                        | - Figure 4 (a, b)                                 |
+| ```exp_04__using_3D_features_for_inchikey1_aggregation.ipynb```             | Here we compare the ranking performance in the ALLDATA setting when using 2D and 3D FCFP fingerprints in combination with LC-MS²Struct. The generated figures can be also found in the supplementary material of the manuscript. | - Extended Data Figure 3                          |
 
 
 ## Instructions to reproduce the figures