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IUPAC · Dec 22, 2023 · 88c0c1e · 88c0c1e
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diff --git a/_images/88ce6db9c4a096dc382f0607d1bcae5505dbe6b66273fe5eb8f3bf60dede8d01.png b/_images/88ce6db9c4a096dc382f0607d1bcae5505dbe6b66273fe5eb8f3bf60dede8d01.png
diff --git a/_images/b678c4cfd692940c77696edd41537c40181ae70df074ea0fc3335ec7ea5054da.png b/_images/b678c4cfd692940c77696edd41537c40181ae70df074ea0fc3335ec7ea5054da.png
diff --git a/_images/sch_excel_import_fig1.jpg → _images/excel_import_fig1.jpg b/_images/sch_excel_import_fig1.jpg → _images/excel_import_fig1.jpg
diff --git a/_images/sch_excel_import_fig2.jpg → _images/excel_import_fig2.jpg b/_images/sch_excel_import_fig2.jpg → _images/excel_import_fig2.jpg
diff --git a/_images/sch_excel_import_fig3.jpg → _images/excel_import_fig3.jpg b/_images/sch_excel_import_fig3.jpg → _images/excel_import_fig3.jpg
diff --git a/_images/sch_excel_import_fig4.jpg → _images/excel_import_fig4.jpg b/_images/sch_excel_import_fig4.jpg → _images/excel_import_fig4.jpg
diff --git a/_images/sch_excel_import_fig5.jpg → _images/excel_import_fig5.jpg b/_images/sch_excel_import_fig5.jpg → _images/excel_import_fig5.jpg
diff --git a/...ges/sch_sheets_citations_crossref_api.jpg → _images/gsheets_citations_crossref_api.jpg b/...ges/sch_sheets_citations_crossref_api.jpg → _images/gsheets_citations_crossref_api.jpg
diff --git a/_images/ing_pubchem_pugrest_fig1.jpg b/_images/ing_pubchem_pugrest_fig1.jpg
diff --git a/_images/utn_opsin_api_fig1.jpg → _images/opsin_api_fig1.jpg b/_images/utn_opsin_api_fig1.jpg → _images/opsin_api_fig1.jpg
diff --git a/_sources/ingredients/ing_figshare.md → _sources/ingredients/figshare.md b/_sources/ingredients/ing_figshare.md → _sources/ingredients/figshare.md
diff --git a/_sources/ingredients/ing_pubchem_pugrest.md b/_sources/ingredients/ing_pubchem_pugrest.md
diff --git a/_sources/ingredients/ing_pubchem.md → _sources/ingredients/pubchem.md b/_sources/ingredients/ing_pubchem.md → _sources/ingredients/pubchem.md
@@ -56,7 +56,7 @@ This paper includes several protocols designed to help users to get familiar wit
 * **Basic Protocol 7**: [Finding compounds annotated with classifications or ontological terms](https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.217#cpz1217-prot-0008)
 * **Basic Protocol 8**: [Finding stereoisomers and isotopomers of a compound through identity search](https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.217#cpz1217-prot-0009)
 
-Finally, one of the developers at PubChem, Dr. Sunghwan Kim, has developed some [tutorials](ing_pubchem_pugrest.md) about the PubChem API,
+Finally, one of the developers at PubChem, Dr. Sunghwan Kim, has developed some [tutorials](pubchem_pugrest) about the PubChem API,
 the Power User Group - Representation State Transfer ([PUG-REST](https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest)) service.
 
 ## References  

diff --git a/_sources/ingredients/pubchem_pugrest.md b/_sources/ingredients/pubchem_pugrest.md
@@ -0,0 +1,9 @@
+# PubChem PUG-REST API
+
+The following samples detail different aspects of using the PubChem PUG-REST Application Programming Interface (API).
+
+- [Part 1 - Basic syntax of PUG-REST request URL](pubchem_pugrest1.ipynb)
+- [Part 2 - Accessing PubChem data using a chemical name](pubchem_pugrest2.ipynb)
+- [Part 3 - Using a SMILES or InChI string as an input query](pubchem_pugrest3.ipynb)
+
+Extensive documentation about the API can be found [here](https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest).
diff --git a/...es/ingredients/ing_pubchem_pugrest1.ipynb → _sources/ingredients/pubchem_pugrest1.ipynb b/...es/ingredients/ing_pubchem_pugrest1.ipynb → _sources/ingredients/pubchem_pugrest1.ipynb
diff --git a/...es/ingredients/ing_pubchem_pugrest2.ipynb → _sources/ingredients/pubchem_pugrest2.ipynb b/...es/ingredients/ing_pubchem_pugrest2.ipynb → _sources/ingredients/pubchem_pugrest2.ipynb
diff --git a/...es/ingredients/ing_pubchem_pugrest3.ipynb → _sources/ingredients/pubchem_pugrest3.ipynb b/...es/ingredients/ing_pubchem_pugrest3.ipynb → _sources/ingredients/pubchem_pugrest3.ipynb
diff --git a/_sources/ingredients/ing_zenodo.md → _sources/ingredients/zenodo.md b/_sources/ingredients/ing_zenodo.md → _sources/ingredients/zenodo.md
diff --git a/_sources/menus/men_iupac_pkadata.ipynb → _sources/menus/iupac_pkadata.ipynb b/_sources/menus/men_iupac_pkadata.ipynb → _sources/menus/iupac_pkadata.ipynb
diff --git a/_sources/recipes/rec_computing_inchis.ipynb → _sources/recipes/computing_inchis.ipynb b/_sources/recipes/rec_computing_inchis.ipynb → _sources/recipes/computing_inchis.ipynb
diff --git a/_sources/recipes/rec_goldbook_api.ipynb → _sources/recipes/goldbook_api.ipynb b/_sources/recipes/rec_goldbook_api.ipynb → _sources/recipes/goldbook_api.ipynb
diff --git a/_sources/recipes/rec_opsin_api.ipynb → _sources/recipes/opsin_api.ipynb b/_sources/recipes/rec_opsin_api.ipynb → _sources/recipes/opsin_api.ipynb
diff --git a/_sources/recipes/rec_uvvis_metadata.ipynb → _sources/recipes/uvvis_metadata.ipynb b/_sources/recipes/rec_uvvis_metadata.ipynb → _sources/recipes/uvvis_metadata.ipynb
@@ -411,7 +411,7 @@
     "plt.ylabel(r'Log $\\epsilon$ ($L\\ mol^{-1}\\ cm^{-1}$)') # Set the name of the y-label\n",
     "plt.title('UV spectrum of salicyclic acid')            # Set the title of the graph\n",
     "plt.grid()                                             # Show grid lines\n",
-    "plt.savefig('rec_uvvis_metadata_fig.png')              # Saves the figure to your current directory.\n",
+    "plt.savefig('uvvis_metadata_fig.png')                  # Saves the figure to your current directory.\n",
     "                                                       # File path can be updated to suit\n",
     "plt.show()                                             # Plot the graph to the screen"
    ]

diff --git a/_sources/school/sch_excel_import.md → _sources/school/excel_import.md b/_sources/school/sch_excel_import.md → _sources/school/excel_import.md
@@ -83,7 +83,7 @@ import .csv, .tsv and other files and not let you choose what the encoding is.
 system there may be some selections that won't work on your computer.
 
 Figure 1
-![fig1](../images/sch_excel_import_fig1.jpg)
+![fig1](../images/excel_import_fig1.jpg)
 Caption: The Excel import dialog (a) and the options for 'File origin' (b)
 
 Using the open file dialog is important if your text file contains unicode (e.g., UTF-8).  If you double-click on a .csv,
@@ -94,7 +94,7 @@ Excel you will be able to use the dialog in Figure 1a to choose the correct enco
 correctly in Excel (see Figure 2b).
 
 Figure 2
-![fig2](../images/sch_excel_import_fig2.jpg)
+![fig2](../images/excel_import_fig2.jpg)
 Caption: Importing a unicode (UTF-8) '.csv' file into Excel directly (a), and using the Excel file oping dialog (b)
 
 ### 2.2 End of line characters
@@ -103,7 +103,7 @@ This can result in extra blank lines begin added by Excel to the imported file w
 CR character, and a 'line-feed' LF character is at the end of line.
 
 Figure 3
-![fig3](../images/sch_excel_import_fig3.jpg)
+![fig3](../images/excel_import_fig3.jpg)
 Caption: Different end-of-line character options from a text file. 
 
 ### 2.3 Data types in Excel
@@ -116,7 +116,7 @@ misinterpreted as dates if the column data type is left as 'General'.  In this s
 addin quotes around the CASRN and adding a '='before the first quote (Figure 4b).
 
 Figure 4
-![fig4](../images/sch_excel_import_fig4.jpg)
+![fig4](../images/excel_import_fig4.jpg)
 Caption: CASRNs in (4a) and advanced options for interpretting numeric values (4b)
 
 ```{Note}
@@ -137,7 +137,7 @@ As an example, the value one thousand, two hundred and thirty-four point fifty-s
 - In Latin America and continental Europe as: 1.234,56
 
 Figure 5
-![fig5](../images/sch_excel_import_fig5.jpg)
+![fig5](../images/excel_import_fig5.jpg)
 Caption: Data types for columns in Excel (a) and advanced options for interpretting numeric values (b)
 
 

diff --git a/_sources/school/sch_sheets_citations.md → _sources/school/gsheets_citations.md b/_sources/school/sch_sheets_citations.md → _sources/school/gsheets_citations.md
@@ -42,7 +42,7 @@ get a JSON file returned (see below).  The JSON file is formatted using the [JSO
 plugin for Firefox and all the fields have been collapsed to make it easy to see the whole file at
 http://api.crossref.org/works/10.1515/pac-2018-1010.
 
-![fig](../images/sch_sheets_citations_crossref_api.jpg)
+![fig](../images/gsheets_citations_crossref_api.jpg)
 
 Caption: JSON output from the Crossref API
 

diff --git a/_sources/standards/std_learn_spectra.md b/_sources/standards/std_learn_spectra.md
@@ -59,13 +59,13 @@ approach that is always possible is to encode the data as one or more tables in
 a tab-delimited text file (TSV) supplemented with the required metadata to undestand and properly interpreted the data. 
 Metadata is usually encoded in XML or JSON data files, although other standard open formats may also be possible. 
 
-More on this approach can be found at [Preparing Chemical Data for FAIR Sharing - A Minimalist Approach](../techniques/tec_sharing_chemdata.md).
+More on this approach can be found at [Preparing Chemical Data for FAIR Sharing - A Minimalist Approach](../techniques/sharing_chemdata).
 
 ## What metadata?
 
 Associated data is critical for reusing spectral data sets. Guidance on this is offered in the reports of the 
 [FAIRSpec IUPAC project](https://iupac.org/project/2019-031-1-024/). Some details are also included in 
-[Creating a UV/Vis (meta)data file structure for small molecule characterisation](../recipes/rec_uvvis_metadata.ipynb).
+[Creating a UV/Vis (meta)data file structure for small molecule characterisation](../recipes/uvvis_metadata.ipynb).
 
 It is always important to include
 

diff --git a/_sources/techniques/tec_dataset_search.ipynb → _sources/techniques/dataset_search.ipynb b/_sources/techniques/tec_dataset_search.ipynb → _sources/techniques/dataset_search.ipynb
diff --git a/_sources/techniques/tec_sharing_chemdata.md → _sources/techniques/sharing_chemdata.md b/_sources/techniques/tec_sharing_chemdata.md → _sources/techniques/sharing_chemdata.md
diff --git a/_sources/utensils/utn_opsin_api.md → _sources/utensils/opsin_api.md b/_sources/utensils/utn_opsin_api.md → _sources/utensils/opsin_api.md
@@ -40,7 +40,7 @@ be used to fix misspelling of systematic names amd it is really useful as a teac
 structure and ask them to name it, checking the names with OPSIN.  For data science OPSIN also has an [API](https://opsin.ch.cam.ac.uk/instructions.html) and returns
 information back in JSON for easy use within scripting languages and other tools.
 
-![fig1](../images/utn_opsin_api_fig1.jpg)
+![fig1](../images/opsin_api_fig1.jpg)
 
 OPSIN can deal with names that include [greek letters and superscripts](https://opsin.ch.cam.ac.uk/instructions.html). 
 It also has the capability to interpret mixtures of substances. This is useful for situations like getting identifiers for

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