new sections

added Organofluorine compounds and PubChem Search - plus other tweaks.

pfas-tree/PFAS_Tree.Rmd

@@ -42,14 +42,22 @@ Environmental Cheminformatics group
 at the [LCSB](https://wwwen.uni.lu/lcsb/), 
 [University of Luxembourg](https://wwwen.uni.lu/) in consultation with 
 several community representatives (see [Contributions](#contrib)
-and [Acknowledgements](#ack)).
+and [Acknowledgements](#ack)). 
+
+The 
+[PFAS Tree](https://pubchem.ncbi.nlm.nih.gov/classification/#hid=120)
+includes all compounds in [PubChem](https://pubchem.ncbi.nlm.nih.gov/) 
+that satisfy various definitions, as explained later in this document.
+Each compound in PubChem has a PubChem Compound Identifier (CID), and the
+blue numbers next to each node header reflects the number of 
+compounds (_i.e._ CIDs) in that node.
 
 <!-- ![The "[PFAS and Fluorinated Organic Compounds in PubChem Tree](https://pubchem.ncbi.nlm.nih.gov/classification/#hid=120)" Landing Page.](fig/PFAS_Tree_Landing.png) -->
 
 
 ## Contents 
 
-This document is organised into several sections, as follows: 
+<!-- This document is organised into several sections, as follows:  -->
 
 | Section | Navigation | PDF Page |
 |-----------|---------|:----:|
@@ -57,12 +65,12 @@ This document is organised into several sections, as follows:
 |_OECD PFAS Definition_ | [Go to heading](#oecddef) | 2 |
 |_Organofluorine Compounds_ | [Go to heading](#orgf) | 5 |
 |_PFAS and Fluorinated Organic Compound Collections_ | [Go to heading](#lists) | 5 |
-|Navigating the Tree | [Go to heading](#search) | 6 |
-|_Search via PubChem Search_ | [Go to heading](#pc-search) | 6 |
-|_Interactions via Entrez_ | [Go to heading](#entrez) | 6 |
-|_Interactions via PUG REST_ | [Go to heading](#pugrest) | 6 |
-|Further Details | [Go to heading](#details) | 7 |
-|Statements and References | [Go to heading](#statements) | 8 | 
+|Navigating the Tree | [Go to heading](#search) | 7 |
+|_Search via PubChem Search_ | [Go to heading](#pc-search) | 7 |
+|_Interactions via Entrez_ | [Go to heading](#entrez) | 8 |
+|_Interactions via PUG REST_ | [Go to heading](#pugrest) | 8 |
+|Further Details | [Go to heading](#details) | 9 |
+|Statements and References | [Go to heading](#statements) | 9 | 
 <!-- |References | [Go to heading](#statements) | 6 |  -->
 
 
@@ -218,9 +226,35 @@ more details.
 This node contains _organofluorine compounds_ as defined in Figure 8 in 
 the 2021 OECD PFAS Report 
 [ENV/CBC/MONO(2021)25](https://www.oecd.org/officialdocuments/publicdisplaydocumentpdf/?cote=ENV/CBC/MONO(2021)25&docLanguage=En) 
- [@oecd_reconciling_2021].
-
-Further content still to come ... 
+[@oecd_reconciling_2021]. 
+Figure 7 in the current report shows an extract from Figure 8 of 
+the OECD report on the left panel, 
+and the corresponding node breakdown in the _Organofluorine compounds_ 
+section of the PubChem PFAS Tree to the right. Note that one additional 
+category was added ("_Other fluorinated substances_") to capture content 
+that did not fit into any other category defined in the OECD figure. 
+
+![The categorization of PFAS (blue shading) and non-PFAS (grey) from the OECD 2021 report [@oecd_reconciling_2021] (left panel) and the "Organofluorine compounds" node (right panel). Numbers from 24 March 2022.](fig/Organofluorine_OECDfig_tree.png)
+
+The _Organofluorine compounds_ node is broken down very differently
+to the _OECD PFAS Definition_ node, since not all the contents are 
+PFAS (and thus do not contain PFAS parts). Each subnode is broken down first 
+by the number of fluorine atoms (1 through to 15, then >15) and then by 
+an exact mass range. If there are no CIDs for the given category, it is not
+present. For instance, the "_Fluorinated aliphatic substances that have a 
+fully fluorinated methyl or methylene carbon atom_" category starts at 
+"_Contains 02 Fluorine atoms_" as no entries in this category could contain 
+only one F. 
+The exact mass is split into the ranges 1-250, 250-500, 500-750, 750-1000
+and >1000.
+
+<!-- The exact mass is split as follows:  -->
+
+<!-- - Exact mass range 1-250 -->
+<!-- - Exact mass range 250-500 -->
+<!-- - Exact mass range 500-750 -->
+<!-- - Exact mass range 750-1000 -->
+<!-- - Exact mass range >1000 -->
 
 
 ### PFAS and Fluorinated Organic Compound Collections {#lists}
@@ -231,7 +265,9 @@ also be added here. The mapping files to construct this are kept
 on the [eci/pubchem](https://gitlab.lcsb.uni.lu/eci/pubchem/) 
 repository on GitLab.
 
-Currently, the content (see Figure 7) comes from:
+![The "PFAS and Fluorinated Organic Compound Collections" node, with all major collections shown (as of 24 March 2022).](fig/PFAS_list_of_lists.png)
+
+Currently, the content (see Figure 8) comes from:
 
 - All [PFAS lists](https://comptox.epa.gov/dashboard/chemical-lists?filtered=&search=PFAS) 
 from the 
@@ -252,17 +288,47 @@ in PubChem;
 
 
 
-![The "PFAS and Fluorinated Organic Compound Collections" node, with all major collections shown (as of 24 March 2022).](fig/PFAS_list_of_lists.png)
-
 ## Navigating the Tree {#search}
 
 While the tree offers possibilities for browsing and searching
 PFAS and other organofluorine content, there are several powerful
-search capabilites to empower this further.
+search capabilites to empower this further, explained in the next 
+sections.
 
 ### Search via PubChem Search {#pc-search}
 
-Content still to come ... 
+Perhaps the most intuitive interaction is directly through 
+clicking on the numbers besides each node. This sends a query 
+directly to the PubChem Search interface and displays the 
+entire node contents, as shown in Figure 9. This query follows 
+"OECD PFAS Definition" > "Molecule contains PFAS parts larger than 
+CF~2~/CF~3~" > "Breakdown by isolated PFAS part count" > 
+"Contains 01 isolated PFAS part" > "Count of molecules 10001-100000" >
+"Contains 01xC04F09-linear" and returns the 10,555 CIDs with 
+a C~4~F~9~ PFAS part. This query could then be downloaded, 
+or sent to Entrez (see next section).
+
+![Querying node contents in PubChem Search. When clicking on the blue numbers (left), a search window will open in a new tab (right, main image). This collection can be browsed, downloaded (see inset) or sent to Entrez (see next section). Clicking on the "?" sign will open a tool tip (left panel, yellow blurb).](fig/Tree_PubChemSearch.png)
+
+The download file contains a number of fields of interest, 
+including: CIDs, names and synonyms, several properties (_e.g._ XlogP), 
+structural information (molecular formula, SMILES, InChI, InChIKey)
+as well as several metadata entries. These relevant ones are explained 
+in the following table: 
+
+| Header | Description | Type |
+|-----------|---------|:----:|
+|annothits| Annotation categories present for this CID | Text |
+|annothitcount | Count of annotation categories for CID | Numeric |
+|cidcdate | CID creation date | YYYYMMDD |
+|sidsrcname | Name of the data source(s) contributing substance | Text |
+|         |  (SID) information for given CID  |   |
+|depcatg | Deposition category, reveals what type of sources | Text |
+|         |  contributed information   |   |
+
+<!-- cid	cmpdname	cmpdsynonym	mw	mf	polararea	complexity	xlogp	heavycnt	hbonddonor	hbondacc	rotbonds	inchi	isosmiles	inchikey	iupacname	meshheadings	annothits	annothitcnt	aids	cidcdate	sidsrcname	depcatg	annotation -->
+
+
 
 ### Interactions via Entrez {#entrez}