Various improvements

... as suggested by (and/or discussed with) Evan.

pfas-tree/PFAS_Tree.Rmd

@@ -61,7 +61,7 @@ This document is organised into several sections, as follows:
 |_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 |
-|Implementation | [Go to heading](#impl) | 7 |
+|Further Details | [Go to heading](#details) | 7 |
 |Statements and References | [Go to heading](#statements) | 8 | 
 <!-- |References | [Go to heading](#statements) | 6 |  -->
 
@@ -105,7 +105,7 @@ CF~3~ groups (5.4 M), these were separated into individual sections.
 Note that here, "**PFAS part**" is used to describe a connected portion of 
 the molecule that satisfies the OECD PFAS definition. A given molecule may have
 more than one PFAS parts present, some examples are given in Figure 2,
-along with the count of parts.
+along with the count of parts. For further information, see [Details](#details).
 
 ![Examples of molecules with varying PFAS parts highlighted, drawn using CDK Depict [@mayfield_cdk].](fig/PFAS_parts_CDK.png)
 
@@ -135,8 +135,8 @@ PFAS part_"), if not, a list of the possibilities is given directly
 (Figure 4, middle left, "_Contains isolated unsaturated-cyclic part_").
 
 The "_Contains only isolated CF~2~_" (or, for the CF~3~ node, only isolated 
-CF~3~) node (Figure 4, middle panel) is broken down by the number of 
-isolated groups (CF~2~ or, for the CF~3~ node, by CF~3~ groups). In both
+CF~3~) is broken down by the number of isolated groups (CF~2~ or, 
+for the CF~3~ node, by CF~3~ groups) - see Figure 4, middle panel. In both
 cases the vast majority of molecules have only one isolated group. 
 
 The "_Contains only isolated CF~2~/CF~3~_" is also broken down by
@@ -197,8 +197,9 @@ breakdown by "_Also contains..._".
 ![The "Molecule contains PFAS parts larger than CF~2~/CF~3~" part of the OECD PFAS Definition node, with dynamic breakdown of subnodes by isolated PFAS part type (numbers from 24 March 2022).](fig/OECDPFAS_PFAS_part_type.png)
 
 
-The dynamic design reduces the scrolling among users and also helps reduce
-the load time for large parts of the tree. It is possible to use some 
+The dynamic navigation approach reduces the scrolling by users and 
+also helps reduce the data loading time, when many entries are 
+present within a node. It is possible to use some 
 advanced search and querying capabilities to improve the interaction
 with the tree, see [Navigating the Tree](#search) below. 
 
@@ -206,8 +207,8 @@ The _PFAS Parts Larger than CF~2~/CF~3~_ is available as
 a [MetFrag](https://msbi.ipb-halle.de/MetFrag/) file for further use 
 [@pubchem_pfas_metfrag_2022]. The CSV can be downloaded from Zenodo
 (DOI:[10.5281/zenodo.6385954](https://doi.org/10.5281/zenodo.6385954))
-for use in MetFragCL, it should be available from the MetFragWeb 
-drop down menu soon. See the description on the Zenodo record for 
+for use in MetFragCL and will be made available from the MetFragWeb 
+drop down menu. See the description on the Zenodo record for 
 more details. 
 
 
@@ -224,30 +225,34 @@ Further content still to come ...
 
 ### PFAS and Fluorinated Organic Compound Collections {#lists}
 
-This section of the PFAS tree gathers together content from various
-locations from within PubChem, with the possibility to add some 
-external content. The mapping files to construct this are kept 
+This section of the PFAS tree contains various lists gathered 
+across PubChem content. Additional community-based PFAS lists may 
+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:
 
-- all [PFAS lists](https://comptox.epa.gov/dashboard/chemical-lists?filtered=&search=PFAS) 
+- All [PFAS lists](https://comptox.epa.gov/dashboard/chemical-lists?filtered=&search=PFAS) 
 from the 
 [CompTox Chemicals Dashboard](https://comptox.epa.gov/dashboard/)
-[@williams_comptox_2017];
-- all [PFAS lists](https://zenodo.org/communities/norman-sle/search?page=1&size=20&q=PFAS) 
+[@williams_comptox_2017] via the 
+[EPA DSSTox Tree](https://pubchem.ncbi.nlm.nih.gov/classification/#hid=105) 
+in PubChem;
+- All [PFAS lists](https://zenodo.org/communities/norman-sle/search?page=1&size=20&q=PFAS) 
 from the NORMAN Suspect List Exchange 
-([NORMAN-SLE](https://www.norman-network.com/nds/SLE/))
-- the CORE PFAS lists from OntoChem [@barnabas_extracting_2022]
+([NORMAN-SLE](https://www.norman-network.com/nds/SLE/)) via the 
+[NORMAN-SLE Tree](https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101) 
+in PubChem;
+- The CORE PFAS lists from OntoChem [@barnabas_extracting_2022];
 - Other collections from within PubChem Classification Trees, including
 [Cameo](https://pubchem.ncbi.nlm.nih.gov/classification/#hid=86),
 [ChEBI](https://pubchem.ncbi.nlm.nih.gov/classification/#hid=2) and
-[MeSH](https://pubchem.ncbi.nlm.nih.gov/classification/#hid=1)
+[MeSH](https://pubchem.ncbi.nlm.nih.gov/classification/#hid=1).
 
 
 
-![The "PFAS and Fluorinated Organic Compound Collections" node, with all major collections shown (status 24 March 2022).](fig/PFAS_list_of_lists.png)
+![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}
 
@@ -335,12 +340,17 @@ write.csv(PFAS_tree, file="PubChem_PFAS_Tree_Details.csv",row.names = F)
 
 
 
-## Implementation {#impl}
+## Further Details {#details}
 
 Content still to come ... 
 
 - test set
 - notes on implementation
+- Exclude molecules from consideration if:
+  - Is a mixture (i.e., has multiple components, which includes any salts)
+  - Contains a radical or isotopically labelled atom
+  - [molecules with non-organic elements not currently being removed]
+