Commit ac456eca authored by Emma Schymanski's avatar Emma Schymanski
Browse files

updated docs

Up to Organofluorine
parent 815cef5e
......@@ -109,7 +109,7 @@ molecules in PubChem containing at least one isolated CF~2~ part (top subnode)
or one isolated CF~3~ (next subnode). These are broken down similarly,
as shown in Figure 4 for the CF~2~ case.
![The isolated CF~2~ section of the OECD PFAS Definition node, with breakdown of the major parts (numbers from 24 March 2022)](fig/OECDPFAS_CF2combi.png)
![The isolated CF~2~ section of the OECD PFAS Definition node, with breakdown of the major parts (numbers from 24 March 2022).](fig/OECDPFAS_CF2combi.png)
The larger PFAS parts (left) are broken down by part type (linear, branched,
_etc._). Within these subcategories, dynamic construction is used.
......@@ -131,9 +131,57 @@ the number of groups, sorted by increasing number of CF~2~ groups
### PFAS Parts Larger than CF~2~/CF~3~
This is the section for larger PFAS parts ...
![The OECD PFAS Definition part of the tree, with top two subnodes (numbers from 24 March 2022)](fig/OECDPFAS_largerPFASparts.png)
The "_Molecule contains PFAS parts larger than CF~2~/CF~3~_" part of the
OECD PFAS node includes approx. 188K molecules, which can be browsed
in two major breakdowns, by isolated PFAS part count (see Figure 5)
and by isolated PFAS part type (see Figure 6).
This part of the tree is constructed dynamically - in other words,
the subnodes present depend on the contents within - to prevent
excessive scrolling. The breakdown by _isolated PFAS part count_ is first
subset by the number of parts (Figure 5, left panel).
Should there be fewer than ~20 categories,
the immediate breakdown is by the formula of the parts (see
Figure 5, bottom right, "_Contains 11 isolated PFAS parts_").
Should there be more than 20 entries, an extra layer is added,
to sort by the type of PFAS part (see Figure 5, top right).
For categories with very large numbers of entries, an additional
initial breakdown by the count of molecules is added (Figure 5,
middle panel). This is again broken down dynamically. If only a
few subcategories exist, these are presented immediately thereafter
(see Figure 5, bottom middle - several linear categories with many
molecules). If, however, more breakdown is needed, an additional
set of part type nodes is added (Figure 5, middle panel, "_Count
of molecules 00001-10_") before the formula breakdown.
Note that throughout the tree, leading zeros are present to
ensure logical sorting.
![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 count (numbers from 24 March 2022).](fig/OECDPFAS_largerPFASparts.png)
The breakdown by _isolated PFAS part type_ is first broken down by the
part type (linear, cyclic, _etc._) (Figure 6, left panel). These are
again split dynamically. With fewer than 20 entries, the list split
according to PFAS part formulas appears. If a greater breakdown is needed,
an extra layer of "_Also contains ..._" or "_Only contains ..._" is
added for extra navigation (Figure 6, top left, "_Contains isolated
branched PFAS part_"). For entries containing many CIDs, a breakdown
by count of molecules is added (Figure 6, mid left, "_Contains isolated
linear PFAS part_"). Generally, the linear entries contain more entries
than the other PFAS part types - and thus tend to have greater breakdown.
Some of these are broken down further (Figure 6, right), such that
a breakdown by the count of PFAS parts is added before the
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
advanced search and querying capabilities to improve the interaction
with the tree, see [Searching the Tree](#search) below.
### Organofluorine Compounds {#orgf}
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