Commit 1b56852f authored by Emma Schymanski's avatar Emma Schymanski
Browse files

updated pfas docs

parent ac456eca
......@@ -53,13 +53,13 @@ This document is organised as follows:
|-----------|---------|:----:|
|PubChem PFAS Tree Nodes | [Go to heading](#treenodes) | 2 |
|_OECD PFAS Definition_ | [Go to heading](#oecddef) | 2 |
|_Organofluorine Compounds_ | [Go to heading](#orgf) | 4 |
|_PFAS and Fluorinated Organic Compound Collections_ | [Go to heading](#lists) | 4 |
|Searching the Tree | [Go to heading](#search) | 4 |
|_Search via PubChem Search_ | [Go to heading](#pc-search) | 4 |
|_Interactions via Entrez_ | [Go to heading](#entrez) | 5 |
|Implementation | [Go to heading](#impl) | 5 |
|Statements and References | [Go to heading](#statements) | 5 |
|_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) | 5 |
|_Search via PubChem Search_ | [Go to heading](#pc-search) | 5 |
|_Interactions via Entrez_ | [Go to heading](#entrez) | 6 |
|Implementation | [Go to heading](#impl) | 6 |
|Statements and References | [Go to heading](#statements) | 6 |
## PubChem PFAS Tree Nodes {#treenodes}
......@@ -68,6 +68,8 @@ The tree is currently split into three main nodes that are constructed and
compiled separately. More nodes are under development and will be released
as they are ready.
Further details are given in the sections below.
To become more familiar with the PubChem Classification Browser features,
see Section [Navigating the Tree](#search).
### OECD PFAS Definition {#oecddef}
......@@ -181,18 +183,41 @@ breakdown by "_Also contains..._".
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.
with the tree, see [Navigating the Tree](#search) below.
The **PFAS Parts Larger than CF~2~/CF~3~** will soon be available as
a [MetFrag](https://msbi.ipb-halle.de/MetFrag/) file for further interactions.
### Organofluorine Compounds {#orgf}
Content still to come ...
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 ...
### PFAS and Fluorinated Organic Compound Collections {#lists}
Content still to come ...
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
on the [eci/pubchem](https://gitlab.lcsb.uni.lu/eci/pubchem/)
repository on GitLab.
More content to come including:
- CompTox
- SLE
- OntoChem
- Other PubChem collecitons
## Searching the Tree {#search}
![The "PFAS and Fluorinated Organic Compound Collections" node, with all major collections shown (status 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
......@@ -206,12 +231,18 @@ Content still to come ...
Content still to come ...
### Interactions via PUG REST {#pugrest}
Content still to come ...
## Implementation {#impl}
Content still to come ...
- test set
- notes on implementation
- MetFrag files
......
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