Commit 815cef5e authored by Emma Schymanski's avatar Emma Schymanski
Browse files

added prod URL

... now that the tree is public - plus other minor tweaks
parent b76d9ed2
......@@ -29,8 +29,9 @@ EEB: ORCID [0000-0002-5959-6190](http://orcid.org/0000-0002-5959-6190)
## Preamble
This document describes the "PFAS and Fluorinated Organic Compounds in
PubChem Tree" (see Figure 1) on the
This document describes the "[PFAS and Fluorinated Organic Compounds in
PubChem Tree](https://pubchem.ncbi.nlm.nih.gov/classification/#hid=120)"
(see Figure 1) on the
[Classification Brower](https://pubchem.ncbi.nlm.nih.gov/classification/)
in [PubChem](https://pubchem.ncbi.nlm.nih.gov/) [@kim_pubchem_2021],
developed in collaboration with the
......@@ -38,9 +39,10 @@ Environmental Cheminformatics group
([ECI](https://wwwen.uni.lu/lcsb/research/environmental_cheminformatics))
at the [LCSB](https://wwwen.uni.lu/lcsb/),
[University of Luxembourg](https://wwwen.uni.lu/) in consultation with
several community representatives (see Acknowledgements).
several community representatives (see [Contributions](#contrib)
and [Acknowledgements](#ack)).
![The "[PFAS and Fluorinated Organic Compounds in PubChem Tree](https://testpubchem.ncbi.nlm.nih.gov/classification/#hid=127)" Landing Page.](fig/PFAS_Tree_Landing.png)
![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
......@@ -51,13 +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) | ... |
|_PFAS and Fluorinated Organic Compound Collections_ | [Go to heading](#lists) | ... |
|Searching the Tree | [Go to heading](#search) | ... |
|_Search via PubChem Search_ | [Go to heading](#pc-search) | ... |
|_Interactions via Entrez_ | [Go to heading](#entrez) | ... |
|Implementation | [Go to heading](#impl) | ... |
|Statements and References | [Go to heading](#statements) | ... |
|_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 |
## PubChem PFAS Tree Nodes {#treenodes}
......@@ -100,7 +102,7 @@ with the top two level subnodes, is shown in Figure 3.
#### Isolated CF~2~ and CF~3~ Nodes
#### Isolated CF~2~ and CF~3~ Nodes:
The top two subnodes of the OECD PFAS Definition allows the browsing of all PFAS
molecules in PubChem containing at least one isolated CF~2~ part (top subnode)
......@@ -174,15 +176,11 @@ Content still to come ...
### Author Contributions {#contrib}
<!-- https://authorservices.wiley.com/author-resources/Journal-Authors/open-access/credit.html -->
ELS: Conceptualization (equal), data curation, methodology, software, validation, writing - original draft preparation, writing - review and editing.
PC: Validation (supporting)
PAT: Data curation, methodology, software
JZ: Data curation, methodology, software
EEB: Conceptualization (equal), data curation, methodology, software (lead), validation, writing - original draft preparation, writing - review and editing.
- ELS: Conceptualization (equal), data curation, methodology, software, validation, writing - original draft preparation, writing - review and editing.
- PC: Validation (supporting)
- PAT: Data curation, methodology, software
- JZ: Data curation, methodology, software
- EEB: Conceptualization (equal), data curation, methodology, software (lead), validation, writing - original draft preparation, writing - review and editing.
### Acknowledgements {#ack}
......@@ -193,7 +191,7 @@ as well as other project members of [ZeroPM](https://zeropm.eu/).
We would also like to acknowledge discussions and contributions from
various members of the ECI and PubChem teams that were not directly
involved in these efforts but have likely contributed indirectly
involved in these efforts but have contributed indirectly
through our many other collaborative efforts!
### References {#ref}
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