Commit 34a0b269 authored by Emma Schymanski's avatar Emma Schymanski
Browse files

updated PubChem search

...to show download file and explain annotation content
parent 7a2e7e92
pfas-tree/.Rhistory
pfas-tree/fig/~$Figure_workup.pptx
......@@ -81,10 +81,10 @@ There is also extensive documentation on the PubChem website, see:
|_PFAS and Fluorinated Organic Compound Collections_ | [Go to heading](#lists) | 5 |
|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 |
|_Interactions via Entrez_ | [Go to heading](#entrez) | 9 |
|_Interactions via PUG REST_ | [Go to heading](#pugrest) | 9 |
|Further Details | [Go to heading](#details) | 10 |
|Statements and References | [Go to heading](#statements) | 10 |
<!-- |References | [Go to heading](#statements) | 6 | -->
......@@ -345,7 +345,7 @@ structural information (molecular formula, SMILES, InChI, InChIKey)
as well as several metadata entries. The relevant metadata fields
of interest to indicate the amount of information available
to support the structures in the tree are explained
in the following table:
in the following table; a preview is shown in Figure 10.
Table: Relevant metadata files in the PubChem Download files
......@@ -361,7 +361,31 @@ Table: Relevant metadata files in the PubChem Download files
<!-- cid cmpdname cmpdsynonym mw mf polararea complexity xlogp heavycnt hbonddonor hbondacc rotbonds inchi isosmiles inchikey iupacname meshheadings annothits annothitcnt aids cidcdate sidsrcname depcatg annotation -->
![PubChem Download file. Top left: CID, names, properties. Middle: structural information and metadata. Bottom: selected metadata with expanded view to show the information content of records. Downloaded from the query shown in Figure 9.](fig/PubChem_Download_File.png)
Note that the categories visible in the "_annothits_" column align
with the individual sections in PubChem records and can
also be viewed in the
[PubChem Table of Contents (TOC) Tree](https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72).
This also means that for every entry with any annotation, the information
available can be viewed for that individual CID.
For example, the annotation information for
CID [105447](https://pubchem.ncbi.nlm.nih.gov/compound/105447)
in Figure 10 can be viewed with the following hyperlinks:
- https://pubchem.ncbi.nlm.nih.gov/compound/105447#section=Classification
- https://pubchem.ncbi.nlm.nih.gov/compound/105447#section=Names-and-Identifiers
- https://pubchem.ncbi.nlm.nih.gov/compound/105447#section=Patents
- https://pubchem.ncbi.nlm.nih.gov/compound/105447#section=Safety-and-Hazards
- https://pubchem.ncbi.nlm.nih.gov/compound/105447#section=Use-and-Manufacturing
As visible in the figure, there are many records where the information
has only been extracted from patents, or for which no annotation exists.
Thus, this metadata can help add a lot of context to the relevance of the
entries for the particular question at hand.
More advanced queries are possible to leverage this information even further,
as explained in the next section.
### Interactions via Entrez {#entrez}
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