Commit ab7e4e8d authored by Emma Schymanski's avatar Emma Schymanski
Browse files

testing pathway file

now with a trim and non-trim version (with pathway codes)
parent 8fad12f0
......@@ -100,15 +100,16 @@ that are relevant, it is possible to download these directly
(you can also just directly download from the PubChem pages and save them):
```{r download chemicals}
#url_path <- "https://pubchem.ncbi.nlm.nih.gov/assay/pcget.cgi?task=pathway_chemical&taxid=6239&start=1&limit=10000000&download=true&downloadfilename=TaxID_6239_pcget_pathway_chemical"
url_path <- "https://pubchem.ncbi.nlm.nih.gov/assay/pcget.cgi?task=pathway_chemical&taxid=6239&start=1&limit=10000000&download=true&downloadfilename=TaxID_6239_pcget_pathway_chemical"
# temporary fix, download an archived version
url_path <- "https://gitlab.lcsb.uni.lu/eci/pubchem-docs/-/raw/main/taxonomy/TaxID_6239_pcget_pathway_chemical.csv"
url_path2 <- "https://gitlab.lcsb.uni.lu/eci/pubchem-docs/-/raw/main/taxonomy/TaxID_6239_pcget_pathway_chemical_trim.csv"
url_wormjam <- "https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?infmt=json&outfmt=csv&query={%22download%22:%22*%22,%22collection%22:%22norman_wormjam%22,%22where%22:{%22ands%22:[{%22taxid%22:%226239%22}]},%22order%22:[%22relevancescore,desc%22],%22start%22:1,%22limit%22:10000000,%22downloadfilename%22:%22TaxID_6239_norman_wormjam%22}"
url_lotus <- "https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?infmt=json&outfmt=csv&query={%22download%22:%22*%22,%22collection%22:%22lotus%22,%22where%22:{%22ands%22:[{%22taxid%22:%226239%22}]},%22order%22:[%22relevancescore,desc%22],%22start%22:1,%22limit%22:10000000,%22downloadfilename%22:%22TaxID_6239_lotus%22}"
download.file(url_path, "TaxID_6239_pcget_pathway_chemical.csv")
download.file(url_path2, "TaxID_6239_pcget_pathway_chemical_trim.csv")
download.file(url_wormjam, "TaxID_6239_eci_wormjam.csv")
download.file(url_lotus, "TaxID_6239_lotus.csv")
```
......
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