No longer able to download PubChem RDF files from NCBI ftp site.

Question

[randykerber]

About a month ago I was able to download PubChem RDF files from the ncbi ftp site. Now I am unable to do so. Also tried a week ago without success. Here's the ftp folder:
ftp://ftp.ncbi.nlm.nih.gov/pubchem/RDF/

Even if I copy-and-paste a command straight from the pubchem website, that no longer works. The commands are from the "PubChemRDF Use Cases" section of the following page:
https://pubchem.ncbi.nlm.nih.gov/rdf/#_Toc421254667

For example, the following command typed into a linux shell should download the pubchem gene data (one relatively small file):

wget -r -A ttl.gz -nH --cut-dirs=2 ftp://ftp.ncbi.nlm.nih.gov/pubchem/RDF/gene

It looks like a new version of pubchem files was put in place on March 25. So perhaps something was changed then.

Just going in with command-line ftp I can navigate through the directory structure. I'm able to download a file from a neighboring directory, but not under the pubchem/RDF directory. Depending on what method I use, I get error messages like "permission denied" or "no such file".

Anyone know what's wrong, what has changed?

Thanks,
- Randy
Data2Discovery www.d2discovery.com)

Answer 1

[GenoMax]

I think the simple explanation here may be that the read permissions on these files were not correctly set when some automated process refreshed the files. If it is any consolation none of the other files in other directories under "RDF" work either. You may want to send a ticket in to NCBI.

[randykerber]

Thanks for the quick response.

Bad "read permissions" were my initial guess, though the file permissions and ownership settings looked exactly the same as for files that would load.

I wasn't finding a forum or any place to ask questions or report issues. But I went back to the site and tried again, and this time I eventually found a link to the help desk at the bottom of the page. As I report below, that worked.

Answer 2

[natasha.sernova]

A lot of things have changed in NCBI recently. Probably this site also has changed.

http://pubchem.ncbi.nlm.nih.gov/

http://pubchem.ncbi.nlm.nih.gov/rdf/

ftp://ftp.ncbi.nlm.nih.gov/pubchem/RDF/ - this link works

It sends me to

ftp://ftp.ncbi.nlm.nih.gov/pubchem/RDF/gene/, where there is a single file:

Файл:pc_gene.ttl.gz from 25.03.16

By the way, the name of the file is not ttl.gz, but pc_gene.ttl.gz,

so "no such file" is not a strange statement, the file has another name now.

I've come there in Windows, the system asked me if I would like to save the file or not.

I've opened it in Windows. I have pc_gene.ttl without any problems.

I did not need any special permission. This file has not been updated since 25th of March,

but this is another question - if there is a new version somewhere.

I have not done it in comand line, this is the only difference.

I will try to repeat it in Linux a little bit later.

Answer 3

[randykerber]

The PubChem ftp site for RDF files has been fixed.

I don't know who fixed it, or what they did, but the same commands that weren't working before now work.

I found a link to contact the "Help Desk". From the PubChem site, click the "Help" tab, then scroll way down to the bottom. On the right is the following link to submit a question:
Write to the Help Desk

A short while later I got an email back from the help desk, saying that they had confirmed there was an issue and they have alerted the PubChem group. A couple of hours later I tried again, and the entire download script worked perfectly.