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Vemonet (vemonet)
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User Since
Oct 26 2018, 11:57 AM (108 w, 6 d)
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Recent Activity

Oct 29 2018

Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

Simple (and dirty) Python scripts to get data out of PubChem turtle files (here InChIKey id, but could be done with other informations)

Oct 29 2018, 9:38 AM · Wiki-Techstorm-2019, Wikidata, patch-welcome

Oct 27 2018

Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

Get the RDF description of a compound

curl -L -H "Accept: text/rdf" -o CID2244.rdf http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID2244
Oct 27 2018, 10:51 AM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

ftp://ftp.ncbi.nlm.nih.gov/pubchem/RDF/descriptor/compound/
Getting DefinedAtomStereoCount

Oct 27 2018, 9:37 AM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

Getting triples linked to a PubMed CID: https://pubchem.ncbi.nlm.nih.gov/rest/rdf/compound/CID2110.html

Oct 27 2018, 9:27 AM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

Informations about the different directories content: ftp://ftp.ncbi.nlm.nih.gov/pubchem/RDF/README

Oct 27 2018, 8:56 AM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

Cannot find the entry for https://pubchem.ncbi.nlm.nih.gov/compound/134797139 in Wikidata (at least not with the PubChem CID, so PubChem data for this entry (and other entries) might be missing

Oct 27 2018, 8:37 AM · Wiki-Techstorm-2019, Wikidata, patch-welcome

Oct 26 2018

Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

Apparently all PubChem hasn't been totally uploaded to WikiData:

Oct 26 2018, 4:01 PM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

Drug drug interactions

Oct 26 2018, 3:54 PM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

Apparently most of PubChem is already uploaded to WikiData
But we could still do an exhaustive comparison to check for part that have not been converted

Oct 26 2018, 3:27 PM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

https://pubchem.ncbi.nlm.nih.gov/rest/rdf/descriptor/CID131475303_Exact_Mass.html

Oct 26 2018, 2:29 PM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

Getting informations about PubChem RDF: https://pubchemdocs.ncbi.nlm.nih.gov/rdf

Oct 26 2018, 2:08 PM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.
Oct 26 2018, 1:48 PM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

PubChem is open, but I don't know what is inside
https://pubchemdocs.ncbi.nlm.nih.gov/downloads

Oct 26 2018, 12:38 PM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a comment to T208036: Scrape chemical names and data for WikiData from chemical databases.

FYI: there is an API to query ChemSpider https://developer.rsc.org/ but it is limited to 1000 calls a month

Oct 26 2018, 12:32 PM · Wiki-Techstorm-2019, Wikidata, patch-welcome
Vemonet added a member for Wikistorm-2018: Vemonet.
Oct 26 2018, 11:59 AM
Vemonet added a watcher for Wikistorm-2018: Vemonet.
Oct 26 2018, 11:58 AM