Question: How To Download Kegg Drug Database
3
gravatar for AP
7.1 years ago by
AP60
AP60 wrote:

Anyone has an idea how do i download the KEGG drug database. i found the ftp folders which had a just few data for the drugs. Am looking for Mysql database for this database.

Thanks

kegg • 8.6k views
ADD COMMENTlink written 7.1 years ago by AP60
5
gravatar for Damian Kao
7.1 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

You can't anymore. At least not for free. Here is an excerpt from their site:

Starting on July 1, 2011 the KEGG FTP site for academic users will be transferred from GenomeNet at Kyoto University to NPO Bioinformatics Japan, and it will be available only to paid subscribers. The publicly funded portion, the medicus directory, will continue to be freely accessible at GenomeNet. The KEGG FTP site for commercial customers managed by Pathway Solutions will remain unchanged. The new FTP site is available for free trial until the end of June.

You can still use their web service. But without resorting to screen scraping or using older versions that you've downloaded previously you can't get a copy of their flatfiles or database.

*edit As cowsandmilk pointed out below, the Drug database is still available for free.

ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by Damian Kao15k
3
gravatar for cowsandmilk
7.1 years ago by
cowsandmilk30
cowsandmilk30 wrote:

I'm going to have to disagree with the people here saying you can't get KEGG DRUG.

As specified in the announcement of part of KEGG becoming non free, the medicus directory remains freely available (for now). As seen at http://www.genome.jp/kegg/download/Readme/README.medicus , KEGG DRUG resides within medicus. I just tested it and was able to access the files listed there without any type of subscription. You can't dig into the linked pathways, since those are not free, but if what you want is KEGG DRUG, it is there and it is free.

Steps:

  1. Get an ftp client
  2. Go to ftp://ftp.genome.jp/pub/kegg/medicus/
  3. Go into the drug directory
  4. Download the file called drug, that is the database in DBGET format. You can write your own scripts to turn it into a database.

The file drug_update.lst is shown as the database having been updated as late as June 29, 2012

ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by cowsandmilk30

Interesting. I think many people -- including myself -- do not make the distinction between KEGG's various components. Let's hope that KEGG MEDICUS funding will be renewed after the three years (two years still to go) and that it does not share the same fate as the remainder of KEGG.

ADD REPLYlink written 7.1 years ago by Joachim2.8k

Thanks for the info. I would like to know is it possible to retireve the information from the KEGG drug database? ie am planning to develop the web application which would look up for the drug names in a article and the drug names detailed information should be linked to the kegg drug database. how would i retrieve the information for that particular drug.

will the fetching the data using URL GET/POST will do?? any other possibilities??

ADD REPLYlink written 7.1 years ago by AP60
1
gravatar for Egon Willighagen
7.1 years ago by
Maastricht
Egon Willighagen5.2k wrote:

You can download a snapshot of KEGG of about a year ago via various Semantic Web websites... for example, you can retrieve it from this Bio2RDF SPARQL end point. You will have to learn a bit of SPARQL, but a

select * where {?s ?p ?o }

query will return all triples.

But as other said, there are plenty of Open alternatives, including WikiPathways.

ADD COMMENTlink written 7.1 years ago by Egon Willighagen5.2k
0
gravatar for AP
7.1 years ago by
AP60
AP60 wrote:

Thank you for that info. Am actually trying to make an application which needs the data present in the database of KEGG, other than downloading or making a new database. how else can i retrive the info and link it to an xml code.

ADD COMMENTlink written 7.1 years ago by AP60

Please use the "comment" function to comment on answers, rather than writing up your response as another answer. People will spot your response easier then and you are not in danger of getting down voted.

ADD REPLYlink written 7.1 years ago by Joachim2.8k
0
gravatar for Joachim
7.1 years ago by
Joachim2.8k
San Francisco, California
Joachim2.8k wrote:

Hi!

As Dk pointed out, KEGG is not available for free anymore.

However, you may find similar information in the publicly available Reactome pathway database ( http://www.reactome.org/ReactomeGWT/entrypoint.html ). Reactome incorporates KEGG Compound and ChEBI. The latter includes drug entries, but I am not sure if they will suffice your needs.

There are also other alternative than the pathway related KEGG and Reactome databases. Perhaps you are interested in DrugBank ( http://www.drugbank.ca ) or any of the other choices listed at http://www.hmdb.ca/databases.

Hope this helps,

Joachim

ADD COMMENTlink written 7.1 years ago by Joachim2.8k

Or WikiPathways, for that matter...

ADD REPLYlink written 7.1 years ago by Egon Willighagen5.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1613 users visited in the last hour