ChEMBL Resources

Resources:
ChEMBL
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SureChEMBL
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ChEMBL-NTD
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ChEMBL-Malaria
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The SARfaris: GPCR, Kinase, ADME
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UniChem
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DrugEBIlity
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ECBD

Sunday, 13 November 2011

Recommendations for a MySQL Chemical Data Cartridge?


What options are there for a MySQL Chemical Structure Cartridge ? - the constraints are that the license needs to be Open (to commercial and non-commercial users). Post away in the comments, then everyone can see the answers.

Update: for a little background on our specific interests - we wish to build a deployable and distributable version (a package or vm) with a preconfigured and loaded current ChEMBL database, capable of performing full chemical search capability. Deployment could be as a Linux style package, or as an Amazon EC2 instance. Our internal systems here at the EBI are based on Oracle, and the MDL (or whatever the current name is :) ) Direct cartridge - this configuration is sometimes beyond the reach of many budgets, and so we are interested in exploring a 'free' but useful version of ChEMBL.

Update 2: So Postgres opens up quite a few more options....

5 comments:

Egon Willighagen said...

There is MyChem:

http://mychem.sourceforge.net/

MyChem is developed by Jerome Pansanel, and with OrChem (Mark + Christoph, EBI) part of the ChemiSQL project, that aim at creating a unified API independent of the actual database platform.

Chris said...

Might be worth looking at Bingo

http://ggasoftware.com/opensource/bingo

fredrik said...

I believe Bingo doesn't support MySQL, only Oracle, MS SQL, and postgreSQL.

jpo said...

I was mailed about MolCart which is a MySQL chemical data cartridge - more details here http://www.molsoft.com/molcart.html

(however, the license looks an issue here, maybe)

greg landrum said...

If you're willing to support postgresql (another popular and powerful open-source database), then another couple options become available: bingo (already mentioned above), and the rdkit (http://www.rdkit.org).

Both support substructure and similarity searching and are actively maintained.