Hello to everybody,
i hope this is the right forum to ask this question.
I want to download the pubchem substance database and put all informations into an mysql database. Is this possible and if how?
Second question is then: Is there an script which automatically update the database?
I didn't found anything about this question.
With best regards, Jochen Schreiber
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Jochen Schreiber •
There is a XML schema (XSD) for the XML files of pubchem; ftp://ftp.ncbi.nih.gov/pubchem/specifications/pug.xsd
you could generate the tables and import the data with a "XSD to SQL" converter. see http://stackoverflow.com/questions/138575/how-can-i-create-database-tables-from-xsd-files
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Pierre Lindenbaum
I want to download SDF files for a list (.xl) of compounds automatically !! is there any python or R script?
The question is of course why you'd want to do that. As mentioned in your own question, updates are a constant hassle.
There are a couple of interfaces available hiding the complexities of the PUG and EUtils gateways into PubChem, so you can work locally with the current PubChem data as if it were a regular file or local database. That is much more convenient (I am guessing that your queries are not top secret...)
Could you provide some additional information and links to some of these interfaces you mention?
I havejust sent an email with a PowerPoint presentation
But the email address in your profile at genome.wustl.edu bouces. How can I reach you?
You an download all the SDF files for the latest PubChem Substance release using any FTP client from
ftp://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/
Then you can using ChemAxon's JChem manager to simply import all the SDFs into a MySQL database.
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Yogesh Pandit •
There is only one way to import large amounts of data into a standard database (i.e. MySQL, PostgreSQL, etc.):
LOAD DATA LOCAL INFILE ... command (or equivalent) to load those files into the databaseIf your data comes as XML (:o), you have to process that data using an XML library like lxml in Python, and create CSV files that contain all the information that you need. "XSD to SQL" converters don't work with complex schema that most XML files contain, and XML databases (e.g. BaseX, eXist) are immature and have limits on the size of the files that you can import.
The same applies to SDF files.
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