My short term goal in a project is to build a local database of the NCBI dbSNP database. The data and schema are available on the FTP site(). I was going to implement the database using MySQL, but I just learnt about MongoDB. Is it possible to somehow convert the sql schema code to mongoDB architecture? Also, are there any real advantages to implementing the dbSNP database as MongoDB?
I've played with mongoDb. It is a nearly schemaless data store - each record (analogous to a row) can have nearly any entry name set except for a unique ID that mongoDb uses. In practice most of your records will have the same labels and names
Leaving SQL for noSQL is turning out not to be a great win. MongoDB will excel in retrieving records quickly and processing records by their content. It has some constraints too compared to SQL. It requires that the main index be stored in RAM, which might or not be an issue. For very large datasets mongoDB can be configured to shard the data automatically - splitting it up over a cluster of machines for high throughput fast processing applications.
If you need flexibility in your data record and you have a good machine (or a good cluster) to put it up on it could offer some advantages. We have a reasonable store of dbSNP on a recent MySQL machine and it performs okay. Not thousands of transactions a second, but we can do reasonable throughput of record processing.