I was hoping people with experience of using biomart/intermine/atlas could tell me some of the advantages and disadvantages of the different tools.
I am looking to find a tool that will provide a ready-made interface for browsing the underlying data source and also has tools for inserting/updating data.
I only have experience of biomart and I know there is no api for data inserts/updates. Intermine has java and perl apis but i don't know if there is anything in these for inserts/updates.
What are the major differences between biomart and intermine? When would you use one over the other? Biomart seems the most ubiquitous.
I have come across ATLAS in my searches but it doesn't seem to be in widespread use. Is this correct?
ANother alternative would be to use middleware tools on top of a CHADO database as discussed here. Or to use Djnago with chado
Thanks in advance for your input
I am already biomart rc5 as a virtual mart on top of the a normalised data source and performance is ok. The virtual mart automatically detects inserts/updates. As the answers given suggest, biomart is for read-only data. I was hoping to use a biomart front-end (because people are familiar with it) for a changing dataset. One option is to use a normal database with ORM tools for modifying the data with a virtual mart on top. ANy comments on this approach welcome.