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With the announcement last week that LION is planning to sell off its bioinformatics business including SRS, a lot of labs are or will be looking for new ways to handle biological data integration. For those not familiar with SRS it is software package that parses and indexes the majority of the biological data sources that exist today and allows you to search all of them through a standard interface. It has the ability to use links between data sets to pull lots of disparate pieces of information together in result sets and generally eases a lot of data warehousing problems. SRS is a commercial product but is available for free to Academic institutions and non-profits. So the question I would like to pose to the nodalpoint community is what have you found to work for your data warehousing needs? Read on for more about data integration... There are a few public systems that have surfaced in recent years that do data integration like Atlas, SeqHound, and BioMart but I haven't seen much use of these systems outside of their home labs yet. BioMart has started to be implmented by a few outside groups because of its affiliation with GMOD but its adoption is still in the early phases. Have any users worked with these or any other systems to address their data integration needs? I would be interested in hearing from you if you have. One of the problems I have with these systems is that you are limited to the data sources they choose to integrate. While the data sources they package with them is significant, plugging in my own data sources is something I do fairly often and thus it ranks pretty high on my feature wish list. After quick reads through the docs of Atlas and SeqHound, it appears that integrating your own data source would take a lot of heavy customization to implement (please correct me if I am wrong). BioMart on the other hand does allow you to plug in your own data sources but it requires that the data be "re-formatted" to fit their data model. This isn't necessarily a bad thing but it does increase the data managment burden compared to systems that are able to deal with the data in their native formats. The other possibility these days is to take advantage of web services that are being exposed for bioinformatics like the NCBI's Eutils project. The types of problems you see with this approach include lack of serivces for some data sources, performance when dealing with large data sets, and implementation differences between services. Performance is the major killer for me especially when you are trying to do automated analysis pipelines or anything else that requires the best performance you can get.moving ca movers California
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