Data extraction is a piece of a larger puzzle called data integration (getting the data you want to a single place, from different systems, the way you want it), which people have been working on since the early 1980s.

greater integration of data, data security, and data sharing through the establishment of a searchable database.

I'll give a little bit of the history to provide context. My own involvement in this started around 2008 after we had shipped our key-value store. My next project was to try to get a working Hadoop setup going, and move some of our recommendation processes there. Having little experience in this area, we naturally budgeted a few weeks for getting data in and out, and the rest of our time for implementing fancy prediction algorithms. So began a long slog. We originally planned to just scrape the data out of our existing Oracle data warehouse. The first discovery was that getting data out of Oracle quickly is something of a dark art. Worse, the data warehouse processing was not appropriate for the production batch processing we planned for Hadoop—much of the processing was non-reversable and specific to the reporting being done. We ended up avoiding the data warehouse and going directly to source databases and log files. Finally, we implemented another pipeline to load data into our key-value store for serving results. This mundane data copying ended up being one of the dominate items for the original development. Worse, any time there was a problem in any of the pipelines, the Hadoop system was largely useless—running fancy algorithms on bad data just produces more bad data. Although we had built things in a fairly generic way, each new data source required custom configuration to set up. It also proved to be the source of a huge number of errors and failures. The site features we had implemented on Hadoop became popular and we found ourselves with a long list of interested engineers. Each user had a list of systems they wanted integration with and a long list of new data feeds they wanted. ETL in Ancient Greece. Not much has changed.

Effective use of data follows a kind of Maslow's hierarchy of needs. The base of the pyramid involves capturing all the relevant data, being able to put it together in an applicable processing environment (be that a fancy real-time query system or just text files and python scripts). This data needs to be modeled in a uniform way to make it easy to read and process. Once these basic needs of capturing data in a uniform way are taken care of it is reasonable to work on infrastructure to process this data in various ways—MapReduce, real-time query systems, etc. It's worth noting the obvious: without a reliable and complete data flow, a Hadoop cluster is little more than a very expensive and difficult to assemble space heater. Once data and processing are available, one can move concern on to more refined problems of good data models and consistent well understood semantics. Finally, concentration can shift to more sophisticated processing—better visualization, reporting, and algorithmic processing and prediction. In my experience, most organizations have huge holes in the base of this pyramid—they lack reliable complete data flow—but want to jump directly to advanced data modeling techniques. This is completely backwards. So the question is, how can we build reliable data flow throughout all the data systems in an organization?

Data integration is making all the data an organization has available in all its services and systems.

First, the domain is a poor candidate because the domain of all entities relevant to neurobiological function is extremely large, highly fragmented into separate subdisciplines, and riddled with lack of consensus (Shirky, 2005).