One of our key missions is to curate open data sources and provide the back to the world so that the brilliant thought leaders in the industry can use data more effectively and efficiently. This means taking the data in its native format (typically XML, txt, csv, Excel), loading it into our Oracle relational database, standardizing the data to important entities like person, place, organization, drug, disease, and then providing that data for download in a standard text file format.
Since we want other companies to be downloading and using our data, I figured I should go through the process myself and see how long it would take me to download and load some karmadata. I chose one of my favorite datasets, ClinicalTrials.gov, which is published by the National Institutes of Health. I chose ClinicalTrials.gov because it is published in XML with a fairly complex schema and there are plenty of free text fields that make standardization ultra-difficult and important.
We’ve attempted to make getting off the ground with karmadata as quick and easy as possible. Our Toolkit contains all the metadata that you should need, as well as the SQL scripts to load the data (currently complete for Oracle, but will be completed for SQL Server, MySQL, etc. in the near future). The hope was that someone could download the data, load it into a relational database, and answer a hard to answer question in less than a day.
I began by heading to karmadata.com and cruising the available files on the download page. Knowing that I wanted to load ClinicalTrials.gov, I clicked into the Source Files section to view the raw source data, and then to Fact Files sections to check out the standardized records that accompany it. I downloaded all of the available files.
Next I downloaded the files provided in the Toolkit section. I read the readme.doc to take me through the process. I found it to be extremely well written. Whoever authored it must be incredibly brilliant and good looking. I identified the scripts for creating the tables for fact and source data, as well as the external table scripts to load the data into those tables.
Then I got started. I created the tables for loading, unzipped the first period of data, and ran the inserts to load the data. Rather than programmatically unzipping and loading the data, I simply manually unzipped and ran the inserts as I went.
Ten minutes after I read the readme document, I had the entire ClinicalTrials.gov dataset loaded into a relational database, and best of all it was standardized to entities for sponsor organization, clinical sites, clinical investigators, geography, disease, drug, and time.
Now the fun part. The last thing that we provide in the toolkit is a couple of queries to get you started to play around with the data. In this case we ask the question, which are the leading sites in running industry sponsored, neurodegenerative disease trials, from 2009 to 2012? I run the query, and boom, I’m looking at a list that looks like a less attractive version of this data visualization.
Now just to recap what it would take to run that from scratch, you would need to go to ClinicalTrials.gov, download the entire dataset in XML, load the XML into a relational database, standardize the start dates to dates, standardize the many versions of each site name to a standard identifier, then group together all of the MeSH terms that fall under neurodegenerative diseases, and then run a query similar to the one we provided.
These are enormous barriers to entry to a functional, effective way of using the data. But what took us countless hours of development, can take you about 10 minutes. (Or you could just find or create a datacard on karmadata.com in about 10 seconds, but you get the point.)
Using our service was a little surreal for me. I was downloading data that I had downloaded, loaded, and standardized, and then was loading it back into an Oracle database. But it left me wishing that I could just use something like karmadata instead of dealing with all the pains that come with unstandardized data sets. Hopefully it will make you feel the same way.