Archives For clinical trials

If you are involved in the study start up process, you know how important it is to have the best investigators.  Having the best investigators allows you to be successful in enrolling patients.  Many have their own investigator database, but when there is difficulty, they usually resort to PubMed, registries, and other data.  This data is difficult to navigate and becomes a time suck.

Indicate Investigators has all the data available, but organizes it in a way that is easy to navigate and will save you time.

Below is the launch page to search by Drug/Drug Class OR Disease.  We curate all publicly available sources that have data on investigators, mining the data from its native html, text or XML, and loading into structured, linked data on each Investigator. We know what trials they participated in, how many trials, and how frequently they work within specific disease indications.

II Blog3

Once you decide what to search for, you will be directed to the results page of all investigators involved in that indication. Continue Reading…

Advertisements

Sponsor Finder is a tool created to allow our users to search and identify sales opportunities at trial sponsors.  Pinpointing opportunities at the right moment can be difficult because once the trial is announced, it is likely that everyone to work with is already lined up.  You can utilize the filters in Sponsor Finder, avoid this problem and stay ahead of the curve.  

One search that is popular among current users, is to look for organizations that have trials completing in the next 6 months.

karmadata___Sponsor_Finder

I will throw out a specific example: “I am on a team with phase 3, breast cancer trial experience…How do I search?”  You would plug the following into Sponsor Finder: phase 1/2 and 2, active, breast cancer trials, that are completing in the next 180 days.  Continue Reading…

Today, we take the time to thank and support all clinical research professionals on International Clinical Trials’ Day.  Many would think that this day was just picked by some organization to celebrate the success of clinical trials throughout the years.  But, in fact May 20th is the date when James Lind started his famous trial on how to treat scurvy.  We have come a long way since having a clinical trial to treat scurvy. Lind paved the way for clinical discovery and finding new means of treatment.

One of the main obstacles with clinical trials today is recruitment.  Organizations are having a difficult time getting the bodies they need for the trials they are conducting. Continue Reading…

karmadata enables users to visualize and simply query the world’s healthcare data.  So why can’t the excel download sheets be simple to navigate as well?  Now they are!  The format of the existing download has greatly improved.  We have cleared away unnecessary columns and provide only the information that is important to you.  We have organized the columns and also added a different tab for clinical trials.  Now the user is able to toggle back and forth between a tab for clinical trials, and a tab for sponsors.

excel downloadThis download is clean, simple, and user friendly.  Feel free to jump up and down (like we did) when you realize how painless this excel sheet is to navigate through.

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.

Image

You could download ClinicalTrials.gov from karmadata, or you could just create this data visualization on karmadata

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.

Disruptive Innovations to Advance Clinical Trials, Envizualized

Conference illustration by Jonny Goldstein of Envizualize

Sean and I recently attended the 2nd Annual Disruptive Innovations to Advance Clinical Trials for Pharma, Biologics, & Devices (DPharm) in Boston. We had a really great time and learned a ton.

Here are a few themes that really stood out for me:

An increasing momentum for collaboration among pharma:

Tom Krohn of Eli Lilly kicked off the conference by bluntly telling us why we need to change the current industry paradigm: because it’s completely unsustainable. Yikes. While radical changes in this industry might feel like trying to pull a 180 in the Titanic, progress is being made.

Elise Felicione of Janssen detailed a cross-pharma investigator databank that is advancing. Janssen, Merck, and Lilly are collaborating on a project that combines their investigator lists into a database hosted by DrugDev.org (we want to be a part of this effort!). While the project has only reached exploratory stages to this point, they have gotten past some very difficult hurdles involving lawyers, red tape, and the like. Did you know about all of the redundant tasks that take place between sponsor and investigator, like how investigators have to go through Good Clinical Practice training with each sponsor that they work with? As a data geek residing on the peripheries of the industry, I did not. Reducing these “redundant burdens” is a no-brainer, but implementing is no easy task. It will take indomitable leaders to overcome the resistance to sharing competitive intelligence, but luckily it appears that such leaders are in place.

Continue Reading…