Peer reviewing the patent system
June 30, 2007
Brady Forrest writes about Peer to Patent, a project developed in cooperation with the USPTO. From the About page
On June 15, 2007, the United States Patent and Trademark Office (USPTO) opens the patent examination process for online public participation for the first time. With the consent of the inventor, the Peer-to-Patent: Community Patent Review pilot, developed by the New York Law School Institute for Information Law and Policy in cooperation with the USPTO, enables the public to submit prior art and commentary relevant to the claims of 250 pending patent applications in Computer Architecture, Software, and Information Security (TC2100). This historic initiative connects an open network of community input to the legal decision-making process.
A lot of effort has been put into the website as well, which has a lot of information, including a bunch of videos, including some by well known patent reform folks such as Pamela Jones and Tim O’Reilly. As Brady points out, getting to some information is not easy and somewhat buried. Hopefully they will improve on the usability of the site in time. The overall look and feel of the site is quite good, so they have a great platform to build upon.
The process is described via the following figure
and here is an excellent example of the kinds of review that are garnering attention
Peer review in the patent process is something that is long overdue. For one, the patent office is understaffed and tends to be very inconsistent. In addition, the concept of “prior art” has always seemed fuzzy to me. Patents in the sciences and for software are a burning issue, which I am not completely sure this process addresses, since there are policy issues to be considered there and philosophical questions as well.
All said and done, it is good to see the USPTO thinking out of the box and setting up a mechanism that is different and involves the community. Will it work? Hopefully, but given recent experiences with such efforts, getting sufficient traction will not be easy. Interestingly, Peer to Patent already has a presence on Second Life
Technorati Tags: Patent, Peer to Patent, USPTO, Peer Review
Few hours to Bio::Blogs #12
June 30, 2007
You can still enter something for Bio::Blogs #12
Technorati Tags: Bio::Blogs
Pharmacovigilance and adverse events
June 29, 2007
I first started writing this post when L’Affaire Avandia initially came to light, but decided to put it off until the incessant coverage had died down. Of course, days became weeks, but better late than never. I will not focus on the specifics of the Avandia situation, but rather on the concept of pharmacovigilance and the role of post-marketing analysis, at least as far as I understand the problem. Listening to a lot of talks on adverse event reporting at the DIA conference also definitely helped crystallize some of these thoughts.
In the recent NEJM paper, Steve Nissen and Kathy Wolksi essentially carried out a meta analysis, where they combined results from multiple independent studies (42 clinical trials) to arrive at their conclusions. That got me thinking. What constitutes appropriate pharmacovigilance and how do we minimize ADRs and make sure that a drug is safe?
The coming years are going to see several changes in clinical trial design and hopefully the approach to drug development itself. While this is not going to happen overnight, those of us who are in the software and informatics business need to understand and appreciate where the industry is headed. In the future, not only will there be data available from randomized clinical trials, and from post-market follow up, but also increasing amounts of molecular data will be included in the results. That means significant amounts of data complexity, diversity and, frankly, noise. In Steve Nissen’s own words on the limitations of meta-analysis (via In the Pipeline)
Our study has important limitations. We pooled the results of a group of trials that were not originally intended to explore cardiovascular outcomes. Most trials did not centrally adjudicate cardiovascular outcomes, and the definitions of myocardial infarction were not available. Many of these trials were small and short-term, resulting in few adverse cardiovascular events or deaths. Accordingly, the confidence intervals for the odds ratios for myocardial infarction and death from cardiovascular causes are wide, resulting in considerable uncertainty about the magnitude of the observed hazard. Furthermore, we did not have access to original source data for any of these trials. Thus, we based the analysis on available data from publicly disclosed summaries of events. The lack of availability of source data did not allow the use of more statistically powerful time-to-event analysis. A meta-analysis is always considered less convincing than a large prospective trial designed to assess the outcome of interest.
At DIA drug safety and pharma reputation were repeatedly listed as the top two issues facing the industry. Companies have started doing a lot of post-marketing analyses, but the success of such studies is still unproven. Companies like Prosanos and Phase Forward are developing applications that perform real-time quantitative analysis and signal detection to identify post-marketing issues, primarily by tracking adverse event databases. People are developing semantic web tools that do much the same. Soon, we will have to worry about the post-marketing success rate of companion diagnostics and how they correlate with successful treatment. In a perfect world, post-marketing intelligence would feed back into the discovery process so we could learn what kind of molecular signatures, phenotypes, etc were common across adverse events if any such pattern exists.
The entire industry is working hard to develop methods that try and make sure that a drug is indeed safe. As far as I can tell, meta-analysis during the trial phase should feed into continued post-marketing analysis along with signal detection of adverse effects. Some of the algorithms being developed are quite advanced, a rich area of research with a lot of direct patient benefit. But we are only at the tip of the iceberg. Our data are only going to get more complex once pharmacogenomics moves into the mainstream of drug development. The coming years are going to be very interesting.
Further reading:
In the pipeline
Respectful Insolence
Disclosure: Many former colleagues work at Prosanos
Technorati Tags: Healthcare, Adverse Event Reporting, Pharmacovigilance
Trendspotting: The return of content
June 29, 2007
Just a note about a trend I have noticed recently. A few years ago, being a life science content company was usually equal to certain failure as a business. In the past year though, I’ve noticed content companies make a comeback, often as Software as a Service companies. Will be interesting to see how they fare. The market can only bear so many providers.
Technorati Tags: Bioinformatics, Content Providers, SaaS
Screencasting for the life scientist
June 28, 2007
First things first. What I am about to tell you about is absolutely not free of any conflicts of interest. So having got that out of the way, I’d like to tell you about Bioscreencast.com, a website that has its roots in Jon Udell and in the curious minds of a few geeks. One of us started posting screencasts to YouTube and the response led to phone calls, discussions, and I suspect, some late dinners in Cambridge, MA. The end result is Bioscreencast.com. The idea has always been that (a) screencasts are a great way for people to see how to use software and web services and (b) scientific knowledge is distributed across minds and geographies and we can all benefit from that.
The goal of Bioscreencast is to allow life scientists to capture how they use various software packages and websites for their research and productivity and share that with the community. Obviously, we spent some time in making sure it was somewhat useful and provided a decent user experience and hopefully with good feedback that will continue to be the case. In the meantime, read this post or go to the website to learn more about Bioscreencast.com and to see what we have there.
Video, podcasts, and the internet in general are going to reshape scientific communication. Readers of this blog should not find this opinion surprising at all. Bioscreencast.com is one attempt to leverage the technology available to us. I hope all of you will participate and make it successful. I’d love to see some examples of molecular simulation out there.
I must add that although I am listed in the “About Us” page, the only credit I can take is providing some very useless ideas on web strategy. The others have done all the hard work.
Technorati Tags: Screencast, Video, Life Science
