MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'data mining'. Sat, 03 Sep 2011 02:01:43 +0100 http://www.medworm.com/index.php?rid=5159275&cid=t_112108_113_f&fid=34625&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FNeilVerselsHealthcareItBlog%2F%7E3%2FRTT7SAYwins%2F As long as there have been EMRs, there have been vendors selling aggregated, de-identified data. And there have been people worried about privacy. That issue came up last week AHIMA Legal EHR Summit right here in Chicago, during a session exploring issues related to data ownership and stewardship in the era of cloud computing. (I’ll have a more complete rundown of the session Monday in InformationWeek Healthcare.) Near the start of the panel, Daniel Orenstein, senior VP and general counsel of Athenahealth tried to put any lingering questions to rest right away. “I think data monetization is kind of a red herring,” Nussbaum said of people who criticize vendors for selling sensitive patient information. According to Nussbaum, de-identified data no longer includes any protec... Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=5159275 Sun, 21 Aug 2011 12:52:18 +0100 5159275 http://www.medworm.com/index.php?rid=5118998&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2Fg-WZvl9XAuY%2F The new president of the American Medical Association is lashing out at critics who claim the AMA has not done enough to persuade physicians to join its five-year-old Physician Data Restriction Program, InformationWeek reports. So far, less than 28,000 doc have joined the PDRP, which enables them to opt out of prescription data mining used in pharmaceutical marketing campaigns. Last week, a commentary in The New England Journal of Medicine commentary suggested the AMA had sabotaged the PDRP. As part of a discussion about the recent US Supreme Court decision to strike down a Vermont data mining law (read here), the authors pointed out that the AMA makes a great deal of money from selling its physician lists, which data miners combine with prescribing data. “To date, few physicians (... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=5118998 Wed, 10 Aug 2011 12:37:32 +0100 5118998 http://www.medworm.com/index.php?rid=4997503&cid=t_112108_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2011%2F07%2Fblogscan-forensic-statistics.html Several interesting points are raised in the newsletter of the American Association of Physicians and Surgeons (AAPS) in a post entitled "Forensic Statistics" in their July 2011 newsletter headlined "Numbers." Healthcare Renewal is cited:Forensic StatisticsWhile claims from RCTs fail to replicate about 20% of the time, the problem with epidemiology is so bad as to constitute a crisis, writes S. Stanley Young (“Everything Is Dangerous: a Controversy,” National Institute of Statistical Sciences, June 2008, www.niss.org). Fewer than 20% of nonrandomized trials [e.g., observational studies - ed.] replicate; i.e. 80%-90% of epidemiologists’ claims are false.More than $1 billion in grant/tax money flows to institutions with reproducibility problems, Young states. A fundamental flaw in the... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4997503 Sun, 03 Jul 2011 14:13:00 +0100 4997503 http://www.medworm.com/index.php?rid=4992692&cid=t_112108_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fsupreme-court-data-mining-ok-even-when-physician-privacy-is-compromised%2F2011.07.01 The Supreme Court has sided with Big Pharma in their challenge to the Vermont Law limiting the pharmaceutical Industry’s access to physician prescribing information. The nation’s high court handed down a verdict Thursday in the Sorrell v. IMS Health case, striking down by a 6-3 vote a 2007 Vermont law that that bans the practice of data mining — the sale and use of prescriber-identifiable information for marketing or promoting a drug, including drug detailing — unless a physician specifically gives his or her permission to use the information. Apparently, Big Pharma’s right to “free speech” trumps my right to privacy. How getting access to my prescribing information has anything to do with free speech is beyond me.  In the twisted logic of the pro-business, anti-citizen Sup... Better Health blogs http://www.medworm.com/rss/comments.php?id=4992692 Fri, 01 Jul 2011 12:00:14 +0100 4992692 http://www.medworm.com/index.php?rid=4984691&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2Fr04LoWLwBgU%2F This is hardly surprising. After the US Supreme Court last week struck down a highly controversial Vermont law that restricts the sale of prescription drug info identifying prescribers and patients for commercial marketing purposes, a similar law in Maine is now being sent back to a federal appeals court for judicial review (see this). In pushing for its legislation, Vermont maintained such laws can protect doctor-patient relationships and consumer privacy, promote patient safety and contain health care costs. But market research firms successfully convinced the Supreme Court that the statute hurt public access to healthcare info and violated commercial speech (back story). Maine and New Hampshire are the only states to have passed similar bills, but these are now coming under pressure. I... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4984691 Wed, 29 Jun 2011 16:38:41 +0100 4984691 http://www.medworm.com/index.php?rid=4968464&cid=t_112108_87_f&fid=36438&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FCato-at-liberty%2F%7E3%2FkY82WaVaaUo%2F By Jim HarperThe Supreme Court’s decision in Sorrell vs. IMS Health is being touted in many quarters as a privacy case, and a concerning one at that. Example: Senator Patrick Leahy (D-VT) released a statement saying “the Supreme Court has overturned a sensible Vermont law that sought to protect the privacy of the doctor-patient relationship.” That’s a stretch. The Vermont law at issue restricted the sale, disclosure, and use of pharmacy records that revealed the prescribing practices of doctors if that information was to be used in marketing by pharmaceutical manufacturers. Under the law, prescription drug salespeople—”detailers” in industry parlance—could not access information about doctors’ prescribing to use in focusing their effort... Cato-at-liberty blogs http://www.medworm.com/rss/comments.php?id=4968464 Fri, 24 Jun 2011 12:37:08 +0100 4968464 http://www.medworm.com/index.php?rid=4968911&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FBc0iyAnR7mo%2F In a 6-to-3 ruling, the US Supreme Court has struck down a highly controversial Vermont law that restricts the sale of prescription drug info identifying prescribers and patients for commercial marketing purposes. The practice is known in the pharma world as data mining and has been growing for the past two decades, ever since data was gathered by market research firms. However, data mining has also sparked heated arguments over free speech, health care costs and information privacy. The decision is a setback for consumer advocates who maintained such laws can protect doctor-patient relationships and consumer privacy, promote patient safety and contain health care costs. Vermont, in fact, passed its law three years ago and then amended it in hopes of staving off court challenges. Similar b... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4968911 Thu, 23 Jun 2011 15:58:18 +0100 4968911 http://www.medworm.com/index.php?rid=4934435&cid=t_112108_113_f&fid=34625&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FNeilVerselsHealthcareItBlog%2F%7E3%2FcaoEF1XUOg0%2F That’s the subject of my weekly post on EMR and HIPAA, based on two stories I’ve written in the last 24 hours and a conference I attended last week in Madison, Wis. Check it out.   Related posts:CDS commentary on EMR and HIPAA blog A business opportunity and a milestone Deborah Peel on Fox Business (Source: Neil Versel's Healthcare IT Blog) Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=4934435 Thu, 16 Jun 2011 21:05:28 +0100 4934435 http://www.medworm.com/index.php?rid=4759043&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FF7d0dGHppWA%2F Top of the morning to you. Gray skies are hovering over the Pharmalot corporate campus, but our spirits remain sunny. And why not? This inspires us to trot out one of our favorite sayings, courtesy of the morning mayor: ‘Every brand new day should be unwrapped like a precious gift.’ So while you tug on the ribbon, here are a few items to get you started. Have a great day, everyone, and smile… Merck To Buy Back Up To $5 Billion In Stock (Reuters) Teva Resumes Manufacturing At California Site (Orange County Business Journal) J&J Agrees To Buy Synthes For $21.3 Billion (Bloomberg News) Supreme Court Skeptical About Vermont Data Mining Law (Bellingham Herald) Lupin May Wait To Sell Birth Control Pills In The US (Bloomberg News) Merck And Biogen Expand Facilities In North... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4759043 Wed, 27 Apr 2011 11:54:02 +0100 4759043 http://www.medworm.com/index.php?rid=4747882&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F9c4NOuPTQQ8%2F The US Supreme Court tomorrow will review a highly controversial issue - the constitutionality of a Vermont law that restricts the sale of prescription drug info identifying prescribers and patients for commercial marketing purposes. The practice is known in the pharma world as data mining and has been building for some two decades ever since data was gathered by market research firms, but has since sparked heated arguments over free speech, health care costs and information privacy. The information at issue includes the name of a prescribing physician, patient age and sex, the type and strength of each drug prescribed, and the date and location of prescription. Pharmacies, of course, are required by law to collect and maintain data about each prescription that is filled, and are allowed c... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4747882 Mon, 25 Apr 2011 16:16:39 +0100 4747882 http://www.medworm.com/index.php?rid=4570532&cid=t_112108_87_f&fid=36438&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FCato-at-liberty%2F%7E3%2Fn6LNbfhzUOA%2F By Jim HarperYou have to wade through a lot to reach the good news at the end of Time reporter Joel Stein's article about "data mining"---or at least data collection and use---in the online world. There's some fog right there: what he calls "data mining" is actually ordinary one-to-one correlation of bits of information, not mining historical data to generate patterns that are predictive of present-day behavior. (See my data mining paper with Jeff Jonas to learn more.) There is some data mining in and among the online advertising industry's use of the data consumers emit online, of course. Next, get over Stein's introductory language about the "vast amount of data that's being collected both online and off by companies in stealth." That's some kind of stealth if a reporter can write a t... Cato-at-liberty blogs http://www.medworm.com/rss/comments.php?id=4570532 Thu, 10 Mar 2011 16:19:15 +0100 4570532 http://www.medworm.com/index.php?rid=4349694&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FxghWdm5jAQA%2F As with any industry, there are always behind-the-scenes players that occupy an important role and one of them is IMS Health, which is best known as a market research firm because it traffics in an enormous amount of data. And to expand its scope, IMS Health is now buying a rival, SDI Health, according to sources who are familiar with the deal. The move will solidify IMS Health’s position as a provider of key data to the pharmaceutical industry, which means drugmakers will have fewer sources for information on patients and prescriptions. This raises the question of the extent to which this deal will cause antitrust concerns. The next biggest player in this market is Wolters Kluwer. The acquistion comes after IMS Health was taken private last year, but has been under pressure to boos... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4349694 Fri, 14 Jan 2011 18:08:25 +0100 4349694 http://www.medworm.com/index.php?rid=4322690&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FUjxdBU3b7R8%2F After several years of courtroom battles, the US Supreme Court has agreed to review whether laws that ban data mining - specifically, the sale of prescription drug info that identifies prescribers and patients for commercial marketing purposes - are unconstitutional (see this). The move, which is not surprising, comes after conflicting rulings issued by different federal appeals courts. Last November, the US Court of Appeals for the Second Circuit shot down a Vermont law after deciding it violated the First Amendment right to free speech (see here). Previously, the US Court of Appeals for the First Circuit upheld similar statutes passed by Maine and New Hampshire (read this). The challenges to the state laws were made by three healthcare research firms - IMS Health, SDI, Wolters Kluwer hea... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4322690 Fri, 07 Jan 2011 23:10:01 +0100 4322690 http://www.medworm.com/index.php?rid=4197361&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F56S6t7OGekU%2F A federal appeals court has ruled that a Vermont law restricting data mining - specifically, the sale of prescription drug info that identifies prescribers and patients for commercial marketing purposes - is unconstitutional. The law was challenged by three healthcare research firms - IMS Health, SDI, Wolters Kluwer health - and the PhRMA trade group, which argued the legislation would hurt public access to healthcare info and violated commercial speech. The decision is a setback for consumer advocates who maintained such laws can protect doctor-patient relationships and consumer privacy, promote patient safety and contain health care costs. Vermont, in fact, passed its law three years ago and then amended it in hopes of staving off court challenges (see here). Similar bills have been intr... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4197361 Tue, 23 Nov 2010 21:29:23 +0100 4197361 http://www.medworm.com/index.php?rid=3899376&cid=t_112108_87_f&fid=36438&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FCato-at-liberty%2F%7E3%2F7Q282tzEUmw%2F It sounds a little bit like the “pre-crime” unit featured in the 2002 film “Minority Report,” but news that Washington, D.C. will implement software to “predict” crime is not quite as worrisome as it might seem at first blush. Beginning several years ago, the researchers assembled a dataset of more than 60,000 various crimes, including homicides. Using an algorithm they developed, they found a subset of people much more likely to commit homicide when paroled or probated. Instead of finding one murderer in 100, the UPenn researchers could identify eight future murderers out of 100. Berk’s software examines roughly two dozen variables, from criminal record to geographic location. The type of crime, and more importantly, the age at which that crime wa... Cato-at-liberty blogs http://www.medworm.com/rss/comments.php?id=3899376 Tue, 24 Aug 2010 18:09:42 +0100 3899376 http://www.medworm.com/index.php?rid=3706759&cid=t_112108_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fonc-hold-hearing-privacy-enhancing-technologies ONC is making history tomorrow with the first-ever federal government sponsored hearing on privacy-enhancing technologies. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3706759 Mon, 28 Jun 2010 14:10:31 +0100 3706759 http://www.medworm.com/index.php?rid=3672068&cid=t_112108_155_f&fid=38412&url=http%3A%2F%2Fpathlabmed.typepad.com%2Fsurgical_pathology_and_la%2F2010%2F06%2Flow-expectations-for-future-of-clinical-data-mininga-study.html I picked this up from Fierce Health IT newsletter: Anvita Health commissioned a newly released HIMSS Analytics study on clinical data mining. HIMSS Analytics convened a focus group of CMOs and and CMIOs of provider and payer organizations for the report.Payers and providers alike generally don't often employ clinical data for real-time decision-making, in part because information is in so many disparate formats, some important data elements are missing and because they believe the costs generally outweigh the benefits. "These challenges are consistent with what we've seen and heard from our payer and provider customers," Noffsinger explains. "Interoperability of data is a hurdle, but it's not insurmountable.""A key finding for us was that both p... The Daily Sign-Out blogs http://www.medworm.com/rss/comments.php?id=3672068 Wed, 16 Jun 2010 20:30:00 +0100 3672068 http://www.medworm.com/index.php?rid=3563951&cid=t_112108_87_f&fid=36438&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FCato-at-liberty%2F%7E3%2FMi9sxOQSUa0%2F By Julian SanchezThere are too few periodical venues for good short fiction these days, so I’d normally be enthusiastic about the Wall Street Journal’s decision to print works of fantasy. Unfortunately, they’ve opted to do so on their editorial page—starting with a long farrago of hypotheticals concerning the putative role of the Foreign Intelligence Surveillance Court in hindering the detection and apprehension of failed Times Square bomber Faisal Shahzad. In fairness to the editors, they acknowledge near the end of the piece that much of it is unvarnished speculation, but their flights of creative fancy extend to many claims presented as fact. Let’s begin with the acknowledged fiction. The Journal editors wonder whether Shahzad might have been under surveillance... Cato-at-liberty blogs http://www.medworm.com/rss/comments.php?id=3563951 Thu, 13 May 2010 16:55:25 +0100 3563951 http://www.medworm.com/index.php?rid=3487186&cid=t_112108_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fhow-will-web-coupons-affect-your-personal-health-information Stephanie Clifford's story in the New York Times tells how the massive, under-the-radar data mining industry just hammered the one of the last nails into the coffin of online "privacy". In case you are naïve enough to imagine you have any privacy at all online - this story proves you have none.   How will "web coupons" affect your personal health information, from prescriptions to DNA to diagnoses?   (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3487186 Tue, 20 Apr 2010 15:26:20 +0100 3487186 http://www.medworm.com/index.php?rid=3483119&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2Fn8a0zw8SdUY%2F A California assemblyman was forced to shelve a bill that would have limited the sale of patient prescription records for marketing purposes because he couldn’t muster the necessary votes, The Californian reports. Although Assemblyman Bill Monning, a Democrat from Carmel, says he may reintroduce his bill in January if he can generate enough support. “We’re going to use this time frame to build more support and do more outreach,” Monning tells the Californian. He pulled the bill just before it was to go to a vote last week in the Assembly’s Committee on Health after realizing he didn’t have enough votes lined up. “We didn’t have the time to cultivate members’ understandings of the issues. There’s some intricacies.” The bill r... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3483119 Mon, 19 Apr 2010 11:52:24 +0100 3483119 http://www.medworm.com/index.php?rid=3139028&cid=t_112108_87_f&fid=36438&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FCato-at-liberty%2F%7E3%2Fufbk6EMGFkw%2F By Jim HarperJohn Brennan, assistant to the president for homeland security and counterterrorism, made the rounds of the Sunday political shows this weekend. He’ll be reviewing the attempted bombing of Northwest flight 253 for the president.  His appearance on ABC’s This Week program revealed his struggle with the limitations on data mining for counterterrorism purposes. His interviewer, Terry Moran, betrayed even less awareness of the challenge. Their conversation is revealing: Moran: Who dropped the ball here? Where did the system fail? Brennan: Well, first of all, there was no single piece of intelligence or “smoking gun,” if you will, that said that Mr. Abdulmutallab was going to carry out this attack against that aircraft. What we had, looking back on it now,... Cato-at-liberty blogs http://www.medworm.com/rss/comments.php?id=3139028 Mon, 04 Jan 2010 13:54:26 +0100 3139028 http://www.medworm.com/index.php?rid=3079582&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FFHcG_n-SOf4%2F An amendment to the Senate health care bill would effectively ban data mining which, as you know, involves the practice of buying prescription records to target sales pitches to doctors, the Associated Press reports. Democrats Herb Kohl of Wisconsin and Dick Durbin of Illinois say their measure will combat “harassing sales practices” and “restrain undue influence” of sales reps. The move comes amid tremendous controversy over data mining. Vermont, for instance, passed a law restricting the sale of prescription drug info that identifies prescribers and patients for commercial marketing purposes. The effort is being challenged by IMS Health, Wolters Kluwer Health and SDI, with support from PhRMA, which contend the law hurts public access to healthcare info (back story... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3079582 Thu, 10 Dec 2009 23:30:17 +0100 3079582 http://www.medworm.com/index.php?rid=3056878&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FH3-o6wZoH3o%2F In a long-promised move, New Jersey Attorney General Anne Milgram released a report from the state’s Division of Consumer Affairs recommending new regs to curtail the potential for conflicts of interest between docs, and drug and device makers. The move comes two years after Milgram formed a task force (see here and interview with Milgram here). “It is critical to minimize the potential for conflicts and it is critical that patients are made aware of any financial relationship between a physician and a pharmaceutical company or medical device manufacturer. Such relationships could bias medical decision-making,” she says in a statement. The report addresses a host of familiar issues - data mining, CME, payments to docs, food and other freebies. On gifts, the AG wants the state&#82... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3056878 Fri, 04 Dec 2009 16:07:49 +0100 3056878 http://www.medworm.com/index.php?rid=3008401&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FnauR90jH7zA%2F Who? Julie Brill, who was Vermont’s assistant attorney general for consumer protection and antitrust, where she spearheaded efforts to publicize pharma payments to docs and reign in some marketing practices, The Pink Sheet writes*. She championed, for instance, a controversial data mining law (see here). Brill worked in Vermont from 1988 to 2009 before moving earlier this year to North Carolina, where she is senior deputy attorney general in charge of the consumer protection division. If she makes the cut, she will become one of five FTC commissioners. Full disclosure: Ed Silverman is an editor at The Pink Sheet (* - subscription required) (Source: Pharmalot) Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3008401 Thu, 19 Nov 2009 12:41:10 +0100 3008401 http://www.medworm.com/index.php?rid=2984777&cid=t_112108_87_f&fid=36438&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FCato-at-liberty%2F%7E3%2FODpp6kuKYzg%2F Commentary on the Fort Hood incident can be categorized three ways: reaction, response, and rejoinder (commentary on the commentary). Reactions generally consist of pundits pouring their preconceptions over what is known of the facts. These are the least worthy of our time, and rejoinders like this one from Stephen M. Walt of Harvard University in the Fort Hood section of The Politico’s Arena blog dispense with them well: Of course [Fort Hood] is being politicized; there is no issue that is immune to exploitation by politicians and media commentators. The problem is that there are an infinite number of “lessons” one can draw from a tragic event like this — the strain on our troops from a foolish war, the impact of hateful ideas from the fringe of a great religion... Cato-at-liberty blogs http://www.medworm.com/rss/comments.php?id=2984777 Wed, 11 Nov 2009 21:39:46 +0100 2984777 http://www.medworm.com/index.php?rid=2963078&cid=t_112108_87_f&fid=36438&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FCato-at-liberty%2F%7E3%2Fx0Xb3dRA9ys%2F Via Secrecy News, “JASON”—a unit of defense contractor the MITRE Corporation—has reported to the Department of Defense on the weakness of data mining for predicting or discovering inchoate terrorist attacks. “[I]t is simply not possible to validate (evaluate) predictive models of rare events that have not occurred, and unvalidated models cannot be relied upon,” says the report. In December 2006, Jeff Jonas and I published a paper making the case that predictive modeling won’t discover rare events like terrorism. The paper, Effective Counterterrorism and the Limited Role of Predictive Data Mining, was featured prominently in a Senate Judiciary Committee hearing early the next year. Privacy gives way to appropriate security measures, as the Fourth Am... Cato-at-liberty blogs http://www.medworm.com/rss/comments.php?id=2963078 Wed, 04 Nov 2009 18:24:23 +0100 2963078 http://www.medworm.com/index.php?rid=2908596&cid=t_112108_88_f&fid=38961&url=http%3A%2F%2Fquantavie.net%2F2009%2F10%2Fpatients-data-markets%2F When 2+2 Equals a Privacy Question—NYTimes The idea of an entirely paperless medical system holds the promise of more efficient and cost-effective care. And, with the incentive of stimulus package money, many companies are rushing to sell clinical information systems to streamline services like patient scheduling, sample tracking, and billing at hospitals and clinics. In some cases, the same companies that sell data management systems to hospitals and physicians also store that information and then repackage it to make money on other services. Transforming healthcare through secondary use of health data—PricewaterhouseCoopers US The data that could be mined from the US health system can be re-used to improve patient care, predict public health trends, reduce healthcare costs... quanta vie blogs http://www.medworm.com/rss/comments.php?id=2908596 Tue, 20 Oct 2009 03:34:05 +0100 2908596 http://www.medworm.com/index.php?rid=2890941&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FiQEWWXzg-tk%2F The groundbreaking legal spat pitting Vermont against drug makers and data providers is being argued in a federal court in New York and, so far, the toughest questions have been directed at Vermont’s Assistant Attorney General, according to The Pink Sheet. You may recall that Vermont passed a law restricting the sale of prescription drug info that identifies prescribers and patients for commercial marketing purposes. The effort is being challenged by IMS Health, Wolters Kluwer Health and SDI, with support from PhRMA, which contend the law hurts public access to healthcare info (back story). During oral arguments, a lawyer for PhRMA contended that Vermont’s law is an “attempt to correct the balance of ideas” and “to shape the message of pharmaceutical companies... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=2890941 Wed, 14 Oct 2009 12:45:39 +0100 2890941 http://www.medworm.com/index.php?rid=2785966&cid=t_112108_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2009%2F09%2F50-million-chemicals-and-accelerating.html (via NatureNews) As reported by the Chemical Abstract Service (CAS) have they reached 50 million registered chemical entities.Here some numbers to think aboutCAS needed 33 years for registering the first 10 million compounds, that is one new compound every 101.5 seconds.the last 9 months CAS registered 10 million compounds, in other words, every 2.3 seconds a new compound was created !So, chemistry has improved its efficiency 44 times !This resulted in a drastically increasing patenting rate as mentioned by David Bradley. O.k. what happens now to your actual lead structure series? Don't panic! Just get enough money for mining CAS directly ... mmmh ... just kidding.Second choice? Extract all 50 million structures from PDF patents, which is really difficult and noisy, I mean it.Third choice?... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2785966 Thu, 10 Sep 2009 19:07:00 +0100 2785966 http://www.medworm.com/index.php?rid=2663989&cid=t_112108_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2009%2F08%2F03%2Fjohns-hopkins-when-a-survey-isnt-really-research%2F So when is a survey not research? When it’s a survey conducted by Johns Hopkins, apparently. We all know Johns Hopkins as one of those premier medical institutions in the U.S. Like the Harvard Medical School or the Mayo Clinic, most Americans recognize the name as being synonymous with quality medicine and research. So what would you think if you received a survey called the “Johns Hopkins 2009 Health America Survey?” You’d think, cool, Johns Hopkins wants me to participate in some of their medical research and tell them about my health. You’d be wrong, though. Trisha Torrey, blogging over at the Patient Empowerment Blog, got such a survey and began wondering about the pitch to purchase one of their 15 “white papers” on the conditions listed in th... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=2663989 Mon, 03 Aug 2009 12:10:03 +0100 2663989 http://www.medworm.com/index.php?rid=2786024&cid=t_112108_109_f&fid=38951&url=http%3A%2F%2Fcarlatpsychiatry.blogspot.com%2F2009%2F07%2Fprescription-data-mining-is-getting.html Prescription data-mining is a marketing tool in which drug companies purchase information from pharmacies that allow them to spy on doctors' prescribing practices. The companies use this information in a variety of sneaky ways. Front line drug reps download this information to their laptops and use it to tailor their marketing pitches before they call on doctors. Higher level marketing executives use the data to craft targeted marketing campaigns involving everything from pseudo-journals to invitations to promotional dinner meetings.It is a deceptive and quite nauseating marketing practice, but it has continued through the years because it seemed for a while that everybody stood to win. Drug companies got invaluable demographic information in order to sell the newest and most expensive dru... The Carlat Psychiatry Blog blogs http://www.medworm.com/rss/comments.php?id=2786024 Thu, 02 Jul 2009 14:27:00 +0100 2786024 http://www.medworm.com/index.php?rid=2195668&cid=t_112108_113_f&fid=36504&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedicalRecordShow%2F%7E3%2F5yygu52TgTE%2F Back in the day when I was a burgeoning kendo student, I read an account about a visiting fencing master. The writer, an established member of a kendo club, was looking forward like everyone else to the visit of this celebrity sensei. While having practiced kendo for nearly seven decades, the guest was appallingly fast, and had a reputation for winning known throughout Japan. He was, in a word, amazing, and every bit as impressive in person as his record suggested. When the guest asked the writer to practice with him, the club member was practically beside himself. What special techniques and feints would he be privileged to witness? What insights into timing, distance, and psyching-out your opponent would he be party to? “I’d like to work the overhead strike,” the guest ... The EMR/EHR Show: Making Your Electronic Medical Records Really Work blogs http://www.medworm.com/rss/comments.php?id=2195668 Wed, 18 Feb 2009 09:31:32 +0100 2195668 http://www.medworm.com/index.php?rid=2182360&cid=t_112108_113_f&fid=34625&url=http%3A%2F%2Fclinicalit.blogspot.com%2F2009%2F02%2Fmore-on-allscriptsand-fight-over-data.html Earlier today, I posted news about Allscripts-Misys Healthcare Solutions intending to sell its Medication Services division to an unnamed purchaser for an unspecified amount. I've since gotten clarification via e-mail from company spokesman Todd Stein: "The release is earlier than we would normally have liked because we're required to reveal all material non-public information about the company prior to undertaking a share repurchase program like the one we also announced yesterday. That's to ensure that shareholders know everything about the company that they need to know in order to make an informed buy-or-sell decision."Indeed, Allscripts announced yesterday a $150 million buyback program and related $150 million increase in its credit commitments.The company also was named in a Bloombe... Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=2182360 Wed, 11 Feb 2009 23:45:00 +0100 2182360 http://www.medworm.com/index.php?rid=2062108&cid=t_112108_113_f&fid=36504&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FMedicalRecordShow%2F%7E3%2F493133839%2F I’ve seen it in a variety of practices, my own being no exception. Free texting to document a patient encounter. You’ve got your clickers, the orientation spiel goes, and ya got your typers. Me, I’m a typer, but the system allows you to document any way you like. To each his own, and I love the look of my own text! So, when your IT folks suggest that you align yourself with the clicker column, so to speak, you might find yourself getting a mite…testy. Vocally belligerent, even — it’s a free country, and I’ll free text, doggone it. What follows are some thoughts about why you might want to reconsider. Reeeally reconsider… “Join Or Die” America’s first political cartoonist, Benjamin Franklin, penned the following image, encou... The EMR/EHR Show: Making Your Electronic Medical Records Really Work blogs http://www.medworm.com/rss/comments.php?id=2062108 Tue, 23 Dec 2008 19:43:17 +0100 2062108 http://www.medworm.com/index.php?rid=2040535&cid=t_112108_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F12%2Fmining-clinical-trials.html "This (clinical data mining) application enables rapid extraction of information about institutions, diseases, clinical approaches, clinical trials dates, predominant cancer types in the trials, clinical opportunities and pharmaceutical market coverage." [10.1186/1745-7580-4-7](via open access news)In 2007 more than seven million people died from cancer. This means there is still a lot to do for helping patients and for reducing this number. This is also the reason why each new treatment option has to follow good design criteria and sufficient testing, called clinical trial design. Typical design criteria could be: assess the safety and effectiveness of a new medication or device on a specific kind of patient (e.g., patients who have been diagnosed with Alzheimer's disease)assess the safet... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2040535 Mon, 15 Dec 2008 19:06:00 +0100 2040535 http://www.medworm.com/index.php?rid=1969316&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F457607692%2F In a move that will likely embolden other states, a federal appeals court upheld a first-in-the-nation law that prohibits prescription data identifying patients or prescribers from being used for marketing purposes. Pharma challenged the law, citing a First Amendment right to track prescription records, while state officials argued the law protected doctor-patient relationships, promoted patient safety and contained health care costs. Drugmakers want this data so they can learn which docs are high prescribers and figure out who to target for the hard sell. Two research firms, also known as data miners, IMS Health and Verispan, challenged the law and called it unconstitutional. They received backing not only from industry, but also free-speech advocates. Consumer and patient groups lined up... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1969316 Tue, 18 Nov 2008 20:35:13 +0100 1969316 http://www.medworm.com/index.php?rid=1952698&cid=t_112108_113_f&fid=36504&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FMedicalRecordShow%2F%7E3%2F449313246%2F Once again, I’m attending the annual NextGen EMR Users Group Meeting on all that’s new and shiny in the world of high-end, integrated electronic medical record and practice management systems. New faces and new directions this year, of course. And a terrific keynote address by Pat Croce, former owner of the Philadelphia 76-ers. But this year, the prize for the most awesome personage goes to Dr. Jan Lee — engaging, encouraging, and passionate about quality health care. And her focus this year is on a revamped version of an older technology: report generation. And if there was ever a cornerstone of The Next Big Wave of electronic records, this is it. Gold Mine What the heck is report generating, and why should you care? You may have heard of a related, sexier phrase: data ... The EMR/EHR Show: Making Your Electronic Medical Records Really Work blogs http://www.medworm.com/rss/comments.php?id=1952698 Tue, 11 Nov 2008 08:30:34 +0100 1952698 http://www.medworm.com/index.php?rid=1535658&cid=t_112108_113_f&fid=34625&url=http%3A%2F%2Fclinicalit.blogspot.com%2F2008%2F06%2Fbad-data-mining.html Recently I received a flier in the mail from Bausch & Lomb, offering me a free sample of an over-the-counter allergy drug called Alaway (ketotifen fumarate ophthalmic solution). "Don't suffer through another allergy season. Stop itchy eyes," the mailer said.How did Bausch & Lomb know I have hay fever? It could only be from my history of purchasing OTC decongestants like Claritin-D and Alavert-D (both are loratadine/pseudoephedrine combos). And the reason why drug companies know I was taking this medication is because federal law now requires a photo ID and a signature to purchase any products containing pseudoephedrine. (Thanks, meth heads, for inconveniencing millions of innocent people.)Clearly, pharmacies are selling their pseudoephedrine purchase logs to pharma marketers. Some might ca... Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=1535658 Fri, 20 Jun 2008 22:09:00 +0100 1535658 http://www.medworm.com/index.php?rid=1475420&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F299922906%2F To appease legislators and some doctors who objected to data mining, which is the practice of gathering and selling prescription data, the American Medical Association created the Prescription Data Restriction Plan. But the program remains contentious, according to Adriane Fugh-Berman an associated professor in the physiology and biophysics department at Georgetown University Medical Center, who also heads out PharmedOut, an independent, publicly funded project that examines pharmaceutical promotion practices. As she noted in a recent paper, docs must opt-out, not sign up. So far, though, less than 2 percent of all US docs have registered - and she notes that those who have opted out aren’t the ones targeted for marketing. Moreover, only sales reps and their immediate superviors are ... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1475420 Wed, 28 May 2008 15:45:07 +0100 1475420 http://www.medworm.com/index.php?rid=1407329&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F280156273%2F A US Senate committee is probing an American Medical Association program that allows docs to opt-out of having their prescribing data sold to drugmakers. Known as the Physician Data Restriction Program, the effort is controversial because the AMA has a financial stake and has also been criticized for not establishing a program that encourages docs to participate, rather than have to opt out. And so Herb Kohl, a Wisconsin Democrat who chairs the Special Committee on Aging, and Dick Durbin, an Illinois Democrat, sent a letter to AMA president Ron Davis asking for info on how the program conducts outreach, protects patient privacy and responds to complaints about drugmakers, along with other details. “To say the least, we are troubled by any attempt to persuade physicians to prescribe a dr... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1407329 Tue, 29 Apr 2008 15:28:10 +0100 1407329 http://www.medworm.com/index.php?rid=1407046&cid=t_112108_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F280023869%2F Detailed blog posts will follow when I have some additional cycles, but thought I’d share some quick thoughts on day 1 of Bio-IT World. My conference started with a workshop on data visualization, which was mostly about the importance of visualization for making sense of multidimensional data sets and what kind of visualizations could be done. My take aways from the talks There was a distinction made between statistical methods and data mining and presenting information to humans. Life science data is inherently multiscalar and reducing dimensions without losing information or creating artifacts is not trivial Importance to create systems that can help scientists go through a workflow and predict visualizations, and help guide the user to the most appropriate visualization for the r... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1407046 Tue, 29 Apr 2008 10:54:07 +0100 1407046 http://www.medworm.com/index.php?rid=1378006&cid=t_112108_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F271811959%2F Lots of talk on data lately. Paul Kedrosky, for example, wants to bring on the data blogs. So in that spirit I wanted to mention some cool data-related sites and APIs and put up some data of my own. Google has its charts API. Swivel and Many Eyes are also familiar to many people who read this blog. To that list I would like to Trendrr, which I first read about on ReadWriteWeb. Haven’t quite tried it out yet, but it definitely looks very interesting. There are a lot of public datasets available, and while accessing them or finding them isn’t as easy as one would like, and the fact that more data should be openly available is always there, it is becoming increasingly available to do things with those data via APIs or services like Freebase (I think that’s where Freebase re... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1378006 Thu, 17 Apr 2008 03:25:52 +0100 1378006 http://www.medworm.com/index.php?rid=1238249&cid=t_112108_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F02%2Fsocial-search-in-drug-design-and-what.html Social search engines, another kind of social software, are trying to include user knowledge for improving search results in the future. One example is Wikia with an announcement of Jimmy WalesSearch is part of the fundamental infrastructure of the Internet. And we are making it open source. In contrast to the problem described by randfish might this improve search quality and reduce search engine tweaking requirements by users. Sometimes users have e.g. to multiply search terms or to find other tweaks, for getting the search results you want. Early initiatives like the the open directory project DMOZ (@Wikipedia) are using already user organized classification schemes for web links. SWiK organizes open source project information in a Wiki-like manner.I am still a little bit puzzled to und... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1238249 Sun, 17 Feb 2008 19:07:00 +0100 1238249 http://www.medworm.com/index.php?rid=1156042&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F217771307%2F Like their neighbors in New Hampshire, Vermont legislators want to restrict the practice in hopes of saving healthcare dollars. But mindful of a court challenge under way to New Hampshire’s law, Vermont’s attorney general has not only delayed implementation, but is drafting changes in hopes of thwarting the same critics, the Associated Press writes. The law was supposed to take effect on Jan. 1, but state attorney general Bill Sorrell decided in September to delay implementation by at least a year, to September 2008. Meanwhile, his office is now deleting a section requiring sales reps to disclose when a competitor might have a cheaper alternative to the medication they are peddling. “We think the proposals we’ve made are consistent with what the legislature was inte... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1156042 Wed, 16 Jan 2008 18:18:21 +0100 1156042 http://www.medworm.com/index.php?rid=1137213&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F213460697%2F A hearing will be held tomorrow morning at a federal appeals court in Boston regarding a challenge to what pharma says is a First Amendment right to track prescription records. Last year, a federal court in New Hampshire struck down a first-in-the-nation law prohibiting prescription data identifying patients or prescribers from being accessed for marketing purposes. State officials argued the law protected doctor-patient relationships and the health and safety of patients, while also helping containing health care costs. For those who haven’t followed this, drugmakers want this data so they can learn which docs are high prescribers and figure out who to target for the hard sell. Two research firms, also known as data miners, IMS Health and Verispan, challenged the law and called it uncon... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1137213 Tue, 08 Jan 2008 23:14:47 +0100 1137213 http://www.medworm.com/index.php?rid=1082982&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F198026570%2F The District of Columbia could become the first jurisdiction in the US to license reps when the district council votes on Tuesday. The council member behind the move says the bill would help protect docs and patients from disreputable agents who help drive up the costs of prescription drugs, but pharma argues the move is unnecessary because it overlaps with federal laws, The Washington Post writes. The council will also vote on banning reps from using a doc’s prescription data for marketing without the doc’s knowledge. At issue, says council member David Catania, is an industry whose reps can mislead docs and patients into buying the most expensive drugs on the market, shunning reasonably priced generics or drugs that could be just as effective. Because a reps salary is depend... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1082982 Mon, 10 Dec 2007 12:44:38 +0100 1082982 http://www.medworm.com/index.php?rid=1048566&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F189815483%2F In a first-person essay in The New York Times magazine, Danny Carlat, a psychiatrist and gadfly who publishes a newsletter about drug research and marketing, recounts how he was wooed by Wyeth to pitch Effexor to other docs. The tale is, basically, one man’s primer on how the process often works - how the reps schmooze, the drugmaker pays and the doc is seduced. For those unfamiliar with the routine, this is worthy reading. For those in the know, this is a reminder of the ceaseless tension between marketing and science. This is how Carlat opens his mea culpa… “On a blustery fall New England day in 2001, a friendly representative from Wyeth Pharmaceuticals came into my office in Newburyport, Mass., and made me an offer I found hard to refuse. He asked me if I’d like to g... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1048566 Sat, 24 Nov 2007 22:36:40 +0100 1048566 http://www.medworm.com/index.php?rid=885517&cid=t_112108_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F158591675%2F We are motoring along today. The transom is overflowing with interesting news of the world. While we prepare more items for your pleasure, here are a few to keep you occupied in the meantime. And if you haven’t already, please take our poll on whether clinical trial databases should be made available on the Internet. West Virginia Curtails Reporting Prescription Data to Drugmakers (Yahoo/AP) Allergan To Pay $370M For Esprit Pharma And Its Bladder Drug (Yahoo/Reuters) FluMist Approved For Children Two To Five Years Old (Yahoo/Reuters) Express Scripts Unit To Pay $10.5M Fine Over HGH (Yahoo/AP) Share / E-mail (Source: Pharmalot) Pharmalot blogs http://www.medworm.com/rss/comments.php?id=885517 Wed, 19 Sep 2007 15:41:58 +0100 885517 http://www.medworm.com/index.php?rid=1147435&cid=t_112108_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F09%2Fopen-source-tournament-rdkit-enters.html Egon is right! It is great that more and more open source tools are entering the drug design arena. On the other hand, we really need some benchmarking and feature comparisons for allowing to learn which tools should be used for which tasks.Noel dashed off an email to Greg Landrum, the main developer (who it turns out is also the developer of YAeHMOP (Yet Another extended Huckel Molecular Orbital Package) ), and he asked him what the story was. Two days ago, he returned from holidays and pointed Noel to the correct website and the documentation, and Noel couldn't believe what he was seeing...Some features that are cool:(1) Molecules based on the Boost Graph Library(2) All the Python stuff works for me on Windows!(3) 2D depiction!!!(4) 2D depiction that mimics 3D conformations!!!(5) 2D --> ... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147435 Fri, 14 Sep 2007 18:40:00 +0100 1147435 http://www.medworm.com/index.php?rid=1147441&cid=t_112108_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F09%2Fintelligent-data-analysis-in.html Two interesting communities in this area are IDAMAP and IDADM. Some scientific information is collected in the following books and article seriesArtificial Intelligence in Medicine, Volume 37, Issue 3, Page 163-222 (July 2006)Knowledge-Based Data Analysis in MedicineEdited by Blaz Zupan, John H. Holmes and Riccardo BellazziArtificial Intelligence in Medicine, Volume 16, Issue 1, Pages 1-120 (May 1999)Data Mining Techniques and Applications in MedicineEdited by Blaž Zupan, Nada Lavrac and Elpida KeravnouJournal of Biomedical Informatics, Volume 40, Issue 5, Pages 453-604 (October 2007)Intelligent Data Analysis in Medicine and Pharmacology (The International Series in Engineering and Computer Science), by Nada Lavrac, Elpida Keravnou, Blaz Zupan (Editor) (Source: Mining Drug Space) Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147441 Sat, 01 Sep 2007 20:17:00 +0100 1147441 http://www.medworm.com/index.php?rid=841722&cid=t_112108_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F08%2Fmeaning-from-pca%2F Back from Madrid. I spent three weeks there on an excellent data analysis course, which I would recommend. Not only did I learn valuable techniques, I also got the chance to spend my evenings by the pool or in Sol eating tapas - which explains the lack of posts this July. I offer this brief tutorial in recompense, continuing the theme of data analysis. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841722 Wed, 01 Aug 2007 15:35:11 +0100 841722 http://www.medworm.com/index.php?rid=841723&cid=t_112108_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F07%2Fexploring-multivariate-data-using-svd-and-som%2F Hola from Madrid, I’ve come here for a data analysis summer school. Last week, there was an interesting class on dimensionality reduction, and since multivariate datasets are prevalent in this -omic era, I thought to post a discussion of what I learnt. The aim of this example is illustrate one technique for visualising multivariate data, singular value decomposition, and a second technique for exploring it, self organising maps. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841723 Tue, 17 Jul 2007 22:57:00 +0100 841723 http://www.medworm.com/index.php?rid=841727&cid=t_112108_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F06%2Fsix-alternatives-to-pubmed-for-searching-scientific-content%2F In my opinion, great coding skills, a thorough knowledge of statistics, and Shakespearian writing ability do not make a great bioinformatician. They help, but the most important things are a relevant scientific question and a good understanding of the literature. If you’re like me, the path to scientific enlightenment begins with typing keywords into PubMed until you get the results you were after - the same way you use Google. However the are other options besides PubMed, here are six other options you might not have heard of, worth a look perhaps? (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841727 Sun, 24 Jun 2007 18:53:17 +0100 841727 http://www.medworm.com/index.php?rid=676131&cid=t_112108_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F123607060%2F Joerg points to a paper by O. Sacher that touches upon an issue that was one of the underlying themes for my Ignite Seattle talk, namely the lack of information on science blogs. Sachter writes One disadvantage of chemical blogs containing structures, reactions, or spectras is that the original information is lost, means the raw data. This restriction is already discussed in the blogosphere and will be hopefully solved soon. The problem goes beyond blogs. Information is scattered across the web in content management systems and in less organized web pages. Joerg refers to a number of data repositories (chemical in his case), but there are many others. The problem is in linking data to sources. There need to be mechanisms that link data to its source and any other references, and also to ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=676131 Sun, 10 Jun 2007 04:48:05 +0100 676131 http://www.medworm.com/index.php?rid=841736&cid=t_112108_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F05%2Fggplot-a-plotting-alternative-to-r-base-and-lattice%2F If you found the tutorial on drawing graphs using R a bit of a kerfuffle, there’s a good introduction on drawing graphs using the ggplot package. An alternative to the R base and lattice packages - so now you’ve got three to choose from. (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841736 Mon, 14 May 2007 17:00:52 +0100 841736 http://www.medworm.com/index.php?rid=841739&cid=t_112108_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F05%2Fbioinformatics-simple-graphs-in-r%2F Graphs and statistics, you can’t really get away from it. Even if you try, like a warm seafood sandwich, it’ll come up later. So here I made up some example data to produce a short tutorial on how to represent common types of information in R. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841739 Fri, 04 May 2007 13:49:11 +0100 841739 http://www.medworm.com/index.php?rid=544262&cid=t_112108_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F109133740%2F I found out about Ali Baba via del.icio.us and a quick blog search showed that Joerg has already mentioned it before. So what is Ali Baba? According the the website “Ali Baba parses PubMed abstracts for biological objects and their relations as discussed in the texts. Ali Baba visualizes the resulting network in graphical form, thus presenting a quick overview over all information contained in the abstracts.” There is a lot more detail about the kind of information available on the About page. The list of features is quite large and appears to be quite useful. For example, you can visualize the known or suspected genes associated with Parkinson’s disease using a simple query like “parkinson disease genetic cause”. The result is the following graph The appli... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=544262 Sun, 15 Apr 2007 01:50:49 +0100 544262 http://www.medworm.com/index.php?rid=841757&cid=t_112108_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F02%2Fthe-dark-side-of-bioinformatics-data-mining%2F An anti-post to my previous post on data mining. The point, to illustrate how data mining can quickly become unrewarding, and worse demotivating. I spend much of my day analysing yeast high throughput data, recently produced in the laboratory. On one hand I’m very lucky to have access to fresh data at many cellular levels. On the other hand, with all this information, I’m easily swept away by the amount of variables I have access to - the dark side of data mining. (more…) (Source: Bioinformatics Zen) Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841757 Tue, 13 Feb 2007 21:26:00 +0100 841757 http://www.medworm.com/index.php?rid=841758&cid=t_112108_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2007%2F01%2Fintroduction-bioinformatics-data-mining%2F In other words, you’re a bioinformatician, and data has been dumped in your lap. Find the patterns, trend, answers, or what ever meaningful knowledge the data is hiding. From experience, I can say that is one of the most frustrating positions to be in. Data mining is a huge field and can easily be bewildering for a beginner. However, high through-put techniques in molecular biology require, more and more, that bioinformatics is required to interpret the data. Furthermore, people working in bioinformatics generally come from computer science, or biology backgrounds. Data mining, however, involves statistics to one degree or another, which means entering a field that is may not be your strong point. Here are some tips from my own forays in the quagmire of data mining in bioinformatics.... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=841758 Mon, 15 Jan 2007 23:14:21 +0100 841758