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Better citations needed: a big upgrade to the PainSci bibliography

Paul Ingraham ARCHIVEDMicroblog posts are archived and rarely updated. In contrast, most long-form articles on PainScience.com are updated regularly over the years.

In 2015, a huge bibliography and “good footnotes” still set PainScience apart.1My footnotes contain either extra commentary and whimsical asides, or citations to science and other sources, like this:

Woolf CJ. Central sensitization: Implications for the diagnosis and treatment of pain. Pain. 2010 Oct;152(2 Suppl):S2–15. PubMed #20961685. PainSci #54851.
And I’ve just upgraded them.

Bibliographic data does not play nicely with modern publishing technology. There’s lots of software for wrangling references on your PC, but it’s still almost impossible to integrate them (efficiently) into blogs and websites. It still has to mostly be done “manually.”

I started investing in a good system to solve this problem in 2005, but it had to be custom job — pure original programming. The result has been a quietly awesome and esoteric boon to my publishing business ever since. My referencing gets noticed by many visitors to the site, because there’s nothing else quite like it anywhere else online. Footnotes in long-form online writing are sparse and spartan.

But it was time for some improvements. Got stay ahead of the curve. This is about what I did, and some behind-the-scenes details.

A craaaazy amount of work

Pulling this off tooks weeks of work spread out over months, but almost everything is better:

That last one was particularly challenging and interesting. Why “Vancouver”? My town?

The old way: dumbed-down references

PainScience isn’t a medical journal, and all of my readers in the early days were “just folks,” so why put on airs? I made my references simple: just the essential information, uncluttered with stuff like 82(123):987-93. (But always with a link to those details, so that a reference could be checked up on — that’s very important, even for just folks.)

It was idealistic and modern. I was declaring what I thought web referencing should be like.

Plus, it is really hard to mass produce the formatting of detailed bibliographic data. So I didn’t.

The new way: more formal = more serious

It’s hard to get taken seriously when you don’t act serious. Regular readers aren’t bothered by formality and detail, not in a footnote, but special visitors — proper experts — definitely notice if I don’t speak their referencing language. Those influential readers won’t know that I’m being clever and innovative and democratic.

“They’ll just think you don’t know how to reference properly,” my wife said about five years ago.

“And they’ll be right,” I said. “I don’t really have a clue. It looks nasty.”

“Time to learn, maybe.”

“Maybe. I should get started on the procrastinating, at least.”

And then I started getting email from people who agreed with my wife. My writing was getting noticed. My website was getting big. Getting referencing right mattered more with each passing year.

[better citations needed]

The Vancouver system of referencing

About six months ago I Googled “standard medical journal referencing format.” After all these years, I wasn’t even sure if there was such a standard. That’s when I discovered “the Vancouver system,” and it kicked off months of work. I had to re-tool the footnote factory & re-train all the bibliography gnomes. (Weirdly, I felt much more comfortable diving into this Sysyphean chore simply because the new standard was named after where I lived.)

So, why Vancouver?

In 1978, editors of medical journals from around the world met in the city of Vancouver, probably close to where I live, and thrashed out the unbelievably numerous details. It was so difficult and tedious that they named the standard after the city they were trapped in. Their work is still the standard today, and it is heavily documented.

I encourage you to click that link and scroll for a while and behold my nightmare. The Vancouver system is about as user-friendly as a swarm of cranky wasps.

The devil is in the details

All my references are generated from a bibliographic database in the fairly exotic BibTeX data format. Every footnote is lovingly crafted by software — essential for mass production. I had to reprogram that software to speak “Vancouver style.”

In programming, an “edge case” is something that requires special handling. You might have 50 lines of code that do something with 95% of your data, and then another 50 lines of code just to cope with a few awkward exceptions in the last 5%. Bibliographic data seems like it’s all edge. It is inherently rotten with the influences of other languages, the strange ways of databases, and oddball conventions grandfathered in from Ye Olde Dayes. My own data collection methods varied over the years: what I kept and how I kept it has come back to haunt me.

I lost entire days to minutiae like accented characters, abbreviations, pagination punctuation, title casing methods, and so on. I nearly lost my mind trying to either hammer my data into the necessary shape, or write clever subroutines that would do the equivalent, or both.

And fairly often I just flat-out disagreed with the Vancouver system. It has some major flaws. My goal was to look like I know the standard — and I do now — but I’m not going to follow it off a typographic cliff.

Old versus new

So here’s an old citation …

Vibe-Fersum et al. Efficacy of classification-based cognitive functional therapy in patients with non-specific chronic low back pain: A randomized controlled trial. European Journal of Pain. 2013. PubMed #23208945.

There’s only one author listed, the journal spelled out instead of abbreviated, and there’s no date, volume, and issue data. Here’s the same paper cited Vancouver style …

Vibe-Fersum K, O'Sullivan P, Skouen JS, Smith A, Kvåle A. Efficacy of classification-based cognitive functional therapy in patients with non-specific chronic low back pain: A randomized controlled trial. Eur J Pain. 2013 Jul;17(6):916–28. PubMed #23208945.

Okay, admittedly it’s not a very exciting difference when all is said and done. 😃 It’s getting thousands of those to look right automatically that’s the impressive part.

100 good citation examples

There’s about 2500 items in the bibliography these days. 400 or so got some extra care and editing during the big upgrade. The 100 best and most interesting are listed here. (I can generate lists like this very easily, one of the superpowers of the system: I just tell the database to generate a score for each record by awarding points for things like how recent is, study quality, summary length, and keywords like “fun” and “odd” and “classic” and “good news.”)

  1. A critical evaluation of the trigger point phenomenon
  2. Spinal manipulation no better for back pain than placebos
  3. Central sensitization
  4. Functional Movement Screen unreliable
  5. Adverse events and cervical manipulation for neck pain
  6. Promising trial of cognitive functional therapy for low back pain
  7. Massage therapy attenuates inflammatory signaling after exercise-induced muscle damage
  8. Forefoot runners have fewer injuries, but causality unclear
  9. Neck strength can reduce chronic neck pain long-term
  10. Regular Swedish versus “tensegrity-based” massage
  11. Location of back and neck pain could not be detected by feel
  12. More than 20% of manual therapy treatments do some harm
  13. Cellular response to simulated myofascial release
  14. Worn out shoes do change the biomechanics of running, but not much
  15. Small, flawed trial of foam rolling shows 8% ROM increase
  16. Comparison of 2 types of massage for chronic low back pain
  17. Trial of therapeutic massage for neck pain
  18. Brief, intense muscular training for cardiovascular fitness
  19. Patellar maltracking in patellofemoral pain with patella alta
  20. Why Most Published Research Findings Are False
  21. Curcumin “likely” reduces muscle soreness after exercise
  22. Thigh and hip exercises effective for patellofemoral pain
  23. Increased trapezius pain sensitivity is not associated with increased tissue hardness
  24. Regular hamstring stretching increased range of motion
  25. The greatest hits of back pain science are a disappointment
  26. Massage therapy probably helps patients with bone cancer
  27. Flexibility gains due to changes in sensation, not muscle length
  28. Safe but useless for knee arthritis: glucosamine, chondroitin sulphate, and celecoxib
  29. The iliotibial band is uniformly, firmly attached to the femur
  30. Intense, brief workouts almost as effective as time-consuming cardio
  31. Trial of glucosamine for low back pain finds no therapeutic effect
  32. Nerve root impingement fairly rare, barely more common in car accident victims
  33. A fascinating landmark study of placebo surgery for knee osteoarthritis
  34. The hazards of NSAIDs, especially diclofenac
  35. Massage vs minimal exercise for poor circulation
  36. Education, not core exercise, reduces back pain incidence in soldiers
  37. Trigger points are acidic and contain pain-causing metabolites
  38. 8 weeks of core strengthening, coordination exercise for chronic low back pain
  39. Do strong quadriceps help patellofemoral pain?
  40. Surprisingly effective back pain injection: intradiscal methylene blue
  41. Quality of online sports medicine information “highly variable”
  42. Only quantity of exercise for back pain produces better results
  43. Failed trial of vertebroplasty for compression fractures
  44. Deyo and Weinstein’s 2001 low back pain tutorial
  45. Disappointing first trial of surgery for tennis elbow
  46. Regular, moderate exercise boosts makes neutrophils busier for longer
  47. Yoga, stretching equally and slightly effective for back pain
  48. Stress fractures: it’s not how hard you hit the ground, but how fast you hit it
  49. Intravascular danger signals guide neutrophils to sites of sterile inflammation
  50. Current evidence does not support Botox for trigger points
  51. Online tutorials for chronic pain reduced pain, anxiety, disability
  52. Prebiotics reduces waking cortisol response
  53. Functional implications of the Q-angle in the patellofemoral joint
  54. Botox for trigger points, update
  55. Strong criticism of “more is better” strength training
  56. Chiropractic subluxation is still “unsupported speculation”
  57. Special core strengthening prevents no more injuries than ordinary sit-ups
  58. Both heat and cold for back and neck strain mildly beneficial
  59. Massage impairs post exercise muscle blood flow and lactic acid removal
  60. General practitioners do not follow guidelines for low back pain care
  61. A review of low quality evidence about exercise for neck pain
  62. Chiropractic identity, role and future: survey
  63. Is hip strength a risk factor for patellofemoral pain?
  64. Regular physical activity prevents chronic pain
  65. Stretching and heart rate variability in inflexible subjects
  66. Smoking associated with low back pain, intervertebral disc disease
  67. Cramps caused by effort, not dehydration and electrolyte shortage
  68. Recent injury had no effect on FMS scores
  69. Asymmetry of psoas and quadratus lumborum unrelated to injury
  70. No clear benefit to muscle relaxants for acute neck strain
  71. The science of trigger point diagnosis is a confusing mess so far
  72. Myoglobin in plasma after trigger point massage
  73. Cherries for soreness? Well, weakness at least
  74. What causes the burn in intense muscle effort?
  75. Dry needling for myofascial pain, review
  76. A disturbing and typical example of sloppy modern acupuncture research
  77. Promising results from athroscopic surgery for IT band syndrome
  78. Does long-distance running lead to cartilage damage? An MRI study
  79. Underwhelming: spinal adjustment and massage for back pain, neck pain
  80. The effect of leg length on back pain: a classic test
  81. Is exercise effective, or just efficacious?
  82. Lumbosacral transition vertebra prevalence, significance
  83. The Conundrum of Calcaneal Spurs
  84. A major, comprehensive report on treatments for knee arthritis
  85. Magnetic resonance imaging in follow-up assessment of sciatica
  86. Minor benefits of pilates for chronic low back pain
  87. Tuning fork, ultrasound diagnosis of stress fractures is unreliable
  88. Hamstring flexibility cannot predict lumbar joint use in reaching
  89. Women adapt effectively and minimally to wearing high heels
  90. Acupuncture for back pain, a poor quality trial
  91. Can trigger point therapy improve restricted ankle joint motion?
  92. Review: patients are “highly satisfied” with physical therapy
  93. Extremely thorough, valuable review of studies of back pain treatments
  94. Stretching, strengthening don’t affect knee and shin injury rates in soldiers in basic training
  95. Exercise reduces anterior knee pain risk
  96. Prospective Predictors of Patellofemoral Pain Syndrome
  97. Kinesio taping in treatment and prevention of sports injuries
  98. Icing delays recovery from muscle soreness
  99. Deep friction massage to treat tendinopathy: still no evidence
  100. Fascia is too tough for mechanical deformation
This is the MICROBLOG: small posts about interesting stuff that comes up while I’m updating & upgrading dozens of featured articles on PainScience.com. Follow along on Twitter, Facebook, or RSS. Sorry, no email subscription option at this time, but it’s in the works.