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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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« Microwaves Aren't Magic | Main | How To Get Useful Data Out of a Drug Patent »

September 30, 2009

Ignoring Patents?

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Posted by Derek

There's a letter in the latest Nature from two researchers in Halifax that makes a point which isn't made often enough. Why do so many papers in the literature ignore patent references?

Why are patent citations so conspicuously absent across academic journals, with most even omitting formatting instructions for these in their author guidelines? Patents present novel, rigorously reviewed unpublished work, as well as providing an unmatched resource for detail.

We randomly selected one month (December 2008) and reviewed all citations in the reviews, articles and letters/reports in Nature (1,773 citations) and Science (1,367). These citations included textbooks, http://arXiv.org preprints and abstracts — but no patents.

They go on to point out that searching the patent literature, which traditionally was rather a pain, is much easier now, as is access to the patents themselves. And they have a point. When I was in graduate school in the 1980s, getting a procedure out of a patent was really considered an absolute last resort - it was a special order in the library, and you had this vague feeling that there was some sort of trickiness going on, that none of those syntheses were ever actually supposed to work, anyway.

Not so. While the patent literature is indeed full of junk, the open literature is, too. They're not exactly peer-reviewed, true - but journal papers have a much lower chance of having to stand up in court, so things sort of even out. And as far as organic synthesis is concerned, patents are full of real procedures to make real things (and often enough, with real spectral data to support the claims). Most of the compounds I've made in my career that have seen any light of day at all have done so in patents, and they're real as can be.

I've complained several times when refereeing papers for publication about the lack of relevant patent citations in them. And I'd advise others to do the same - this branch of the scientific literature deserves its due.

Comments (23) + TrackBacks (0) | Category: Patents and IP | The Scientific Literature


COMMENTS

1. Canageek on September 30, 2009 1:50 PM writes...

I think it might be cultural. I'm working on an undergrad in chem and I've already had a professor advise us to avoid patent citations because they are so unreliable, with companies advertising great compounds they have invented and very little proof.

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2. Greg Hlatky on September 30, 2009 1:53 PM writes...

Quite so! While chemical patents are legal and not scientific publications, they certainly are publications that contain chemistry and deserve the same citation consideration that journal articles do. Now that patents can be viewed and downloaded online, there's no excuse for ignoring them except, possibly, the inability of most academics and their students to read and understand them.

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3. Biologist on September 30, 2009 2:06 PM writes...

To my eyes (untrained by law school), patents are pretty much unreadable. The claims seems to hide, rather than reveal, what really has been invented, the introduction obfuscates the real state of the art, etc. I think many scientists feel that way and avoid reading patents.

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4. milkshake on September 30, 2009 2:26 PM writes...

for that reason I tend to ignore the intro and the patent claim and skip right to the experimentals.
By looking at the structures of compounds in examples one can often get some sense of the SAR and the project history.

You can see right away if the procedures were written by a competent chemist, some sloppy hack in hurry, or a lawyer. When the yields are missing and there are no spectra and the reaction/workup details are vague, it means crap - to be approached with great caution (I have seen blatant mistakes in patents, and half-baked irreproducible stuff.) And a present-tense written "prophetic" examples are not worth bothering with at all.

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5. HelicalZz on September 30, 2009 2:26 PM writes...

I would think that Science and Nature, journals known to focus on the more novel research, would not have a high ratio of patent references. Still the point is fair, I've not published for too long, but did not tend to reference patents. Often, and particularly in terms of a technique or interpretation of a result, there will be a literature reference that follows on the data incorporated into the patent. Since the literature tends to have more discussion I can certainly see where a literature reference would be preferred over a patent one when given the option of either/or.

Plus, patents are just painful to read. The intentional redundancy of language and bland interpretive delivery makes most scientific literature read like a Robert Ludlum novel by comparison.

Zz
P.S. Substitute Dan Brown for Ludlum if you are too young to appreciate the difference.

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6. HelicalZz on September 30, 2009 2:31 PM writes...

OCD: bland 'un'interpretive delivery

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7. startup on September 30, 2009 3:34 PM writes...

Part of the problem is that many patents are so damn long. In the old times it was quite common to see a 3-page patent with a synthesis or two in it. Nowadays 300-page monstrosity doesn't surprise anyone. A good question actually - how big is the longest chemical patent out there? And I can't entirely agree with you on access, while it is free, getting full texts is still a pain, although admittedly less so at USPTO website where all the patents I would trust are anyway.

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8. Sili on September 30, 2009 4:11 PM writes...

HelicalZz, you're the first one to put Dan Brown in a context that makes me sorta wanna have a look. I used to love Ludlum as a kid.

For what little it's worth the organistas at my place read the patents - one of them even wrote a little programme to automatically retrieve the whole thing instead of just one page at a time (I have no idea what the deal was - I didn't use it, myself). This was a group working on anti-retrovirals (I think).

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9. Arjun on September 30, 2009 7:22 PM writes...

My experiences, consistent with some of those above, have been that patents are often deliberately obfuscatory. They may suggest a synthetic approach, but I have never found a reliable prep in a patent. I would usually see language like "1-10g of amine A was added to 50-500 mL of an appropriate solvent and stirred for between 2 and 20 hours and a temperature not less than 0 degrees and not more than 100 degrees."

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10. Old Pharma Guy on September 30, 2009 7:54 PM writes...

Being a pharma guy, I agree about the utility of patents. Furthermore, it's wise to search the patent literature to look for advances in the science before manuscripts are published. I've taught a few of my academic collaborators how to mine the databases and they've been surprised.

Often, I've found materials published in patent filings months or a year before the paper was published.

On a separate note, journals should take patent data more seriously, since it does represent prior release of IP to the public domain prior to publication in scholarly journals. Think about this if your PCT patent filing is published and you state that you have not published your data prior to submission to the journal.

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11. RTW on September 30, 2009 8:15 PM writes...

I think there has been a change in culture with regards to Patent literature procedure writing. Early in my career, it seemed to be true that patent procedures almost never worked and seemed to be written in such a way as to leave the greatest level of leway of interpretation. Things like the reaction was run with 1 to 20 eq of the following bases.... In pick one from this list of solvents at a temoperature from 20 to 60 degrees C.... Upon isolation of the desired product gave from 10 to 90 % yield.....

Later I began to notice that much more level of detail and less use of obsure language was appearing in patent procedures. Additionally patent department was requiring more detail and selection of the BEST procedures, rather than just one that worked. Biological data was still reported in such a way as to obscure the compound we would probably use as a lead. We didn't want to make it too easy on our competitors....

7. Startup is correct in his observation, and the change I have observed is the result. When one wrote rather generic procedures and methods. A patent could be many fewer pages. Now with each compound explicitly exemplified they are huge.

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12. BCP on September 30, 2009 9:43 PM writes...

I'd agree with others, there are several reasons why patents aren't cited:

Lack of clear "to the point" writing - for reasons stated above

Questions around reproducibility or whether the work was actually done (although it should have been), and in the case of process patents, these are some of the best published procedures around IMO.

Also, how about lack of an open "peer review" process? As long as the patent examiner doesn't find that you are claiming work that has been done previously, there's no review by others to provide feedback/criticism to the authors. Frankly we can all think of journals that barely seem to make this grade as well, but I suspect this may also be a factor in academic circles. Consequently I find that the quality of many patents are judged by the organizations from which they originated.

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13. Smoki on October 1, 2009 3:33 AM writes...

I agree that some patents might be unreliable, but scientist even ignore some older very important patents that have already proven to be solid. I included a patent citation in my PhD thesis and I didn't even know how should I format it. In several years of reading loads of articles, I cannot remember a single patent citation appearing in them.

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14. ChemSpiderman on October 1, 2009 6:14 AM writes...

It is much easier to access patent information online nowadays and, for chemists specifically, efforts have been made to make structure-searchable patent data available. Structure-searchable sites providing links to patents have been made available by both IBM and SureChem. The ChemSpider site was recently linked up to the SureChem site as discussed here: http://tinyurl.com/y8gnpqt. If people are using structure-based online resources such integrated resources are going to remove the hurdles to accessing information for inclusion in references.

Relative to Smoki's comments....I don't recall reading any formatting rules for patents in the instructions for authors sections for most journals...

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15. DrCMS on October 1, 2009 6:16 AM writes...

As an idustrial chemist I find patents much more useful than acedemic papers. They are free to get hold of and contain the details of experiments that worked and has probably been done on a large scale. I think too many people look at a patent think "this isn't laid out like the journal articles I'm used to reading" and then give up.

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16. lysine on October 2, 2009 12:42 AM writes...

Part of the under-representation of patent citations may be due to the "double publication" effect - ie. a public(ion appearing on the same stuff as the patent. I always cite the paper rather than the patent in those cases.

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17. Curly Arrow on October 2, 2009 7:13 AM writes...

I try to be optimistic about patents and I keep returning to them for experimental procedures and I keep failing to reproduce the chemistry. I have never succesfully used a patent procedure (except my own). Maybe I've just been unlucky?
I agree there is tons of rubbish in the journals but it's easily accessible, it's easy to find the experimental procedure and the compounds are well characterised.
As a consequence I only head for the patents when I can't find a reasonable journal procedure. D!

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18. lysine on October 3, 2009 10:40 PM writes...

Oh, and there's also the issue of generic claims. If you find a compound in a paper there's a fair chance it's been made (computational studies notwithstanding) but if a patent comes up in a SciFinder compound search there's a chance it's a general claim and hasn't actually been made. Of course Tet Letters with no data are just as bad...

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19. researchfella on October 3, 2009 11:53 PM writes...

In my view, the best place to find medicinal chemistry information such as SAR is in Bioorg. Med. Chem. Lett., and the best place to find the experimental procedures for most of the compounds in those articles is in the patent literature. Once in a while you might find all of it in J. Med. Chem., but the the patent literature is invaluable for experimental procedures.

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20. CMCguy on October 4, 2009 10:12 AM writes...

I think #16 lysine hit the nail on the head for much of the lack of Patent cites but agree there still is problems with general avoidance and should be part of undergrad/grad education particularly with greater ease of access now (my undergrad days I had to get a couple Patents from intra-library loan from Law School which took two weeks and didn't add anything new). As Derek's follow-on post indicates there is a learned skill to searching and reading Patents. I currently am most concerned about infringement so often only look at the claims which is all that matters from IP view.

As far as reproducibility of Patents I have mixed observations. As general procedures most are as as good as Literature though closer to communications than full papers. Following Medchem patents will produce the target compound(s) although yields and other data can be off. On the other hand Process Patents often seemed to suffer that same mode where "one skilled" in the art would have to perform substantial additional effort to achieve the results reported much less be applicable to large scale productions.

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21. pi* on October 4, 2009 2:49 PM writes...

Science and Nature, as HelicalZz said, focus on the highly novel, presumably things that patents aren't relevent for.
They also only allow 20-30 references for an entire article.
Much less than half of science or nature papers even deal with subjects relevant to patents (technology or 'hard science' based topics).
This seams to me like a relevant subject, but they chose to look at journals in which patents, for very good reasons, aren't going to be referenced.

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22. anon on October 5, 2009 7:59 AM writes...

Two comments.

1) It's nice that issued patents show up as full PDF's in Google now-- VERY helpful.

2) I was recently annoyed to read a paper that REALLY should have cited an older patent of mine-- the new work was pretty close--- and made NO mention, whatsoever. They could have "Scifinder'ed" before going to press!

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23. MikeyMedchem on December 15, 2009 3:58 PM writes...

catching up on reading of my Nature RSS feed, I came across a letter from David Piehler(see doi:10.1038/462276b) that addressed this topic in a direction different than the original letter Derek brought up. An excerpt:

"An employee publishing a patent citation may be exposing his or her employer to liability for triple damages, and many firms ask their technologists to remain ignorant of the patent literature. US patent law awards triple damages for the period in which an infringer wilfully violates intellectual property. Ignorance is a valid defence against such a claim, so, before contemplating legal action, owners of intellectual property will often alert potential infringers, preemptively starting a wilful-violation clock. Widespread patent citation could even lead corporate lawyers to advise corporate scientists to avoid even reading or citing papers that cite patents."

The letter also goes on to comment on the various scientific shortcomings that may become apparent but do not result in retraction or correction, and that patents are not peer reviewed (and therefore, as mentioned by numerous comments above, _reader beware!_)


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