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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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September 6, 2012

Databases and Money

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Posted by Derek

The NIH has been cutting back on its funding (via the National Libraries of Medicine) for a number of external projects. One of those on the chopping block is the Biological Magnetic Resonance Bank (BMRB), at Wisconsin:

The BMRB mission statement is to “collect, annotate, archive and disseminate (worldwide in the public domain)” NMR data on biological macromolecules and metabolites, to “empower scientists” and to “support further development of the field.” Despite its indisputable success in achieving these goals, the BMRB is facing serious funding challenges.

Since 1990, the BMRB has received continuous support from the National Library of Medicine (NLM), at the US National Institutes of Health, in the form of five-year grants. However, the BMRB obtained its latest grant renewal in 2009, accompanied by a sharp reduction in the funding level. It was also to be the last renewal, as the NLM announced that funding for all external centers would be phased out as their grants expire. Thus, as of today, the BMRB has no means of financial support after September 2014.

That editorial link above, from Nature Structural and Molecular Biology, also has a several other database projects formerly supported by the NLM. These are far enough outside my own field that I've never had call to use any of them as a medicinal chemist, but (as that last link shows) they are indeed used, and by plenty of researchers.

This problem won't be going away, since the volume of data produced these days shows no sign of any inflection points. Molecular genetics, protein biology, and structural biology in general are producing vast piles of material. Having as much of it as possible brought together and curated is clearly in the best interest of scientific research - but again, who pays?

Comments (19) + TrackBacks (0) | Category: Biological News


COMMENTS

1. road on September 6, 2012 3:03 PM writes...

The link to the article is broken. The correct link is:

http://www.nature.com/nsmb/journal/v19/n9/full/nsmb.2371.html

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2. bacillus on September 6, 2012 4:15 PM writes...

Does the BMRB currently charge users, or is this precluded under the NIH contract? If reasonable user fees could be charged, investigators could build these charges into their grant budgets. The proponents of the BMRB in the accompanying article believe that its work is critical to them, so I'm sure they'd be ready to pony up! Talk is cheap, and a user fee system would better illustrate the usefulness or otherwise of the product. Who doesn't love low cost scientific services? However, the minute they have to start charging on a complete cost recovery basis, it's amazing how usage can plummet. I've seen this happen plenty of times when investigators start having to pay commercial rates for animal per diems. I do sympathize with them, since we had an NIH grant worth several million dollars that was yanked at the Council review stage having aced the study section review (a first according to the NIH program officer), clearly another example of the hard times at NIH and the hard decisions they are being forced to make.

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3. Martin on September 6, 2012 4:35 PM writes...

Seems a shame but one thing I have noticed that makes BMRB less useful to medicinal chemists is the fact that it doesn't actually warehouse NMR structures per se, but rather the raw chemical shift data, assignment and restraints data usually. So if for example you wanted to get hold of someones NMR structure of a smallish peptide which falls below the size cutoff of what RCSB/PDB will accept, your chances of getting a set of 20 structures plus an average from BRMB are slim. You could of course get a friendly local NMR person to run the raw data through Xplor/CNS etc for you but that is not exactly convenient.

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4. Anonymous on September 6, 2012 7:34 PM writes...

These are US taxpayer subsidized, correct? Yet they are open to the world, too? It would be nice if the other developed nations chipped in.

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5. gippgig on September 6, 2012 9:23 PM writes...

Computer power is so cheap nowadays why would databases need funding in the first place?

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6. Londonlad on September 6, 2012 11:17 PM writes...

'Computer power is so cheap nowadays why would databases need funding in the first place?'

Mitt, welcome to In the Pipeline! Great to have a politician interested in the sort of stuff we care about.

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7. CB on September 7, 2012 12:00 AM writes...

The BMRB has been incredibly important for advancing basic developments in NMR.
For instance: Chemical shift prediction of secondary structure and dihedral angles.
The calculation of protein structures based entirely on NMR chemical shift assignments.
The BMRB aided these developments.

A fee system on the data acts as a wet blanket on basic research, innovation and discovery. If you want to test a speculative idea, or you're just curious and want to check the database for correlations or variations, the cost is an issue. Researchers aren't going to satisfy their curiousity about questions indirectly related to their research if a purchase order is involved. Serendipity is diminished.

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8. Morten G on September 7, 2012 4:19 AM writes...

@4. Anonymous
Really hope you aren't a scientist. Hope even less that you are a politician. "Are you saying that a dirty European scientist used research funded by American taxpayers for some purpose I don't understand!? To the war chariots!"

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9. MolecularGeek on September 7, 2012 8:22 AM writes...

@5 gippgig
Raw computing power is much more affordable than in the past, but it certainly isn't free, and the cost of building and maintaining a curated data repository on top of the raw platform is not trivial. It's easy to start serving raw data from an old PC beside your desk at work, but when people actually start depending on that data being there to do their work, their demands get expensive. Ask anyone here in the industry with a company that has been running more than 5 years how much they spend to keep their compound registries working.

MG

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10. SP on September 7, 2012 9:17 AM writes...

I assume Pubchem is one of the most relevant to drug discovery, is it commonly used by med chemists or HTS biologists?

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11. MolecularGeek on September 7, 2012 10:08 AM writes...

PubChem is an intramural project, and so won't be directly affected by this. It certainly gets around , but how much directly by HTS and MedChem folks, as opposed to being grist for the modeling and data-mining crowds is a harder question.

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12. HTSguy on September 7, 2012 10:14 AM writes...

I'm in the academic world these days and when someone discusses a possible screen with me, the first thing I do is look in PubChem to see if a similar screen has already been run.

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13. Anonymous on September 7, 2012 10:25 AM writes...

@5

Basically you need to hire a full-time IT professional (or three) to keep the database running smoothly. Someone has to fix things when the computers crash at 2 AM, and upgrade hardware/software to keep up with a database with growing information and demand.

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14. Tom Womack on September 7, 2012 12:42 PM writes...

@4: in the case of the (larger, older) Protein Databank, there is the PDB at Rutgers, PDB Europe at the EBI near Cambridge, and PDB Japan at the University of Osaka.

Salaries are always the expensive part of this kind of project - the BMRB database dump is four gigabytes long, you could mail out a memory stick with the whole database on to every user annually for the price of one administrator, or host it on Amazon S3 for much less than the cost of providing liquid helium to one high-field NMR machine.

But what you can't do is sanity-check new entries that way. Huge databases of easily-checked Truths are trivial (see www.factordb.com for a nice example), huge libraries of information that needs curating are very much not.

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15. Anon on September 9, 2012 5:41 AM writes...

Just a nit -

It's the "National Library of Medicine", not Libraries.

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16. Vlad on September 9, 2012 7:38 AM writes...

NIH should support development of data standards and enforce use of these standards by NIH-supported research. Private entities will assemble standardized data into database and provide access either for fee or advertisement-based. I am not familiar with the specific type of data. But working a lot with genomic data I argue that data cleaning/curation is most time consuming (i.e expensive) part of database support.

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17. Tom Womack on September 9, 2012 9:37 AM writes...

For-fee data availability would ruin a lot of these services, because one of the great uses for big amalgamated databases is in doing statistics on the whole lot. Advertised-based isn't terribly helpful either in that context, since no advertiser will pay for hits produced by wget as you pull the database down.

This is more difficult than it looks - there are a number of protein-structure statistics papers which tell you much more about the REFMAC restraint function than about the geometry of proteins.

Inevitably the curatorial organisations are very busy; so an option where the curators of the data are the only institution that can work with the data cheaply enough to get the analyses to work well is not really acceptable.

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18. Anonymous on September 9, 2012 3:11 PM writes...

Morten G:

I didn't say that. (BTW, I am in Europe for the week and thorougly enjoying it). The snark here is incredible by many on this blog - although there are many good contributors, too. The point is, why not have all those benefiting (North American, European, Australasian developed countries) share the cost if there is the potential that the benifit is to be lost for all? That's a rhetorical question, but maybe not to the expert snarkologists. To me there is an obvious answer (although it may not be a poliitically easy answer).

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19. DensityDuck on September 10, 2012 12:41 PM writes...

Orbital mechanics was developed by doing curve fits to recorded data of planetary positions--and that data was recorded to years, usually decades, sometimes centuries. And to fully understand that mass of data, we had to invent calculus.

Meaning that, if we hadn't had that huge repository of curated data, then we wouldn't have calculus.

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