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Biotech Data Mining

Zonk posted more than 8 years ago | from the squirmy-thought-worms dept.

Biotech 33

Roland Piquepaille writes "In the last ten years, biotech companies have been busy accumulating mountains of data. And it's becoming more and more difficult to find useful information about interactions between genes and proteins for example. It's one of the reasons why the European Union has started the BioGrid project. In Mining biotech's data mother lode, IST Results describes this project. Among current results, the researchers involved in it have delivered a better search engine for PubMed by analyzing over-expressing genes and predicting the protein interactions that are likely occurring. And many of the tools developed by BioGrid are available for public use -- even by yourself. For more information, this overview contains additional details, pictures and references about this project."

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qlarp (-1, Offtopic)

Anonymous Coward | more than 8 years ago | (#14372891)

Happy New Year, Azores!

If I had access to all that data... (0, Troll)

PCM2 (4486) | more than 8 years ago | (#14372895)

...I'd want to find the first biotech post ever. Now that would really be interesting!

stop accepting spam blogs (-1, Troll)

Anonymous Coward | more than 8 years ago | (#14372905)

roland piquepalle is a spammer and a scammer (look up the "TDA" company he blogged about that he has associations with that ripped people off). why do we accept his garbage?

Hopefully! (3, Funny)

Anonymous Coward | more than 8 years ago | (#14372914)

Hopefully this is the last Rololand Picapal article for the rest of the year.

Lets celebrate by not clicking through to his poorly made blog!

Re:Hopefully! (0)

Anonymous Coward | more than 8 years ago | (#14372963)

Well... There is no link to his blog in the summary, so unless you are really looking for it, it is pretty hard to click through to his blog. (yes, I do know about the author link. That is not in the summary, and is not likely to be clicked.)

Re:Hopefully! (1)

Briareos (21163) | more than 8 years ago | (#14373828)

Funny enough, the ZDNet blog link says "Posted by Roland Picklepail" right at the top... *ick*

np: Lawrence - Two Minutes In August (Pingipung Plays: The Piano)

Google? (-1, Offtopic)

Ruff_ilb (769396) | more than 8 years ago | (#14372917)

I hate to be a Google whore here, but couldn't google tech be adapted to search pretty much anything?

As for the tools being free for public use, are we talking free as in beer, or free as in Linux? Either way, I'm glad, but libre free would be exceptionally amazing.

Re:Google? (1)

lvgreen (942462) | more than 8 years ago | (#14372946)

As the owner of a small Medical Device R&D company I can tell you that this is great news! It is vary hard to compete with the larger R&D companies out there and searchengins are from $1000 to $10,000 a month. There are engins that you can buy reports peice meal but they are $40 and up. So if it really is free I am all over that.

Re:Google? (1)

Forbman (794277) | more than 8 years ago | (#14381793)

If you were a chemist, how would you have felt 150 years ago when the chemical table was being "discovered", that patents could have been applied for and recieved on elements?

I guess that's my beef with Biotech and the patenting of genetic sequences in general. If you have a specific product developed off of one, then it should be patentable (i.e., genetic marker XYZ54 is a good target for identifying likely Slashdot trolls), but what if it also is a good marker for other traits? Should one group of researchers be locked out entirely because someone else identified a novel, unique use for a chemical that wasn't thought up before, or should they have to publish in a way that allows the original patent holder to expand the scope of their patent retroactively to include the new use?

I understand that patents for chemicals include the process path to make said chemical. There are chemicals where if you discover a different, novel path, then you also get to make said chemical, but not use it the way the original patentee uses it (phenobarbital used to treat seizure disorders by one company, and another company develops their own flavor of phenobarbital, say, to treat colon motility disorders).

It could very well be a meaningful new use, in which case either the original patentee can buy out...er, exclusively license, the new use, or it's just cheaper to buy the chemical from the original patentee for the new use...

Re:Google? (1)

GooddSkittles (942360) | more than 8 years ago | (#14372960)

NEW FROM GOOGLE GoogleGenes Beta Search your own genetic code to discover any flaws or mistakes in your programming, and learn to debug yourself. Make yourself taller! Change your natural hair color! Change your eye color! Anything you dislike about yourself can now be changed with the help of Google!

Re:Google? (1)

Memnos (937795) | more than 8 years ago | (#14374580)

The problem is not so much finding the relevant data, although that is very important. The "holy grail" is being able to exchange the data in a meaningful way - to be able to the mine the data that exists across disparate researchers and their systems. This is not in the search engine solution space. The EU and the US are making some slow progress on this, but it is remains a vexing problem. (I am not a Mirobiologist, but I do help them _try_ to design compatible systems -- NOT easy.)

Re:Google? (1)

Memnos (937795) | more than 8 years ago | (#14374626)

Addendum: Prova is great but not surprisingly BioGrid is not the be all and end all.

Great, idea my left sock has been missing too (1)

RedLaggedTeut (216304) | more than 8 years ago | (#14375132)

Maybe Google could find my left sock for me too? I lost it somewhere in my aparment it must be easy for google, and I'd pay a few dollars too.

"Google, the search company"

and while we are at it, make it:

"Google, the search and destroy company"

It's New Year's Eve... (1)

GET THE FACTS! (850779) | more than 8 years ago | (#14372931)

It's New Year's Eve and you're worried about biotech data mining?!?

GET SOME PRIORITIES, PEOPLE!!!

Ummm... (1, Insightful)

NotQuiteReal (608241) | more than 8 years ago | (#14372940)

Like the calendar changing days is more important?

Do you cream your pants if your total bill at Wal-Mart ends in double zero?

Re:It's New Year's Eve... (1, Insightful)

Dunbal (464142) | more than 8 years ago | (#14372957)

GET SOME PRIORITIES, PEOPLE!!!

      What is even worse is that both you and I are here reading this...

Re:It's New Year's Eve... (0)

Anonymous Coward | more than 8 years ago | (#14373092)

the worst is I am here, not only reading, but commenting on your fagdance!

Re:It's New Year's Eve... (1)

radiotyler (819474) | more than 8 years ago | (#14373098)

I'm in Iraq. There's no beer here. What's your excuse?

Roland the Plogger is Back! (4, Interesting)

Animats (122034) | more than 8 years ago | (#14372958)

He's Back! I thought we were rid of Roland the Plogger, still trying to drive traffic to his blog. But no. Must be some new editor on the night shift who let this one through.

Re:Roland the Plogger is Back! (0)

Anonymous Coward | more than 8 years ago | (#14373049)

Must be some new editor

nope, it's just zonk.

FIRST!! (1)

pupupupupupupupupupu (939687) | more than 8 years ago | (#14372964)

Nyah!

Re:FIRST!! (0)

Anonymous Coward | more than 8 years ago | (#14372971)

Swing and a miss, lunch meat.

Re:FIRST!! (0)

Anonymous Coward | more than 8 years ago | (#14372986)

No, that would be Mr. 9:40 from the Azores.

Ahh, I remember the /. post several months back that was taken back - disappeared after 5 minutes and everyone who wanted to post about how idiotic it was had to go to the next post to rant. Would have been nice to see something like that happen to this one.

But, hey lighten up on Roland the Headless Blogger, after all, his life is so worthless that he is doing /. on New Years eve.

first post as an anonymous coward

Say what you want (too bad he got a minus one) at least Mr. Azores just got done shooing all the drunken reprobates out and trying to figure out how to clean up the mess - aw hell - I'll just check out /. said he.

Mod me Down or Mod me Funny... (2, Funny)

NotQuiteReal (608241) | more than 8 years ago | (#14372965)

... either way I don't win "karma".

A lot of posts from here on out are implicit or explict observations that it is "New Years" at different times in different time zones all accross the globe. Just ignore them.

Anyhow, for the on-topic part... the article describes what I think is reasonable follow-up to other research. E.g. Bio-tech is a science just like other, and needs to be confirmed and used as a starting point for further research.

But that is boring to say.

MERRY NEWYEAR!!!!!!! (1)

pupupupupupupupupupu (939687) | more than 8 years ago | (#14372984)

ke ke ke ke ke ke ke ke (^______^)-V-

pay the man (1)

hostingreviews (941757) | more than 8 years ago | (#14373036)

I think these scientists deserve kudos, karma and lots of money. It's men and women that do boring jobs like this that will someday benifit humanity in ways we can't yet understand.

I dont see why not (1)

Septicmadman (912044) | more than 8 years ago | (#14373057)

They have been accumualting lot of data. Well this is a forgone conclusion in any area of scientific research esepcially on of demand and has a direct relation to economic stability.

The ability to search data for a highly pertinent area of research also a good idea. Perhaps the best ways to do this is not to establish one effective means of searching, but multiple.

That being said just predicting results should be sufficient. It should be the means for basing an industry, and has proven to be succseful, in well, everything.

Maybe it is just me, but the breakthoughs will always come from the entrepenaurs or at least that is the my ideology for humanity.

  Completly Out of Context

Misread that topic (1)

FryerTuck (883048) | more than 8 years ago | (#14373509)

At first glance I thought it said Biatch Data Mining.. and subsequently had privacy concerns for ex-girlfriends.

I worked for a bioinformatics company ... (3, Informative)

TallMatthew (919136) | more than 8 years ago | (#14373731)

... and I'm not sure this data is that useful.

What they're hoping for is to find commonalities among individuals with certain traits, genetic diseases obviously, but also predisposition for certain drug therapies. Medications work for some people and not for others. It would be marvelous if you could do a genetic scan of someone and predict whether a certain drug therapy would work on them. It could also bring drugs to market that aren't already because they don't help some people and are in fact dangerous to others.

Great idea, but there are serious obstacles. First, the dataset that comes off a DNA sample is enormous. You can currently sample DNA in about 500,000 places, each location represented by letters, those letters representing the type of molecule present in a certain position on the double helix. There are about a half-dozen of those, so what you end up with is half a million of these letters juxtaposed. And it's not as easy as "if there's an n at position 232.922, this drug won't work for you." It's more like "if there's a series of letters in one place, and there's a series of letters in another, then you can either have a series in this place or a series that one, etc.".

Unfortunately, you don't know how long the series is and you don't know where, you don't know what depends on what. You just don't know. It's a statistical nightmare. You should see the algorithms they throw at those things.

And of course, environment may play a role in such things, too, so you don't even know if what you're looking for means anything.

Great idea, hope it works, not holding my breath.

Re:I worked for a bioinformatics company ... (1)

espressojim (224775) | more than 8 years ago | (#14374563)

Actually, you can 'sample DNA' (I think you mean genotype) at any one of the 3 billion bases in the genome, provided you can develop an assay.

The 500K you refer to could be from one of the (now standard) affymetrix 500K chips that have a standardized set of variants to test. They exclude a number of other markers, but via indirect evidence (knowledge of haplotype structure in the population), you can test other areas as well, and increase your coverage of the whole genome.

I'll agree that the statistics are complicated. What you need are ways to define your patients that are matched to each other, except for the phenotype in question you want to test. I find that this information is usually lacking (hell, even the researchers are often saying "I wish that I had more phenotypic data available for my cohort!")

What I'm interested in is looking at their algorithms, and seeing if there's anything I can use for our own work. If they have some well implemented tests that I don't, then that saves me the effort of developing them myself.

Left-handed DNA (2, Interesting)

srblackbird (569638) | more than 8 years ago | (#14374305)

The DNA in the fist picture is LEFT handed instead of right. That's WRONG!
http://www.lecb.ncifcrf.gov/~toms/LeftHanded.DNA.h tml [ncifcrf.gov]

Re:Left-handed DNA (0)

Anonymous Coward | more than 8 years ago | (#14375993)

Awesome site :) Thanks -I hadn't realised it was so widespread!

Questions (1)

adityaramani (807674) | more than 8 years ago | (#14393946)

There are a NUMBER of large scale efforts to perform the same in the US. I find it very weird that BioGrid, an European System is being tested on PubMed, a database maintained by the NIH/NCBI in the US. I am finding it weird that the author would choose to quote an obscure project in Europe. The integrated modeling of Biological systems is an extremely complicated problem, with data varying from sequence to microarray to literature to god knows what, and the author makes it look so simple. That is not the case. Even the integrated study of 2 data sources (say sequence and protein expression) is an extremely complicated problem.
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