Slashdot Mirror
Datamining Medline for Gene Interactions - Pubgene
An Anonymous Coward wrote: "According to an article in the 5 May 2001 issue of New Scientist , biologists in Norway have developed a computer program to datamine Medline to predict interactions between genes. Some of the relationships hadn't been predicted before and were found to be real. The scientists' PubGene database and tools are available for experimentation." Wow.
Interesting technique, but it depends in large part on the use of a standard nomenclature. If a protein is known as "p89" in one article, and as "acetylcholinesterase II" in another article, a link cannot be established so easily.
This technigue, morover, appears only to collate published interactions-- helpful, perhaps, in guiding the conduct of basic research, and the avoidence of duplicate studies-- but less useful when the goal of a researcher is determining the function of unknown genes, or putative protein products. In those cases, protein fold databases or motif databases are much more useful.
Can one give Pubgene a pdb or fasta file-- and find papers on homolougous genes or structurally similar proteins-- or must one use BLAST, or a fold recognition algoritm prior to searching Pubgene?
This is interesting. I used to work at a place trying to do "meaning based search" in the medical field. They were working on among other things ontology based search and a search for protein-gene relationships.
/labbook and a host of others are working on this stuff to sell to pharama companys to do better search and allow quicker more accurate drug creation.
There was a paper in the office of some proffesor who used a brill learning algorithn with existing genes and then had it try to guess what a ramdom genes did. It did very well in the test despite the "primitive" ai.
3rdmill and spotfire
There is a lot of computing power in the life sciences field,and a lot of data created with gene-clips and assay data. People can't sort it all out anymore some computer analysis makes everything faster. Look at the human genome.
College isn't so bad, it all depends on where you go. No one makes you live in the dorms at a public university (at least not a UC). I understand your problem with the casual interest vs. career, but you do have opportunities to learn outside. I'm taking a class in Roman History because it's required for me to graduate as a general requirement. Ancient history is something I'm fond of, but not something I'd major in. You do have the opportunities to look around though. I know tons of people who spend their first two years just looking around. Changing majors is a normal and constant thing. The goal of college isn't generally to trap you in to what you want to do, but let you feel around a bit (a lot more than in high school!) and finally pick a course. Even then there are options. I'm majoring in molecular biology, with a specialization in computing, and an English minor :-)
"I may not have morals, but I have standards."
"I may not have morals, but I have standards."
It's good that this is done in the open. I would be uncomfortable with genetic engineering being an open source discipline (ie. downloading a gene set and coding your own modifications to it then compiling it into a living creature), but I'd much rather have the knowledge out in the open than locked up for who knows what to happen to it.
Even Slashdot wants to hide some things
Genome@home
First off, yeah... that reaction pretty much sums it up. "Wow."
But I find it interesting that their method was so simple. It didn't involve any real complicated methods... basically a glorified text scanner. Yet, it was able to predict some new interactions that hadn't existed before. Still, it was only 7 times better than random guessing... I wonder if that could be improved any?
Humorless sig goes here.