March 04, 2011

Databases: The Facebook of the Molecules involved in Life

The objective of biomedical scientists is to discover new medicines to cure diseases and to be able to detect them with new techniques which are more rapid, cheap and precise. In this field of research an enormous amount of information is generated with very powerful equipments (such as the ones used for the HUMAN GENOME PROJECT), producing huge files containing the sequence of nucleic acids (DNA, RNA) and protein sequences, protein 3D structures, and so on. So, where can we store all of this information? And how can we access them quickly? Where can we read scientific articles without going to the local library? The answer to all of these questions is the same: databases.

The databases are mainly maintained by big research associations such as EBI (the European Bioinformatics Institute) which is European or the NCBI (National Center for biotechnology information) which is American. As it was mentioned previously in our Scientific Collaborations article, the interaction between different organisms allows this to be possible.

In the NCBI database you can explore the gene region (literally walking among the chromosomes , as if you were using Google Maps), see the variations among people, check the protein database, You can also find PubMed, the bibliographic database; GenBank, the nucleotide sequence database; and the BLAST algorithm for sequence comparison, and so on. Similar results can be found in the Ensembl database.
If you are interested in proteins, you can check out the uniprot/swissprot database, where you can find biological information, the secondary structure of the protein (based on real-life experiments), the sequence of the protein and the bibliography. And even more interestingly, you can check the 3D structure of the proteins (based on real-life experiments as well) in the Protein Data Bank, you can find related information of the protein, bibliographic references, and the most exciting part, you can play with the Jmol viewer, moving the protein, and if you have the right pair of glasses, you can watch it in real 3D (yes, like in Avatar).

And exactly as on Facebook, you can check the “Friends” list of the molecule of interest, which could be the protein coded by this gene, related publications, gene ontology (gene and gene product information in several species), and so on, because all of this information is interconnected. The swissprot database is famous for having the links well up-to-dated. Moreover, you can find the “Photos” of the molecule of interest. 

Before spending a lot of time and money in crazy experiments you can take a look on this databases to see if somebody else did the same experiment on the same molecule before or in a similar one which you can transfer information from. The best part is that if you don't know how to use these tools you can just click on the tutorial link and they have even videos where you can learn how to play with them! Scientists use these tools everyday in the lab before designing an experiment or when analyzing  results, and even more, bioinformaticians (nerdy scientists than only use computers for their research) can even publish articles only by analyzing the information of this databases and using other programs to generate predictions, models or deep analysis of this information.

To summarize, databases are a user-friendly and open access way to obtain biologically relevant information which is used worldwide in research institutes, hospitals, industries and universities.

Diana Rosentul

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