NCBI: Wikipedia for Scientists
I stumbled upon this website during my senior year in high school and it’s an absolute gold mine. The National Centre for Biotechnology Information, NCBI, is my go-to when I’m writing labs or research papers. Unlike Wikipedia which is shunned throughout the academic world for not being reliable, NCBI is the new wikipedia- there are visual aids, comparison software as well as scientific structures and notations.
When you first visit the page,it looks quite daunting- almost like the ‘95 internet explorer.
However, accessing NCBI is relatively easy. To further help their users, NCBI has tutorials and pdfs outlining the steps required to use the tools and resources adequately. Throughout the rest of this blog, I will share some tips on effectively accessing NCBI. I will be detailing the use of a couple of the Popular Resources on PubMed which include, PubMed and Nucleotide.
PubMed is the database for Medicine and Health. The database compromises of health science journals, medical literature, clinical queries, clinical trial, reviews, etc. This makes it a great resource for academics in the health sciences and biomedical profession.
Suppose you are writing a research paper on cystic fibrosis in humans and you need cited, peer-reviewed, and recent papers. The following video takes you through the efficient way of searching on PubMed.
The great about PubMed is that it allows you to filter out texts and journals that have restricted access. Moreover, you can save your results, upto 500 items, on Clipboard temporarily. This way you are organized and can filter out the results that do not add key information to your research paper.
Now, suppose you need to back up your research paper with clinical literature about cystic fibrosis. The following video shows the steps for effective clinical queries searches.
As you can see, NCBI allows you to broaden or narrow your scope, making it more accessable. Furthermore, you can look for articles strictly pertaining to Diagnosis, Prognosis, etc. which can be selected for in the Categories.
So now you have gotten everything for the theoretical aspect of your paper. However, you need to find a specific sequence on the cystic fibrosis gene, CFTR, that causes mutation. Let’s say, the mutation arises in the mRNA in the sequence, TATAATCT, NCBI is equipped with software that let’s you find this specific sequence through Nucleotide.
Nucleotide is another database with a collection of sequences and genomes data which is the foundation for biomedical and bioinformatic research.The video below shows the step-by-step procedure on accessing genes through Nucleotide.
When searching, it is useful to familiarize yourself with some keywords that fine-tune your search such as refseqgene that was used in the above video. Refseqgene is a keyword that defines genomic sequences which are well understood to be used as reference standards.
Since you are studying cystic fibrosis in humans, you must be sure to view the genes found in humans. There are filters to the left of the screen where you can pick animals or humans. In the video, you see that some numbers are highlighted, those indicate the size of gene, such as the entire CFTR gene is 257, 188 base pairs long whereas the spliced mRNA is only 6,132 base pairs long. Lastly, to the right of the page under “Analyze this sequence”, the “Find in this Sequence” is used for finding very specific sequences that might contribute to mutations and diseases.
Finally, you have finished your research paper with authentic, cited and reliable information that is not outdated, and still, you have not penetrated the surface of what NCBI holds for its users. Truly, NCBI is a gift from God.