The European Bioinformatics Institutute (EBI) at the European Molecular Biology Laboratory (EMBL) offers researchers databases that cover areas from DNA/RNA to gene ontologies and chemical biology. It includes links to all the literature covering these topics as well as data from research that falls under its nine categories.
There are tutorials on their pages that enable first time users to easily manuver their way around their website.
EMBL-EBI is equivalent to the NCBI suite of databases that includes PubMed.
Typing in a key word, phrase or the name of a gene in EBI leads to pages about your search item as seen in Figure 1. Selecting or specifying which species you want more information for concerning your gene of interest also takes one to a page with information on the structuttre of the gene and other pertinent information (Figure 2). Links to other EMBL search engines as well as external pages offer more information on different parts of the gene of interest e.g. disease associations, polymorphisms, reguulatory elements, SNPs, etc. Molecular interactions in which the gene or protein of interest is involved in can also be searched on EBI.
Molecular InteractionsEditMolecular interactions in which a gene or protein of interest is involved in can be investigated further, and articles which reference such interactions as well as the experiments deminstrating those interactions can also be accessed from EBI with their PMID and gene accession numbers . This data can be accessed through IntAct on EMBL-EBI (Figure 3). One such example is the entry on Wnt5A;s interaction with APC and dishevelled gene products for the regulation of cell migration and adhesion (1) shown in Figure 3.
Diseases and PathwaysEdit
Searches on EBI also bring up all records related to diseases, pathways and reactions that your gene of interest or protein has been reported to be involved in.
If a disease in which a gene plays a role is Mendelian in nature, the entry in EBI is linked to the disease entry in OMIM (Figure 4-5)
Figure 4, Diseases in which Wnt5A plays a role
Figure 5. Results for Wnt5A diseases in OMIM
Table format of Mendelian diseases due to Wnt5A mutations
Like a search on NCBI, current literature related to your search entry can be perused on EBI. Any relevant articles are highlighted and all results for the entry can be retrieved by selecting the Literature button on the right hand side of the page or underneath the first srticle highlighted on the results page for the key word. An example of articles returned upon selecting the literature option is shown in Figure 6.
A recent development from researchers at EMBL-EBI was the storage of data in the form of DNA (2). To do this, researchers encoded information from computer files in a DNA sequence and were able to synthesize this DNA. Upon sequencing the DNA, they were able to retrieve the information stored in the DNA code.
1. Matsumoto S, Fumoto K et al. (2010) Binding of APC and dishevelled mediates Wnt5a-regulated focal adhesion dynamics in migrating cells (pdf). EMBO J. 29(7):1192-204 PMID 20224554
2. Goldman N, Bertone P et al. (2013) Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 494: 77-80