Elsevier this week further integrated the scientific literature with bioinformatics databases by launching Genome Viewer, a browser that displays information from GenBank within journal articles.
Elsevier collaborated with the National Center for Biotechnology Information to create the browser.
When article authors tag gene sequences, Elsevier matches these genes with information in GenBank and then displays the sequences in an interactive browser that includes links to the source database for users who want to dive deeper into the data.
The browser enables readers to get specific information about each DNA strand by hovering over it, and also allows readers to flip the strands, zoom in on a sequence, or go to specific positions to define tracks of interest within the sequence.
Users can also download the complete list of genes or genomes referenced in an article along with their respective GenBank accession numbers.
IJsbrand Jan Aalbersberg, Elsevier's vice president for content innovation, said in a statement that the new addition should enhance readers' experience because "they don't have to search for the gene information outside of the article."
It's also a boon for authors since the added information "enriches their article[s]," he said.
Andre van Wijnen, an associate professor of cell biology at the University of Massachusetts Medical Center and editor-in-chief of Elsevier journal Gene explained that the Genome Viewer gives users a "quick examination of sequences and primer design for genes of interest" and "permits easy alternation between long-range genomic organization and zooming to the highest magnification to obtain base-pair information."
Additionally, "the hotlink with the NCBI database is particularly useful, as it further expands functionality and permits creation of multiple sliding windows with different genomic ranges," he said.
The Genome Viewer falls under Elsevier's "Article of the Future" project, which has been ongoing for two years and aims to incorporate "digital enhancements" into the peer-reviewed literature, Aalbersberg explained to BioInform.
"The Internet has improved a lot on the scientific communication [side], but mostly in the discoverability and in the searchability and in the dissemination of the scientific articles, but the actual article hasn’t changed [much]," he said.
"Scientists ... use all sorts of digital tools [and] enhancements in their research and computational biology is a strong example of that," he added. "The author [and] the reader benefit if we put those digital enhancements that are already in the workflows from the scientist into the scientific article[s]."
As part of the Article of the Future project, Elsevier has also launched a protein viewer that displays protein information from the Protein Data Bank in relevant articles.
It works in the same way the genome viewer does; authors simply tag the gene or protein sequences in their articles and these tagged sequences are then linked to the PDB, to obtain all information and images of protein structures contained in the resources, Aalbersberg explained.
Elsevier already links gene and protein sequences that researchers tag to the appropriate databases and will continue to do that, but the addition of the viewer "bring[s] ... information inside the article such that the user who wants an initial look at all the information doesn’t need to go back and forth between the article itself and the NCBI database," he said.
The Genome Viewer isn't intended to compete with bioinformatics databases, Aalbersberg stressed; rather, Elsevier hopes to bring databases and repositories "one step closer to the user." He anticipates these types of applications will become the norm in the future.
Elsevier plans to eventually develop viewers for other databases that it currently links to in addition to GenBank and PDB, Aalbersberg said, such as the Arabidopsis Information Resource, the Cambridge Crystallographic Data Centre, ClinicalTrials.gov, Online Mendelian Inheritance in Man, the Molecular Interactions Database, and UniProt.
However the decision to develop additional viewers for these resources will be based on the desires of readers, he said, as well as other factors, such as where their data is deposited.
Additionally, each database has unique requirements that need to be taken into account that would make it difficult to simply apply the same viewer across the board, Aalbersberg said. For example, developing a viewer for data from ClinicalTrials.gov would likely require a different treatment because much of the data stored in the resource is text-based.
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