PubMed: bridging the information gap.

O n-line literature searches of bibliographic databases such as PubMed (www.ncbi.nlm.nih.gov/entrez/query.fcgi) are now integral to the lives of clinicians. A huge amount of knowledge can be gleaned from even a basic PubMed search, while the use of advanced functions can add speed and focus. The 11 million or so abstracts that constitute PubMed undoubtedly make it one of the most significant barrier-free on-line biomedical resources. However, the scientific abstract is but one flavour of information that we use in our professional lives: full-length research articles, clinical trials databases, molecular biology data and so on all contribute to a rich information landscape. One challenge of the information age is to make the best use of new technologies to present and integrate these diverse information resources in ways that were not previously possible. Forging links between disparate pieces of information can po-tentiate new ideas that may cross traditional disciplinary boundaries. At the National Center for Biotechnology Information (NCBI) (www.ncbi.nlm.nih.gov/), one of our goals is to weave together published information — be it scientific articles, books or molecular sequence data — in such a way that the information is enhanced and the potential for making discoveries is increased. Although PubMed is a mighty stand-alone service, it is significantly enriched by the addition of links to related resources. These can contribute background, refinement and depth. In this short article, we will discuss how we are in the process of integrating PubMed with other information resources in order to build a layered approach to biomedical data. When an author submits a paper reporting a new gene sequence, it is usually a prerequisite of acceptance that the sequence is submitted to one of the public databases such as Genbank (The new sequence is then cited in the article in the form of an accession number, ensuring that any interested researchers have access to the sequence. Genbank entries in turn usually cite one or more research papers to add biological context to the data, so the GenBank sequence records incorporate links to the PubMed abstracts of the cited papers. We can make use of these to enable reciprocal links from PubMed back to the sequence information, not only for nucleotide sequences, but also for protein sequences and protein structures in their respective public repositories. In individual PubMed records, the links are labelled Nucleotide, Protein or Structure (Fig. 1). In this way, the biological data provide foundation and …