PubMed

Medline covers primarily biomedical literature, containing more than 13 million citations (October, 2002) of articles from more than 4600 journals published since 1958 [18]. The database covers basic biomedical research, clinical sciences, dentistry, pharmacy, veterinary medicine, pre-clinical sciences, and life science. Medline, a subset of PubMed, is a bibliographic database produced by the US Nationcil Library of Medicine (NLM). The database is available free of charge via SciFinder Scholar or PubMed [19]. 

Also databases of scientific literature (such as PUBMED, MEDLINE) provide additional functionality, e.g. they can search for similar articles based on word-usage analysis. Text recognition systems are being developed that automatically extract knowledge about protein function from the abstracts of scientific articles, notably on protein-protein interactions. 

Bibliographic Indices. This publication is listed in bibliographic services, including Current Contents and PubMed/MEDLINE. 

NLP systems are being developed to address the increasingly challenging problem of data mining for systems level content from the published literature, that is, integrating across the global expert database of biomedical research [71]. One recent approach to this problem was to develop a web-based tool, PubNet, that is able to visualize concept and theme networks derived from the PubMed literature [72]. 

It is worth noting that the past few years have witnessed tremendous development of web-based information resources. Notably, the PubMed search tool [4] has made the investigation of any life sciences topic much easier. It offers keyword and author (as well as structure and sequence) searches and covers a wide range of medicinal chemistry-related journals. This resource, coupled with e-journals, affords the medicinal chemist the tools to keep up with any research topics of interest. Because of the public nature of the Web, now a chemist can sometimes find critical journal articles on the Web that do not show up until much later in traditional literature sources. It is not uncommon that scientific meeting presentations can be found on the Web. Indeed, the Internet tools we have all become familiar with also have made the professional life of the medicinal chemist much easier. 

Figure 21.1 The emergence of computer simulation in the peer-reviewed biomedical literature as represented in NCBFs PubMed. The database is available at http //www.pubmed.org, and the searches were carried out on September 17, 2005.

It is essential that, with the use of evidence-based medicine to inform decisions in health care, the processes used in program development be as transparent as possible. Information about the limited evidence and inherent uncertainty should be disclosed and available for scrutiny, even within the software itself. In fact, in an attempt to maximize transparency, some have advocated open source development and publication of interactive software models [49, 50]. Certainly, details of methodologies, sources, and other techniques employed for development of the underlying models must be acknowledged. However, the proprietary nature of many of these programs must be taken into consideration and measures put into place to ensure confidentiality. Requested publication of all NIH-sponsored research online (in PubMed) [51] within a reasonable time frame after journal acceptance will help to ensure that these data are available in the public domain in short order. 

National Center for Biotechnology Information. PubMed Central, URL http //www.pubmedcen-tral.nih.gov/, accessed 3-10-2001. 

FIGURE 13.3 Time-course of publications L or Z and eye. The graph was produced by entering the search term lutein or zeaxanthin and eye, searching in all fields of the international biomedical research article database Pubmed for the years 1950-2008. The abstracts of the retrieved articles were checked to ensure that they were indeed relevant to the search term. The number of articles found was noted and plotted against the year of publication. 

Based on this hypothesis, from the year 1990 onward, lutein and zeaxanthin have received increasing attention in the scientific literature as possible contributors to risk reduction of AMD, an attention that continues as indicated by the still increasing number of hits in PubMed for the keywords eye and lutein or zeaxanthin (Figure 13.3) and by a steady flux of review articles on the subject (some of the more recent reviews are O Connell et al. [2006], Trumbo and Ellwood [2006], Whitehead et al. [2006], Bhosale and Bernstein [2007], Coleman and Chew [2007], Loughman et al. [2007], Renzi and Johnson [2007], Afzal and Afzal [2008], and Loane et al. [2008]). 

Fig. 10.1. The number of Pubmed Medline citations containing the keyword Fluorescence resonance energy transfer or Fluorescence resonance energy transfer + Plants anywhere in the text over the past 27 years. Although the technique has become very popular generally, its potential has yet to be fully exploited in plant research.

Some Internet search sites that I have found particularly useful include the National Center for Biotechnology information (NCBI) Entrez cross-database search page (http //www.ncbi. nlm.nih.gov/sites/gquery), which includes PubMed Central containing a limited number of free, full text journal articles. In addition, High Wire Press run by Stanford University also contains many free articles from established journals (http //highwire.stanford.edu/) and is able to search the PubMed database simultaneously. 

The literature is extensive for instance, a query for gliotoxin to PubMed in February, 2005, returned 289 hits . Reviews are available.20 22 All that can be done here is to illustrate representative types (Scheme 3). 

Access to Medline and PubMed is provided through the National Library of Medicine at http //www.nlm.nih.gov. MEDLINE contains bibliographic citations and author abstracts from more than 4000 biomedical journals published in the United States and 70 other countries. The service provides titles and abstracts for over 130 chemistry journals. 

The number of enzymes and functional proteins that are reportedly regulated by S-nitrosation is on the rise. For example, a search of PUBMED with the key word S-nitrosation revealed some 70 reports of in vitro regulation of enzymes, proteins and cellular processes that are affected by S-nitrosation. Some of these processes that have been well characterized include, nuclear regulatory proteins the NMDA receptor and the ertrocyte anion exchange protein 1 (AE1) (see review by Gaston, 2003). 

Search engine of the National Center for Biotechnology Information, including a few databases PubMed (MEDLINE biomedical literature), PubMed Central (free digital archive of life sciences journal literature), Books, OMIM (Online Mendelian Inheritance in Man, a catalog of genetically linked diseases),... 

Nguyen TV, Andresen BS, Corydon TJ, Ghisla S, Abd-El Razik N, Mohsen AW, Cederbaum SD, Roe DS, Roe CR, Lench NJ, Vockley J. Identification of isobutyryl-CoA dehydrogenase and its deficiency in humans. Mol Genet Metab. 2002 Sep-Oct 77(l-2) 68-79. PubMed citation... 

Roe CR, Cederbaum SD, Roe DS, Mardach R, Galindo A, Sweetman L. Isolated isobutyryl-CoA dehydrogenase deficiency an unrecognized defect in human valine metabohsm. Mol Genet Metab. 1998 Dec 65(4) 264-71. PubMed citation... 

Sass JO, Sander S, Zschocke J. Isobutyryl-CoA dehydrogenase deficiency isobutyrylglydnuria and ACAD8 gene mutations in two infants. J Inherit Metab Dis. 2004 27(6) 741-5. PubMed citation... 

Koeberl DD, Young SP, Gregersen NS, Vockley J, Smith WE, Benjamin DK Jr, An Y, Weavil SD, Chaing SH, Bah D, McDonald MT, Kishnani PS, Chen YT, Millington DS. Rare disorders of metabolism with elevated butyryl- and isobutyryl-carnitine detected by tandem mass spectrometry newborn screening. Pediatr Res. 2003 Aug 54(2) 219-23. Epub 2003 May 7. PubMed citation... 

Telford EA, Moynihan LM, Markham AF, Lench NJ. Isolation and characterisation of a cDNA encoding the precursor for a novel member of the acyl-CoA dehydrogenase gene family. Biochim Biophys Acta. 1999 Sep 3 1446(3) 371-6. PubMed citation... 

One of the quickest and most comprehensive ways to find academic studies in both English and other languages is to use PubMed, maintained by the National Library of Medicine.5 The advantage of PubMed over previously mentioned sources is that it covers a greater number of domestic and foreign references. It is also free to use. If the publisher has a Web site that offers full text of its journals, PubMed will provide links to that site, as well as to sites offering other related data. User registration, a subscription fee, or some other type of fee may be required to access the full text of articles in some journals. 

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