Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols

Background  

The evaluation of information retrieval techniques has traditionally relied on human judges to determine which documents are relevant to a query and which are not. This protocol is used in the Text Retrieval Evaluation Conference (TREC), organized annually for the past 15 years, to support the unbiased evaluation of novel information retrieval approaches. The TREC Genomics Track has recently been introduced to measure the performance of information retrieval for biomedical applications.     

MRSD: a web server for metabolic route search and design

SUMMARY: We present a tool called MRSD (Metabolic Route Search and Design) to search and design routes based on the weighted compound transform diagraph. The search submodule returns routes between a source and product compound within seconds in the network of one or multiple organisms based on data from KEGG. The design submodule designs a route from an appointed compound in an interactive mode. The two complementary functions, Metabolic Route Search and Design, can be broadly used in biosynthesis, bio-pharmaceuticals and the other related fields. AVAILABILITY: bioinfo.ustc.edu.cn/softwares/MRSD/.     

Characterizing phosphoproteins and phosphoproteomes using mass spectrometry.

The reversible phosphorylation of proteins plays a major role in many vital cellular processes by modulating protein function and transmitting signals within cellular pathways and networks. Because phosphorylation is dynamic and the sites of modification cannot be predicted by an organism's genome, proteomic measurements are required to identify sites of and changes in the phosphorylation state of proteins. The low stoichiometry of phosphorylation sites that accompany the multifarious nature of protein phosphorylation in biological systems continues to challenge the dynamic range of present mass spectrometry (MS) technologies and proteomic measurements, despite the preponderance of research and analytical methods devoted to this area. This review addresses some of the strategies and limitations involving the use of MS to map and quantify changes in protein phosphorylation sites for samples that range from a single protein to an entire proteome, and presents several compelling reasons as to why comprehensive phosphorylation site analysis has proven to be so elusive without a hypothesis-driven experimental approach to elicit more meaningful and confident results.     

Query Chem: a Google-powered web search combining text and chemical structures

Query Chem (www.QueryChem.com) is a Web program that integrates chemical structure and text-based searching using publicly available chemical databases and Google's Web Application Program Interface (API). Query Chem makes it possible to search the Web for information about chemical structures without knowing their common names or identifiers. Furthermore, a structure can be combined with textual query terms to further restrict searches. Query Chem's search results can retrieve many interesting structure-property relationships of biomolecules on the Web.     

Multiple definitions of food web statistics: An unnecessary problem for food web research

Three of the statistics that are regularly used to describe food web structure have been defined in two different ways. The use of these statistics by several authors illustrates some of the problems caused by the existence of two different definitions for what is, at least in name, the same statistic.     

Stable isotopes in physiological ecology and food web research

Mention the word 'isotopes' and most people will think of short-lived radioactive isotopes. Yet far more abundant than the radioactive forms and perhaps much more useful for ecological studies are the stable isotopes. Early interest in stable isotope analyses developed in the geological sciences, and their application in environmental biology has developed slowly until recently. Over the past few years, innovative applications of stable isotope analyses to studies of biological processes have been expanding rapidly, and there is every indication that stable isotope approaches will lead to major advances over the next decade in our understanding of physiological processes and fluxes through ecological systems. Studies of plant and animal physiological ecology and food webs will benefit greatly.