SUMMARY: Progress in high-throughput genomic technologies has led to the development of a variety of resources that link genes to functional information contained in the biomedical literature. However, tools attempting to link small molecules to normal and diseased physiology and published data relevant to biologists and clinical investigators, are still lacking. With metabolomics rapidly emerging as a new omics field, the task of annotating small molecule metabolites becomes highly relevant. Our tool Metab2MeSH uses a statistical approach to reliably and automatically annotate compounds with concepts defined in Medical Subject Headings, and the National Library of Medicine's controlled vocabulary for biomedical concepts. These annotations provide links from compounds to biomedical literature and complement existing resources such as PubChem and the Human Metabolome Database.

The biomedical research community relies on a diverse set of resources, both within their own institutions and at other research centers. In addition, an increasing number of shared electronic resources have been developed. Without effective means to locate and query these resources, it is challenging, if not impossible, for investigators to be aware of the myriad resources available, or to effectively perform resource discovery when the need arises. In this paper, we describe the development and use of the Biomedical Resource Ontology (BRO) to enable semantic annotation and discovery of biomedical resources. We also describe the Resource Discovery System (RDS) which is a federated, inter-institutional pilot project that uses the BRO to facilitate resource discovery on the Internet. Through the RDS framework and its associated Biositemaps infrastructure, the BRO facilitates semantic search and discovery of biomedical resources, breaking down barriers and streamlining scientific research that will improve human health.

Abstract Motivation: The elucidation of biological concepts enriched with differentially expressed genes has become an integral part of the analysis and interpretation of genomic data. Of additional importance is the ability to explore networks of relationships among previously defined biological concepts from diverse information sources, and to explore results visually from multiple perspectives. Accomplishing these tasks requires a unified framework for agglomeration of data from various genomic resources, novel visualizations, and user functionality. Results: We have developed ConceptGen, a web-based gene set enrichment and gene set relation mapping tool that is streamlined and simple to use. ConceptGen offers over 20 000 concepts comprising 14 different types of biological knowledge, including data not currently available in any other gene set enrichment or gene set relation mapping tool. We demonstrate the functionalities of ConceptGen using gene expression data modeling TGF-beta-induced epithelial-mesenchymal transition and metabolomics data comparing metastatic versus localized prostate cancers. Availability: ConceptGen is part of the NIH's National Center for Integrative Biomedical Informatics (NCIBI) and is freely available at http://conceptgen.ncibi.org. For terms of use, visit http://portal.ncibi.org/gateway/pdf/Terms%20of%20use-web.pdf Contact: [email protected]; [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

UNLABELLED: MiSearch is an adaptive biomedical literature search tool that ranks citations based on a statistical model for the likelihood that a user will choose to view them. Citation selections are automatically acquired during browsing and used to dynamically update a likelihood model that includes authorship, journal and PubMed indexing information. The user can optionally elect to include or exclude specific features and vary the importance of timeliness in the ranking. AVAILABILITY: http://misearch.ncibi.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

When virtual teams need to establish trust at a distance, it is advantageous for them to use rich media to communicate. We studied the emergence of trust in a social dilemma game in four different communication situations: face-to-face, video, audio, and text chat. All three of the richer conditions were significant improvements over text chat. Video and audio conferencing groups were nearly as good as face-to-face, but both did show some evidence of what we term delayed trust (slower progress toward full cooperation) and fragile trust (vulnerability to opportunistic behavior)