PMID: 17317333;PMCID: PMC2047827;Abstract:
Gene/protein interactions provide critical information for a thorough understanding of cellular processes. Recently, considerable interest and effort has been focused on the construction and analysis of genome-wide gene networks. The large body of biomedical literature is an important source of gene/protein interaction information. Recent advances in text mining tools have made it possible to automatically extract such documented interactions from free-text literature. In this paper, we propose a comprehensive framework for constructing and analyzing large-scale gene functional networks based on the gene/protein interactions extracted from biomedical literature repositories using text mining tools. Our proposed framework consists of analyses of the network topology, network topology-gene function relationship, and temporal network evolution to distill valuable information embedded in the gene functional interactions in the literature. We demonstrate the application of the proposed framework using a testbed of P53-related PubMed abstracts, which shows that the literature-based P53 networks exhibit small-world and scale-free properties. We also found that high degree genes in the literature-based networks have a high probability of appearing in the manually curated database and genes in the same pathway tend to form local clusters in our literature-based networks. Temporal analysis showed that genes interacting with many other genes tend to be involved in a large number of newly discovered interactions. © 2007 Elsevier Inc. All rights reserved.
Abstract:
Nanotechnology holds the promise to revolutionize a wide range of products, processes and applications. It is recognized by over sixty countries as critical for their development at the beginning of the 21st century. A significant public investment of over $1 billion annually is devoted to nanotechnology research in the United States. This paper provides an analysis of the National Science Foundation (NSF) funding of nanoscale science and engineering (NSE) and its relationship to the innovation as reflected in the United States Patent and Trade Office (USPTO) patent data. Using a combination of bibliometric analysis and visualization tools, we have identified several general trends, the key players, and the evolution of technology topics in the NSF funding and commercial patenting activities. This study documents the rapid growth of innovation in the field of nanotechnology and its correlation to funding. Statistical analysis shows that the NSF-funded researchers and their patents have higher impact factors than other private and publicly funded reference groups. This suggests the importance of fundamental research on nanotechnology development. The number of cites per NSF-funded inventor is about 10 as compared to 2 for all inventors of NSE-related patents recorded at USPTO, and the corresponding Authority Score is 20 as compared to 1.8. © Springer 2005.
Abstract:
The basic problem in information retrieval is that large-scale searches can only match terms specified by the user to terms appearing in documents in the digital library collection. Intermediate sources that support term suggestion can thus enhance retrieval by providing alternative search terms for the user. Term suggestion increases the recall, while interaction enables the user to attempt to not decrease the precision. We are building a prototype user interface that will become the Web interface for the University of Illinois Digital Library Initiative (DLI) testbed. It supports the principle of multiple views, where different kinds of term suggestors can be used to complement search and each other. This paper discusses its operation with two complementary term suggestors, subject thesauri and co-occurrence lists, and compares their utility. Thesauri are generated by human indexers and place selected terms in a subject hierarchy. Co-occurrence lists are generated by computer and place all terms in frequency order of occurrence together. This paper concludes with a discussion of how multiple views can help provide good quality Search for the Net. This is a paper about the design of a retrieval system prototype that allows users to simultaneously combine terms offered by different suggestion techniques, not about comparing the merits of each in a systematic and controlled way. It offers no experimental results.
