Pathways database system

The study of citation networks is of interest to the scientific community. However, the underlying mechanism driving individual citation behavior remains imperfectly understood, despite the recent proliferation of quantitative research methods. Traditional network models normally use graph theory to consider articles as nodes and citations as pairwise relationships between them. In this paper, we propose an alternative evolutionary model based on hypergraph theory in which one hyperedge can have an arbitrary number of nodes, combined with an aging effect to reflect the temporal dynamics of scientific citation behavior. Both theoretical approximate solution and simulation analysis of the model are developed and validated using two benchmark datasets from different disciplines, i.e. publications of the American Physical Society (APS) and the Digital Bibliography & Library Project (DBLP). Further analysis indicates that the attraction of early publications will decay exponentially. Moreover, the experimental results show that the aging effect indeed has a significant influence on the description of collective citation patterns. Shedding light on the complex dynamics driving these mechanisms facilitates the understanding of the laws governing scientific evolution and the quantitative evaluation of scientific outputs.

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Pathways Database System

Özsoyoğlu

Nadeau

Özsoyoǧlu

2003

OMICS: A Journal of Integrative Biology

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During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers. In this paper, we introduce an integrated system, called "Pathways Database System," with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail.

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Pathways database system

Cited by 6 publications

References 2 publications

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Pathways Database System

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