A knowledgebase system to enhance scientific discovery: Telemakus

Telemakus Research Program, Division of Biomedical & Health Informatics, University of Washington, Seattle, WA, USA. .
Biomedical Digital Libraries 02/2004; 1(1):2. DOI: 10.1186/1742-5581-1-2
Source: PubMed


With the rapid expansion of scientific research, the ability to effectively find or integrate new domain knowledge in the sciences is proving increasingly difficult. Efforts to improve and speed up scientific discovery are being explored on a number of fronts. However, much of this work is based on traditional search and retrieval approaches and the bibliographic citation presentation format remains unchanged.

Case study.

The Telemakus KnowledgeBase System provides flexible new tools for creating knowledgebases to facilitate retrieval and review of scientific research reports. In formalizing the representation of the research methods and results of scientific reports, Telemakus offers a potential strategy to enhance the scientific discovery process. While other research has demonstrated that aggregating and analyzing research findings across domains augments knowledge discovery, the Telemakus system is unique in combining document surrogates with interactive concept maps of linked relationships across groups of research reports.

Based on how scientists conduct research and read the literature, the Telemakus KnowledgeBase System brings together three innovations in analyzing, displaying and summarizing research reports across a domain: (1) research report schema, a document surrogate of extracted research methods and findings presented in a consistent and structured schema format which mimics the research process itself and provides a high-level surrogate to facilitate searching and rapid review of retrieved documents; (2) research findings, used to index the documents, allowing searchers to request, for example, research studies which have studied the relationship between neoplasms and vitamin E; and (3) visual exploration interface of linked relationships for interactive querying of research findings across the knowledgebase and graphical displays of what is known as well as, through gaps in the map, what is yet to be tested. The rationale and system architecture are described and plans for the future are discussed.

Download full-text


Available from: Debra Revere
  • Source
    • "To evaluate the literature concerning the genotoxic and/or mutagenic effects of glucose and fructose metabolites on biochemical processes related to nucleic acid metabolism, we performed data mining of the literature. Some of the literature search engines rely on strings of words and/or natural language processing to extract useful biological information from full-text biological literature (Telemakus, XplorMed, and Ali Baba) [16] [17] [18], while others use multiplex Boolean queries in order to mine biological information (PubMatrix) [15]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Glucose and fructose are major dietary carbohydrates that are essential for general metabolism. The elevated consumption of these two monosaccharides by the human population is related to the development of pluri-metabolic syndromes (e.g., diabetes mellitus and obesity). Glucose and fructose are metabolized by specific biochemical pathways to generate energy and metabolites. Many of these metabolites are mono- and bi-phosphorylated compounds, which renders them likely to generate reactive carbonyl species (RCS). Under physiological conditions, RCS react non-enzymatically with macromolecules and small molecules by means of Maillard reactions, forming stable glycated/fructated compounds called advanced glycation end products (AGEs). DNA and dNTPs are prone to react with RCS, forming DNA- and dNTP-AGEs, and many of these compounds are genotoxic and/or mutagenic. Unfortunately, little is understood about the genotoxicity and/or mutagenicity of carbohydrate intermediate metabolites or their interactions with DNA repair and carbohydrate metabolic-associated proteins. To elucidate these associations between carbohydrate metabolic pathways, DNA repair mechanisms, and dNTP-/DNA-AGEs, a systems biology study was performed by employing algorithms to mine literature data and construct physical protein-protein interactions. The results obtained in this work allow us to construct a model suggesting that yeast carbohydrate metabolic-associated enzymes activate different mechanisms for DNA repair and dNTP synthesis and act during DNA replication to protect the genome against the effects of RCS.
    Full-text · Article · Aug 2008 · Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis
  • Source
    • "Aging research is an important area of biology which involves multiple molecular and experimental entities such as genes, proteins, drugs, organisms, diseases and experiments, to name a few [7] [5]. SENECA contains the information about both the facts on the biomolecular entities relevant for the aging process, along with their relationships, and the information about the individual experiment settings and results. "
    [Show abstract] [Hide abstract]
    ABSTRACT: In an attempt further the understanding of the wealth of data that describes the aging process we have developed a relational database to organize and document the genomic and proteomic facts and experimental results reported in the aging research literature. Our schema design is intended to coordinate with, and complement, the state of the art text information and data extraction techniques developed to support studies on aging. The root cause of aging is the declining energy metabolism resulting from the oxidative stress and free radical damage to macromolecules in and adjacent to the mitochondria. Mitochondria contain over flve hundred speciflc proteins, the vast majority being coded by nuclear genes. Our database contains genomic and proteomic information expressly concerned with energy metabolism, and mitochondrial components in particular, that are afiected in aging. It is intended to be linked to, and complement a literature summary style database, in order to support directed extraction of data, results and text from full article published papers on age related energy metabolism and mitochondrial components.
    Full-text · Article ·
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We describe Semantic MEDLINE, a Web application that manages the results of PubMed searches by summarizing and visu-alizing semantic predications extracted from MEDLINE citations and linking them to several structured resources to provide an integrated environment. To demonstrate its utility, we present a scenario in which we use Semantic MEDLINE to gain insights into relaxin, a hormone whose function in humans has not been fully elucidated. We propose Semantic MEDLINE as an enabling information resource and exploration tool for biomedical scientists, health care profes-sionals, and consumers. (For access, send e-mail to
    Full-text · Article · Nov 2007
Show more