title: An architecture for biological information extraction and representation.
abstract: BACKGROUND
  Technological advances in biomedical research are generating a plethora of heterogeneous data at a high rate. There is a critical need for extraction, integration and management tools for information discovery and synthesis from these heterogeneous data.
  
  
  RESULTS
  In this paper, we present a general architecture, called ALFA, for information extraction and representation from diverse biological data. The ALFA architecture consists of: (i) a networked, hierarchical, hyper-graph object model for representing information from heterogeneous data sources in a standardized, structured format; and (ii) a suite of integrated, interactive software tools for information extraction and representation from diverse biological data sources. As part of our research efforts to explore this space, we have currently prototyped the ALFA object model and a set of interactive software tools for searching, filtering, and extracting information from scientific text. In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation, and representation of information from scientific text. We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation.
  
  
  BACKGROUND
  aditya_vailaya@agilent.com.
authors.affiliation: Agilent Laboratories 3500 Deer Creek Road, MS 26U-16, Palo Alto, CA 94304, USA. aditya_vailaya@agilent.com
authors.forename: Aditya
authors.initials: A
authors.lastname: Vailaya
authors.forename: Peter
authors.initials: P
authors.lastname: Bluvas
authors.forename: Robert
authors.initials: R
authors.lastname: Kincaid
authors.forename: Allan
authors.initials: A
authors.lastname: Kuchinsky
authors.forename: Michael
authors.initials: M
authors.lastname: Creech
authors.forename: Annette
authors.initials: A
authors.lastname: Adler
mesh_terms: D000043:Abstracting and Indexing / Q000379:methods; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods; D003628:Database Management Systems; D016208:Databases, Factual; D004282:Documentation / Q000379:methods; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D009323:Natural Language Processing; D010506:Periodicals as Topic; D012984:Software; D014584:User-Computer Interface; D018875:Vocabulary, Controlled