title: PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction.
abstract: There is an increasing interest in using literature mining techniques to complement information extracted from annotation databases or generated by bioinformatics applications. Here we present PLAN2L, a web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. Our system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned. PLAN2L does not require registration and is freely accessible at http://zope.bioinfo.cnio.es/plan2l.
authors.affiliation: Structural Biology and Biocomputing programme, Spanish National Cancer Center (CNIO), Melchor Fernandez Almagro 3, Madrid, 28029, Spain. mkrallinger@cnio.es
authors.forename: Martin
authors.initials: M
authors.lastname: Krallinger
authors.forename: Carlos
authors.initials: C
authors.lastname: Rodriguez-Penagos
authors.forename: Ashish
authors.initials: A
authors.lastname: Tendulkar
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
mesh_terms: D026342:AGAMOUS Protein, Arabidopsis / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000378:metabolism; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D012984:Software; D018511:Systems Integration; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D026342:AGAMOUS Protein, Arabidopsis; D029681:Arabidopsis Proteins; C417768:LUG protein, Arabidopsis; D014157:Transcription Factors