title: SciMiner: web-based literature mining tool for target identification and functional enrichment analysis.
abstract: SciMiner is a web-based literature mining and functional analysis tool that identifies genes and proteins using a context specific analysis of MEDLINE abstracts and full texts. SciMiner accepts a free text query (PubMed Entrez search) or a list of PubMed identifiers as input. SciMiner uses both regular expression patterns and dictionaries of gene symbols and names compiled from multiple sources. Ambiguous acronyms are resolved by a scoring scheme based on the co-occurrence of acronyms and corresponding description terms, which incorporates optional user-defined filters. Functional enrichment analyses are used to identify highly relevant targets (genes and proteins), GO (Gene Ontology) terms, MeSH (Medical Subject Headings) terms, pathways and protein-protein interaction networks by comparing identified targets from one search result with those from other searches or to the full HGNC [HUGO (Human Genome Organization) Gene Nomenclature Committee] gene set. The performance of gene/protein name identification was evaluated using the BioCreAtIvE (Critical Assessment of Information Extraction systems in Biology) version 2 (Year 2006) Gene Normalization Task as a gold standard. SciMiner achieved 87.1% recall, 71.3% precision and 75.8% F-measure. SciMiner's literature mining performance coupled with functional enrichment analyses provides an efficient platform for retrieval and summary of rich biological information from corpora of users' interests.
  
  
  BACKGROUND
  http://jdrf.neurology.med.umich.edu/SciMiner/. A server version of the SciMiner is also available for download and enables users to utilize their institution's journal subscriptions.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA. juhur@umich.edu
authors.forename: Junguk
authors.initials: J
authors.lastname: Hur
authors.forename: Adam D
authors.initials: AD
authors.lastname: Schuyler
authors.forename: David J
authors.initials: DJ
authors.lastname: States
authors.forename: Eva L
authors.initials: EL
authors.lastname: Feldman
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005796:Genes; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D016239:MEDLINE; D011506:Proteins / Q000502:physiology*; D039781:PubMed; D011642:Publications; D012984:Software; D014481:United States
chemical_list: D011506:Proteins