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Linguist"},{"key":"ref71","first-page":"474","article-title":"Learning dictionaries for information extraction by multi-level bootstrapping.","author":"E Riloff","year":"1999"},{"key":"ref72","article-title":"The Synonym Finder;","author":"JI Rodale","year":"1986"},{"key":"ref73","article-title":"Webster's New World Roget's A-Z Thesaurus;","author":"C Laird","year":"1999"},{"key":"ref74","article-title":"21st Century Synonym and Antonym Finder;","author":"BA Kipfer","year":"1993"},{"key":"ref75","article-title":"The Oxford dictionary of synonyms and antonyms.","author":"A Spooner","year":"2007"},{"key":"ref76","article-title":"A Dictionary of Synonyms and Antonyms; Fried J, editor.","author":"J Devlin","year":"1987"},{"key":"ref77","article-title":"Scholastic dictionary of synonyms, antonyms, and homonyms.","author":"I Scholastic","year":"2001"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/ijl\/3.4.235","article-title":"WordNet: an online lexical 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