A knowledge-driven approach to biomedical document conceptualization

Raychaudhuri, 2002, Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature, Genome Res, 12, 203, 10.1101/gr.199701 Theodosiou, 2007, Gene functional annotation by statistical analysis of biomedical articles, Int J Med Inform, 76, 601, 10.1016/j.ijmedinf.2006.04.011 Zheng H-T, Borchert C, Kim H-G. Exploiting gene ontology to conceptualize biomedical document collections. In: Domingue J, Anutariya C (Eds.), ASWC (3rd Asian Semantic Conference), vol. 5367 of Lecture Notes in Computer Science. Springer; 2008, p. 375–89. Srinivasan, 2001, Meshmap: a text mining tool for medline, 642 Vanteru, 2008, Semantically linking and browsing pubmed abstracts with gene ontology, BMC Genom, 9, S10, 10.1186/1471-2164-9-S1-S10 The open biomedical ontologies. http://www.obofoundry.org/ [accessed 29.09.09]. Ashburner, 2000, Gene ontology: tool for the unification of biology. The gene ontology consortium, Nat Genet, 25, 25, 10.1038/75556 PubMed. http://www.ncbi.nlm.nih.gov/sites/entrez/ [accessed 29.09.09]. Izumitani, 2004, Assigning gene ontology categories (go) to yeast genes using text-based supervised learning methods, 503 Chen, 2007, Automated linking pubmed documents with go terms using SVM, J Data Sci, 5, 259, 10.6339/JDS.2007.05(2).331 Doms, 2005, Gopubmed: exploring pubmed with the gene ontology, Nucleic Acids Res, 33, 783, 10.1093/nar/gki470 Delfs, 2004, Gopubmed: ontology-based literature search applied to geneontology and pubmed, 169 Smith, 2003, Automatically linking medline abstracts to the gene ontology Medical Subject Headings. http://www.nlm.nih.gov/mesh/ [accessed 29.09.09]. Srinivasan, 2002, Exploring text mining from medline, 722 Uramoto, 2004, A text-mining system for knowledge discovery from biomedical documents, IBM Syst J, 43, 516, 10.1147/sj.433.0516 Kankar, 2002, Medmesh summarizer: text mining for gene clusters, 548 Abasolo, 2000, Melisa: an ontology-based agent for information retrieval in medicine, 73 Djebbari, 2005, MeSHer: identifying biological concepts in microarray assays based on pubmed references and mesh terms, Bioinformatics, 21, 3324, 10.1093/bioinformatics/bti503 Olsen, 1993, Visualization of a document collection: the VIBE system, Inf Process Manage, 29, 69, 10.1016/0306-4573(93)90024-8 Grobelnik, 2004, Visualization of news articles, Informatica, 28, 32 Fortuna, 2005, Visualization of text document corpus, Informatica, 29, 497 Zhu, 2007, Storylines: visual exploration and analysis in latent semantic spaces, Comput Graphics, 31, 338, 10.1016/j.cag.2007.01.025 Shaw, 1999, Interactive volumetric information visualization for document corpus management, Int J Digit Libr, 2, 144, 10.1007/s007990050043 Forsyth, 1986, Adding an edge in machine learning: applications in expert systems and information retrieval, 198 Hotho, 2005, Learning concept hierarchies from text corpora using formal concept analysis, J Artif Intell Res, 24, 305, 10.1613/jair.1648 Sanderson, 1999, Deriving concept hierarchies from text, 206 Stop_Word_List. http://www.lextek.com/manuals/onix/stopwords2.html. Technical report [accessed 29.09.09]. Phan X-H. Crftagger: Crf English pos tagger. http://crftagger.sourceforge.net/ [accessed 29.09.09]. Miller, 1995, Wordnet: a lexical database for english, Commun ACM, 38, 39, 10.1145/219717.219748 X.-H. Phan. Crfchunker: Crf English phrase chunker. http://crfchunker.sourceforge.net/ [accessed 29.09.09]. Baeza-Yates, 1999 Deerwester, 1990, Indexing by latent semantic analysis, J Am Soc Inf Sci, 41, 391, 10.1002/(SICI)1097-4571(199009)41:6<391::AID-ASI1>3.0.CO;2-9 McGuinness DL, van Harmelen F. Owl web ontology language overview. http://www.w3.org/TR/owl-features/ [accessed 29.09.09]. Zamir, 1998, Web document clustering: a feasibility demonstration, 46 Osinski, 2005, A concept-driven algorithm for clustering search results, IEEE Intell Syst, 20, 48, 10.1109/MIS.2005.38 Schockaert S. Het Clusteren van Zoekresultaten met behulp van Vaagmieren (Clustering of search results using fuzzy ants). Master thesis, University of Ghent; 2004. Lang NC. A tolerance rough set approach to clustering web search results. Master thesis, Warsaw University; 2004. Carrot2. http://project.carrot2.org/ [accessed 29.09.09]. Steinbach M, Karypis G, Kumar V. A comparison of document clustering techniques. In: KDD workshop on text mining; 2000. Pantel, 2002, Document clustering with committees, 199 Weiss D. Descriptive clustering as a method for exploring text collections. Ph.D. thesis, Poznań University of Technology, Poznań, Poland; 2006. Landauer, 1998, An introduction to latent semantic analysis, Discourse Proces, 25, 259, 10.1080/01638539809545028 Java Matrix Package. http://math.nist.gov/javanumerics/jama/ [accessed 29.09.09].