Exploiting gene ontology to conceptualize biomedical document collections

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5367 LNCS, Issue , 2008, Pages 375-389

  Zheng, Hai Tao ^a   Borchert, Charles ^a   Kim, Hong Gee ^a  

^a Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING ALGORITHMS; INFORMATION THEORY; MULTI AGENT SYSTEMS; SEMANTIC WEB; SEMANTICS;

AUTOMATICALLY GENERATE; BIOMEDICAL INFORMATIONS; BIOMEDICAL SCIENCES; BIOMEDICAL TEXTS; CONCEPTUAL STRUCTURES; DOCUMENT COLLECTIONS; GENE ONTOLOGIES; GENE ONTOLOGY ANNOTATIONS; INFORMATION OVERLOADS; LATENT SEMANTIC ANALYSIS; SEMANTIC RELATIONSHIPS;

ONTOLOGY;

EID: 58049117786     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-89704-0_26     Document Type: Conference Paper

References (29)

1. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1), 25-29 (2000)
2. Zheng, H.T., Borchert, C., Kim, H.G.: A concept-driven automatic ontology generation approach for conceptualization of document corpora (unpublished manuscript, 2008)
3. Zamir, O., Etzioni, O.: Web document clustering: a feasibility demonstration. In: SIGIR 1998: Proceedings of the 21st annual international ACM SIGIR conference on Research and development in information retrieval, pp. 46-54. ACM, New York (1998)
4. Zamir, O., Etzioni, O.: Grouper: a dynamic clustering interface to web search results. Comput. Netw. 31(11-16), 1361-1374 (1999)
5. Schockaert, S.: Het clusteren van zoekresultaten met behulp van vaagmieren (clustering of search results using fuzzy ants). Master thesis, University of Ghent (2004)
6. Lang, N.C.: A tolerance rough set approach to clustering web search results. Master thesis, Warsaw University (2004)
7. Osinski, S., Weiss, D.: A concept-driven algorithm for clustering search results. IEEE Intelligent Systems 20(3), 48-54 (2005)
8. Plaisant, C., Fekete, J.D., Grinstein, G.: Promoting insight-based evaluation of visualizations: From contest to benchmark repository. IEEE Transactions on Visualization and Computer Graphics 14(1), 120-134 (2008)
9. Olsen, K.A., Korfhage, R.R., Sochats, K.M., Spring, M.B., Williams, J.G.: Visualization of a document collection: the vibe system. Inf. Process. Manage. 29(1), 69-81 (1993)
10. Grobelnik, M., Maldenic, D.: Visualization of news articles. Informatica 28, 32-35 (2004)
11. Fortuna, B., Grobelnik, M., Mladenic, D.: Visualization of text document corpus. Informatica 29, 497-504 (2005)
12. Zhu, W., Chen, C.: Storylines: Visual exploration and analysis in latent semantic spaces. Computers & Graphics 31(3), 338-349 (2007)
13. Shaw, C.D., Kukla, J.M., Soboroff, I., Ebert, D.S., Nicholas, C.K., Zwa, A., Miller, E.L., Roberts, D.A.: Interactive volumetric information visualization for document corpus management. Int. J. on Digital Libraries 2(2-3), 144-156 (1999)
14. Fluit, C., Sabou, M., van Harmelen, F.: Ontology-based information visualisation: Towards semantic web applications. In: Visualising the Semantic Web, 2nd edn. (2005)
15. Thai, V., Handschuh, S., Decker, S.: IVEA: An information visualization tool for personalized exploratory document collection analysis. In: Bechhofer, S., Hauswirth, M., Hoffmann, J., Koubarakis, M. (eds.) ESWC 2008. LNCS, vol. 5021, pp. 139-153. Springer, Heidelberg (2008)
16. Bada, M., Turi, D., McEntire, R., Stevens, R.: Using reasoning to guide annotation with gene ontology terms in goat. SIGMOD Rec. 33(2), 27-32 (2004)
17. Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R., Apweiler, R.: The gene ontology annotation (goa) database: sharing knowledge in uniprot with gene ontology. Nucleic Acids Res. 32 (database issue) (2004)
18. Gene-Ontology-Annotation.Tool, http://www.geneontology.org/go.tools. annotation.shtml
19. Hill, D.P., Smith, B., McAndrews-Hill, M.S., Blake, J.A.: Gene ontology annotations: what they mean and where they come from. BMC bioinformatics 9 (suppl. 5) (2008)
20. Seki, K., Mostafa, J.: An application of text categorization methods to gene ontology annotation. In: SIGIR 2005: Proceedings of the 28th annual international ACM SIGIR conference on Research and development in information retrieval, pp. 138-145. ACM, New York (2005)
21. Phan, X.H.: Crftagger: Crf english pos tagger (2006), http://crftagger.sourceforge.net/
22. Phan, X.H.: Crfchunker: Crf english phrase chunker (2006), http://crfchunker.sourceforge.net/
23. Salton, G., Wong, A., Yang, C.S.: A vector space model for automatic indexing. Commun. ACM 18(11), 613-620 (1975)
24. OWL-Web-Ontology-Language, http://www.w3.org/tr/owl-ref/
25. 2, http://project.carrot2.org/
26. PubMed, http://www.ncbi.nlm.nih.gov/sites/entrez/
27. Steinbach, M., Karypis, G., Kumar, V.: A comparison of document clustering techniques. In: KDD Workshop on Text Mining (2000)
28. Rosse, C., Mejino, J.L.V.: A reference ontology for biomedical informatics: the foundational model of anatomy. J. of Biomedical Informatics 36(6), 478-500 (2003)
29. Stearns, M., Price, C., Spackman, K., Wang, A.: Snomed clinical terms: overview of the development process and project status. In: Proc. AMIA Symp., pp. 662-666 (2001)