Semantic annotation of biosystematics literature without training examples

Journal of the American Society for Information Science and Technology

Volumn 61, Issue 3, 2010, Pages 522-542

  Cui, Hong ^a   Boufford, David ^b   Selden, Paul ^c  

^a UNIVERSITY OF ARIZONA   (United States)

^b HARVARD UNIVERSITY   (United States)

^c UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LINEAR TIME; MANUAL LABORS; MORPHOLOGICAL DESCRIPTION; PLAIN TEXT; SEMANTIC ANNOTATIONS; SYNTACTIC PARSERS; TRAINING EXAMPLE; UNSUPERVISED ALGORITHMS;

SEMANTICS;

ALGORITHMS;

EID: 76649117733     PISSN: 15322882     EISSN: 15322890     Source Type: Journal    
DOI: 10.1002/asi.21246     Document Type: Article

References (28)

1. Biodiversity Heritage Library. (2008). Biodiversity Heritage Library. Retrieved July 10, 2008, from Biodiversity Heritage Library: http://www.bhl.si.edu/
2. Cui, H. (2008). Unsupervised semantic markup of literature for biodiversity digital libraries. Proceedings of the Eighth ACM/IEEE-CS Joint Conference on Digital libraries, (pp. 25-28). New York: ACM Press.
3. Cui, H., & Heidorn, P. (2007). The reusability of induced knowledge for automatic semantic markup of taxonomie descriptions. Journal of the American Society for Information Science and Technology, 58(1), 133-149. (Pubitemid 46051790)
4. Cui, H., Heidorn, P., & Zhang, H. (2002). An approach to automatic classification for information retrieval. Proceedings of the Second ACM/IEEE Joint Conference on DigitalLibraries, (pp. 96-97). New York: ACM Press.
5. Curry, G., & Connor, R. (2008). Automated extraction of data from text using an XML parser: An earth science example using fossil descriptions. Geosphere, 4(1), 159-169.
6. Flora of North America Editorial Committee. (2006). Flora of North America North of Mexico guide for contributors. Retrieved July 10, 2007, from http://www.fna.org/FNA/Guide/guide-2006.pdf
7. Kiger, R.W., & Porter, D.M. (2001). Categorical glossary for the flora of North America project. Retrieved January 3, 2009, from http://huntbot. andrew.cmu.edu/HIBD/Departments/DB-INTRO/IntroFNA.shtml
8. Koning, D., Sarkar, L., & Moritz, T. (2005). TaxonGrad: Extracting taxonomie names from text. Biodiversity Informatics, 2, 79-82.
9. Lydon, S., Wood, M., Huxley, R., & Sutton, D. (2003). Data patterns in multiple botanical descriptions: Implications for automatic processing of legacy data. Systematics and Biodiversity, 1(2), 151-157.
10. Mabee, P., Ashburner, M., Cronk, Q., Gkoutos, G., Haendal, M., Segerdall, E., et al. (2007). Phenotype ontologies: The bridge between genomics and evoluation. Trends in Ecology and Evoluation, 22(7), 345-350. (Pubitemid 46929011)
11. Moore, R.C., Teichert, C., Robison, R.A., Kaesler, R.L., & Seiden, P.A. (1952-2008). Treatise on invertebrate paleontology. Lawrence, KS: University of Kansas/Boulder, CO: Geological Society of America.
12. OPC - Plant characteristics, (n.d.). Retrieved May 21, 2009, from http://herbaria.plants.ox.ac.uk/vfh/image/?glossary=show
13. PATO. (2006). Phenotypic quality ontology main page. Retrieved June 10, 2009, from http://www.bioontology.org/wiki/index.php/PATO: Main-Page
14. Probst, K., Ghani, R., Krema, M., Fano, A.E., & Liu, Y. (2007). Semisupervised learning of attribute-value pairs from product descriptions. In M.M. Veloso (Ed.), Proceedings of the 20th International Joint Conferences on Artificial Intelligence (pp. 2839-2843). Rochester Hills, MI: IJCAI.
15. Raju, S., Pingali, P., & Varma, V. (2009). An unsupervised approach to product attribute extraction. In M. Boughanem, C. Beirut, J. Mothe, & C. Soule-Dupuy (Eds.), Proceedings of the 31th European Conference on IR Research on Advances in Information Retrieval. Lecture Notes in Computer Science, 5478, 796-800.
16. Riloff, E., & Jones, R. (1999). Learning dictionaries for information extraction by multi-level bootstrapping. Proceedings of the Sixteenth National Conference on Artificial Intelligence (pp. 474-479). Menlo Park, CA: Association for the Advancement of Artificial Intelligence.
17. Sautter, G., Agosti, D., & Böhm, K. (2006). A combining approach to find all taxon names (FAT). Biodiversity Informatics, 3, 46-58.
18. Sautter, G., Agosti, D., & Böhm, K. (2007). Semi-automated XML markup of biosystematics legacy literature with the GoldenGATE Editor. In R.B Altman, A.K. Dunker, L. Hunter, T. Murray, & T.E. Klein. (Eds.), Proceedings of the Pacific Symposium on Biocomputing (PSB 2007) (pp. 391-402). Hackensack, NJ: World Scientific.
19. Soderland, S. (1999). Learning information extraction rules for semistructured and free text. Machine Learning, 34(1-3), 233-272.
20. StanfordParser. (n.d.). The Stanford Parser: A statistical parser. Retrieved June 30, 2009, from http://nlp.stanford.edu/software/lex-parser.shtml
21. Tang, X., & Heidorn, P.B. (2007). Using automatically extracted information in species page retrieval. Retrieved July 10, 2008, from http://www. tdwg.org/proceedings/article/view/195/0
22. Taylor, A. (1995). Extracting knowledge from biological descriptions. Proceedings of 2nd International Conference on Building and Sharing Very Large-Scale Knowledge Bases (pp. 114-119).
23. Text Retrieval Conference, (n.d.). TREC entity retrieval. Retrieved June 30, 2009, from http://ilps.science.uva.nl/trec-entity/
24. Treebank, P. (n.d.). The Penn Treebank Project. Retrieved June 30, 2009, from http://www.cis.upenn.edu/~treebank/
25. Vanel, J.-M. (2004). Worldwide botanical knowledge base. Retrieved July 5, 2007, from http://wwbota.free.fr/
26. Wood, M., Lydon, S., Tablan, V., Maynard, D., & Cunningham, H. (2004). Populating a database from parallel texts using ontology-based information extraction. In F. Meziane, & E. M'tais (Eds.), Proceedings of Natural Language Processing and Information Systems, 9th International Conference on Applications of Natural Languages to Information Systems. Lecture Notes in Computer Science, 3136, 254-264.
27. WordNet. (n.d.). WordNet: A lexical database for the English language. Retrieved June 30, 2009, from http://wordnet.princeton.edu/
28. Yona, S. (2002). Sentence. Retrieved September 4, 2009, from http://cpansearch.perl.org/src/SHLOMOY/Lingua-EN-Sentence-0.25/lib/Lingua/EN/ Sentence.pm