Publications

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1994
Verspoor, CM.  1994.  A cognitively relevant lexical semantics. Master's thesis. Abstract
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1996
Verspoor, C.  1996.  Lexical limits on the influence of context. Proc. of CogSci. :116–120. Abstract
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Verspoor, CM.  1996.  A perspective on PPs. Edinburgh Working Papers in Cognitive Science. :229. Abstract
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Narasimhan, B, Di Tomaso V, Verspoor CM.  1996.  Unaccusative or Unergative? Verbs of Manner of Motion Quaderni del Laboratorio di Llinguistica. 10 Abstract

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1997
Verspoor, CM.  1997.  Contextually-dependent lexical semantics. : University of Edinburgh. College of Science and Engineering. School of Informatics. Abstract
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Verspoor, C.  1997.  Conventionality-governed logical metonymy. Proc. of the 2nd International Workshop on Computational Semantics. :300–312. Abstract
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1998
Verspoor, CM.  1998.  Predictivity vs. Stipulativity in the Lexicon. Language. 152:162. Abstract
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Wan, S, Verspoor CM.  1998.  Automatic English-Chinese name transliteration for development of multilingual resources. Proceedings of the 36th Annual Meeting of the Association for Computational Linguistics and 17th International Conference on Computational Linguistics-Volume 2. :1352–1356.: Association for Computational Linguistics Abstract

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Dale, R, Green SJ, Milosavljevic M, Paris C, Williams S, Verspoor C.  1998.  Dynamic document delivery: Generating natural language texts on demand. Database and Expert Systems Applications, 1998. Proceedings. Ninth International Workshop on. :131–136.: IEEE Abstract

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Verspoor, C, Dale R, Green S, Milosavljevic M, Paris C, Williams S.  1998.  Intelligent Agents for Information Presentation: Dynamic Description of Knowledge Base Objects. the proceed. :75–86. Abstract

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Dale, R, Green SJ, Milosavljevic M, Paris C, Williams S, Verspoor C.  1998.  The realities of generating natural language from databases. Proceedings of the 11th Australian Joint Conference on Artificial Intelligence. :13–17. Abstract

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2003
Verspoor, CM, Joslyn C, Papcun GJ.  2003.  The gene ontology as a source of lexical semantic knowledge for a biological natural language processing application. SIGIR workshop on Text Analysis and Search for Bioinformatics. :51–56. Abstractlaur_03-4480.pdf

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Verspoor, C, Joslyn C, Papcun G.  2003.  Interactions Between the Gene Ontology and a Domain Corpus for a Biological Natural Language Processing Application. proceedings Sixth Annual Bio-Ontologies Meeting. Abstract

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2004
Verspoor, K, Cohn J, Joslyn C, Mniszewski S, Rechtsteiner A, Rocha LM, Simas T.  2004.  The LANL BioCreAtIvE submission. Abstract

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Verspoor, K, Cohn J, Mniszewski SM, Joslyn CA.  2004.  Nearest Neighbor Categorization for Function Prediction. Proc. 5th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP 05). Abstract

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2005
Verspoor, K.  2005.  Towards a semantic lexicon for biological language processing. Comparative and functional genomics. 6:61–66., Number 1-2: Wiley Online Library Abstract
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Verspoor, K, Cohn J, Mniszewski S, Joslyn C.  2005.  POSOLE: Automated Ontological Annotation for Function Prediction. Automated Function Prediction. 16:20., Number 1 Abstract

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Verspoor, K, Joslyn C, Cohn J, Mniszewski S, Rechtsteiner A, Simas T, Rocha L.  2005.  Protein annotation as term categorization in the gene ontology using word proximity networks. BMC bioinformatics. 6:S20., Number Suppl 1: BioMed Central Ltd Abstract

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2006
Verspoor, K, Cohen KB, Goertzel B, Mani I.  2006.  BioNLP’06 Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis. Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology. , New York, NY
Verspoor, K, Cohn J, Mniszewski S, Joslyn C.  2006.  A categorization approach to automated ontological function annotation. Protein Science. 15:1544–1549., Number 6: Wiley Online Library Abstract

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Gessler, DDG, Joslyn CA, Verspoor KM, Schmidt SE.  2006.  Deconstruction, Reconstruction, and Ontogenesis for Large, Monolithic, Legacy Ontologies in Semantic Web Service Applications. National Center for Genome Research. Abstract

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Verspoor, K, Sanfilippo A, Elmore M, MacKerrow E.  2006.  Deploying Natural Language Processing for Social Science Analysis. proceedings 2006 Chicago Colloquium on Digital Humanities and Computer Science. Abstract

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Joslyn, CA, Gessler DDG, Schmidt SE, Verspoor KM.  2006.  Distributed Representations of Bio-Ontologies for Semantic Web Services. Joint BioLINK and 9th Bio-Ontologies Meeting (JBB 06): 2006. Abstract

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Maguitman, AG, Rechtsteiner A, Verspoor K, Strauss C, Rocha LM.  2006.  Large-scale testing of Bibliome informatics using Pfam protein families. Pacific Symposium on Biocomputing. 11:76–87. Abstract

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2007
Joslyn, CA, Verspoor KM, Gessler DDG.  2007.  Knowledge Integration in OpenWorlds: Utilizing the Mathematics of Hierarchical Structure. Semantic Computing, 2007. ICSC 2007. International Conference on. :105–112.: IEEE Abstract

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Abi-Haidar, A, Maguitman A, Kaur J, Radivojac P, Retchsteiner A, Verspoor K, Wang Z, Rocha L.  2007.  Uncovering protein-protein interactions in the bibliome. Proceedings of the Second BioCreative Challenge Evaluation Workshop, Volume ISBN 84-933255-6. 2:247–255. Abstract

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2008
Joslyn, C, Paulson P, Verspoor K.  2008.  Exploiting Term Relations for Semantic Hierarchy Construction. Semantic Computing, 2008 IEEE International Conference on. :42–49.: IEEE Abstract

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Joslyn, C, Gregory M, McGrath L, Paulson P, Verspoor K.  2008.  Semantic Hierarchies: Induction, Measurement, and Management. Abstract

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Lin, S, Verspoor K.  2008.  A semantics-enhanced language model for unsupervised word sense disambiguation. Computational Linguistics and Intelligent Text Processing. :287–298.: Springer Abstract

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Abi-Haidar, A, Kaur J, Maguitman A, Radivojac P, Rechtsteiner A, Verspoor K, Wang Z, Rocha LM.  2008.  Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks. Genome biology. 9:S11., Number Suppl 2: BioMed Central Ltd Abstract

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2009
Verspoor, K, Baumgartner Jr W, Roeder C, Hunter L.  2009.  Abstracting the types away from a UIMA type system. From Form to Meaning: Processing Texts Automatically. C. Chiarcos, Eckhart de Castilho, Stede, M. :249–256. Abstract

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Cohen, KB, Verspoor K, Johnson HL, Roeder C, Ogren PV, Baumgartner Jr WA, White E, Tipney H, Hunter L.  2009.  High-precision biological event extraction with a concept recognizer. Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task. :50–58.: Association for Computational Linguistics Abstract

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Verspoor, K, Dvorkin D, Cohen KB, Hunter L.  2009.  Ontology quality assurance through analysis of term transformations. Bioinformatics. 25:i77., Number 12: Oxford Univ Press Abstract

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Verspoor, K, Cohen KB, Hunter L.  2009.  The textual characteristics of traditional and Open Access scientific journals are similar. BMC bioinformatics. 10:183., Number 1: BioMed Central Ltd Abstract

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Ferrucci, D, Lally A, Verspoor K, Nyberg DE.  2009.  Unstructured Information Management Architecture (UIMA) Version 1.0, March 2, 2009. : OASIS Technical Standard
2010
Ramakrishnan, C, Baumgartner Jr WA, Blake JA, Burns GAPC, Cohen KB, Drabkin H, Eppig J, Hovy E, Hsu CN, Hunter LE, Ingulfsen T, Pokkunuri S, Onda H, Riloff E, Roeder C, Verspoor K.  2010.  Building the Scientific Knowledge Mine (SciKnowMine): a Community-driven Framework for Text Mining Tools in Direct Service to Biocuration. Malta. Language Resources and Evaluation. Abstract

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Verspoor, K, Roeder C, Johnson HL, Cohen KB, Baumgartner Jr WA, Hunter LE.  2010.  Exploring species-based strategies for gene normalization. Computational Biology and Bioinformatics, IEEE/ACM Transactions on. 7:462–471., Number 3: IEEE Abstract

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Livingston, KM, Johnson HL, Verspoor K, Hunter LE.  2010.  Leveraging Gene Ontology Annotations to Improve a Memory-Based Language Understanding System. Semantic Computing (ICSC), 2010 IEEE Fourth International Conference on. :40–45.: IEEE Abstract

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Cohen, KB, Johnson H, Verspoor K, Roeder C, Hunter L.  2010.  The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC bioinformatics. 11:492., Number 1: BioMed Central Ltd Abstract

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Cohen, KB, Baumgartner Jr WA, Roeder C, Hunter LE, Verspoor K.  2010.  Test suite design for ontology concept recognition systems. Language Resources and Evaluation Conference (LREC). Abstract

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Roeder, C, Jonquet C, Shah NH, Baumgartner Jr WA, Verspoor K, Hunter L.  2010.  A UIMA wrapper for the NCBO annotator. Bioinformatics. 26:1800–1801., Number 14: Oxford Univ Press Abstract

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Görg, C, Tipney H, Verspoor K, Baumgartner W, Cohen K, Stasko J, Hunter L.  2010.  Visualization and language processing for supporting analysis across the biomedical literature. Knowledge-Based and Intelligent Information and Engineering Systems. :420–429.: Springer Abstract

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2011
Cohen, KB, Christiansen T, Baumgartner Jr WA, Verspoor K, Hunter LE.  2011.  Fast and simple semantic class assignment for biomedical text. ACL HLT 2011. :38. Abstract

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Lu, Z, Kao HY, Wei CH, Huang M, Liu J, Kuo CJ, Hsu CN, Tsai R, Dai HJ, Okazaki N, others, Verspoor K, Livingston K, Wilbur WJ.  2011.  The gene normalization task in BioCreative III. BMC Bioinformatics. 12(Suppl 8):S2., Number Suppl 8: BioMed Central LtdWebsite
Cohen, KB *, Verspoor K *, Johnson HL, Roeder C, Ogren PV, Baumgartner WA, White E, Tipney H, Hunter L.  2011.  High-precision biological event extraction: Effects of system and data. Computational Intelligence. 27(4):681–701. Abstractbionlp09_coin_paper.pdf

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Ravikumar, KE, Liu H, Cohn JD, Wall ME, Verspoor K.  2011.  Pattern Learning through Distant Supervision for Extraction of Protein-Residue Associations in the Biomedical Literature. Machine Learning and Applications and Workshops (ICMLA), 2011 10th International Conference on. 2:59–65.: IEEE Abstract

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Verspoor, CM, Sims BH, Ambrosiano JJ, Cleland TJ.  2011.  System and method for knowledge based matching of users in a network. : Los Alamos National Security LLC (Los Alamos, NM) Abstract

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Kano, Y, Bjorne J, Ginter F, Salakoski T, Buyko E, Hahn U, Cohen KB, Verspoor K, Roeder C, Hunter LE, others, Ohta T, Tsujii J.  2011.  U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC bioinformatics. 12:481., Number 1: BioMed Central Ltd Abstract

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2012
Liu, H, Christiansen T, Baumgartner Jr WA, Verspoor K.  2012.  BioLemmatizer: a lemmatization tool for morphological processing of biomedical text. Journal of Biomedical Semantics. 3(3) AbstractWebsite

Background
The wide variety of morphological variants of domain-specific technical terms contributes to the complexity of performing natural language processing of the scientific literature related to molecular biology. For morphological analysis of these texts, lemmatization has been actively applied in the recent biomedical research.

Results
In this work, we developed a domain-specific lemmatization tool, BioLemmatizer, for the morphological analysis of biomedical literature. The tool focuses on the inflectional morphology of English and is based on the general English lemmatization tool MorphAdorner. The BioLemmatizer is further tailored to the biological domain through incorporation of several published lexical resources. It retrieves lemmas based on the use of a word lexicon, and defines a set of rules that transform a word to a lemma if it is not encountered in the lexicon. An innovative aspect of the BioLemmatizer is the use of a hierarchical strategy for searching the lexicon, which enables the discovery of the correct lemma even if the input Part-of-Speech information is inaccurate. The BioLemmatizer achieves an accuracy of 97.5% in lemmatizing an evaluation set prepared from the CRAFT corpus, a collection of full-text biomedical articles, and an accuracy of 97.6% on the LLL05 corpus. The contribution of the BioLemmatizer to accuracy improvement of a practical information extraction task is further demonstrated when it is used as a component in a biomedical text mining system.

Conclusions
The BioLemmatizer outperforms other tools when compared with eight existing lemmatizers. The BioLemmatizer is released as an open source software and can be downloaded from http://biolemmatizer.sourceforge.net.