Publications

  • strict warning: Declaration of vsite::router() should be compatible with space_og::router($op, $object = NULL, $is_active = true) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 262.
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  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method view::load() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/views/views.module on line 879.
  • strict warning: Non-static method view::load() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/views/views.module on line 879.
  • strict warning: Non-static method view::load() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/views/views.module on line 879.
  • strict warning: Declaration of views_handler_argument::init() should be compatible with views_handler::init(&$view, $options) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/views/handlers/views_handler_argument.inc on line 745.
  • strict warning: Declaration of views_handler_filter::options_validate() should be compatible with views_handler::options_validate($form, &$form_state) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/views/handlers/views_handler_filter.inc on line 589.
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  • strict warning: Declaration of views_handler_filter_boolean_operator::value_validate() should be compatible with views_handler_filter::value_validate($form, &$form_state) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/views/handlers/views_handler_filter_boolean_operator.inc on line 149.
  • strict warning: Declaration of views_plugin_row::options_validate() should be compatible with views_plugin::options_validate(&$form, &$form_state) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/views/plugins/views_plugin_row.inc on line 135.
  • strict warning: Declaration of views_plugin_row::options_submit() should be compatible with views_plugin::options_submit(&$form, &$form_state) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/views/plugins/views_plugin_row.inc on line 135.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
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  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
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Verspoor, K, Jimeno Yepes A, Cavedon L, McIntosh T, Herten-Crabb A, Thomas Z, Plazzer J-P.  2013.  Annotating the biomedical literature for the human variome. Database: The Journal of Biological Databases and Curation. 2013 AbstractWebsite

This article introduces the Variome Annotation Schema, a schema that aims to capture the core concepts and relations relevant to cataloguing and interpreting human genetic variation and its relationship to disease, as described in the published literature. The schema was inspired by the needs of the database curators of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) database, but is intended to have application to genetic variation information in a range of diseases. The schema has been applied to a small corpus of full text journal publications on the subject of inherited colorectal cancer. We show that the inter-annotator agreement on annotation of this corpus ranges from 0.78 to 0.95 F-score across different entity types when exact matching is measured, and improves to a minimum F-score of 0.87 when boundary matching is relaxed. Relations show more variability in agreement, but several are reliable, with the highest, cohort-has-size, reaching 0.90 F-score. We also explore the relevance of the schema to the InSiGHT database curation process. The schema and the corpus represent an important new resource for the development of text mining solutions that address relationships among patient cohorts, disease and genetic variation, and therefore, we also discuss the role text mining might play in the curation of information related to the human variome. The corpus is available at http://opennicta.com/home/health/variome.

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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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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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, 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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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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Verspoor, KM, Cohn JD, Ravikumar KE, Wall ME.  2012.  Text Mining Improves Prediction of Protein Functional Sites. PLoS ONE. 7( e32171), Number 2: Public Library of Science AbstractWebsite

We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

Verspoor, C.  1996.  Lexical limits on the influence of context. Proc. of CogSci. :116–120. Abstract
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Verspoor, K.  2014.  Diving deep into data to crack the gene code on disease, 14 February 2014. The Conversation.
Verspoor, CM.  1997.  Contextually-dependent lexical semantics. : University of Edinburgh. College of Science and Engineering. School of Informatics. Abstract
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Verspoor, K, Jimeno Yepes A, Ong C-S, Macintyre G.  2013.  Prioritising genetic mutations by mining the biomedical literature, 18 April. HISA Big Data. , Melbourne, Australiabig_data_2013_verspoor.pdf
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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Verspoor, K, Cohen KB, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Eckert M, Xue N, Baumgartner WA, Bada M, Palmer M, Hunter LE.  2012.  A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinformatics. 13:207.Journal Website
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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Verspoor, CM.  1996.  A perspective on PPs. Edinburgh Working Papers in Cognitive Science. :229. 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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Verspoor, K, Livingston K.  2012.  Towards Adaptation of Linguistic Annotations to Scholarly Annotation Formalisms on the Semantic Web, 12-13 July 2012. Linguistic Annotation Workshop at the Association for Computational Linguistics annual meeting. , Jeju Island, Korea
Verspoor, CM.  1998.  Predictivity vs. Stipulativity in the Lexicon. Language. 152:162. Abstract
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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, K, Blaschke C, Hirschman L, Shatkay H, Valencia A.  2013.  Proceedings of the BioLINK SIG 2013: Roles for text mining in biomedical knowledge discovery and translational medicine. BioLINK SIG 2013. , Berlin, Germany: ISMB BioLINK SIGbiolink2013_proceedings.pdf
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, MacKinlay A, Cohn JD, Wall ME.  2013.  Detection of protein catalytic sites in the biomedical literature, Jan 3-7, 2013. Pacific Symposium on Biocomputing. , Hawaii
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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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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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, CM.  1994.  A cognitively relevant lexical semantics. Master's thesis. Abstract
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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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Verspoor, C.  1997.  Conventionality-governed logical metonymy. Proc. of the 2nd International Workshop on Computational Semantics. :300–312. Abstract
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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, Joslyn C, Mniszewski S, Rechtsteiner A, Rocha LM, Simas T.  2004.  The LANL BioCreAtIvE submission. Abstract

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