Publications

  • strict warning: Declaration of vsite::router() should be compatible with space_og::router($op, $object = NULL, $is_active = true) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 262.
  • strict warning: Non-static method vsite::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 242.
  • strict warning: Non-static method space_og::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/openscholar_vsite/vsite/plugins/vsite.inc on line 218.
  • strict warning: Non-static method space_type_purl::excluded_paths() should not be called statically in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/spaces/spaces_og/plugins/space_og.inc on line 185.
  • strict warning: Declaration of os_boxes_modal_siteinfo::config_path() should be compatible with os_boxes_modalframe::config_path($box) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/os/modules/os_modalframe/plugins/os_boxes_modal_siteinfo.inc on line 65.
  • strict warning: Declaration of os_boxes_modal_sitelogo::config_path() should be compatible with os_boxes_modalframe::config_path($box) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/os/modules/os_modalframe/plugins/os_boxes_modal_sitelogo.inc on line 56.
  • strict warning: Declaration of os_modal_wysiwyg::config_path() should be compatible with os_boxes_modalframe::config_path($box) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/os/modules/os_modalframe/plugins/os_modal_wysiwyg.inc on line 69.
  • strict warning: Declaration of os_modal_wysiwyg::submit() should be compatible with os_boxes_modalframe::submit($form, $form_state) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/os/modules/os_modalframe/plugins/os_modal_wysiwyg.inc on line 69.
  • 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: Only variables should be passed by reference in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/wysiwyg_fields/includes/system.inc on line 11.
  • 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 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, &$form_state) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/views/handlers/views_handler_filter.inc on line 589.
  • strict warning: Declaration of views_handler_filter::options_submit() should be compatible with views_handler::options_submit($form, &$form_state) in /home/uceda/webapps/openscholar_php_5_2/sites/all/modules/contrib/views/handlers/views_handler_filter.inc on line 589.
  • strict warning: Declaration of views_handler_filter_boolean_operator::value_validate() should be compatible with views_handler_filter::value_validate($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.
  • 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.
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Bada, M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA, Cohen KB, Verspoor K, Blake JA, Hunter LE.  2012.  Concept Annotation in the CRAFT corpus. BMC Bioinformatics. 13(161) AbstractWebsite

Background
Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text.

Results
This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement.

Conclusions
As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.