Concept annotation in the CRAFT corpus

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Bada, Michael ^a   Eckert, Miriam ^b   Evans, Donald ^a   Garcia, Kristin ^a   Shipley, Krista ^a   Sitnikov, Dmitry ^c   Baumgartner Jr, William A ^a   Cohen, K B ^a   Verspoor, Karin ^a,d   Blake, Judith A ^c   Hunter, Lawrence E ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c JACKSON LABORATORY   (United States)

^d CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED METHODS; BIOMEDICAL JOURNAL; BIOMEDICAL ONTOLOGIES; BIOMEDICAL TEXT MININGS; CELL TYPES; CHEMICAL ENTITY; COMPARABLE CORPORA; GENE ONTOLOGY; GOLD STANDARDS; HIGH QUALITY; JOURNAL ARTICLES; NLP SYSTEMS; OPEN ACCESS; TEXT-MINING;

DATA MINING; GOLD;

NATURAL LANGUAGE PROCESSING SYSTEMS;

ARTICLE; BIOLOGY; DATA MINING; FACTUAL DATABASE; INFORMATION RETRIEVAL; LINGUISTICS; METHODOLOGY; NATURAL LANGUAGE PROCESSING; SEMANTICS;

COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, FACTUAL; INFORMATION STORAGE AND RETRIEVAL; NATURAL LANGUAGE PROCESSING; SEMANTICS; VOCABULARY, CONTROLLED;

EID: 84863516719     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-161     Document Type: Article

References (79)

1. Ananiadou S, McNaught J. Text Mining for Biology and Biomedicine 2006, Artech House, Boston, London.
2. Hunter L, Cohen KB. Biomedical Language Processing: What's Beyond PubMed?. Mol Cell 2006, 21(5):589-594. 10.1016/j.molcel.2006.02.012, 1702322, 16507357.
3. Jensen LJ, Šarić J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 2006, 7:119-129. 10.1038/nrg1768, 16418747.
4. Zweigenbaum P, Demner-Fushman D, Yu H, Cohen KB. Frontiers of biomedical text mining: current progress. Brief Bioinform 2007, 8(5):358-375. 10.1093/bib/bbm045, 2516302, 17977867.
5. Hersh W. Information retrieval: a health and biomedical perspective 2008, Springer, , 3.
6. Bodenreider O. Biomedical Ontologies in action: role in knowledge management, data integration and decision support. Yearb Med Inform 2008, 47:67-79.
7. Smith B, Ashburner M, Rosse C, Bard C, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S, . The OBI Consortium The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotech 2007, 25:1251-1255. The OBI Consortium.
8. Curtis RK, Orešič M, Vidal-Puig A. Pathways to the analysis of microarray data. Trends Biotech 2005, 23(8):429-435.
9. Khatri P, Drǎghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinform 2005, 21(18):3587-3595.
10. Huang DW, Sherman BT, Lempicki R. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucl Acids Res 2009, 37(1):1-13. 10.1093/nar/gkn923, 2615629, 19033363.
11. Leach SM, Tipney H, Feng W, Baumgartner WA, Kasliwal P, Schuyler RP, Williams T, Spritz RA, Hunter L. Biomedical discovery acceleration, with applications to craniofacial development. PLoS Comput Biol 2009, 5(3):e1000215. 10.1371/journal.pcbi.1000215, 2653649, 19325874.
12. Tomanek K, Wermter J, Hahn U. A reappraisal of sentence and token splitting for life sciences documents. Stud Health Technol Inform 2007, 129(Pt 1):524-528.
13. Kulick S, Bies A, Liberman M, Mandel M, McDonald R, Palmer M, Schein A, Ungar L, Winters S, White P. Integrated Annotation for Biomedical Information Extraction , .
14. Coden AR, Pakhomov SV, Ando RK, Duffy PH, Chute CG. Domain-specific language models and lexicons for tagging. J Biomed Inform 2005, 36:422-430.
15. Lease M, Charniak E. Parsing Biomedical Literature 2005, 58-69. , .
16. Roberts A, Gaizauskas R, Hepple M, Guo Y. Combining terminology resources and statistical methods for entity recognition: an evaluation 2008, , .
17. Craven M, Kumlien J. Constructing Biological Knowledge Bases by Extracting Information from Text Sources 1999, , .
18. Bard J, Rhee SY, Ashburner M. An ontology for cell types. Genome Biol 2005, 6(2):R21. 10.1186/gb-2005-6-2-r21, 551541, 15693950.
19. Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehal AD. Logical Development of the Cell Ontology. BMC Bioinform 2011, 12:6.
20. Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M. ChEBI: a database and ontology for chemical entities of biological interest. Nucl Acids Res 2008, 36(Database Issue):D344-D350. 2238832, 17932057.
21. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvarov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucl Acids Res 2009, 37(Database Issue):D5-15. 2686545, 18940862.
22. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol 2005, 6:R44. 10.1186/gb-2005-6-5-r44, 1175956, 15892872.
23. Mungall CJ, Batchelor C, Eilbeck K. Evolution of the Sequence Ontology terms and relationships. J Biomed Inform 2011, 44(1):87-93. 10.1016/j.jbi.2010.03.002, 3052763, 20226267.
24. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2011, 39(Database issue):D52-57. 3013746, 21115458.
25. The Gene Ontology Consortium Gene Ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651, The Gene Ontology Consortium.
26. The Gene Ontology Consortium Enhancements for 2012. Nucleic Acids Res 2010, 40(Database issue):D559-D564. The Gene Ontology Consortium.
27. Verspoor K, Cohen KB, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Baumgartner WA, Ogren PV, Bada M, Palmer M, Hunter LE. A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. Accepted BMC Bioinform 2011,
28. Cohen KB, Lanfranchi A, Corvey W, Baumgartner WA, Roeder C, Ogren PV, Palmer V, Hunter L. Annotation of all coreference in biomedical text: Guideline selection and adaptation 2010, 37-41. , .
29. Smith B. Beyond Concepts: Ontology as Reality Representation , .
30. Smith B. From concepts to clinical reality: an essay on the benchmarking of biomedical terminologies. J Biomed Inform 2006, 39(3):299-306. 10.1016/j.jbi.2005.11.008, 16386470.
31. Bada M, Hunter L. Using the Gene Ontology to Annotate Biomedical Journal Articles 2009, , .
32. Bada M, Hunter L. Desiderata for ontologies to be used in semantic annotation of biomedical documents. J Biomed Inform 2011, 44(1):94-101. 10.1016/j.jbi.2010.10.002, 20971216.
33. Dligach D, Nielsen RD, Palmer M. To Annotate More Accurately or to Annotate More 2010, , .
34. Dligach D, Palmer M. Reducing the Need for Double Annotation 2011, , .
35. PubMed Central Open Access Articles http://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/.
36. GENIA Project Markup Language , , http://www-tsujii.is.s.u-tokyo.ac.jp/~genia/topics/GPML/.
37. Ogren PV. Knowtator: A plug-in for creating training and evaluation data sets for Biomedical Natural Language systems 2006, , .
38. Ferrucci D, Lally A. Building an example application with the unstructured information management architecture. IBM Systems J 2004, 43:455-475.
39. Kano Y, Miwa M, Cohen K, Hunter L, Ananiadou A, Tsujii J. U-Compare: a modular NLP workflow construction and evaluation system. IBM J Res Dev 2011, 55(3):11:1-11:10.
40. Clark T, Kinoshita J. Alzforum and SWAN: The Present and Future of Scientific Web Communities. Brief Bioinform 2007, 8(3):163-171. 10.1093/bib/bbm012, 17510163.
41. Stenetorp P, Pyysalo S, Topić G, Ohta T, Ananiadou S, Tsujii J. Brat: a Web-based Tool for NLP-Assisted Text Annotation , .
42. Smith LH, ETanabe L, Rindflesch T, Wilbur WJ. MedTag: A Collection of Biomedical Annotations 32-37. , .
43. Pyysalo S, Ginter F, Heimonen J, Björne J, Boberg J, Järvinen J, Salakoski T. BioInfer: a corpus for information extraction in the biomedical domain. BMC Bioinform 2007, 8:50.
44. Roberts A, Gaizauskas R, Hepple M, Demetriou G, Guo Y, Roberts I, Setzer A. Building a semantically annotated corpus of clinical texts. J Biomed Inform 2009, 42:950-966. 10.1016/j.jbi.2008.12.013, 19535011.
45. The FetchProt Corpus Documentation and Annotation Guidelines http://fetchprot.sics.se/Corpus/ Release20051107/FetchProtCorpusDocumentationv1.0d.pdf.
46. Fourth i2b2/VA Shared Task and Workshop , , https://www.i2b2.org/NLP/Relations/.
47. Tanabe L, Xie N, Thom LH, Matten W, Wilbur WJ. GENETAG: a tagged corpus for gene/protein named entity recognition. BMC Bioinform 2005, 6(Suppl 1):S3.
48. Kim JD, Ohta T, Tateisi Y, Tsujii J. GENIA corpus-a semantically annotated corpus for bio-textmining. Bioinform 2003, 19(Suppl 1):i180-i182.
49. Kim JD, Ohta T, Tsujii J. Corpus annotation for mining biomedical events from literature. BMC Bioinform 2008, 9:10.
50. Thompson P, Iqbal SA, McNaught J, Ananiadou S. Construction of an annotated corpus to support biomedical information extraction. BMC Bioinform 2009, 10:349.
51. Alex B, Grover C, Haddow B, Kabadjov M, Klein E, Matthews M, Roebuck S, Tobin R, Wang X. The ITI TXM Corpora: Tissue Expressions and Protein-Protein Interactions 2008, Proceedings of the Workshop on Building & Evaluation of Resources for Biomedical Text Mining, LREC.
52. Smith L, Rindflesch T, Wilbur WJ. MedPost: a part-of-speech tagger for bioMedical text. Bioinform 2004, 20(14):2320-2321.
53. Yapex Collections of MEDLINE abstracts , , http://www.sics.se/humle/projects/prothalt/ README_yapex_text_collection.txt.
54. Rebholz-Schuhmann D, Jimeno-Yepes AJ, van Mulligen EM, Kang N, Kors J, Milward D, Corbett P, Buyko E, Tomanek K, Beisswanger E, Hahn U. The CALBC Silver Standard Corpus - Harmonizing Multiple Semantic Annotations in a Large Biomedical Corpus. J Bioinform Comput Biol 2010, 8(1):163-179. 10.1142/S0219720010004562, 20183881.
55. Pradhan S, Hovy E, Marcus M, Palmer M, Ramshaw L, Weischedel R. OntoNotes: A Unified Relational Semantic Representation 2007, 517-526.
56. OntoNotes Release 2.0 http://yertle.ldc.upenn.edu/Catalog/docs/LDC2008T04/OntoNotes-Release-2.0.pdf.
57. Blaschke C, Valencia A. Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study. Comp Funct Genom 2001, 2:196-206.
58. Corney DPA, Buxton B, Langdon WB, Jones DT. BioRAT: extracting biological information from full-length papers. Bioinform 2004, 20(17):3206-3213.
59. Shah PK, Perez-Iratxeta C, Bork P, Andrade MA. Information extraction from full text scientific articles: Where are the keywords?. BMC Bioinform 2003, 4:20.
60. Cohen KB, Johnson HL, Verspoor K, Roeder C, Hunter LE. The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinform 2010, 11:492.
61. Bada M, Livingston K, Hunter L. From Text to Knowledge: Toward Systematic Composition of Complex Representations 2011, , .
62. Lord PW, Stevens RD, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinform 2003, 19(10):1275-1283.
63. Alterovitz G, Xiang M, Mohan M, Ramoni MF. GO PaD: the Gene Ontology Partition Database. Nucleic Acids Res 2007, 35(suppl 1):D322-D327. 1669720, 17098937.
64. Tateisi Y, Ohta T, Collier N, Nobata C, Tsujii J. Building an Annotated Corpus in the Molecular-Biology Domain 2000, , .
65. Soldatova L, Liakata M. An ontology methodology and CISP - the proposed Core Information about Scientific Papers. JISC Project Report 2007,
66. Cohen KB, Christiansen T, Hunter LE. Parenthetically speaking: Classifying the contents of parentheses for text mining 2011, , .
67. Mouse Genome Informatics http://www.informatics.jax.org/.
68. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, . the Mouse Genome Database Group The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucl Acids Res 2012, 40(Database Issue):D881-D886. 3245042, 22075990, the Mouse Genome Database Group.
69. Smith CL, Eppig JT. The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med 2010, 1(3):390-399.
70. Bada M, Eckert M, Palmer M, Hunter LE. An Overview of the CRAFT Concept Annotation Guidelines 2010, Proceedings of the Linguistic Annotation Workshop IV, Association for Computational Linguistics (ACL) Conference.
71. Gennari JH, Musen MA, Fergerson RW, Grosso WE, Crubézy M, Eriksson H, Noy NF, Tu SW. The Evolution of Protégé: An Environment for Knowledge-Based Systems Development. Internat J Human-Comp Studies 2003, 58(1):89-123.
72. Sarntivijai S, Ade AS, Athey BD, States DJ. The Cell Line Ontology and its use in tagging cell line names in biomedical text. AMIA Annu Symp Proc 2007, 11:1103.
73. Mani I, Hu Z, Jang SB, Samuel K, Krause M, Philips J, Wu CH. Protein name tagging guidelines: lessons learned. Comp Funct Genom 2005, 6:72-76.
74. Grenon P, Smith B, Goldberg L. Biodynamic Ontology: Applying BFO in the Biomedical Domain. Ontologies in Medicine 2004, 20-38. Ios Press, Amsterdam, Pisanelli DM.
75. NCBI Taxonomy Database http://www.ncbi.nlm.nih.gov/taxonomy.
76. Ereshefsky M. The Poverty of the Linnaean Hierarchy: A Philosophical Study of Biological Taxonomy 2001, Cambridge University Press, Cambridge.
77. Schulz S, Stenzhorn H, Boeker M. The ontology of biological taxa. Bioinform 2008, 24(13):i313-i321.
78. Bada M, Eilbeck K. Toward a Richer Representation of Sequence Variation in the Sequence Ontology 2010, , , Proceedings of the Annotation, Interpretation and Management of Mutations Workshop, 9th European Conference on Computational Biology (ECCB).
79. Bada M, Eilbeck K. Efforts toward a More Consistent and Interoperable Sequence Ontology 2012, , .