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Items: 1 to 20 of 47


In the pursuit of a semantic similarity metric based on UMLS annotations for articles in PubMed Central Open Access.

Garcia Castro LJ, Berlanga R, Garcia A.

J Biomed Inform. 2015 Oct;57:204-18. doi: 10.1016/j.jbi.2015.07.015. Epub 2015 Aug 1.


A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.

Verspoor K, Cohen KB, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Eckert M, Xue N, Baumgartner WA Jr, Bada M, Palmer M, Hunter LE.

BMC Bioinformatics. 2012 Aug 17;13:207. doi: 10.1186/1471-2105-13-207.


Parenthetically speaking: classifying the contents of parentheses for text mining.

Cohen KB, Christiansen T, Hunter LE.

AMIA Annu Symp Proc. 2011;2011:267-72. Epub 2011 Oct 22.


The Gene Ontology: enhancements for 2011.

Gene Ontology Consortium..

Nucleic Acids Res. 2012 Jan;40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. Epub 2011 Nov 18.


The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse.

Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; Mouse Genome Database Group..

Nucleic Acids Res. 2012 Jan;40(Database issue):D881-6. doi: 10.1093/nar/gkr974. Epub 2011 Nov 10.


Logical development of the cell ontology.

Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD.

BMC Bioinformatics. 2011 Jan 5;12:6. doi: 10.1186/1471-2105-12-6.


Entrez Gene: gene-centered information at NCBI.

Maglott D, Ostell J, Pruitt KD, Tatusova T.

Nucleic Acids Res. 2011 Jan;39(Database issue):D52-7. doi: 10.1093/nar/gkq1237. Epub 2010 Nov 28.


Desiderata for ontologies to be used in semantic annotation of biomedical documents.

Bada M, Hunter L.

J Biomed Inform. 2011 Feb;44(1):94-101. doi: 10.1016/j.jbi.2010.10.002. Epub 2010 Oct 26.


The structural and content aspects of abstracts versus bodies of full text journal articles are different.

Cohen KB, Johnson HL, Verspoor K, Roeder C, Hunter LE.

BMC Bioinformatics. 2010 Sep 29;11:492. doi: 10.1186/1471-2105-11-492.


Evolution of the Sequence Ontology terms and relationships.

Mungall CJ, Batchelor C, Eilbeck K.

J Biomed Inform. 2011 Feb;44(1):87-93. doi: 10.1016/j.jbi.2010.03.002. Epub 2010 Mar 10.


CALBC silver standard corpus.

Rebholz-Schuhmann D, Jimeno Yepes AJ, Van Mulligen EM, Kang N, Kors J, Milward D, Corbett P, Buyko E, Beisswanger E, Hahn U.

J Bioinform Comput Biol. 2010 Feb;8(1):163-79.


The mammalian phenotype ontology: enabling robust annotation and comparative analysis.

Smith CL, Eppig JT.

Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):390-9. doi: 10.1002/wsbm.44. Review.


Construction of an annotated corpus to support biomedical information extraction.

Thompson P, Iqbal SA, McNaught J, Ananiadou S.

BMC Bioinformatics. 2009 Oct 23;10:349. doi: 10.1186/1471-2105-10-349.


Building a semantically annotated corpus of clinical texts.

Roberts A, Gaizauskas R, Hepple M, Demetriou G, Guo Y, Roberts I, Setzer A.

J Biomed Inform. 2009 Oct;42(5):950-66. doi: 10.1016/j.jbi.2008.12.013. Epub 2009 Jan 23.


Biomedical discovery acceleration, with applications to craniofacial development.

Leach SM, Tipney H, Feng W, Baumgartner WA, Kasliwal P, Schuyler RP, Williams T, Spritz RA, Hunter L.

PLoS Comput Biol. 2009 Mar;5(3):e1000215. doi: 10.1371/journal.pcbi.1000215. Epub 2009 Mar 27.


Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.

Huang da W, Sherman BT, Lempicki RA.

Nucleic Acids Res. 2009 Jan;37(1):1-13. doi: 10.1093/nar/gkn923. Epub 2008 Nov 25.


Database resources of the National Center for Biotechnology Information.

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, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J.

Nucleic Acids Res. 2009 Jan;37(Database issue):D5-15. doi: 10.1093/nar/gkn741. Epub 2008 Oct 21. Erratum in: Nucleic Acids Res. 2009 May;37(9):3124.


The Cell Line Ontology and its use in tagging cell line names in biomedical text.

Sarntivijai S, Ade AS, Athey BD, States DJ.

AMIA Annu Symp Proc. 2007 Oct 11:1103.


Protein name tagging guidelines: lessons learned.

Mani I, Hu Z, Jang SB, Samuel K, Krause M, Phillips J, Wu CH.

Comp Funct Genomics. 2005;6(1-2):72-6. doi: 10.1002/cfg.452.

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