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Items: 1 to 20 of 45


A categorical analysis of coreference resolution errors in biomedical texts.

Choi M, Zobel J, Verspoor K.

J Biomed Inform. 2016 Apr;60:309-18. doi: 10.1016/j.jbi.2016.02.015. Epub 2016 Feb 27.


PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources.

Kahanda I, Funk C, Verspoor K, Ben-Hur A.

F1000Res. 2015 Jul 16;4:259. doi: 10.12688/f1000research.6670.1. eCollection 2015.


Special issue on bio-ontologies and phenotypes.

Soldatova LN, Collier N, Oellrich A, Groza T, Verspoor K, Rocca-Serra P, Dumontier M, Shah NH.

J Biomed Semantics. 2015 Dec 17;6:40. doi: 10.1186/s13326-015-0040-2. eCollection 2015.


Optimizing graph-based patterns to extract biomedical events from the literature.

Liu H, Verspoor K, Comeau DC, MacKinlay AD, Wilbur W.

BMC Bioinformatics. 2015;16 Suppl 16:S2. doi: 10.1186/1471-2105-16-S16-S2. Epub 2015 Oct 30.


A close look at protein function prediction evaluation protocols.

Kahanda I, Funk CS, Ullah F, Verspoor KM, Ben-Hur A.

Gigascience. 2015 Sep 14;4:41. doi: 10.1186/s13742-015-0082-5. eCollection 2015.


Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct.

Funk CS, Kahanda I, Ben-Hur A, Verspoor KM.

J Biomed Semantics. 2015 Mar 18;6:9. doi: 10.1186/s13326-015-0006-4. eCollection 2015.


The CHEMDNER corpus of chemicals and drugs and its annotation principles.

Krallinger M, Rabal O, Leitner F, Vazquez M, Salgado D, Lu Z, Leaman R, Lu Y, Ji D, Lowe DM, Sayle RA, Batista-Navarro RT, Rak R, Huber T, Rocktäschel T, Matos S, Campos D, Tang B, Xu H, Munkhdalai T, Ryu KH, Ramanan SV, Nathan S, Žitnik S, Bajec M, Weber L, Irmer M, Akhondi SA, Kors JA, Xu S, An X, Sikdar UK, Ekbal A, Yoshioka M, Dieb TM, Choi M, Verspoor K, Khabsa M, Giles CL, Liu H, Ravikumar KE, Lamurias A, Couto FM, Dai HJ, Tsai RT, Ata C, Can T, Usié A, Alves R, Segura-Bedmar I, Martínez P, Oyarzabal J, Valencia A.

J Cheminform. 2015 Jan 19;7(Suppl 1 Text mining for chemistry and the CHEMDNER track):S2. doi: 10.1186/1758-2946-7-S1-S2. eCollection 2015.


Assessing the impact of case sensitivity and term information gain on biomedical concept recognition.

Groza T, Verspoor K.

PLoS One. 2015 Mar 19;10(3):e0119091. doi: 10.1371/journal.pone.0119091. eCollection 2015.


Associating disease-related genetic variants in intergenic regions to the genes they impact.

Macintyre G, Jimeno Yepes A, Ong CS, Verspoor K.

PeerJ. 2014 Oct 23;2:e639. doi: 10.7717/peerj.639. eCollection 2014.


Mutation extraction tools can be combined for robust recognition of genetic variants in the literature.

Jimeno Yepes A, Verspoor K.

Version 2. F1000Res. 2014 Jan 21 [revised 2014 Jun 10];3:18. doi: 10.12688/f1000research.3-18.v2. eCollection 2014.


Big data in medicine is driving big changes.

Martin-Sanchez F, Verspoor K.

Yearb Med Inform. 2014 Aug 15;9:14-20. doi: 10.15265/IY-2014-0020.


Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013.

Verspoor K, Shatkay H, Hirschman L, Blaschke C, Valencia A.

Bioinformatics. 2015 Jan 15;31(2):297-8. doi: 10.1093/bioinformatics/btu412. Epub 2014 Jul 14.


Mapping biomedical vocabularies: a semi-automated term matching approach.

Ofoghi B, Lopez-Campos GH, Martin Sanchez FJ, Verspoor K.

Stud Health Technol Inform. 2014;202:16-9.


BioC interoperability track overview.

Comeau DC, Batista-Navarro RT, Dai HJ, Doğan RI, Yepes AJ, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M, Peng Y, Rak R, Rinaldi F, Tsai RT, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ.

Database (Oxford). 2014 Jun 30;2014. pii: bau053. doi: 10.1093/database/bau053. Print 2014. Review.


Roles for text mining in protein function prediction.

Verspoor KM.

Methods Mol Biol. 2014;1159:95-108. doi: 10.1007/978-1-4939-0709-0_6. Review.


Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters.

Funk C, Baumgartner W Jr, Garcia B, Roeder C, Bada M, Cohen KB, Hunter LE, Verspoor K.

BMC Bioinformatics. 2014 Feb 26;15:59. doi: 10.1186/1471-2105-15-59.


Literature mining of genetic variants for curation: quantifying the importance of supplementary material.

Jimeno Yepes A, Verspoor K.

Database (Oxford). 2014 Feb 10;2014:bau003. doi: 10.1093/database/bau003. Print 2014.


Representing annotation compositionality and provenance for the Semantic Web.

Livingston KM, Bada M, Hunter LE, Verspoor K.

J Biomed Semantics. 2013 Nov 22;4:38. doi: 10.1186/2041-1480-4-38. eCollection 2013.


BioC: a minimalist approach to interoperability for biomedical text processing.

Comeau DC, Islamaj Doğan R, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ.

Database (Oxford). 2013 Sep 18;2013:bat064. doi: 10.1093/database/bat064. Print 2013.

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