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Items: 1 to 20 of 23


PPInterFinder--a mining tool for extracting causal relations on human proteins from literature.

Raja K, Subramani S, Natarajan J.

Database (Oxford). 2013 Jan 15;2013:bas052. doi: 10.1093/database/bas052. Print 2013.


The eFIP system for text mining of protein interaction networks of phosphorylated proteins.

Tudor CO, Arighi CN, Wang Q, Wu CH, Vijay-Shanker K.

Database (Oxford). 2012 Dec 5;2012:bas044. doi: 10.1093/database/bas044. Print 2012.


Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts.

Wei CH, Harris BR, Li D, Berardini TZ, Huala E, Kao HY, Lu Z.

Database (Oxford). 2012 Nov 17;2012:bas041. doi: 10.1093/database/bas041. Print 2012.


Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR.

Van Auken K, Fey P, Berardini TZ, Dodson R, Cooper L, Li D, Chan J, Li Y, Basu S, Muller HM, Chisholm R, Huala E, Sternberg PW; WormBase Consortium.

Database (Oxford). 2012 Nov 17;2012:bas040. doi: 10.1093/database/bas040. Print 2012.


SR4GN: a species recognition software tool for gene normalization.

Wei CH, Kao HY, Lu Z.

PLoS One. 2012;7(6):e38460. doi: 10.1371/journal.pone.0038460. Epub 2012 Jun 5.


Open semantic annotation of scientific publications using DOMEO.

Ciccarese P, Ocana M, Clark T.

J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S1. doi: 10.1186/2041-1480-3-S1-S1.


Using ODIN for a PharmGKB revalidation experiment.

Rinaldi F, Clematide S, Garten Y, Whirl-Carrillo M, Gong L, Hebert JM, Sangkuhl K, Thorn CF, Klein TE, Altman RB.

Database (Oxford). 2012 Apr 23;2012:bas021. doi: 10.1093/database/bas021. Print 2012.


Text mining for the biocuration workflow.

Hirschman L, Burns GA, Krallinger M, Arighi C, Cohen KB, Valencia A, Wu CH, Chatr-Aryamontri A, Dowell KG, Huala E, Lourenço A, Nash R, Veuthey AL, Wiegers T, Winter AG.

Database (Oxford). 2012 Apr 18;2012:bas020. doi: 10.1093/database/bas020. Print 2012.


Biocurators and biocuration: surveying the 21st century challenges.

Burge S, Attwood TK, Bateman A, Berardini TZ, Cherry M, O'Donovan C, Xenarios L, Gaudet P.

Database (Oxford). 2012 Mar 20;2012:bar059. doi: 10.1093/database/bar059. Print 2012.


NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A.

Syst Biol. 2012 Jul;61(4):675-89. doi: 10.1093/sysbio/sys025. Epub 2012 Feb 22.


BioCreative III interactive task: an overview.

Arighi CN, Roberts PM, Agarwal S, Bhattacharya S, Cesareni G, Chatr-Aryamontri A, Clematide S, Gaudet P, Giglio MG, Harrow I, Huala E, Krallinger M, Leser U, Li D, Liu F, Lu Z, Maltais LJ, Okazaki N, Perfetto L, Rinaldi F, Sætre R, Salgado D, Srinivasan P, Thomas PE, Toldo L, Hirschman L, Wu CH.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S4. doi: 10.1186/1471-2105-12-S8-S4.


Overview of the BioCreative III Workshop.

Arighi CN, Lu Z, Krallinger M, Cohen KB, Wilbur WJ, Valencia A, Hirschman L, Wu CH.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S1. doi: 10.1186/1471-2105-12-S8-S1.


Integration of gene normalization stages and co-reference resolution using a Markov logic network.

Dai HJ, Chang YC, Tsai RT, Hsu WL.

Bioinformatics. 2011 Sep 15;27(18):2586-94. doi: 10.1093/bioinformatics/btr358. Epub 2011 Jun 17.


GeneTUKit: a software for document-level gene normalization.

Huang M, Liu J, Zhu X.

Bioinformatics. 2011 Apr 1;27(7):1032-3. doi: 10.1093/bioinformatics/btr042. Epub 2011 Feb 8.


An Overview of BioCreative II.5.

Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, Valencia A.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep;7(3):385-99.


eGIFT: mining gene information from the literature.

Tudor CO, Schmidt CJ, Vijay-Shanker K.

BMC Bioinformatics. 2010 Aug 9;11:418. doi: 10.1186/1471-2105-11-418.


Phenex: ontological annotation of phenotypic diversity.

Balhoff JP, Dahdul WM, Kothari CR, Lapp H, Lundberg JG, Mabee P, Midford PE, Westerfield M, Vision TJ.

PLoS One. 2010 May 5;5(5):e10500. doi: 10.1371/journal.pone.0010500.


HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features.

Tsai RT, Lai PT, Dai HJ, Huang CH, Bow YY, Chang YC, Pan WH, Hsu WL.

BMC Bioinformatics. 2009 Dec 3;10 Suppl 15:S9. doi: 10.1186/1471-2105-10-S15-S9.


Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation.

Van Auken K, Jaffery J, Chan J, Müller HM, Sternberg PW.

BMC Bioinformatics. 2009 Jul 21;10:228. doi: 10.1186/1471-2105-10-228.


Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge.

Krallinger M, Morgan A, Smith L, Leitner F, Tanabe L, Wilbur J, Hirschman L, Valencia A.

Genome Biol. 2008;9 Suppl 2:S1. doi: 10.1186/gb-2008-9-s2-s1. Epub 2008 Sep 1.

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