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Items: 1 to 20 of 200

1.

Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.

Névéol A, Wilbur WJ, Lu Z.

Database (Oxford). 2012 Jun 8;2012:bas026. doi: 10.1093/database/bas026.

2.

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.

3.

Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup.

Yeh AS, Hirschman L, Morgan AA.

Bioinformatics. 2003;19 Suppl 1:i331-9.

4.

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.

Lu Z, Hirschman L.

Database (Oxford). 2012 Nov 17;2012:bas043. doi: 10.1093/database/bas043.

5.

PubTator: a web-based text mining tool for assisting biocuration.

Wei CH, Kao HY, Lu Z.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W518-22. doi: 10.1093/nar/gkt441.

6.

pubmed2ensembl: a resource for mining the biological literature on genes.

Baran J, Gerner M, Haeussler M, Nenadic G, Bergman CM.

PLoS One. 2011;6(9):e24716. doi: 10.1371/journal.pone.0024716.

7.

Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?

Winnenburg R, Wächter T, Plake C, Doms A, Schroeder M.

Brief Bioinform. 2008 Nov;9(6):466-78. doi: 10.1093/bib/bbn043. Review.

8.

OntoMate: a text-mining tool aiding curation at the Rat Genome Database.

Liu W, Laulederkind SJ, Hayman GT, Wang SJ, Nigam R, Smith JR, De Pons J, Dwinell MR, Shimoyama M.

Database (Oxford). 2015 Jan 25;2015. pii: bau129. doi: 10.1093/database/bau129.

9.

Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the comparative toxicogenomics database.

Davis AP, Wiegers TC, Johnson RJ, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, Murphy CG, Mattingly CJ.

PLoS One. 2013 Apr 17;8(4):e58201. doi: 10.1371/journal.pone.0058201.

10.

NCBI GEO: mining tens of millions of expression profiles--database and tools update.

Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R.

Nucleic Acids Res. 2007 Jan;35(Database issue):D760-5.

11.

NCBI GEO: mining millions of expression profiles--database and tools.

Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D562-6.

12.

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.

Torii M, Li G, Li Z, Oughtred R, Diella F, Celen I, Arighi CN, Huang H, Vijay-Shanker K, Wu CH.

Database (Oxford). 2014 Aug 13;2014. pii: bau081. doi: 10.1093/database/bau081.

13.

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.

Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H.

Genome Biol. 2008;9 Suppl 2:S5. doi: 10.1186/gb-2008-9-s2-s5.

14.

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.

15.

Curation accuracy of model organism databases.

Keseler IM, Skrzypek M, Weerasinghe D, Chen AY, Fulcher C, Li GW, Lemmer KC, Mladinich KM, Chow ED, Sherlock G, Karp PD.

Database (Oxford). 2014 Jun 12;2014. pii: bau058. doi: 10.1093/database/bau058.

16.

NCBI GEO: archive for high-throughput functional genomic data.

Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R.

Nucleic Acids Res. 2009 Jan;37(Database issue):D885-90. doi: 10.1093/nar/gkn764.

17.

The Xenbase literature curation process.

Bowes JB, Snyder KA, James-Zorn C, Ponferrada VG, Jarabek CJ, Burns KA, Bhattacharyya B, Zorn AM, Vize PD.

Database (Oxford). 2013 Jan 9;2013:bas046. doi: 10.1093/database/bas046.

18.

Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases.

Gobeill J, Pasche E, Vishnyakova D, Ruch P.

Database (Oxford). 2013 Jul 9;2013:bat041. doi: 10.1093/database/bat041.

19.

Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*.

Barrett T, Edgar R.

Methods Mol Biol. 2006;338:175-90.

20.

Opportunities for text mining in the FlyBase genetic literature curation workflow.

McQuilton P; FlyBase Consortium..

Database (Oxford). 2012 Nov 17;2012:bas039. doi: 10.1093/database/bas039.

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