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Results: 1 to 20 of 36

1.

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.

2.

CHEMDNER: The drugs and chemical names extraction challenge.

Krallinger M, Leitner F, Rabal O, Vazquez M, Oyarzabal J, Valencia A.

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

3.

FUN-L: gene prioritization for RNAi screens.

Lees JG, Hériché JK, Morilla I, Fernández JM, Adler P, Krallinger M, Vilo J, Valencia A, Ellenberg J, Ranea JA, Orengo C.

Bioinformatics. 2015 Feb 8. pii: btv073. [Epub ahead of print]

PMID:
25667547
4.

Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation.

Hériché JK, Lees JG, Morilla I, Walter T, Petrova B, Roberti MJ, Hossain MJ, Adler P, Fernández JM, Krallinger M, Haering CH, Vilo J, Valencia A, Ranea JA, Orengo C, Ellenberg J.

Mol Biol Cell. 2014 Aug 15;25(16):2522-36. doi: 10.1091/mbc.E13-04-0221. Epub 2014 Jun 18.

5.

BioCreative-IV virtual issue.

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

Database (Oxford). 2014 May 22;2014. pii: bau039. doi: 10.1093/database/bau039. Print 2014. No abstract available. Erratum in: Database (Oxford). 2014;2014:bau072.

6.

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.

7.

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.

Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K, Subramani S, Natarajan J, Cejuela JM, Dubey P, Wu C.

Database (Oxford). 2013 Jan 17;2013:bas056. doi: 10.1093/database/bas056. Print 2013.

8.

BioCreative-2012 virtual issue.

Wu CH, Arighi CN, Cohen KB, Hirschman L, Krallinger M, Lu Z, Mattingly C, Valencia A, Wiegers TC, John Wilbur W.

Database (Oxford). 2012 Dec 5;2012:bas049. doi: 10.1093/database/bas049. Print 2012. No abstract available.

9.

Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining.

Izarzugaza JM, Krallinger M, Valencia A.

Front Physiol. 2012 Aug 22;3:323. doi: 10.3389/fphys.2012.00323. eCollection 2012.

10.

MyMiner: a web application for computer-assisted biocuration and text annotation.

Salgado D, Krallinger M, Depaule M, Drula E, Tendulkar AV, Leitner F, Valencia A, Marcelle C.

Bioinformatics. 2012 Sep 1;28(17):2285-7. Epub 2012 Jul 12.

11.

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.

12.

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.

Krallinger M, Leitner F, Vazquez M, Salgado D, Marcelle C, Tyers M, Valencia A, Chatr-aryamontri A.

Database (Oxford). 2012 Mar 21;2012:bas017. doi: 10.1093/database/bas017. Print 2012.

13.

Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology.

Rojas AM, Santamaria A, Malik R, Jensen TS, Körner R, Morilla I, de Juan D, Krallinger M, Hansen DA, Hoffmann R, Lees J, Reid A, Yeats C, Wehner A, Elowe S, Clegg AB, Brunak S, Nigg EA, Orengo C, Valencia A, Ranea JA.

PLoS One. 2012;7(3):e31813. doi: 10.1371/journal.pone.0031813. Epub 2012 Mar 9.

14.

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.

15.

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.

Krallinger M, Vazquez M, Leitner F, Salgado D, Chatr-Aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M, Schneider G, Rinaldi F, Leaman R, Gonzalez G, Matos S, Kim S, Wilbur WJ, Rocha L, Shatkay H, Tendulkar AV, Agarwal S, Liu F, Wang X, Rak R, Noto K, Elkan C, Lu Z, Dogan RI, Fontaine JF, Andrade-Navarro MA, Valencia A.

BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S3. doi: 10.1186/1471-2105-12-S8-S3.

16.

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.

17.

The FEBS Letters/BioCreative II.5 experiment: making biological information accessible.

Leitner F, Chatr-aryamontri A, Mardis SA, Ceol A, Krallinger M, Licata L, Hirschman L, Cesareni G, Valencia A.

Nat Biotechnol. 2010 Sep;28(9):897-9. doi: 10.1038/nbt0910-897. No abstract available.

PMID:
20829821
18.

The FEBS Letters SDA corpus: a collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community.

Leitner F, Krallinger M, Cesareni G, Valencia A.

FEBS Lett. 2010 Oct 8;584(19):4129-30. doi: 10.1016/j.febslet.2010.08.026. Epub 2010 Aug 20. No abstract available.

19.

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.

PMID:
20704011
20.

FragKB: structural and literature annotation resource of conserved peptide fragments and residues.

Tendulkar AV, Krallinger M, de la Torre V, López G, Wangikar PP, Valencia A.

PLoS One. 2010 Mar 18;5(3):e9679. doi: 10.1371/journal.pone.0009679.

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