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Results: 1 to 20 of 257

1.

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. Epub 2008 Sep 1.

PMID:
18834496
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
18834487
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.

Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R.

BMC Bioinformatics. 2005;6 Suppl 1:S17. Epub 2005 May 24.

PMID:
15960829
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
22438567
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Overview of the protein-protein interaction annotation extraction task of BioCreative II.

Krallinger M, Leitner F, Rodriguez-Penagos C, Valencia A.

Genome Biol. 2008;9 Suppl 2:S4. doi: 10.1186/gb-2008-9-s2-s4. Epub 2008 Sep 1.

PMID:
18834495
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Evaluation of BioCreAtIvE assessment of task 2.

Blaschke C, Leon EA, Krallinger M, Valencia A.

BMC Bioinformatics. 2005;6 Suppl 1:S16. Epub 2005 May 24.

PMID:
15960828
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases.

Chatr-Aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M.

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

PMID:
22151178
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22151647
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
22151968
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Mining physical protein-protein interactions from the literature.

Huang M, Ding S, Wang H, Zhu X.

Genome Biol. 2008;9 Suppl 2:S12. doi: 10.1186/gb-2008-9-s2-s12. Epub 2008 Sep 1.

PMID:
18834490
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Overview of BioCreAtIvE: critical assessment of information extraction for biology.

Hirschman L, Yeh A, Blaschke C, Valencia A.

BMC Bioinformatics. 2005;6 Suppl 1:S1. Epub 2005 May 24.

PMID:
15960821
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
23327936
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Terminological resources for text mining over biomedical scientific literature.

Rinaldi F, Kaljurand K, Sætre R.

Artif Intell Med. 2011 Jun;52(2):107-14. doi: 10.1016/j.artmed.2011.04.011. Epub 2011 Jun 11.

PMID:
21652190
[PubMed - indexed for MEDLINE]
14.

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. Epub 2008 Dec 6. Review.

PMID:
19060303
[PubMed - indexed for MEDLINE]
Free Article
15.

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.

PMID:
12855478
[PubMed - indexed for MEDLINE]
Free Article
16.

Efficient extraction of protein-protein interactions from full-text articles.

Hakenberg J, Leaman R, Vo NH, Jonnalagadda S, Sullivan R, Miller C, Tari L, Baral C, Gonzalez G.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep;7(3):481-94. doi: 10.1109/TCBB.2010.51.

PMID:
20498514
[PubMed - indexed for MEDLINE]
17.

Overview of the gene ontology task at BioCreative IV.

Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z.

Database (Oxford). 2014 Aug 25;2014. pii: bau086. doi: 10.1093/database/bau086. Print 2014.

PMID:
25157073
[PubMed - in process]
Free PMC Article
18.

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.

PMID:
22151929
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database.

Jamieson DG, Gerner M, Sarafraz F, Nenadic G, Robertson DL.

Database (Oxford). 2012 Apr 23;2012:bas023. doi: 10.1093/database/bas023. Print 2012.

PMID:
22529179
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Linking genes to literature: text mining, information extraction, and retrieval applications for biology.

Krallinger M, Valencia A, Hirschman L.

Genome Biol. 2008;9 Suppl 2:S8. doi: 10.1186/gb-2008-9-s2-s8. Epub 2008 Sep 1. Review.

PMID:
18834499
[PubMed - indexed for MEDLINE]
Free PMC Article

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