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Volumn 9, Issue 6, 2008, Pages

Anni 2.0: A multipurpose text-mining tool for the life sciences

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASTHMA; BIOMEDICINE; COMPUTER PROGRAM; DNA MICROARRAY; ELEPHANTIASIS; GENE CLUSTER; GENE EXPRESSION; GENETIC ANALYSIS; HEPATITIS B; HEPATITIS C; HUMAN; HUMAN T CELL LEUKEMIA VIRUS INFECTION; INTERNET; LEISHMANIASIS; LISTERIOSIS; MEDICAL INFORMATION; MEDLINE; METASTASIS; PROSTATE CANCER; SCHISTOSOMIASIS; SPASTIC PARAPLEGIA; UPREGULATION; DOCUMENTATION; EVALUATION; INFORMATION RETRIEVAL; METHODOLOGY;

EID: 47349105353     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-6-r96     Document Type: Article
Times cited : (102)

References (51)
  • 2
    • 31144458029 scopus 로고    scopus 로고
    • Extraction of transcript diversity from scientific literature
    • 10.1371/journal.pcbi.0010010 16103899 1183516
    • Shah PK Jensen LJ Boué S Bork P Extraction of transcript diversity from scientific literature. PLoS Comput Biol 2005, 1:e10. 10.1371/journal.pcbi.0010010 16103899 1183516
    • (2005) PLoS Comput Biol , vol.1
    • Shah, P.K.1    Jensen, L.J.2    Boué, S.3    Bork, P.4
  • 3
    • 15044341082 scopus 로고    scopus 로고
    • Integration of text- and data-mining using ontologies successfully selects disease gene candidates
    • 10.1093/nar/gki296 15767279 1065256
    • Tiffin N Kelso JF Powell AR Pan H Bajic VB Hide WA Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res 2005, 33:1544-1552. 10.1093/nar/gki296 15767279 1065256
    • (2005) Nucleic Acids Res , vol.33 , pp. 1544-1552
    • Tiffin, N.1    Kelso, J.F.2    Powell, A.R.3    Pan, H.4    Bajic, V.B.5    Hide, W.A.6
  • 4
    • 0036649742 scopus 로고    scopus 로고
    • Association of genes to genetically inherited diseases using data mining
    • 12006977
    • Perez-Iratxeta C Bork P Andrade MA Association of genes to genetically inherited diseases using data mining. Nat Genet 2002, 31:316-319. 12006977
    • (2002) Nat Genet , vol.31 , pp. 316-319
    • Perez-Iratxeta, C.1    Bork, P.2    Andrade, M.A.3
  • 5
    • 31144432293 scopus 로고    scopus 로고
    • Literature mining for the biologist: From information retrieval to biological discovery
    • 10.1038/nrg1768 16418747
    • Jensen LJ Saric J Bork P Literature mining for the biologist: From information retrieval to biological discovery. Nat Rev Genet 2006, 7:119-129. 10.1038/nrg1768 16418747
    • (2006) Nat Rev Genet , vol.7 , pp. 119-129
    • Jensen, L.J.1    Saric, J.2    Bork, P.3
  • 6
    • 33645841072 scopus 로고    scopus 로고
    • Status of text-mining techniques applied to biomedical text
    • 10.1016/j.drudis.2006.02.011 16580973
    • Erhardt RAA Schneider R Blaschke C Status of text-mining techniques applied to biomedical text. Drug Discov Today 2006, 11:315-325. 10.1016/ j.drudis.2006.02.011 16580973
    • (2006) Drug Discov Today , vol.11 , pp. 315-325
    • Erhardt, R.A.A.1    Schneider, R.2    Blaschke, C.3
  • 7
    • 0037545622 scopus 로고    scopus 로고
    • Generating hypotheses by discovering implicit associations in the literature: A case report of a search for new potential therapeutic uses for thalidomide
    • 10.1197/jamia.M1158 12626374 342048
    • Weeber M Vos R Klein H Berg LTWDJVD Aronson AR Molema G Generating hypotheses by discovering implicit associations in the literature: A case report of a search for new potential therapeutic uses for thalidomide. J Am Med Inform Assoc 2003, 10:252-259. 10.1197/jamia.M1158 12626374 342048
    • (2003) J Am Med Inform Assoc , vol.10 , pp. 252-259
    • Weeber, M.1    Vos, R.2    Klein, H.3    de Jong-van den Berg, L.T.W.4    Aronson, A.R.5    Molema, G.6
  • 8
    • 1542365353 scopus 로고    scopus 로고
    • Text mining: Generating hypotheses from MEDLINE
    • 10.1002/asi.10389
    • Srinivasan P Text mining: Generating hypotheses from MEDLINE. JASIST 2004, 55:396-413. 10.1002/asi.10389
    • (2004) JASIST , vol.55 , pp. 396-413
    • Srinivasan, P.1
  • 9
    • 1342330525 scopus 로고    scopus 로고
    • Knowledge discovery by automated identification and ranking of implicit relationships
    • 10.1093/bioinformatics/btg421 14960466
    • Wren JD Bekeredjian R Stewart JA Shohet RV Garner HR Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics 2004, 20:389-398. 10.1093/bioinformatics/btg421 14960466
    • (2004) Bioinformatics , vol.20 , pp. 389-398
    • Wren, J.D.1    Bekeredjian, R.2    Stewart, J.A.3    Shohet, R.V.4    Garner, H.R.5
  • 10
    • 13444278595 scopus 로고    scopus 로고
    • Using literature-based discovery to identify disease candidate genes
    • 10.1016/j.ijmedinf.2004.04.024 15694635
    • Hristovski D Peterlin B Mitchell JA Humphrey SM Using literature-based discovery to identify disease candidate genes. Int J Med Inform 2005, 74:289-298. 10.1016/j.ijmedinf.2004.04.024 15694635
    • (2005) Int J Med Inform , vol.74 , pp. 289-298
    • Hristovski, D.1    Peterlin, B.2    Mitchell, J.A.3    Humphrey, S.M.4
  • 12
    • 0025265976 scopus 로고
    • Medical literature as a potential source of new knowledge
    • 225324 2403828
    • Swanson DR Medical literature as a potential source of new knowledge. Bull Med Libr Assoc 1990, 78:29-37. 225324 2403828
    • (1990) Bull Med Libr Assoc , vol.78 , pp. 29-37
    • Swanson, D.R.1
  • 13
    • 0022786956 scopus 로고
    • Fish oil, Raynaud's syndrome, and undiscovered public knowledge
    • 3797213
    • Swanson DR Fish oil, Raynaud's syndrome, and undiscovered public knowledge. Perspect Biol Med 1986, 30:7-18. 3797213
    • (1986) Perspect Biol Med , vol.30 , pp. 7-18
    • Swanson, D.R.1
  • 14
    • 0024492974 scopus 로고
    • Fish-oil dietary supplementation in patients with Raynaud's phenomenon: A double-blind, controlled, prospective study
    • 10.1016/0002-9343(89)90261-1 2536517
    • DiGiacomo RA Kremer JM Shah DM Fish-oil dietary supplementation in patients with Raynaud's phenomenon: A double-blind, controlled, prospective study. Am J Med 1989, 86:158-164. 10.1016/ 0002-9343(89)90261-1 2536517
    • (1989) Am J Med , vol.86 , pp. 158-164
    • DiGiacomo, R.A.1    Kremer, J.M.2    Shah, D.M.3
  • 15
    • 0038017587 scopus 로고    scopus 로고
    • Mining microarray expression data by literature profiling
    • research0055.1-0055.16 10.1186/gb-2002-3-10-research0055
    • Chaussabel D Sher A Mining microarray expression data by literature profiling. Genome Biol 2002, 3. research0055.1 0055.16 10.1186/ gb-2002-3-10-research0055
    • (2002) Genome Biol , vol.3
    • Chaussabel, D.1    Sher, A.2
  • 16
    • 0043163729 scopus 로고    scopus 로고
    • The computational analysis of scientific literature to define and recognize gene expression clusters
    • 10.1093/nar/gkg636 12888516 169898
    • Raychaudhuri S Chang JT Imam F Altman RB The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Res 2003, 31:4553-4560. 10.1093/nar/gkg636 12888516 169898
    • (2003) Nucleic Acids Res , vol.31 , pp. 4553-4560
    • Raychaudhuri, S.1    Chang, J.T.2    Imam, F.3    Altman, R.B.4
  • 17
    • 18744403058 scopus 로고    scopus 로고
    • Co-occurrence based meta-analysis of scientific texts: Retrieving biological relationships between genes
    • 10.1093/bioinformatics/bti268 15657104
    • Jelier R Jenster G Dorssers LCJ van der Eijk CC van Mulligen EM Mons B Kors JA Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes. Bioinformatics 2005, 21:2049-2058. 10.1093/bioinformatics/bti268 15657104
    • (2005) Bioinformatics , vol.21 , pp. 2049-2058
    • Jelier, R.1    Jenster, G.2    Dorssers, L.C.J.3    van der Eijk, C.C.4    van Mulligen, E.M.5    Mons, B.6    Kors, J.A.7
  • 18
    • 33847004014 scopus 로고    scopus 로고
    • Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation
    • 10.1186/1471-2105-8-14 17233900 1784107
    • Jelier R Jenster G Dorssers LCJ Wouters BJ Hendriksen PJ Mons B Delwel R Kors JA Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation. BMC Bioinformatics 2007, 8:14. 10.1186/1471-2105-8-14 17233900 1784107
    • (2007) BMC Bioinformatics , vol.8 , pp. 14
    • Jelier, R.1    Jenster, G.2    Dorssers, L.C.J.3    Wouters, B.J.4    Hendriksen, P.J.5    Mons, B.6    Delwel, R.7    Kors, J.A.8
  • 19
  • 21
    • 41149175599 scopus 로고    scopus 로고
    • Literature-based concept profiles for gene annotation: The issue of weighting
    • 10.1016/j.ijmedinf.2007.07.004 17827057
    • Jelier R Schuemie MJ Roes PJ van Mulligen EM Kors JA Literature-based concept profiles for gene annotation: The issue of weighting. Int J Med Inform 2008, 77:354-362. 10.1016/j.ijmedinf.2007.07.004 17827057
    • (2008) Int J Med Inform , vol.77 , pp. 354-362
    • Jelier, R.1    Schuemie, M.J.2    Roes, P.J.3    van Mulligen, E.M.4    Kors, J.A.5
  • 22
    • 33947726437 scopus 로고    scopus 로고
    • Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE
    • 10.1002/pmic.200600693 17370270
    • Schuemie M Chichester C Lisacek F Coute Y Roes PJ Sanchez JC Kors J Mons B Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE. Proteomics 2007, 7:921-931. 10.1002/pmic.200600693 17370270
    • (2007) Proteomics , vol.7 , pp. 921-931
    • Schuemie, M.1    Chichester, C.2    Lisacek, F.3    Coute, Y.4    Roes, P.J.5    Sanchez, J.C.6    Kors, J.7    Mons, B.8
  • 23
    • 0345863927 scopus 로고    scopus 로고
    • The Unified Medical Language System (UMLS): Integrating biomedical terminology
    • 10.1093/nar/gkh061 14681409 308795
    • Bodenreider O The Unified Medical Language System (UMLS): Integrating biomedical terminology. Nucleic Acids Res 2004, 32: Database issue D267-D270. 10.1093/nar/gkh061 14681409 308795
    • (2004) Nucleic Acids Res , vol.32
    • Bodenreider, O.1
  • 25
    • 47249132919 scopus 로고    scopus 로고
    • Filtering the UMLS metathesaurus for MetaMap
    • National Library of Medicine
    • Aronson AR Filtering the UMLS metathesaurus for MetaMap. Technical Report. National Library of Medicine 2006. http://skr.nlm.nih.gov/papers/ references/filtering06.pdf
    • (2006) Technical Report
    • Aronson, A.R.1
  • 27
    • 34248198854 scopus 로고    scopus 로고
    • Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification
    • 10.1016/j.jbi.2006.09.002 17079192
    • Schuemie MJ Mons B Weeber M Kors JA Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification. J Biomed Inform 2007, 40:316-324. 10.1016/ j.jbi.2006.09.002 17079192
    • (2007) J Biomed Inform , vol.40 , pp. 316-324
    • Schuemie, M.J.1    Mons, B.2    Weeber, M.3    Kors, J.A.4
  • 33
    • 33745256260 scopus 로고    scopus 로고
    • CENP-F is a novel microtubule-binding protein that is essential for kinetochore attachments and affects the duration of the mitotic checkpoint delay
    • 10.1007/s00412-006-0049-5 16601978
    • Feng J Huang H Yen TJ CENP-F is a novel microtubule-binding protein that is essential for kinetochore attachments and affects the duration of the mitotic checkpoint delay. Chromosoma 2006, 115:320-329. 10.1007/ s00412-006-0049-5 16601978
    • (2006) Chromosoma , vol.115 , pp. 320-329
    • Feng, J.1    Huang, H.2    Yen, T.J.3
  • 34
    • 33747177050 scopus 로고    scopus 로고
    • Differential mitotic checkpoint protein requirements in somatic and germ cells
    • 10.1042/BST0340583 16856867
    • Jeganathan KB van Deursen JM Differential mitotic checkpoint protein requirements in somatic and germ cells. Biochem Soc Trans 2006, 34:583-586. 10.1042/BST0340583 16856867
    • (2006) Biochem Soc Trans , vol.34 , pp. 583-586
    • Jeganathan, K.B.1    van Deursen, J.M.2
  • 35
    • 0033575347 scopus 로고    scopus 로고
    • Identification of a vertebrate sister-chromatid separation inhibitor involved in transformation and tumorigenesis
    • 10.1126/science.285.5426.418 10411507
    • Zou H McGarry TJ Bernal T Kirschner MW Identification of a vertebrate sister-chromatid separation inhibitor involved in transformation and tumorigenesis. Science 1999, 285:418-422. 10.1126/science.285.5426.418 10411507
    • (1999) Science , vol.285 , pp. 418-422
    • Zou, H.1    McGarry, T.J.2    Bernal, T.3    Kirschner, M.W.4
  • 36
    • 0034213929 scopus 로고    scopus 로고
    • Degradation of human Aurora2 protein kinase by the anaphase-promoting complex-ubiquitin-proteasome pathway
    • 10.1038/sj.onc.1203609 10851084
    • Honda K Mihara H Kato Y Yamaguchi A Tanaka H Yasuda H Furukawa K Urano T Degradation of human Aurora2 protein kinase by the anaphase-promoting complex-ubiquitin-proteasome pathway. Oncogene 2000, 19:2812-2819. 10.1038/sj.onc.1203609 10851084
    • (2000) Oncogene , vol.19 , pp. 2812-2819
    • Honda, K.1    Mihara, H.2    Kato, Y.3    Yamaguchi, A.4    Tanaka, H.5    Yasuda, H.6    Furukawa, K.7    Urano, T.8
  • 37
    • 0030113930 scopus 로고    scopus 로고
    • Identification of a novel ubiquitin-conjugating enzyme involved in mitotic cyclin degradation
    • 10.1016/S0960-9822(02)00513-4 8723350
    • Yu H King RW Peters JM Kirschner MW Identification of a novel ubiquitin-conjugating enzyme involved in mitotic cyclin degradation. Curr Biol 1996, 6:455-466. 10.1016/S0960-9822(02)00513-4 8723350
    • (1996) Curr Biol , vol.6 , pp. 455-466
    • Yu, H.1    King, R.W.2    Peters, J.M.3    Kirschner, M.W.4
  • 38
    • 0036284778 scopus 로고    scopus 로고
    • The anaphase-promoting complex: Proteolysis in mitosis and beyond
    • 10.1016/S1097-2765(02)00540-3 12049731
    • Peters JM The anaphase-promoting complex: Proteolysis in mitosis and beyond. Mol Cell 2002, 9:931-943. 10.1016/S1097-2765(02)00540-3 12049731
    • (2002) Mol Cell , vol.9 , pp. 931-943
    • Peters, J.M.1
  • 39
    • 34247863874 scopus 로고    scopus 로고
    • Mitotic regulation of the anaphase-promoting complex
    • 10.1007/s00018-007-6443-1 17334950
    • Baker DJ Dawlaty MM Galardy P van Deursen JM Mitotic regulation of the anaphase-promoting complex. Cell Mol Life Sci 2007, 64:589-600. 10.1007/ s00018-007-6443-1 17334950
    • (2007) Cell Mol Life Sci , vol.64 , pp. 589-600
    • Baker, D.J.1    Dawlaty, M.M.2    Galardy, P.3    van Deursen, J.M.4
  • 40
    • 34250883376 scopus 로고    scopus 로고
    • Oncogenic regulators and substrates of the anaphase promoting complex/ cyclosome are frequently overexpressed in malignant tumors
    • 10.2353/ajpath.2007.060767 17456782 1854971
    • Lehman NL Tibshirani R Hsu JY Natkunam Y Harris BT West RB Masek MA Montgomery K Rijn van de M Jackson PK Oncogenic regulators and substrates of the anaphase promoting complex/cyclosome are frequently overexpressed in malignant tumors. Am J Pathol 2007, 170:1793-1805. 10.2353/ajpath.2007.060767 17456782 1854971
    • (2007) Am J Pathol , vol.170 , pp. 1793-1805
    • Lehman, N.L.1    Tibshirani, R.2    Hsu, J.Y.3    Natkunam, Y.4    Harris, B.T.5    West, R.B.6    Masek, M.A.7    Montgomery, K.8    Rijn, M.9    Jackson, P.K.10
  • 41
    • 34247355517 scopus 로고    scopus 로고
    • Ubiquitination by the anaphase-promoting complex drives spindle checkpoint inactivation
    • Reddy SK Rape M Margansky WA Kirschner MW Ubiquitination by the anaphase-promoting complex drives spindle checkpoint inactivation. Nature 2007, 446:921-925. 10.1038/nature05734 17443186
    • (2007) Nature , vol.446 , pp. 921-925
    • Reddy, S.K.1    Rape, M.2    Margansky, W.A.3    Kirschner, M.W.4
  • 42
    • 33646675327 scopus 로고    scopus 로고
    • Treatment of chronic hepatitis C in non-responsive patients with pegylated interferon associated with ribavirin and thalidomide: Report of six cases of total remission
    • 16699635
    • Caseiro MM Treatment of chronic hepatitis C in non-responsive patients with pegylated interferon associated with ribavirin and thalidomide: report of six cases of total remission. Rev Inst Med Trop Sao Paulo 2006, 48:109-112. 16699635
    • (2006) Rev Inst Med Trop Sao Paulo , vol.48 , pp. 109-112
    • Caseiro, M.M.1
  • 44
    • 33646852822 scopus 로고    scopus 로고
    • Effects of combined therapy with thalidomide and glucantime on leishmaniasis induced by Leishmania major in BALB/c mice
    • 16514283
    • Solgi G Kariminia A Abdi K Darabi M Ghareghozloo B Effects of combined therapy with thalidomide and glucantime on leishmaniasis induced by Leishmania major in BALB/c mice. Korean J Parasitol 2006, 44:55-61. 16514283
    • (2006) Korean J Parasitol , vol.44 , pp. 55-61
    • Solgi, G.1    Kariminia, A.2    Abdi, K.3    Darabi, M.4    Ghareghozloo, B.5
  • 45
    • 28244497036 scopus 로고    scopus 로고
    • Thalidomide enhances both primary and secondary host resistances to Listeria monocytogenes infection by a neutrophil-related mechanism in female B6C3F1 mice
    • 10.1016/j.taap.2005.04.014 15921716
    • Guo TL Chi RP Karrow NA Zhang LX Pruett SB Germolec DR White KL Jr Thalidomide enhances both primary and secondary host resistances to Listeria monocytogenes infection by a neutrophil-related mechanism in female B6C3F1 mice. Toxicol Appl Pharmacol 2005, 209:244-254. 10.1016/ j.taap.2005.04.014 15921716
    • (2005) Toxicol Appl Pharmacol , vol.209 , pp. 244-254
    • Guo, T.L.1    Chi, R.P.2    Karrow, N.A.3    Zhang, L.X.4    Pruett, S.B.5    Germolec, D.R.6    White Jr., K.L.7
  • 46
    • 0032858907 scopus 로고    scopus 로고
    • Role of Leishmania donovani and its lipophosphoglycan in CD4+ T-cell activation-induced human immunodeficiency virus replication
    • 96879 10496904
    • Wolday D Akuffo H Demissie A Britton S Role of Leishmania donovani and its lipophosphoglycan in CD4+ T-cell activation-induced human immunodeficiency virus replication. Infect Immun 1999, 67:5258-5264. 96879 10496904
    • (1999) Infect Immun , vol.67 , pp. 5258-5264
    • Wolday, D.1    Akuffo, H.2    Demissie, A.3    Britton, S.4
  • 47
    • 33745639228 scopus 로고    scopus 로고
    • Retrieval with gene queries
    • 10.1186/1471-2105-7-220 16630348 1482725
    • Sehgal AK Srinivasan P Retrieval with gene queries. BMC Bioinformatics 2006, 7:220. 10.1186/1471-2105-7-220 16630348 1482725
    • (2006) BMC Bioinformatics , vol.7 , pp. 220
    • Sehgal, A.K.1    Srinivasan, P.2
  • 49
    • 3042786293 scopus 로고    scopus 로고
    • A gene network for navigating the literature
    • 10.1038/ng0704-664 15226743
    • Hoffmann R Valencia A A gene network for navigating the literature. Nat Genet 2004, 36:664. 10.1038/ng0704-664 15226743
    • (2004) Nat Genet , vol.36 , pp. 664
    • Hoffmann, R.1    Valencia, A.2
  • 50
    • 33845976670 scopus 로고    scopus 로고
    • Knowledge discovery based on an implicit and explicit conceptual network
    • 10.1002/asi.20421
    • Koike A Takagi T Knowledge discovery based on an implicit and explicit conceptual network. JASIST 2007, 58:51-65. 10.1002/asi.20421
    • (2007) JASIST , vol.58 , pp. 51-65
    • Koike, A.1    Takagi, T.2
  • 51
    • 47349114097 scopus 로고    scopus 로고
    • Biosemantics http://www.biosemantics.org
    • Biosemantics


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