-
1
-
-
15744374330
-
Facts from text - Is text mining ready to deliver
-
Rebholz-Schuhmann, D. Facts from text - is text mining ready to deliver. PLoS Biol. 3, e65 (2005).
-
(2005)
PLoS Biol.
, vol.3
-
-
Rebholz-Schuhmann, D.1
-
2
-
-
0034734040
-
Automated extraction of information in molecular biology
-
Andrade, M. A. & Bork, P. Automated extraction of information in molecular biology. FEBS Lett. 476, 12-17 (2000).
-
(2000)
FEBS Lett.
, vol.476
, pp. 12-17
-
-
Andrade, M.A.1
Bork, P.2
-
3
-
-
3943106585
-
Accomplishments and challenges in literature data mining for biology
-
Hirschman, L., Park, J. C., Tsujii, J., Wong, L. & Wu, C. H. Accomplishments and challenges in literature data mining for biology. Bioinformatics 18, 1553-1561 (2002).
-
(2002)
Bioinformatics
, vol.18
, pp. 1553-1561
-
-
Hirschman, L.1
Park, J.C.2
Tsujii, J.3
Wong, L.4
Wu, C.H.5
-
4
-
-
0036325427
-
Genomics and natural language processing
-
Yandell, M. D. & Majoros, W. H. Genomics and natural language processing. Nature Rev. Genet. 3, 601-610 (2002).
-
(2002)
Nature Rev. Genet.
, vol.3
, pp. 601-610
-
-
Yandell, M.D.1
Majoros, W.H.2
-
5
-
-
22244459539
-
Text-mining and information-retrieval services for molecular biology
-
Krallinger, M. & Valencia, A. Text-mining and information-retrieval services for molecular biology. Genome Biol. 6, 224 (2005).
-
(2005)
Genome Biol.
, vol.6
, pp. 224
-
-
Krallinger, M.1
Valencia, A.2
-
6
-
-
21844458914
-
Concerted mechanism of swe1/wee1 regulation by multiple kinases in budding yeast
-
Asano, S. et al. Concerted mechanism of swe1/wee1 regulation by multiple kinases in budding yeast. EMBO J. 24, 2194-2204 (2005).
-
(2005)
EMBO J.
, vol.24
, pp. 2194-2204
-
-
Asano, S.1
-
7
-
-
0029989103
-
An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts
-
Wilbur, W. J. & Yang, Y. An analysis of statistical term strength and its use in the indexing and retrieval of molecular biology texts. Comput. Biol. Med. 26, 209-222 (1996).
-
(1996)
Comput. Biol. Med.
, vol.26
, pp. 209-222
-
-
Wilbur, W.J.1
Yang, Y.2
-
8
-
-
0000970864
-
The effectiveness of document neighboring in search enhancement
-
Wilbur, W. J. & Coffee, L. The effectiveness of document neighboring in search enhancement. Inf. Process. Manage. 30, 253-266 (1994).
-
(1994)
Inf. Process. Manage.
, vol.30
, pp. 253-266
-
-
Wilbur, W.J.1
Coffee, L.2
-
9
-
-
0033642065
-
High-throughput functional annotation of novel gene products using document clustering
-
Renner, A. & Aszodi, A. High-throughput functional annotation of novel gene products using document clustering. Pac. Symp. Biocomput. 5, 50-68 (2000).
-
(2000)
Pac. Symp. Biocomput.
, vol.5
, pp. 50-68
-
-
Renner, A.1
Aszodi, A.2
-
10
-
-
0035229819
-
Textquest: Document clustering of Medline abstracts for concept discovery in molecular biology
-
Iliopoulos, I. Enright, A. J. & Ouzounis, C. A. Textquest: document clustering of Medline abstracts for concept discovery in molecular biology. Pac. Symp. Biocomput. 6, 384-395 (2001).
-
(2001)
Pac. Symp. Biocomput.
, vol.6
, pp. 384-395
-
-
Iliopoulos, I.1
Enright, A.J.2
Ouzounis, C.A.3
-
11
-
-
0041627778
-
Evaluation of the vector space representation in text-based gene clustering
-
Glenisson, P., Antal, P., Mathys, J., Moreau, Y. & De Moor, B. Evaluation of the vector space representation in text-based gene clustering. Pac. Symp. Biocomput. 8, 391-402 (2003).
-
(2003)
Pac. Symp. Biocomput.
, vol.8
, pp. 391-402
-
-
Glenisson, P.1
Antal, P.2
Mathys, J.3
Moreau, Y.4
De Moor, B.5
-
12
-
-
0035002541
-
Mining literature for protein-protein interactions
-
Marcotte, E. M., Xenarios, I. & Eisenberg, D. Mining literature for protein-protein interactions. Bioinformatics 17, 359-363 (2001).
-
(2001)
Bioinformatics
, vol.17
, pp. 359-363
-
-
Marcotte, E.M.1
Xenarios, I.2
Eisenberg, D.3
-
13
-
-
31144471688
-
-
Bhalotia, G., Nakov, P. I., Schwartz, A. S. & Hearst, M. A. BioText team report for the TREC 2003 genomics track [online], 〈http://trec.nist. gov/pubs/trec12/papers/ucal-berkeley.genomics.pdf〉 (2003).
-
(2003)
BioText Team Report for the TREC 2003 Genomics Track [Online]
-
-
Bhalotia, G.1
Nakov, P.I.2
Schwartz, A.S.3
Hearst, M.A.4
-
14
-
-
2942549190
-
PreBIND and Textomy - Mining the biomedical literature for protein-protein interactions using a support vector machine
-
Donaldson, I. et al. PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics 4, 11 (2003).
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 11
-
-
Donaldson, I.1
-
16
-
-
23144432078
-
PubFinder: A tool for improving retrieval rate of relevant PubMed abstracts
-
Goetz, T. & von der Lieth, C.-W. PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts. Nucleic Acids Res. 33, W774-W778 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Goetz, T.1
Von Der Lieth, C.-W.2
-
17
-
-
31144458029
-
Extraction of transcript diversity from scientific literature
-
Shah, P. K., Jensen, L. J., Boue, S. & Bork, P. Extraction of transcript diversity from scientific literature. PLoS Comp. Biol. 1, e10 (2005).
-
(2005)
PLoS Comp. Biol.
, vol.1
-
-
Shah, P.K.1
Jensen, L.J.2
Boue, S.3
Bork, P.4
-
18
-
-
14844329372
-
Ranking the whole MEDLINE database according to a large training set using text indexing
-
Suomela, B. P. & Andrade, M. A. Ranking the whole MEDLINE database according to a large training set using text indexing. BMC Bioinformatics 6, 75 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 75
-
-
Suomela, B.P.1
Andrade, M.A.2
-
22
-
-
0032795144
-
MedMiner: An internet text-mining tool for biomedical information, with application to gene expression profiling
-
Tanabe, L. et al. MedMiner: An internet text-mining tool for biomedical information, with application to gene expression profiling. Biotechniques 27, 1210-1217 (1999).
-
(1999)
Biotechniques
, vol.27
, pp. 1210-1217
-
-
Tanabe, L.1
-
23
-
-
14044254746
-
Textpresso: An ontology-based information retrieval and extraction system for biological literature
-
Muller, H. M., Kenny, E. E. & Sternberg, P. W. Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol. 2, e309 (2004). This paper presents an advanced full-text IR tool that is designed for the Caenorhabditis elegans research community.
-
(2004)
PLoS Biol.
, vol.2
-
-
Muller, H.M.1
Kenny, E.E.2
Sternberg, P.W.3
-
24
-
-
0035448614
-
XplorMed: A tool for exploring MEDLINE abstracts
-
Perez-Iratxeta, C., Bork, P. & Andrade, A. M. XplorMed: a tool for exploring MEDLINE abstracts. Trends Biochem. Sci. 26, 573-575 (2001).
-
(2001)
Trends Biochem. Sci.
, vol.26
, pp. 573-575
-
-
Perez-Iratxeta, C.1
Bork, P.2
Andrade, A.M.3
-
25
-
-
3042786293
-
A gene network for navigating the literature
-
Hoffmann, R. & Valencia, A. A gene network for navigating the literature. Nature Genet. 36, 664 (2004).
-
(2004)
Nature Genet.
, vol.36
, pp. 664
-
-
Hoffmann, R.1
Valencia, A.2
-
26
-
-
23144448699
-
GoPubMed: Exploring PubMed with the Gene Ontology
-
Doms, A. & Schroeder, M. GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res. 33, W783-W786 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Doms, A.1
Schroeder, M.2
-
27
-
-
27744543196
-
Text mining for metabolic pathways, signaling cascades, and protein networks
-
Hoffmann, R. et al. Text mining for metabolic pathways, signaling cascades, and protein networks. Sci. STKE 283, pe21 (2005).
-
(2005)
Sci. STKE
, vol.283
-
-
Hoffmann, R.1
-
28
-
-
0031633368
-
Toward information extraction: Identifying protein names from biological papers
-
Fukuda, K., Tamura, A., Tsunoda, T. & Takagi, T. Toward information extraction: identifying protein names from biological papers. Pac. Symp. Biocomput. 3, 707-718 (1998).
-
(1998)
Pac. Symp. Biocomput.
, vol.3
, pp. 707-718
-
-
Fukuda, K.1
Tamura, A.2
Tsunoda, T.3
Takagi, T.4
-
29
-
-
0036678776
-
Tagging gene and protein names in biomedical text
-
Tanabe, L. & Wilbur, W. J. Tagging gene and protein names in biomedical text. Bioinformatics 18, 1124-1132 (2002).
-
(2002)
Bioinformatics
, vol.18
, pp. 1124-1132
-
-
Tanabe, L.1
Wilbur, W.J.2
-
30
-
-
0002670150
-
Extracting the names of genes and gene products with a hidden Markov model
-
Coller, N., Nobata, C. & Tsujii, J. Extracting the names of genes and gene products with a hidden Markov model. Int. Conf. Comput. Linguist. 18, 201-207 (2000).
-
(2000)
Int. Conf. Comput. Linguist.
, vol.18
, pp. 201-207
-
-
Coller, N.1
Nobata, C.2
Tsujii, J.3
-
31
-
-
1042269470
-
GAPSCORE: Finding gene and protein names one word at a time
-
Chang, J. T., Schutze, H. & Altman, R. B. GAPSCORE: finding gene and protein names one word at a time. Bioinformatics 20, 216-225 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 216-225
-
-
Chang, J.T.1
Schutze, H.2
Altman, R.B.3
-
32
-
-
33947305118
-
Identifying gene and protein mentions in text using conditional random fields
-
McDonald, R. & Pereira, F. Identifying gene and protein mentions in text using conditional random fields. BMC Bioinformatics 6, S6 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
-
-
McDonald, R.1
Pereira, F.2
-
33
-
-
25144520247
-
ABNER: An open source tool for automatically tagging genes, proteins, and other entity names in text
-
Settles, B. ABNER: an open source tool for automatically tagging genes, proteins, and other entity names in text. Bioinformatics 21, 3191-3192 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 3191-3192
-
-
Settles, B.1
-
34
-
-
33947307025
-
Recognition of protein/gene names from text using an ensemble of classifiers
-
Zhou, G., Shen, D., Zhang, J,, Su, J. & Tan, S. Recognition of protein/gene names from text using an ensemble of classifiers. BMC Bioinformatics 6, S7 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Zhou, G.1
Shen, D.2
Zhang, J.3
Su, J.4
Tan, S.5
-
35
-
-
0034707204
-
Using BLAST for identifying gene and protein names in journal articles
-
Krauthammer, M., Rzhetsky, A., Morozov, P. & Friedman, C. Using BLAST for identifying gene and protein names in journal articles. Gene 259, 245-252 (2000).
-
(2000)
Gene
, vol.259
, pp. 245-252
-
-
Krauthammer, M.1
Rzhetsky, A.2
Morozov, P.3
Friedman, C.4
-
36
-
-
0036854484
-
Finding relevant references to genes and proteins in Medline using a Bayesian approach
-
Leonard, J. E., Colombe, J. B. & Levy, J. L. Finding relevant references to genes and proteins in Medline using a Bayesian approach. Bioinformatics 18, 1515-1522 (2002).
-
(2002)
Bioinformatics
, vol.18
, pp. 1515-1522
-
-
Leonard, J.E.1
Colombe, J.B.2
Levy, J.L.3
-
37
-
-
9544222527
-
Protein names precisely peeled off free text
-
Mika, S. & Rost, B. Protein names precisely peeled off free text. Bioinformatics 20, i241-i247 (2004).
-
(2004)
Bioinformatics
, vol.20
-
-
Mika, S.1
Rost, B.2
-
38
-
-
33947317767
-
Exploring the boundaries: Gene and protein identification in biomedical text
-
Finkel, J. et al. Exploring the boundaries: gene and protein identification in biomedical text. BMC Bioinformatics 6, S5 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Finkel, J.1
-
39
-
-
33947315795
-
Automatically annotating documents with normalized gene lists
-
Crim, J., McDonald, R. & Pereira, F. Automatically annotating documents with normalized gene lists. BMC Bioinformatics 6, S13 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Crim, J.1
McDonald, R.2
Pereira, F.3
-
40
-
-
33947373992
-
A simple approach for protein name identification: Prospects and limits
-
Fundel, K., Güttler, D., Zimmer, R. & Apostolakis, J. A simple approach for protein name identification: prospects and limits. BMC Bioinformatics 6, S15 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Fundel, K.1
Güttler, D.2
Zimmer, R.3
Apostolakis, J.4
-
41
-
-
33947258447
-
ProMiner: Rule-based protein and gene entity recognition
-
Hanisch, D., Fundel, K., Mevissen, H. T., Zimmer, R. & Fluck, J. ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 6, S14 (2005). This paper describes a simple biomedical ER system that relies primarily on a carefully curated list of synonyms. It was one of the methods that performed best in the BioCreAtIvE assessment.
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Hanisch, D.1
Fundel, K.2
Mevissen, H.T.3
Zimmer, R.4
Fluck, J.5
-
42
-
-
13444256580
-
Gene name ambiguity of eukaryotic nomenclatures
-
Chen, L., Liu, H. & Friedman, C. Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics 21, 248-256 (2005). These authors provide a quantitative overview of the causes of gene-name ambiguity, and suggest how researchers and publishers can help to minimize this problem.
-
(2005)
Bioinformatics
, vol.21
, pp. 248-256
-
-
Chen, L.1
Liu, H.2
Friedman, C.3
-
43
-
-
24644505245
-
Resolving abbreviations to their senses in Medline
-
Gaudan, S., Kirsch, H. & Rebholz-Schuhmann, D. Resolving abbreviations to their senses in Medline. Bioinformatics 21, 3658-3664 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 3658-3664
-
-
Gaudan, S.1
Kirsch, H.2
Rebholz-Schuhmann, D.3
-
44
-
-
25444465132
-
Thesaurus-based disambiguation of gene symbols
-
Schijvenaars, B. J. A. et al. Thesaurus-based disambiguation of gene symbols. BMC Bioinformatics 6, 149 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 149
-
-
Schijvenaars, B.J.A.1
-
45
-
-
33947250174
-
GENETAG: A tagged corpus for gene/protein named entity recognition
-
Tanabe, L., Xie, N., Thom, L. H., Matten, W. & Wilbur, W. J. GENETAG: a tagged corpus for gene/protein named entity recognition. BMC Bioinformatics 6, S3 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Tanabe, L.1
Xie, N.2
Thom, L.H.3
Matten, W.4
Wilbur, W.J.5
-
46
-
-
0033290514
-
Constructing biological knowledge bases by extracting information from text sources
-
Craven, M. Kumlien, J. Constructing biological knowledge bases by extracting information from text sources. in Proc. Int. Conf. Intell. Syst. Mol. Biol. 7, 77-86 (1999).
-
(1999)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.7
, pp. 77-86
-
-
Craven, M.1
Kumlien, J.2
-
47
-
-
25444468307
-
Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information
-
Cooper, J. W. & Kershenbaum, A. Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information. BMC Bioinformatics 6, 143 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 143
-
-
Cooper, J.W.1
Kershenbaum, A.2
-
48
-
-
25144516911
-
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome
-
Ramani, A. K., Bunescu, R. C., Mooney, R. J. & Marcotte, E. M. Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol. 6, R40 (2005).
-
(2005)
Genome Biol.
, vol.6
-
-
Ramani, A.K.1
Bunescu, R.C.2
Mooney, R.J.3
Marcotte, E.M.4
-
49
-
-
0035229924
-
Detecting gene relations from Medline abstracts
-
Stephens, M., Palakal, M., Mukhopadhyay, S., Raje, R. & Mostafa, J. Detecting gene relations from Medline abstracts. Pac. Symp. Biocomput. 6, 483-495 (2001).
-
(2001)
Pac. Symp. Biocomput.
, vol.6
, pp. 483-495
-
-
Stephens, M.1
Palakal, M.2
Mukhopadhyay, S.3
Raje, R.4
Mostafa, J.5
-
50
-
-
0036522638
-
The frame-based module of the SUISEKI information extraction system
-
Blaschke, C. & Valencia, A. The frame-based module of the SUISEKI information extraction system. IEEE Intell. Syst. 17, 14-20 (2002).
-
(2002)
IEEE Intell. Syst.
, vol.17
, pp. 14-20
-
-
Blaschke, C.1
Valencia, A.2
-
51
-
-
0033655017
-
Biobibliometrics: Information retrieval and visualization from co-occurrence of gene names in Medline abstracts
-
Stapley, B. J. & Benoit, G. Biobibliometrics: information retrieval and visualization from co-occurrence of gene names in Medline abstracts. Pac. Symp. Biocomput. 5, 529-540 (2000).
-
(2000)
Pac. Symp. Biocomput.
, vol.5
, pp. 529-540
-
-
Stapley, B.J.1
Benoit, G.2
-
52
-
-
0035042776
-
A literature network of human genes for high-throughput analysis of gene expression
-
Jenssen, T. K., Lægreid, A., Komorowski, J. & Hovig, E. A literature network of human genes for high-throughput analysis of gene expression. Nature Genet. 28, 21-28 (2001). This paper describes an IE system, PubGene, that is based on simple co-occurrence, and shows how it can be used for the interpretion of microarray expression data.
-
(2001)
Nature Genet.
, vol.28
, pp. 21-28
-
-
Jenssen, T.K.1
Lægreid, A.2
Komorowski, J.3
Hovig, E.4
-
53
-
-
4644231028
-
Prolinks: A database of protein functional linkages derived from coevolution
-
Bowers, P. M. et al. Prolinks: a database of protein functional linkages derived from coevolution. Nucleic Acids Res. 5, R35 (2003).
-
(2003)
Nucleic Acids Res.
, vol.5
-
-
Bowers, P.M.1
-
54
-
-
13444249988
-
STRING: Known and predicted protein-protein associations, integrated and transferred across organisms
-
von Mering, C. et al. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 33, D433-D437 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Von Mering, C.1
-
55
-
-
0346752107
-
From gene networks to gene function
-
Schlitt, T. et al. From gene networks to gene function. Genome Res. 13, 2568-2576 (2003).
-
(2003)
Genome Res.
, vol.13
, pp. 2568-2576
-
-
Schlitt, T.1
-
56
-
-
1042269463
-
Shared relationship analysis: Ranking set cohesion and commonalities within a literature-derived relationship network
-
Wren, J. D. & Garner, H. R. Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinformatics 20, 191-198 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 191-198
-
-
Wren, J.D.1
Garner, H.R.2
-
57
-
-
25444530343
-
CoPub Mapper: Mining MEDLiNE based on search term co-publication
-
Alako, B. T. et al. CoPub Mapper: mining MEDLiNE based on search term co-publication. BMC Bioinformatics 6, 51 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 51
-
-
Alako, B.T.1
-
58
-
-
15044341082
-
Integration of text- and data-mining using ontologies successfully selects disease gene candidates
-
Tiffin, N. et al. Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res. 33, 1544-1552 (2005). This study combines tissue-expression data with disease-tissue relationships that were extracted from the literature to predict candidate disease genes.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 1544-1552
-
-
Tiffin, N.1
-
59
-
-
0036371537
-
Mining Medline: Abstracts, sentences, or phrases?
-
Ding, J., Berleant, d., Nettleton, D. & Wurtelle, E. Mining Medline: abstracts, sentences, or phrases? Pac. Symp. Biocomput. 7, 326-337 (2002).
-
(2002)
Pac. Symp. Biocomput.
, vol.7
, pp. 326-337
-
-
Ding, J.1
Berleant, D.2
Nettleton, D.3
Wurtelle, E.4
-
60
-
-
33947301798
-
Learning statistical models for annotating proteins with function information using biomedical text
-
Ray, S. & Craven, M. Learning statistical models for annotating proteins with function information using biomedical text. BMC Bioinformatics 6, S18 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Ray, S.1
Craven, M.2
-
61
-
-
84860538817
-
Beyond the clause: Extraction of phosphorylation information from Medline abstracts
-
Narayanaswamy, M., Ravikumar, K. E. & Vijay-Shanker, K. Beyond the clause: extraction of phosphorylation information from Medline abstracts. Bioinformatics 21, i319-i327 (2005).
-
(2005)
Bioinformatics
, vol.21
-
-
Narayanaswamy, M.1
Ravikumar, K.E.2
Vijay-Shanker, K.3
-
62
-
-
33645104154
-
Extraction of regulatory gene/protein networks from Medline
-
26 July. (doi:10.1093/bioinformatics/bti597)
-
Saric, J., Jensen, L. J., Ouzounova, R., Rojas, I. & Bork, P. Extraction of regulatory gene/protein networks from Medline. Bioinformatics 26 July 2005 (doi:10.1093/bioinformatics/bti597).
-
(2005)
Bioinformatics
-
-
Saric, J.1
Jensen, L.J.2
Ouzounova, R.3
Rojas, I.4
Bork, P.5
-
63
-
-
0033657546
-
EDGAR: Extraction of drugs, genes and relations from the biomedical literature
-
Rindflesch, T. C., Tanabe, L., Weinstein, J. N. & Hunter, L. EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac. Symp. Biocomput. 1, 517-528 (2000).
-
(2000)
Pac. Symp. Biocomput.
, vol.1
, pp. 517-528
-
-
Rindflesch, T.C.1
Tanabe, L.2
Weinstein, J.N.3
Hunter, L.4
-
64
-
-
0034564486
-
A pragmatic information extraction strategy for gathering data on genetic interactions
-
Proux, D., Rechenmann, F. & Julliard, L. A pragmatic information extraction strategy for gathering data on genetic interactions. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8, 179-285 (2000).
-
(2000)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.8
, pp. 179-285
-
-
Proux, D.1
Rechenmann, F.2
Julliard, L.3
-
65
-
-
0035236527
-
Event extraction from biomedical papers using a full parser
-
Yakushiji, A., Tateisi, Y., Miyao, Y. & Tsujii, J. Event extraction from biomedical papers using a full parser. Pac. Symp. Biocomput. 6, 408-419 (2001).
-
(2001)
Pac. Symp. Biocomput.
, vol.6
, pp. 408-419
-
-
Yakushiji, A.1
Tateisi, Y.2
Miyao, Y.3
Tsujii, J.4
-
66
-
-
1842559914
-
Extracting human protein interactions from MEDLINE using a full-sentence parser
-
Daraselia, N. et al. Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics 20, 604-611 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 604-611
-
-
Daraselia, N.1
-
67
-
-
0035236048
-
GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles
-
Friedman, C., Kra, P., Yu, H., Krauthammer, M. & Rzhetsky, A. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 17, S74-S82 (2001).
-
(2001)
Bioinformatics
, vol.17
-
-
Friedman, C.1
Kra, P.2
Yu, H.3
Krauthammer, M.4
Rzhetsky, A.5
-
68
-
-
12144290446
-
GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data
-
Rzhetsky, A. et al. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J. Biomed. Inform. 37, 43-53 (2004). This paper is a good introduction to NLP-based IE and to the design of complex IE systems such as GeneWays.
-
(2004)
J. Biomed. Inform.
, vol.37
, pp. 43-53
-
-
Rzhetsky, A.1
-
69
-
-
0242559066
-
Extraction of protein interaction information from unstructured text using a context-free grammar
-
Temkin, J. M. & Gilder, M. R. Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics 19, 2046-2053 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 2046-2053
-
-
Temkin, J.M.1
Gilder, M.R.2
-
70
-
-
25144508650
-
Discovering patterns to extract protein-protein interactions from the literature: Part II
-
Hao, Y., Zhu, X., Huang, M. & Li, M. Discovering patterns to extract protein-protein interactions from the literature: part II. Bioinformatics 21, 3294-3300 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 3294-3300
-
-
Hao, Y.1
Zhu, X.2
Huang, M.3
Li, M.4
-
71
-
-
0000206156
-
Automatic extraction of protein interactions from scientific abstracts
-
Thomas, J., Milward, D., Ouzounis, C., Pulman, S. & Carroll, M. Automatic extraction of protein interactions from scientific abstracts. Pac. Symp. Biocomput. 5, 707-709 (2000).
-
(2000)
Pac. Symp. Biocomput.
, vol.5
, pp. 707-709
-
-
Thomas, J.1
Milward, D.2
Ouzounis, C.3
Pulman, S.4
Carroll, M.5
-
73
-
-
0022786956
-
Fish oil, Raynaud's Syndrome, and undiscovered public knowledge
-
Swanson, D. R. Fish oil, Raynaud's Syndrome, and undiscovered public knowledge. Perspect. Biol. Med. 30, 7-18 (1986). This is the original text-mining paper, which shows how new knowledge can be inferred from the existing literature.
-
(1986)
Perspect. Biol. Med.
, vol.30
, pp. 7-18
-
-
Swanson, D.R.1
-
75
-
-
0024031265
-
Migrane and magnesium: Eleven neglected connections
-
Swanson, D. R. Migrane and magnesium: eleven neglected connections. Perspect. Biol. Med. 31, 526-557 (1988).
-
(1988)
Perspect. Biol. Med.
, vol.31
, pp. 526-557
-
-
Swanson, D.R.1
-
76
-
-
0025323307
-
Somatomedin C and arginine: Implicit connections between mutually isolated literatures
-
Swanson, D. R. Somatomedin C and arginine: implicit connections between mutually isolated literatures. Perspect. Biol. Med. 33, 157-186 (1990).
-
(1990)
Perspect. Biol. Med.
, vol.33
, pp. 157-186
-
-
Swanson, D.R.1
-
77
-
-
0029818226
-
Linking estrogen to Alzheimer's disease: An informatics approach
-
Smalheiser, N. R. & Swanson, D. R. Linking estrogen to Alzheimer's disease: an informatics approach. Neurology 47, 809-810 (1996).
-
(1996)
Neurology
, vol.47
, pp. 809-810
-
-
Smalheiser, N.R.1
Swanson, D.R.2
-
78
-
-
21144462294
-
Intervening in the life cycle of scientific knowledge
-
Swanson, D. R. Intervening in the life cycle of scientific knowledge. Library Trends 41, 606-631 (1988).
-
(1988)
Library Trends
, vol.41
, pp. 606-631
-
-
Swanson, D.R.1
-
79
-
-
0028109119
-
Assessing a gap in the biomedical literature: Magnesium deficiency and neurological disease
-
Smalheiser, N. R. & Swanson, D. R. Assessing a gap in the biomedical literature: Magnesium deficiency and neurological disease. Neurosci. Res. Commun. 15, 1-9 (1994).
-
(1994)
Neurosci. Res. Commun.
, vol.15
, pp. 1-9
-
-
Smalheiser, N.R.1
Swanson, D.R.2
-
80
-
-
0034577278
-
Text-based discovery in biomedicine: The architecture of the DAD-system
-
Weeber, M. et al. Text-based discovery in biomedicine: the architecture of the DAD-system. Proc. AMIA Symp. 20, S903-S907 (2000).
-
(2000)
Proc. AMIA Symp.
, vol.20
-
-
Weeber, M.1
-
81
-
-
6344276917
-
Mining MEDLINE for implicit links between dietary substances and diseases
-
Srinivasan, P. & Libbus, B. Mining MEDLINE for implicit links between dietary substances and diseases. Bioinformatics 20, i290-i296 (2004).
-
(2004)
Bioinformatics
, vol.20
-
-
Srinivasan, P.1
Libbus, B.2
-
82
-
-
13244268327
-
Extending the mutual information measure to rank inferred literature relationships
-
Wren, J. D. Extending the mutual information measure to rank inferred literature relationships. BMC Bioinformatics 5, 145 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 145
-
-
Wren, J.D.1
-
83
-
-
13444278595
-
Using literature-based discovery to identify disease candidate genes
-
Hristovski, D., Peterlin, B., Mitchell, J. A. & Humphrey, S. M. Using literature-based discovery to identify disease candidate genes. Int. J. Med. Inform. 74, 289-298 (2005).
-
(2005)
Int. J. Med. Inform.
, vol.74
, pp. 289-298
-
-
Hristovski, D.1
Peterlin, B.2
Mitchell, J.A.3
Humphrey, S.M.4
-
84
-
-
0036231909
-
HSF and Msn2/4p can exclusively or cooperatively activate the yeast HSP104 gene
-
Grably, M. R., Stanhill, A., Tell, O. & Engelberg, D. HSF and Msn2/4p can exclusively or cooperatively activate the yeast HSP104 gene. Mol. Microbiol. 44, 21-35 (2002).
-
(2002)
Mol. Microbiol.
, vol.44
, pp. 21-35
-
-
Grably, M.R.1
Stanhill, A.2
Tell, O.3
Engelberg, D.4
-
85
-
-
0035339092
-
Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase
-
Chi, Y. et al. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 15, 1078-1092 (2001).
-
(2001)
Genes Dev.
, vol.15
, pp. 1078-1092
-
-
Chi, Y.1
-
86
-
-
17444387368
-
Genetic factors that regulate the attenuation of the general stress response of yeast
-
Bose, S., Dutko, J. A. & Zitomer, R. S. Genetic factors that regulate the attenuation of the general stress response of yeast. Genetics 169, 1215-1226 (2005).
-
(2005)
Genetics
, vol.169
, pp. 1215-1226
-
-
Bose, S.1
Dutko, J.A.2
Zitomer, R.S.3
-
87
-
-
19944399062
-
The Ccr4-Not complex independently controls both Msn2-dependent transcriptional activation - Via a newly identified Glc7/Bud14 type I protein phosphatase module - and TFIID promoter distribution
-
Lenssen, E. et al. The Ccr4-Not complex independently controls both Msn2-dependent transcriptional activation - via a newly identified Glc7/Bud14 type I protein phosphatase module - and TFIID promoter distribution. Mol. Cell. Biol. 25, 488-498 (2005).
-
(2005)
Mol. Cell. Biol.
, vol.25
, pp. 488-498
-
-
Lenssen, E.1
-
88
-
-
0033913190
-
Shared roles of yeast glycogen synthase kinase 3 family members in nitrogen-responsive phosphorylation of meiotic regulator Ume6p
-
Xiao, Y. & Mitchell, A. P. Shared roles of yeast glycogen synthase kinase 3 family members in nitrogen-responsive phosphorylation of meiotic regulator Ume6p. Mol. Cell. Biol. 20, 5447-5453 (2000).
-
(2000)
Mol. Cell. Biol.
, vol.20
, pp. 5447-5453
-
-
Xiao, Y.1
Mitchell, A.P.2
-
89
-
-
0035100029
-
Expression of the INO2 regulatory gene of Saccharomyces cerevisiae is controlled by positive and negative promoter elements and an upstream open reading frame
-
Eiznhamer, D. A., Ashburner, B. P., Jackson, J. C., Gardenour, K. R. & Lopes, J. M. Expression of the INO2 regulatory gene of Saccharomyces cerevisiae is controlled by positive and negative promoter elements and an upstream open reading frame. Mol. Microbiol. 39, 1395-1405 (2001).
-
(2001)
Mol. Microbiol.
, vol.39
, pp. 1395-1405
-
-
Eiznhamer, D.A.1
Ashburner, B.P.2
Jackson, J.C.3
Gardenour, K.R.4
Lopes, J.M.5
-
90
-
-
0033553144
-
Transcriptional regulation of the squalene synthase gene (ERG9) in the yeast Saccharomyces cerevisiae
-
Kennedy, M. A., Barbuch, R. & Bard, M. Transcriptional regulation of the squalene synthase gene (ERG9) in the yeast Saccharomyces cerevisiae. Biochim. Biophys. Acta 1445, 110-122 (1999).
-
(1999)
Biochim. Biophys. Acta
, vol.1445
, pp. 110-122
-
-
Kennedy, M.A.1
Barbuch, R.2
Bard, M.3
-
91
-
-
0037303467
-
Life cycles of successful genes
-
Hoffmann, R. & Valencia, A. Life cycles of successful genes. Trends Genet. 19, 79-81 (2003).
-
(2003)
Trends Genet.
, vol.19
, pp. 79-81
-
-
Hoffmann, R.1
Valencia, A.2
-
92
-
-
13244284551
-
Dynamic complex formation during the yeast cell cycle
-
de Lichtenberg, U., Jensen, L. J., Brunak, S. & Bork, P. Dynamic complex formation during the yeast cell cycle. Science 307, 724-727 (2005).
-
(2005)
Science
, vol.307
, pp. 724-727
-
-
De Lichtenberg, U.1
Jensen, L.J.2
Brunak, S.3
Bork, P.4
-
93
-
-
0034142323
-
Repression by Suppressor of Hairless and activation by Notch are required to define a single row of single-minded expressing cells in the Drosophila embryo
-
Morel, V. & Schweisguth, F. Repression by Suppressor of Hairless and activation by Notch are required to define a single row of single-minded expressing cells in the Drosophila embryo. Genes Dev. 14, 377-388 (2000).
-
(2000)
Genes Dev.
, vol.14
, pp. 377-388
-
-
Morel, V.1
Schweisguth, F.2
-
94
-
-
0037155908
-
Differential activities of Murine Single Minded 1 (SIM1) and SIM2 on a hypoxic response element
-
Woods, S. L. & Witelaw, M. L. Differential activities of Murine Single Minded 1 (SIM1) and SIM2 on a hypoxic response element. J. Biol. Chem. 277, 10236-10243 (2002).
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 10236-10243
-
-
Woods, S.L.1
Witelaw, M.L.2
-
95
-
-
0031690080
-
Automatic extraction of keywords from scientific text: Application to the knowledge domain of protein families
-
Andrade, M. A. & Valencia, A. Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. Bioinformatics 14, 600-607 (1998).
-
(1998)
Bioinformatics
, vol.14
, pp. 600-607
-
-
Andrade, M.A.1
Valencia, A.2
-
96
-
-
0034766349
-
Mining functional information associated with expression arrays
-
Blaschke, C., Oliveros, J. C. & Valencia, A. Mining functional information associated with expression arrays. Funct. Integr. Genomics 1, 256-268 (2001).
-
(2001)
Funct. Integr. Genomics
, vol.1
, pp. 256-268
-
-
Blaschke, C.1
Oliveros, J.C.2
Valencia, A.3
-
97
-
-
0035022821
-
Use of keyword hierarchies to interpret gene expression patterns
-
Masys, D. R. et al. Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics 17, 319-326 (2001).
-
(2001)
Bioinformatics
, vol.17
, pp. 319-326
-
-
Masys, D.R.1
-
98
-
-
0038017587
-
Mining microarray expression data by literature profiling
-
research0055.1-research0055.16
-
Chaussabel, D. & Sher, A. Mining microarray expression data by literature profiling. Genome Biol. 3, research0055.1-research0055.16 (2002).
-
(2002)
Genome Biol.
, vol.3
-
-
Chaussabel, D.1
Sher, A.2
-
99
-
-
0036796319
-
Using text analysis to identify functionally coherent gene groups
-
Raychaudhuri, S., Schutze, H. & Altman, R. B. Using text analysis to identify functionally coherent gene groups. Genome Res. 12, 1582-1590 (2002).
-
(2002)
Genome Res.
, vol.12
, pp. 1582-1590
-
-
Raychaudhuri, S.1
Schutze, H.2
Altman, R.B.3
-
100
-
-
0043163729
-
The computational analysis of scientific literature to define and recognize gene expression clusters
-
Raychaudhuri, S., Chang, J. T., Imam, F. & Altman, R. B. The computational analysis of scientific literature to define and recognize gene expression clusters. Nucleic Acids Res. 31, 4553-4560 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 4553-4560
-
-
Raychaudhuri, S.1
Chang, J.T.2
Imam, F.3
Altman, R.B.4
-
101
-
-
4844222294
-
TXTGate: Profiling gene groups with text-based information
-
Glenisson, P. et al. TXTGate: profiling gene groups with text-based information. Genome Biol. 5, R43 (2004).
-
(2004)
Genome Biol.
, vol.5
-
-
Glenisson, P.1
-
102
-
-
6344229209
-
Molecular triangulation: Bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease
-
Krauthammer, M., Kaufmann, C. A., Gilliam, T. C. & Rzhetsky, A. Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. Proc. Natl Acad. Sci. USA 101, 15148-15153 (2004). The study shows how literature-based molecular networks and genetic linkage mapping can be integrated to find candidate disease genes.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 15148-15153
-
-
Krauthammer, M.1
Kaufmann, C.A.2
Gilliam, T.C.3
Rzhetsky, A.4
-
103
-
-
0036649742
-
Association of genes to genetically inherited diseases using text mining
-
Perez-Iratxeta, C., Bork, P. & Andrade, M. A. Association of genes to genetically inherited diseases using text mining. Nature Genet. 31, 316-319 (2002).
-
(2002)
Nature Genet.
, vol.31
, pp. 316-319
-
-
Perez-Iratxeta, C.1
Bork, P.2
Andrade, M.A.3
-
104
-
-
26444581337
-
G2D: A tool for mining genes associated to disease
-
Perez-Iratxeta, C., Wjst, M., Bork, P. & Andrade, M. A. G2D: A tool for mining genes associated to disease. BMC Genetics 6, 45 (2005). Reference 103 integrates genetic linkage-mapping data with data from the literature to suggest candidate genes for inherited diseases. Reference 104 shows later improvements of the method.
-
(2005)
BMC Genetics
, vol.6
, pp. 45
-
-
Perez-Iratxeta, C.1
Wjst, M.2
Bork, P.3
Andrade, M.A.4
-
105
-
-
21844471754
-
Systematic association of genes to phenotypes by genome and literature mining
-
Korbel, J. O. et al. Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol. 3, e134 (2005). These authors present a method for linking genotypes to phenotypes by comparing species profiles of genes and literature-derived keywords.
-
(2005)
PLoS Biol.
, vol.3
-
-
Korbel, J.O.1
-
106
-
-
0642368715
-
Information extraction from full text scientific articles: Where are the keywords?
-
Shah, P. K., Perez-Iratxeta, C., Bork, P. & Andrade, M. A. Information extraction from full text scientific articles: Where are the keywords? BMC Bioinformatics 4, 20 (2003).
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 20
-
-
Shah, P.K.1
Perez-Iratxeta, C.2
Bork, P.3
Andrade, M.A.4
-
107
-
-
8844252296
-
Distribution of information in biomedical abstracts and full-text publications
-
Schuemie, M. J. et al. Distribution of information in biomedical abstracts and full-text publications. Bioinformatics 20, 2597-2604 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 2597-2604
-
-
Schuemie, M.J.1
-
108
-
-
19544373503
-
Tough mining
-
Dickman, S. Tough mining. PLoS Biol. 1, 144-147 (2005).
-
(2005)
PLoS Biol.
, vol.1
, pp. 144-147
-
-
Dickman, S.1
-
109
-
-
0033931867
-
Assessing the accuracy of prediction algorithms for classification: An overview
-
Baldi, P., Brunak, S., Chauvin, Y., Andersen, C. A. F. & Nielsen, H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16, 412-424 (2000).
-
(2000)
Bioinformatics
, vol.16
, pp. 412-424
-
-
Baldi, P.1
Brunak, S.2
Chauvin, Y.3
Andersen, C.A.F.4
Nielsen, H.5
-
110
-
-
4944235422
-
Evaluation of text data mining for database curation: Lessons learned from the KDD Challenge Cup
-
Yeh, A. S., Hirschman, L. & Morgan, A. A. Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup. Bioinformatics 19, i331-i339 (2003).
-
(2003)
Bioinformatics
, vol.19
-
-
Yeh, A.S.1
Hirschman, L.2
Morgan, A.A.3
-
111
-
-
33947304181
-
Overview of BioCreAtIvE: Critical assessment of information extraction for biology
-
Hirschman, L., Yeh, A., Blaschke, C. & Valencia, A. Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics 6, S1 (2005).
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Hirschman, L.1
Yeh, A.2
Blaschke, C.3
Valencia, A.4
-
112
-
-
11244311539
-
Of truth and pathways: Chasing bits of information through myriads of articles
-
Krauthammer, M. et al. Of truth and pathways: chasing bits of information through myriads of articles. Bioinformatics 18, S249-S257 (2002).
-
(2002)
Bioinformatics
, vol.18
-
-
Krauthammer, M.1
-
113
-
-
0037178707
-
Worldwide scientific publishing activity
-
Perez-Iratxeta, C. & Andrade, M. A. Worldwide scientific publishing activity. Science 297, 519 (2002).
-
(2002)
Science
, vol.297
, pp. 519
-
-
Perez-Iratxeta, C.1
Andrade, M.A.2
-
114
-
-
0038110071
-
The way we write
-
Netzel, R., Perez-Iratxeta, C., Bork, P. & Andrade, M. A. The way we write. EMBO Rep. 4, 446-451 (2003).
-
(2003)
EMBO Rep.
, vol.4
, pp. 446-451
-
-
Netzel, R.1
Perez-Iratxeta, C.2
Bork, P.3
Andrade, M.A.4
-
115
-
-
1842788834
-
Coauthorship networks and patterns of scientific collaboration
-
Newman, M. E. J. Coauthorship networks and patterns of scientific collaboration. Proc. Natl Acad. Sci. USA 101, 5200-5205 (2004).
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 5200-5205
-
-
Newman, M.E.J.1
|