Text mining and its potential applications in systems biology

Modern Information Retrieval

Baeza-Yates, R. A., & Ribeiro-Neto, B. A. (1999) · Cited by 11,505

The unified medical language system (UMLS): integrating biomedical terminology

Bodenreider, O. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh061 · Cited by 4,356

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg015 · Cited by 3,060

Taverna: a tool for the composition and enactment of bioinformatics workflows

Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K., Pocock, M. R., Wipat, A., et al. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth361 · Cited by 1,602

GENIA corpus—a semantically annotated corpus for bio-textmining

Kim, J.-D., Ohta, T., Tateisi, Y., & Tsujii, J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1023 · Cited by 1,232

Computational cluster validation in post-genomic data analysis

Handl, J., Knowles, J., & Kell, D. B. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti517 · Cited by 898

Untangling text data mining

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Fish Oil, Raynaud's Syndrome, and Undiscovered Public Knowledge

Swanson, D. R. (1986) · Perspectives in Biology and Medicine · doi:10.1353/pbm.1986.0087 · Cited by 866

Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation.

Mendes, P., & Kell, D. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.10.869 · Cited by 676

Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature

Müller, H.-M., Kenny, E. E., & Sternberg, P. W. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020309 · Cited by 653

Proceedings of the 2006 Conference on Empirical Methods in Natural Language Processing - EMNLP '06

(2006) · doi:10.3115/1610075 · Cited by 650

Literature mining for the biologist: from information retrieval to biological discovery

Jensen, L. J., Saric, J., & Bork, P. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1768 · Cited by 631

Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis‐driven science in the post‐genomic era

Kell, D. B., & Oliver, S. G. (2004) · BioEssays · doi:10.1002/bies.10385 · Cited by 535

Overview of BioCreAtIvE: critical assessment of information extraction for biology

Hirschman, L., Yeh, A., Blaschke, C., & Valencia, A. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-s1-s1 · Cited by 530

Metabolomics and systems biology: making sense of the soup

KELL, D. (2004) · Current Opinion in Microbiology · doi:10.1016/j.mib.2004.04.012 · Cited by 529

A SIMPLE ALGORITHM FOR IDENTIFYING ABBREVIATION DEFINITIONS IN BIOMEDICAL TEXT

SCHWARTZ, A. S., & HEARST, M. A. (2002) · Biocomputing 2003 · doi:10.1142/9789812776303_0042 · Cited by 508

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. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.suppl_1.s74 · Cited by 507

Toward information extraction: identifying protein names from biological papers.

Fukuda, K., Tamura, A., Tsunoda, T., & Takagi, T. (1998) · PubMed · Cited by 494

Pacific Symposium on Biocomputing 2002/2003/2004

Dunker, A. K. (2004) · doi:10.2172/833844 · Cited by 482

Automated extraction of information on protein–protein interactions from the biological literature

Ono, T., Hishigaki, H., Tanigami, A., & Takagi, T. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.2.155 · Cited by 398

Migraine and Magnesium: Eleven Neglected Connections

Swanson, D. R. (1988) · Perspectives in Biology and Medicine · doi:10.1353/pbm.1988.0009 · Cited by 382

Text Mining for Biology And Biomedicine

Ananiadou, S., & McNaught, J. (2005) · Cited by 369

BioMOBY: An open source biological web services proposal

Wilkinson, M. D. (2002) · Briefings in Bioinformatics · doi:10.1093/bib/3.4.331 · Cited by 351

Genome-Scale Metabolic Model of Helicobacter pylori 26695

Schilling, C. H., Covert, M. W., Famili, I., Church, G. M., Edwards, J. S., & Palsson, B. O. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.16.4582-4593.2002 · Cited by 325

Proceedings of the 38th Annual Meeting on Association for Computational Linguistics - ACL '00

(2000) · doi:10.3115/1075218 · Cited by 323

Biomedical Language Processing: What's Beyond PubMed?

Hunter, L., & Cohen, K. B. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.02.012 · Cited by 308

Text mining and ontologies in biomedicine: Making sense of raw text

Spasic, I., Ananiadou, S., McNaught, J., & Kumar, A. (2005) · Briefings in Bioinformatics · doi:10.1093/bib/6.3.239 · Cited by 299

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data

Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboué, P. A., Weng, W., Wilbur, W. J., et al. (2004) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2003.10.001 · Cited by 291

Accomplishments and challenges in literature data mining for biology

Hirschman, L., Park, J. C., Tsujii, J., Wong, L., & Wu, C. H. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.12.1553 · Cited by 287

Mining literature for protein–protein interactions

Marcotte, E. M., Xenarios, I., & Eisenberg, D. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.4.359 · Cited by 284

Tuning support vector machines for biomedical named entity recognition

Kazama, J., Makino, T., Ohta, Y., & Tsujii, J. (2002) · doi:10.3115/1118149.1118150 · Cited by 258

Recognizing names in biomedical texts: a machine learning approach

Zhou, G., Zhang, J., Su, J., Shen, D., & Tan, C. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth060 · Cited by 251

Discovering patterns to extract protein–protein interactions from full texts

Huang, M., Zhu, X., Hao, Y., Payan, D. G., Qu, K., & Li, M. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth451 · Cited by 241

Extracting human protein interactions from MEDLINE using a full-sentence parser

Daraselia, N., Yuryev, A., Egorov, S., Novichkova, S., Nikitin, A., & Mazo, I. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg452 · Cited by 237

System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Szállási, Z., Stelling, J., & Periwal, V. (2007) · Medical Entomology and Zoology · Cited by 236

Implementing the iHOP concept for navigation of biomedical literature

Hoffmann, R., & Valencia, A. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1142 · Cited by 236

Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

Borodina, I., Krabben, P., & Nielsen, J. (2005) · Genome Research · doi:10.1101/gr.3364705 · Cited by 234

EVENT EXTRACTION FROM BIOMEDICAL PAPERS USING A FULL PARSER

Yakushiji, A., Tateisi, Y., Miyao, Y., & Tsujii, J.-I. (2000) · Biocomputing 2001 · doi:10.1142/9789814447362_0040 · Cited by 224

Disambiguating proteins, genes, and RNA in text: a machine learning approach

Hatzivassiloglou, V., Duboué, P. A., & Rzhetsky, A. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.suppl_1.s97 · Cited by 224

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

Herrgård, M. J., Lee, B.-S., Portnoy, V., & Palsson, B. Ø. (2006) · Genome Research · doi:10.1101/gr.4083206 · Cited by 223

PubMatrix: a tool for multiplex literature mining

Becker, K. G., Hosack, D. A., Dennis, G., Lempicki, R. A., Bright, T. J., Cheadle, C., & Engel, J. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-61 · Cited by 202

Generating Hypotheses by Discovering Implicit Associations in the Literature: A Case Report of a Search for New Potential Therapeutic Uses for Thalidomide

Weeber, M. (2003) · Journal of the American Medical Informatics Association · doi:10.1197/jamia.m1158 · Cited by 184

BioRAT: extracting biological information from full-length papers

Corney, D. P. A., Buxton, B. F., Langdon, W. B., & Jones, D. T. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth386 · Cited by 175

Genomics and natural language processing

Yandell, M. D., & Majoros, W. H. (2002) · Nature Reviews Genetics · doi:10.1038/nrg861 · Cited by 168

Systematic Association of Genes to Phenotypes by Genome and Literature Mining

Korbel, J. O., Doerks, T., Jensen, L. J., Perez‐Iratxeta, C., Kaczanowski, S., Hooper, S. D., Andrade-Navarro, M. A., & Bork, P. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030134 · Cited by 157

EXTRACTION OF GENE-DISEASE RELATIONS FROM MEDLINE USING DOMAIN DICTIONARIES AND MACHINE LEARNING

Chun, H.-W., Tsuruoka, Y., Kim, J.-D., Shiba, R., NAGATA, N., Hishiki, T., & Tsujii, J. (2005) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812701626_0002 · Cited by 151

Metabolomics, modelling and machine learning in systems biology – towards an understanding of the languages of cells: Delivered on 3 July 2005 at the 30th FEBS Congress and 9th IUBMB conference in Budapest

Kell, D. B. (2006) · FEBS Journal · doi:10.1111/j.1742-4658.2006.05136.x · Cited by 148

Mining MEDLINE for implicit links between dietary substances and diseases

Srinivasan, P., & Libbus, B. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth914 · Cited by 134

A BIOLOGICAL NAMED ENTITY RECOGNIZER

Narayanaswamy, M., Ravikumar, K. E., & Vijay‐Shanker, K. (2002) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812776303_0040 · Cited by 119

Gene name identification and normalization using a model organism database

Morgan, A. A., Hirschman, L., Colosimo, M., et al. (2004) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2004.08.010 · Cited by 118

Information extraction in molecular biology

Blaschke, C. (2002) · Briefings in Bioinformatics · doi:10.1093/bib/3.2.154 · Cited by 112

Rutabaga by any other name: extracting biological names

Hirschman, L., Morgan, A. A., & Yeh, A. (2002) · Journal of Biomedical Informatics · doi:10.1016/s1532-0464(03)00014-5 · Cited by 106

PAX of mind for pathway researchers

Luciano, J. (2005) · Drug Discovery Today · doi:10.1016/s1359-6446(05)03501-4 · Cited by 104

Extracting synonymous gene and protein terms from biological literature

Yu, H. Q., & Agichtein, E. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1047 · Cited by 104

BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case

Wilkinson, M. D., Schoof, H., Ernst, R., & Haase, D. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.059170 · Cited by 98

Improving the performance of dictionary-based approaches in protein name recognition

Tsuruoka, Y., & Tsujii, J. (2004) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2004.08.003 · Cited by 97

POPS: A COMPUTATIONAL TOOL FOR MODELING AND PREDICTING PROTEASE SPECIFICITY

BOYD, S. E., Pike, R. N., Rudy, G. B., Whisstock, J. C., & de la Banda, M. G. (2005) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s021972000500117x · Cited by 95

Pacific Symposium on Biocomputing

(2015) · F1000Research Channels · doi:10.12688/f1000research.channels.77 · Cited by 95

Taverna/myGrid: Aligning a Workflow System with the Life Sciences Community

Oinn, T., Li, P., Kell, D. B., Goble, C., Goderis, A., Greenwood, R. M., Hull, D., Stevens, R., Turi, D., & Zhao, J. (2007) · Springer eBooks · doi:10.1007/978-1-84628-757-2_19 · Cited by 93

Semantic retrieval for the accurate identification of relational concepts in massive textbases

Miyao, Y., Ohta, T., Masuda, K., Tsuruoka, Y., YOSHIDA, K., Ninomiya, T., & Tsujii, J. (2006) · International Conference on Computational Linguistics · doi:10.3115/1220175.1220303 · Cited by 91

Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks

Hoffmann, R., Krallinger, M., Andres, E., Tamames, J., Blaschke, C., & Valencia, A. (2005) · Science's STKE · doi:10.1126/stke.2832005pe21 · Cited by 88

Mining functional information associated with expression arrays

Blaschke, C., Oliveros, J. C., & Valencia, A. (2001) · Functional & Integrative Genomics · doi:10.1007/s101420000036 · Cited by 80

Heuristics for Identification of Acronym-Definition Patterns within Text: Towards an Automated Construction of Comprehensive Acronym-Definition Dictionaries

Wren, J. D., & Garner, H. R. (2002) · Methods of Information in Medicine · doi:10.1055/s-0038-1634373 · Cited by 74

Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy

Bekhuis, T. (2006) · Biomedical Digital Libraries · doi:10.1186/1742-5581-3-2 · Cited by 67

TXTGate: profiling gene groups with text-based information

Glenisson, P., Coessens, B., Vooren, S. V., Mathys, J., Moreau, Y., & Moor, B. D. (2004) · Genome biology · doi:10.1186/gb-2004-5-6-r43 · Cited by 67

Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser

McDonald, D. M., Chen, H., Su, H., & Marshall, B. B. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth409 · Cited by 66

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes

Arakawa, K., Yamada, Y., Shinoda, K., Nakayama, Y., & Tomita, M. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-168 · Cited by 59

The Role of Modeling in Systems Biology

Kell, D. B., & Knowles, J. D. (2006) · The MIT Press eBooks · doi:10.7551/mitpress/6604.003.0003 · Cited by 54

Finding Kinetic Parameters Using Text Mining

Hakenberg, J., Schmeier, S., Kowald, A., Klipp, E., & Leser, U. (2004) · OMICS A Journal of Integrative Biology · doi:10.1089/1536231041388366 · Cited by 51

Web services in the life sciences

Ćurčin, V., Ghanem, M. M., & Guo, Y. (2005) · Drug Discovery Today · doi:10.1016/s1359-6446(05)03481-1 · Cited by 42

KDE Bioscience: Platform for bioinformatics analysis workflows

Lu, Q., Hao, P., Ćurčin, V., He, W., Li, Y., Luo, Q., Guo, Y., & Li, Y. (2005) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2005.09.001 · Cited by 33

A Fishing Buddy for Hypothesis Generators

Brent, R., & Lok, L. (2005) · Science · doi:10.1126/science.1110535 · Cited by 31

Comparison of character-level and part of speech features for name recognition in biomedical texts

Collier, N., & Takeuchi, K. (2004) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2004.08.008 · Cited by 31

BIOIE: RETARGETABLE INFORMATION EXTRACTION AND ONTOLOGICAL ANNOTATION OF BIOLOGICAL INTERACTIONS FROM THE LITERATURE

Kim, J., & Park, J. C. (2004) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720004000739 · Cited by 27

Query Chem: a Google-powered web search combining text and chemical structures

Klekota, J., Roth, F. P., & Schreiber, S. L. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl155 · Cited by 18

Text Influenced Molecular Indexing (TIMI): A Literature Database Mining Approach that Handles Text and Chemistry

Singh, S. B., Hull, R., & Fluder, E. M. (2003) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci025587a · Cited by 16

Visualizing information across multidimensional post-genomic structured and textual databases

Tao, Y., Friedman, C., & Lussier, Y. A. (2004) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti210 · Cited by 13

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1492 · Cited by 588

Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases

Kell, D. B. (2009) · BMC Medical Genomics · doi:10.1186/1755-8794-2-2 · Cited by 554

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

Currin, A., Swainston, N., Day, P. J., & Kell, D. B. (2015) · Chemical Society Reviews · doi:10.1039/c4cs00351a · Cited by 388

Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson’s, Huntington’s, Alzheimer’s, prions, bactericides, chemical toxicology and others as examples

Kell, D. B. (2010) · Archives of Toxicology · doi:10.1007/s00204-010-0577-x · Cited by 361

Controlled vocabularies and semantics in systems biology

Courtot, M., Juty, N., Knüpfer, C., Waltemath, D., Zhukova, A., Dräger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.77 · Cited by 316