nach oben

Discover Computing

Erschienen in:

01.02.2009 | Introduction

TREC genomics special issue overview

verfasst von: William Hersh, Ellen Voorhees

Erschienen in: Discover Computing | Ausgabe 1/2009

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config

KI-gestützte Suche

Aus

Excerpt

Recent advances in biotechnology have changed the fundamental nature of biological research. Whereas scientists used to be able to manage their modest amount of experimental data in paper notebooks or simple spreadsheets, new tools such as gene chips for measuring gene expression (Mobasheri et al. 2004) or sequence variation (Pennisi 2007) have fundamentally altered their work. Not only do these gene chips generate massive amounts of data (as much as tens of thousands of data points per biological sample), they uncover potential associations and interactions with a wide variety of genes, diseases, and other biological entities. The field devoted to managing, utilizing, and evaluating this data is called bioinformatics (Baxevanis and Ouellette 2005), which is sometimes described as the intersection of biology (or biomedicine) and computer science. …

Nächster Artikel Exploring criteria for successful query expansion in the genomic domain

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Allan, J. (2003). HARD Track overview in TREC 2003—high accuracy retrieval from documents. The Twelfth Text REtrieval Conference-TREC 2003 (pp. 24–37). Gaithersburg, MD: National Institute of Standards and Technology. http://trec.nist.gov/pubs/trec12/papers/HARD.OVERVIEW.pdf.

Allan, J. (2004). HARD Track overview in TREC 2004—high accuracy retrieval from documents. The Thirteenth Text REtrieval Conference (TREC 2004). Gaithersburg, MD: National Institute of Standards and Technology. http://trec.nist.gov/pubs/trec13/papers/HARD.OVERVIEW.pdf.

Ando, R., Dredze, M., et al. (2005). TREC 2005 genomics track experiments at IBM Watson. The Fourteenth Text Retrieval Conference Proceedings (TREC 2005). Gaithersburg, MD: National Institute for Standards and Technology. http://trec.nist.gov/pubs/trec14/papers/ibm-tjwatson.geo.pdf.

Anonymous. (2008). The gene ontology project in 2008. Nucleic Acids Research, 36, D440–D444.

Aronson, A., Demmer, D., et al. (2004). Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations. The Thirteenth Text Retrieval Conference (TREC 2004). Gaithersburg, MD: National Institute of Standards and Technology. http://trec.nist.gov/pubs/trec13/papers/nlm-umd-ul.geo.pdf.

Aronson, A., Demner-Fushman, D., et al. (2005). Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents. The Fourteenth Text REtrieval Conference Proceedings (TREC 2005). Gaithersburg, MD: National Institute for Standards and Technology. http://trec.nist.gov/pubs/trec14/papers/nlm-umd.geo.pdf.

Bahls, C., Weitzman, J., et al. (2003). Biology’s models. Scientist (Philadelphia, PA), 5. http://www.the-scientist.com/yr2003/jun/feature_030602.html.

Baxevanis, A., & Ouellette, B. (2005). Bioinformatics: A practical guide to the analysis of genes and proteins (3rd ed.). Hoboken, NJ: Wiley.

Buckley, C., & Voorhees, E. (2005). Retrieval system evaluation. In E. Voorhees & D. Harman (Eds.), TREC: Experiment and evaluation in information retrieval (pp. 53–75). Cambridge, MA: MIT Press.

Buttcher, S., Clarke, C., et al. (2004). Domain-specific synonym expansion and validation for biomedical information retrieval (MultiText experiments for TREC 2004). The Thirteenth Text Retrieval Conference (TREC 2004). Gaithersburg, MD: National Institute of Standards and Technology. http://trec.nist.gov/pubs/trec13/papers/uwaterloo-clarke.geo.pdf.

Cohen, A., & Hersh, W. (2006). The TREC 2004 genomics track categorization task: Classifying full-text biomedical documents. Journal of Biomedical Discovery and Collaboration, 1, 4. http://www.j-biomed-discovery.com/content/1/1/4. doi:10.1186/1747-5333-1-4.

Cohen, A., Hersh, W., et al. (2006). Reducing workload in systematic review preparation using automated citation classification. Journal of the American Medical Informatics Association, 13, 206–219. doi:10.1197/jamia.M1929.CrossRef

Fujita, S. (2004). Revisiting again document length hypotheses—TREC 2004 genomics track experiments at Patolis. The Thirteenth Text Retrieval Conference (TREC 2004). Gaithersburg, MD: National Institute of Standards and Technology. http://trec.nist.gov/pubs/trec13/papers/patolis.geo.pdf.

Galperin, M. (2008). The molecular biology database collection: 2008 update. Nucleic Acids Research, 36, D2–D4. doi:10.1093/nar/gkm1037.CrossRef

Hersh, W. (2001). Interactivity at the text retrieval conference (TREC). Information Processing and Management, 37, 365–366. doi:10.1016/S0306-4573(00)00052-2.CrossRef

Hersh, W. (2003). Information retrieval: A health and biomedical perspective (2nd ed.). New York: Springer-Verlag. http://www.irbook.info.

Hersh, W., & Bhupatiraju, R. (2003). TREC genomics track overview. The Twelfth Text Retrieval Conference (TREC 2003) (pp. 14–23). Gaithersburg, MD: NIST. http://trec.nist.gov/pubs/trec12/papers/GENOMICS.OVERVIEW3.pdf.

Hersh, W., Bhuptiraju, R., et al. (2004). TREC 2004 genomics track overview. The Thirteenth Text Retrieval Conference (TREC 2004). Gaithersburg, MD: National Institute for Standards and Technology. http://trec.nist.gov/pubs/trec13/papers/GEO.OVERVIEW.pdf.

Hersh, W., Cohen, A., et al. (2005). TREC 2005 genomics track overview. The Fourteenth Text Retrieval Conference (TREC 2005). Gaithersburg, MD: National Institute for Standards and Technology. http://trec.nist.gov/pubs/trec14/papers/GEO.OVERVIEW.pdf.

Hersh, W., Bhupatiraju, R., et al. (2006a). Enhancing access to the bibliome: the TREC 2004 genomics track. Journal of Biomedical Discovery and Collaboration, 1, 3. http://www.j-biomed-discovery.com/content/1/1/3. doi:10.1186/1747-5333-1-3.

Hersh, W., Cohen, A., et al. (2006b). TREC 2006 genomics track overview. The Fifteenth Text Retrieval Conference (TREC 2006) (pp. 52–78). Gaithersburg, MD: National Institute for Standards & Technology. http://trec.nist.gov/pubs/trec15/papers/GEO.OVERVIEW.pdf.

Hersh, W., Cohen, A., et al. (2007). TREC 2007 genomics track overview. The Sixteenth Text Retrieval Conference (TREC 2007). Gaithersburg, MD: National Institute for Standards and Technology. http://ir.ohsu.edu/genomics/trec-07-genomics.pdf.

Hill, D., Begley, D., et al. (2004). The mouse gene expression database (GXD): Updates and enhancements. Nucleic Acids Research, 32, D568–D571. doi:10.1093/nar/gkh069.CrossRef

Hirschman, L., Park, J., et al. (2002). Accomplishments and challenges in literature data mining for biology. Bioinformatics (Oxford, England), 18, 1553–1561. doi:10.1093/bioinformatics/18.12.1553.CrossRef

Hirschman, L., Yeh, A., et al. (2005). Overview of BioCreAtIvE: Critical assessment of information extraction for biology. BMC Bioinformatics, 6, S1. http://www.biomedcentral.com/1471-2105/6/S1/S1. doi:10.1186/1471-2105-6-S1-S1.

Huang, X., Zhong, M., et al. (2005). York University at TREC 2005: Genomics track. The Fourteenth Text REtrieval Conference Proceedings (TREC 2005). Gaithersburg, MD: National Institute for Standards and Technology. http://trec.nist.gov/pubs/trec14/papers/yorku-huang2.geo.pdf.

Jiang, J., & Zhai, C. (2007). An empirical study of tokenization strategies for biomedical information retrieval. Information Retrieval, 10, 341–363. doi:10.1007/s10791-007-9027-7.CrossRef

Krupke, D., Naf, D., et al. (2005). The mouse tumor biology database: Integrated access to mouse cancer biology data. Experimental Lung Research, 31, 259–270. doi:10.1080/01902140490495633.CrossRef

Lin, J., & Wilbur, W. (2007). PubMed related articles: A probabilistic topic-based model for content similarity. BMC Bioinformatics, 8, 423. http://www.biomedcentral.com/1471-2105/8/423. doi:10.1186/1471-2105-8-423.

Lu, Y., Fang, H., et al. (2008a). An empirical study of gene synonym query expansion in biomedical information retrieval. Information Retrieval. doi:10.1007/s10791-008-9075-7.

Lu, Z., Kim, W., et al. (2008b). Evaluation of query expansion using MeSH in PubMed. Information Retrieval. doi:10.1007/s10791-008-9074-8.

Maglott, D., Ostell, J., et al. (2007). Entrez gene: Gene-centered information at NCBI. Nucleic Acids Research, 35, D26–D31. doi:10.1093/nar/gkl993.CrossRef

Mitchell, J., Aronson, A., et al. (2003). Gene indexing: Characterization and analysis of NLM’s GeneRIFs. Proceedings of the AMIA 2003 Annual Symposium (pp. 460–464). Washington, DC: Hanley & Belfus.

Mobasheri, A., Airley, R., et al. (2004). Post-genomic applications of tissue microarrays: Basic research, prognostic oncology, clinical genomics and drug discovery. Histology and Histopathology, 19, 325–335.

Moult, J., Fidelis, K., et al. (2003). Critical assessment of methods of protein structure prediction (CASP)-round V. Proteins, 53, 334–339. doi:10.1002/prot.10556.CrossRef

Nakov, P., Schwartz, A., et al. (2004). BioText team experiments for the TREC 2004 genomics track. The Thirteenth Text Retrieval Conference (TREC 2004). Gaithersburg, MD: National Institute of Standards and Technology. http://trec.nist.gov/pubs/trec13/papers/ucal-berkeley.geo.pdf.

Pennisi, E. (2007). Breakthrough of the year—human genetic variation. Science, 318, 1842–1843. doi:10.1126/science.318.5858.1842.CrossRef

Rekapalli, H., Cohen, A., et al. (2007). A comparative analysis of retrieval features used in the TREC 2006 Genomics Track passage retrieval task. Proceedings of the AMIA 2007 Annual Symposium. Chicago, IL: American Medical Informatics Association.

Roberts, P., Cohen, A., et al. (2008). Tasks, topics and relevance judging for the TREC Genomics Track: Five years of experience evaluating biomedical text information retrieval systems. Information Retrieval. doi:10.1007/s10791-008-9072-x.

Seki, K., Costello, J., et al. (2004). TREC 2004 genomics track experiments at IUB. The Thirteenth Text Retrieval Conference (TREC 2004). Gaithersburg, MD: National Institute of Standards and Technology. http://trec.nist.gov/pubs/trec13/papers/indianau-seki.geo.pdf.

Shatkay, H., Chen, N., et al. (2006). Integrating image data into biomedical text categorization. Bioinformatics (Oxford, England), 22, e446–e453. doi:10.1093/bioinformatics/btl235.CrossRef

Stokes, N., Li, Y., et al. (2008). Exploring criteria for successful query expansion in the genomic domain. Information Retrieval. doi:10.1007/s10791-008-9073-9.

Strivens, M., & Eppig, J. (2004). Visualizing the laboratory mouse: Capturing phenotype information. Genetica, 122, 89–97. doi:10.1007/s10709-004-1435-7.CrossRef

Venclovas, C., Zemla, A., et al. (2003). Assessment of progress over the CASP experiments. Proteins, 53, 585–595. doi:10.1002/prot.10530.CrossRef

Voorhees, E., & Harman, D. (Eds.). (2005). TREC: Experiment and evaluation in information retrieval. Cambridge, MA: MIT Press.

Wheeler, D., Barrett, T., et al. (2008). Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 36, D13–D21. doi:10.1093/nar/gkm1000.CrossRef

Yeh, A., Hirschman, L., et al. (2003). Evaluation of text data mining for database curation: Lessons learned from the KDD challenge cup. Bioinformatics (Oxford, England), 19, I331–I339. doi:10.1093/bioinformatics/btg1046.CrossRef

Zheng, Z., Brady, S., et al. (2005). Applying probabilistic thematic clustering for classification in the TREC 2005 genomics track. The Fourteenth Text REtrieval Conference Proceedings (TREC 2005). Gaithersburg, MD: National Institute for Standards and Technology. http://trec.nist.gov/pubs/trec14/papers/queensu.geo.pdf.

Titel: TREC genomics special issue overview
verfasst von: William Hersh
Ellen Voorhees
Publikationsdatum: 01.02.2009
Verlag: Springer Netherlands
Erschienen in: Discover Computing / Ausgabe 1/2009
Print ISSN: 2948-2984
Elektronische ISSN: 2948-2992
DOI: https://doi.org/10.1007/s10791-008-9076-6

Springer Professional

Excerpt

Bitte loggen Sie sich ein, um Zugang zu Ihrer Lizenz zu erhalten.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"

Weitere Artikel der Ausgabe 1/2009

An empirical study of gene synonym query expansion in biomedical information retrieval

Tasks, topics and relevance judging for the TREC Genomics Track: five years of experience evaluating biomedical text information retrieval systems

Exploring criteria for successful query expansion in the genomic domain

Evaluation of query expansion using MeSH in PubMed