Skip to main content

Protein Data Integration Problem

  • Chapter
Biomedical Data and Applications

Part of the book series: Studies in Computational Intelligence ((SCI,volume 224))

  • 666 Accesses

Abstract

In this chapter, we consider the challenges of information integration in proteomics from the prospective of researchers using information technology as an integral part of their discovery process. Specifically, data integration, meta-data specification, data provenance and data quality, and ontology are discussed here. These are the fundamental problems that need to be solved by the bioinformatics community so that modern information technology can have a deeper impact on the progress of biological discovery.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Appel, R.D., Bairoch, A., Hochstrasser, D.F.: A new generation of information retrieval tools for biologists: the example of the expasy www server. Trends in Biochemical Sciences 19, 258–260 (1994)

    Article  Google Scholar 

  • Apweiler, R., Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Natale, D.A., O’Donovan, C., Redaschi, N., Yeh, L.S.: UniProt: The Universal Protein knowledgebase. Nucleic Acids Research 32, 115–119 (2004)

    Article  Google Scholar 

  • Ashburner, M.: FlyBase. Genome News 13, 19–20 (1993)

    Google Scholar 

  • Ashburner, M., Ball, C.A., Blake, J.A., Butler, H., Cherry, J.C., Corradi, J., Dolinski, K.: Creating the Gene Ontology Resource: Design and Implementation. Genome Research 11, 1425–1433 (2001)

    Article  Google Scholar 

  • Baclawski, K., Cigna, J., Kokar, M.M., Magner, P., Indurkhya, B.: Knowledge Representation and Indexing Using the Unified Medical Language System. In: Pacific Symposium on Biocomputing, PSB Online Proceedings. Honolulu, Hawaii (2000)

    Google Scholar 

  • Bada, M., Hunter, L.: Enrichment of OBO Ontologies. Journal of Biomedical Informatics (July 26, 2006) (E-publication ahead of print)

    Google Scholar 

  • Bairoch, A., Bucher, P., Hofmann, K.: The PROSITE database, its status in 1995. Nucleic Acids Research, 189–196 (1996)

    Google Scholar 

  • Bairoch, A., Bucher, P., Hofmann, K.: The PROSITE database, its status in 1997. Nucleic Acids Research 25, 217–221 (1997)

    Article  Google Scholar 

  • Baker, P.G., Brass, A., Bechhofer, S., Goble, C., Paton, N., Stevens, R.: TAMBIS - transparent access to multiple bioinformatics information sources. In: Glasgow, J., Littlejohn, T., Major, F., Lathrop, R., Sankoff, D., Sensen, C.W. (eds.) 6th International Conference on Intelligent Systems for Molecular Biology. AAAI, Montreal (1998)

    Google Scholar 

  • Baker, P.G., Goble, C.A., Bechhofer, S., Paton, N.W., Stevens, R., Brass, A.: An Ontology for Bioinformatics Applications. Bioinformatics 15, 510–520 (1999)

    Article  Google Scholar 

  • Benson, D., Karsch-Mizrachi, I., Lipman, D., Ostell, J., Wheeler, D.: Genbank. Nucleic Acids Research 34, 16–20 (2006)

    Article  Google Scholar 

  • Blake, J.A., Eppig, J.T., Richardson, J.E., Davisson, M.T.: The Mouse Genome Database (MGD): a community resource. Status and enhancements. The Mouse Genome Informatics Group. Nucleic Acids Research 26, 130–137 (1998)

    Article  Google Scholar 

  • Bodenreider, O.: The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Research 32, 267–270 (2004)

    Article  Google Scholar 

  • Brenner, S.E.: World Wide Web and molecular biology. Science 268, 622–623 (1995)

    Article  Google Scholar 

  • Buneman, P., Davidson, S., Hart, K., Overton, C., Wong, L.: A Data Transformation System for Biological Data Sources. In: 21st International Conference on Very Large Data Bases (VLDB 1995). Morgan Kaufmann, Zurich (1995)

    Google Scholar 

  • Buneman, P., Davidson, S., Hillebrand, G., Suciu, D.: A query language and optimization techniques for unstructured data. In: Widom, J. (ed.) 1996 ACM SIGMOD international Conference on Management of Data. ACM Press, Montreal (1996)

    Google Scholar 

  • Camon, E., Magrane, M., Barrell, D., Lee, V., Dimmer, E., Maslen, J., Binns, D., Harte, N., Lopez, R., Apweiler, R.: The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Research 32, 262–266 (2004)

    Article  Google Scholar 

  • Chen, I.A., Markowitz, V.M.: An overview of the Object Protocol Model (OPM) and the OPM data management tools. Information Systems 20, 393–418 (1995)

    Article  Google Scholar 

  • Cochrane, G., Aldebert, P., Althorpe, N., Andersson, M., Baker, W., Baldwin, A., Bates, K., Bhattacharyya, S., Browne, P., Van Den Broek, A., Castro, M., Duggan, K., Eberhardt, R., Faruque, N., Gamble, J., Kanz, C., Kulikova, T., Lee, C., Leinonen, R., Lin, Q., Lombard, V., Lopez, R., Mchale, M., Mcwilliam, H., Mukherjee, G., Nardone, F., Pastor, M.P.G., Sobhany, S., Stoehr, P., Tzouvara, K., Vaughan, R., Wu, D., Zhu, W., Apweiler, R.: EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Research 34, 10–15 (2005)

    Article  Google Scholar 

  • Collins, F.S., Morgan, M., Patrinos, A.: The Human Genome Project: Lessons from Large-Scale Biology. Science 300, 286–290 (2003)

    Article  Google Scholar 

  • Davidson, S., Crabtree, J., Brunk, B., Schug, J., Tannen, V., Overton, C., Stoeckert, C.: K2/Kleisli and GUS: Experiments in Integrated Access to Genomic Data Sources. IBM Systems Journal 40, 512–531 (2001)

    Article  Google Scholar 

  • Denny, J.C., Smithers, J.D., Miller, R.: "Understanding" medical school curriculum content using Knowledge Map. Journal of the American Medical Informatics Association 10, 351–362 (2003)

    Article  Google Scholar 

  • Discala, C., Ninnin, M., Achard, F., Barillot, E., Vaysseix, G.: DBCat: a catalog of biological databases. Nucleic Acids Research 27, 10–11 (1999)

    Article  Google Scholar 

  • Etzold, T., Argos, P.: SRS: An Indexing and Retrieval Tool for Flat File Data Libraries. Computer Application of Biosciences 9, 49–57 (1993)

    Google Scholar 

  • Fan, W.: Path Constraints for Databases with or without Schemas. University of Pennsylvania, Philadelphia (1999)

    Google Scholar 

  • Flanders, D.J., Weng, S., Petel, F.X., Cherry, J.M.: AtDB, the Arabidopsis thaliana Database, and graphical-web-display of progress by the Arabidopsis Genome Initiative. Nucleic Acids Research 26, 80–84 (1998)

    Article  Google Scholar 

  • Fraser, A.G., Marcotte, E.M.: A probabilistic view of gene function. Nature Genetics 36, 559–564 (2004)

    Article  Google Scholar 

  • Frazier, M.E., Johnson, G.M., Thomassen, D.G., Oliver, C.E., Patrinos, A.: Realizing the Potential of Genome Revolution: The Genomes to Life Program. Science 300, 290–293 (2003a)

    Article  Google Scholar 

  • Frazier, M.E., Thomassen, D.G., Patrinos, A., Johnson, G.M., Oliver, C.E., Uberbacher, E.: Setting Up the Pace of Discovery: the Genomes to Life Program. In: 2nd IEEE Computer Society Bioinformatics Conference (CSB 2003). IEEE CS Press, Stanford (2003)

    Google Scholar 

  • Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., Kanehisa, M.: DBGET/LinkDB: an Integrated Database Retrieval System. In: Pacific Symposium of Biocomputing, PSB Electronic Proceedings, Hawaii (1998)

    Google Scholar 

  • George, D.G., Mewes, H.-W., Kihara, H.: A standardized format for sequence data exchange. Protein Seq. Data Anal. 1, 27–29 (1987)

    Google Scholar 

  • George, D.G., Orcutt, B.C., Mewes, H.-W., Tsugita, A.: An object-oriented sequence database definition language (sddl). Protein Seq. Data Anal. 5, 357–399 (1993)

    Google Scholar 

  • Goble, C.A., Stevens, R., Ng, G., Bechhofer, S., Paton, N.W., Baker, P.G., Peim, M., Brass, A.: Transparent access to multiple bioinformatics information sources. IBM Systems Journal 40, 532–551 (2001)

    Google Scholar 

  • Gray, P.M.D., Paton, N.W., Kemp, G.J.L., Fothergill, J.E.: An object-oriented database for protein structure analysis. Protein Engineering 3, 235–243 (1990)

    Article  Google Scholar 

  • Gruber, T.R.: A Translation Approach to Portable Ontology Specifications. Knowledge Acquisition 5, 199–220 (1993)

    Article  Google Scholar 

  • Haas, L., Schwarz, P., Kodali, P., Kotlar, E., Rice, J., Swope, W.: DiscoveryLink: A system for integrated access to life sciences data sources. IBM Systems Journal 40, 489–511 (2001)

    Google Scholar 

  • Hafner, C.D., Fridman, N.: Ontological foundations for biology knowledge models. In: 4th International Conference on Intelligent Systems for Molecular Biology. AAAI, St. Louis (1996)

    Google Scholar 

  • Harger, C., Skupski, M., Bingham, J., Farmer, A., Hoisie, S., Hraber, P., Kiphart, D., Krakowski, L., Mcleod, M., Schwertfeger, S., Seluja, S., Siepel, A., Singh, G., Stamper, D., Steadman, P., Thayer, N., Thompson, R., Wargo, P., Waugh, M., Zhuang, J.J., Schad, P.A.: The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Research 26, 21–26 (1998)

    Article  Google Scholar 

  • Harte, N., Silventoinen, V., Quevillon, E., Robinson, S., Kallio, K., Fustero, X., Patel, P., Jokinen, P., Lopez, R.: Public webbased services from the European Bioinformatics Institute. Nucleic Acids Research 32, W3–W9 (2004)

    Article  Google Scholar 

  • Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A.: IntAct-an open source molecular interaction database. Nucleic Acids Research 32, 452–455 (2004)

    Article  Google Scholar 

  • Huysmans, M., Richelle, J., Wodak, S.J.: SESAM: a relational database for structure and sequence of macromolecules. Proteins 11, 59–76 (1991)

    Article  Google Scholar 

  • Jenssen, T.K., Laegreid, A., Komorowski, J., Hovig, E.: A literature network of human genes for high-throughput analysis of gene expression. Nature Genetics 28, 21–28 (2001)

    Article  Google Scholar 

  • Kanehisa, M., Fickett, J.W., Goad, W.B.: A relational database system for the maintenance and verification of the Los Alamos sequence library. Nucleic Acids Research 12, 149–158 (1984)

    Article  Google Scholar 

  • Karp, P.: Database links are a foundation for interoperability. Trends in Biotechnology 14, 273–279 (1996)

    Article  Google Scholar 

  • King, O.D., Foulger, R.E., Dwight, S., White, J., Roth, F.P.: Predicting gene function from patterns of annotation. Genome Research 13, 896–904 (2003)

    Article  Google Scholar 

  • Letovsky, S.I.: Beyond the information maze. Journal of Computational Biology 2, 539–546 (1995)

    Article  Google Scholar 

  • Lewis, S.E.: Gene Ontology: looking backwards and forwards. Genome Biology 6, 103.1–103.4 (2004)

    Google Scholar 

  • Li, Q., Shilane, P., Noy, N.F., Musen, M.A.: Ontology acquisition from on-line knowledge sources. In: AMIA 2000 Annual Symposium, Los Angeles, CA (2000)

    Google Scholar 

  • Lindberg, C.: The Unified Medical Language System (UMLS) of the National Library of Medicine. Journal of American Medical Record Association 61, 40–42 (1990)

    Google Scholar 

  • Lindberg, D.A., Humphreys, B.L., Mccray, A.T.: The Unified Medical Language System. Methods of information in medicine 32, 281–291 (1993)

    Google Scholar 

  • Lindsley, D.L., Zimm, G.G.: The genome of Drosophila melanogaster. Academic Press, San Diego (1992)

    Google Scholar 

  • Mani, I., Hu, Z., Hu, W.: PRONTO: A Large-scale Machine-induced Protein Ontology. In: 2nd Standards and Ontologies for Functional Genomics Conference (SOFG 2004), UK (2004)

    Google Scholar 

  • Markowitz, V.M., Ritter, O.: Characterizing heterogeneous molecular biology data systems. Journal of Computational Biology 2, 547–556 (1995)

    Article  Google Scholar 

  • Mckusick, V.A.: Mendelian Inheritance in Man. In: A Catalog of Human Genes and Genetic Disorders. Johns Hopkins University Press, Baltimore (1998)

    Google Scholar 

  • Miyazaki, S., Sugawara, H., Gojobori, T., Tateno, Y.: DNA Databank of Japan (DDBJ) in XML. Nucleic Acids Research 31, 13–16 (2003)

    Article  Google Scholar 

  • Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L.: InterPro, progress and status in 2005. Nucleic Acids Research 33, 201–205 (2005)

    Article  Google Scholar 

  • Nelson, S.J., Johnston, D., Humphreys, B.L.: Relationships in Medical Subject Headings. In: Bean, C.A., Green, R. (eds.) Relationships in the organization of knowledge. Kluwer Academic Publishers, New York (2001)

    Google Scholar 

  • Nestorov, S., Ullman, J., Wiener, J., Chawathe, S.: Representative objects: concise representations of semistructured, hierarchical data. In: 13th International Conference on Data Engineering. IEEE CS Press, Birmingham (1997)

    Google Scholar 

  • O’Neil, M., Payne, C., Read, J.: Read Codes Version 3: a user led terminology. Methods of information in medicine 34, 187–192 (1995)

    Google Scholar 

  • Ohkawa, H., Ostell, J., Bryant, S.: MMDB: an ASN.1 specification for macromolecular structure. In: 3rd International Conference on Intelligent Systems for Molecular Biology. AAAI, Cambridge (1995)

    Google Scholar 

  • Ostell, J.: GenInfo ASN.1 Syntax: Sequences. NCBI Technical Report Series. National Library of Medicine, NIH (1990)

    Google Scholar 

  • Overton, G.C., Aaronson, J.S., Haas, J., Adams, J.: Qgb: a system for querying sequence database fields and features. Journal of Computational Biology 1, 3–14 (1994)

    Google Scholar 

  • Pennisi, E.: Genome Data Shake Tree of Life. Science 280, 672–674 (1998)

    Article  Google Scholar 

  • Pongor, S.: Novel databases for molecular biology. Nature 332, 24 (1998)

    Article  Google Scholar 

  • Rawlings, C.J.: Designing databases for molecular biology. Nature 334, 447 (1998)

    Google Scholar 

  • Rebhan, M., Chalifa-Caspi, V., Prilusky, J., Lancet, D.: GeneCards: encyclopedia for Genes, Proteins, and Diseases. Weizmann Institute of Science, Bioinformatics Unit and Genome Center Rehovot, Israel, (1997)

    Google Scholar 

  • Rector, A.L., Bechhofer, S., Goble, C.A., Horrocks, I., Nowlan, W.A., Solomon, W.D.: The GRAIL Concept Modelling Language for Medical Terminology. Artificial Intelligence in Medicine 9, 139–171 (1997)

    Article  Google Scholar 

  • Roberts, R.J., Macelis, D.: REBASE - restriction enzymes and methylases. Nucleic Acids Research 26, 338–350 (1998)

    Article  Google Scholar 

  • Schuler, G.D., Boguski, M.S., Stewart, E.A., Stein, L.D., Gyapay, G., Rice, K., White, R.E., Rodriguez-Tome, P., Aggarwal, A., Bajorek, E., Bentolila, S., Birren, B.B., Butler, A., Castle, A.B., Chiannilkulchai, N., Chu, A., Clee, C., Cowles, S., Day, P.J.R., Dibling, T., Drouot, N., Dunham, I., Duprat, S., East, C., Edwards, C., Fan, J.-B., Fang, N., Fizames, C., Garrett, C., Green, L., Hadley, D., Harris, M., Harrison, A.P., Brady, S., Hicks, A., Holloway, E., Hui, L., Hussain, S., Louis-Dit-Sully, C., Ma, J., Macgilvery, A., Mader, C., Maratukulam, A., Matise, T.C., Mckusick, K.B., Morissette, J., Mungall, A., Muselet, D., Nusbaum, D.: A gene map of the human genome. Science 274, 540–546 (1996a)

    Article  Google Scholar 

  • Schuler, G.D., Epstein, J.A., Ohkawa, H., Kans, J.A.: Entrez: molecular biology database and retrieval system. Methods in Enzymology 266, 141–162 (1996b)

    Article  Google Scholar 

  • Schulze-Kremer, S.: Ontologies for Molecular Biology. In: Pacific Symposium of Biocomputing, PSB 1998 Electronic Proceedings, Hawaii (1998)

    Google Scholar 

  • Shomer, B., Harper, R.A., Cameron, G.N.: Information services of the European Bioinformatics Institute. Methods in Enzymology 266, 3–27 (1996)

    Article  Google Scholar 

  • Sidhu, A.S., Dillon, T.S., Chang, E.: Protein Ontology. In: Chen, J., Sidhu, A.S. (eds.) Biological Database Modeling. Artech House, New York (2007)

    Google Scholar 

  • Sidhu, A.S., Dillon, T.S., Setiawan, H., Sidhu, B.S.: Comprehensive Protein Database Representation. In: Gramada, A., Bourne, P.E. (eds.) 8th International Conference on Research in Computational Molecular Biology 2004 (RECOMB 2004). ACM Press, San Diego (2004a)

    Google Scholar 

  • Sidhu, A.S., Dillon, T.S., Sidhu, B.S., Setiawan, H.: A Unified Representation of Protein Structure Databases. In: Reddy, M.S., Khanna, S. (eds.) Biotechnological Approaches for Sustainable Development. Allied Publishers, India (2004b)

    Google Scholar 

  • Sidhu, A.S., Dillon, T.S., Sidhu, B.S., Setiawan, H.: An XML based semantic protein map. In: Zanasi, A., Ebecken, N.F.F., Brebbia, C.A. (eds.) 5th International Conference on Data Mining, Text Mining and their Business Applications (Data Mining 2004). WIT Press, Malaga (2004c)

    Google Scholar 

  • Sonnhammer, E.L.L., Eddy, S.R., Birney, E., Bateman, A., Durbin, R.: Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Research 26, 320–322 (1998)

    Article  Google Scholar 

  • Spackman, K.A.: SNOMED RT. College of American Pathologists, Northfield (2000)

    Google Scholar 

  • Spackman, K.A., Campbell, K.E., Cote, R.A.: SNOMED RT: a reference terminology for health care. In: Masys, D.R. (ed.) AMIA 1997 Annual Fall Symposium, Nashville, TN (1997)

    Google Scholar 

  • Stoesser, G., Baker, W., Van Den Broek, A., Garcia-Pastor, M., Kanz, C., Kulikova, T.: The EMBL Nucleotide Sequence Database: Major new developments. Nucleic Acids Research 31, 17–22 (2003)

    Article  Google Scholar 

  • Tisdall, J.D.: Mastering Perl for bioinformatics. O’Reilly, Sebastopol (2003)

    Google Scholar 

  • Trombert-Paviot, B., Rodrigues, J.M., Rogers, J.E., Baud, R., Van Der Haring, E., Rassinoux, A.M., Abrial, V., Clavel, L., Idir, H.: GALEN: a third generation terminology tool to support a multipurpose national coding system for surgical procedures. International Journal of Medical Informatics 58–59, 71–85 (2000)

    Google Scholar 

  • Bray, T., Paoli, J., Sperberg-Mcqueen, C.M., Maler, E., Yergeau, F. (eds.): W3C-XML, Extensible Markup Language (XML) 1.0. W3C Recommendation, August 16, 2006; edited in place September 29, 2006. 4th edn., World Wide Web Consortium (2006)

    Google Scholar 

  • Fallside, D.C., Walmsley, P. (eds.): W3C-XMLSCHEMA, XML Schema Part 0: Primer. W3C Recommendation, 2nd edn., October 28, 2004. World Wide Web Consortium (2004)

    Google Scholar 

  • Wang, A.: Mapping Between SNOMED RT and Clinical Terms Version 3: A Key Component of the SNOMED CT Development Process. In: Bakken, S. (ed.) AMIA Annual Fall Symposium 2001 (2001)

    Google Scholar 

  • Westbrook, J., Ito, N., Nakamura, H., Henrick, K., Berman, H.M.: PDBML: the representation of archival macromolecular structure data in XML. Bioinformatics 21, 988–992 (2005)

    Article  Google Scholar 

  • Whetzel, P.L., Parkinson, H., Causton, H.C., Fan, L., Fostel, J., Fragoso, G., Game, L., Heiskanen, M., Morrison, N., Rocca-Serra, P., Sansone, S., Taylor, C., White, J., Stoeckert, C.J.: The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22, 866–873 (2006)

    Article  Google Scholar 

  • Williams, N.: Bioinformatics: How to Get Databases Talking the Same Language. Science 275, 301–302 (1997)

    Article  Google Scholar 

  • Wingender, E.: Gene Regulation in Eukaryotes. Wiley-VCH, Weinheim (1993)

    Google Scholar 

  • Wingender, E., Dietze, P., Karas, H., Knüppel, R.: TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Research 24, 238–241 (1996)

    Article  Google Scholar 

  • Yang, S., Bhowmick, S.S., Madria, S.: Bio2X: a rule-based approach for semi-automatic transformation of semi-structured biological data to XML. Data and Knowledge Engineering 52, 249–271 (2005)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Sidhu, A.S., Bellgard, M. (2009). Protein Data Integration Problem. In: Sidhu, A.S., Dillon, T.S. (eds) Biomedical Data and Applications. Studies in Computational Intelligence, vol 224. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02193-0_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-02193-0_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02192-3

  • Online ISBN: 978-3-642-02193-0

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics