Abstract
Semantic Web technologies are appealing for biomedical researchers since they promise to solve many of the daily problems they face while accessing and integrating biological information that is distributed over the Internet and managed by using tools which are extremely heterogeneous and largely not compatible. On the other hand, the complexity of biomedical information and its heterogeneity, together with the need of keeping current production services steadily up and running, make the transition from current semantic-less to future semantic-aware services a huge problem.
In this paper, authors present the characteristics of biomedical information that make adoption of semantic web technologies both desirable and complex at the same time. They then present the tools and the applications that have been developed so far, including biomedical ontologies, RDF/OWL data stores, query systems and semantic-aware tools and browsers. Finally, they present community efforts and the perspectives that can be sought for short- and mid-term developments in the field.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Spear, A.D.: Ontology for the Twenty First Century: An Introduction with Recommendations, Saarbruecken, Germany (2006), http://www.ifomis.uni-saarland.de/bfo/manual/manual.pdf
Lodish, H., Berk, A., Kaiser, C.A., Krieger, M., Scott, M.P., Bretscher, A., Ploegh, H., Matsudaira, P.: Molecular Cell Biology, 6th edn. W.H.Freeman, New York (2000)
Rebholz-Schuhmann, D., Arregui, M., Gaudan, S., Kirsh, H., Jimeno, A.: Text processing through Web services: calling Whatizit. Bioinformatics 24(2), 296–298 (2008)
Fink, J.L., Kushch, S., Williams, P.R., Bourne, P.E.: BioLit: integrating biological literature with databases. Nucleic Acids Res. (May 31, 2008)
Bourne, P.: Will a biological database be different from a biological journal? PloS Comp. Biol. 1(3), 34 (2005)
Bons, M.: Which gene did you mean? BMC Bioinformatics 6, 142 (2005)
Bourne, P.E., Fink, J.L., Gerstein, M.: Open Access: Taking Full Advantage of the Content. PloS Comput. Biol. 4(3), 1000037 (2008)
Ball, A.C., Sherlock, G., Parkinson, H., Rocca-Serra, P., Brooksbank, C., Causton, H.C., Cavaliaeri, D., Gaasterland, T., Hingamp, P., Holstege, F., Ringwald, M., Spellman, P., Stoeckert, C.J., Stewart, J.E., Taylor, R., Brazma, A., Quackenbush, J.: An open letter to the scientific journals. Bioinformatics 18(1), 1409 (2002)
Internationl Human Genome Sequencing Consortium, Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)
Lin, S., Lopez, Q., Lorenc, R., McWilliam, D., Mukherjee, H., Nardone, G., Plaister, F., Robinson, S., Sobhany, S., Vaughan, S., Wu, R., Zhu, D.: Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acid Res. 36(Database issue), D5–D12 (2008)
Parkinson, H., Kapushesky, M., Shojatalab, M., Abeygunawardena, N., Coulson, R., Farne, A., Holloway, E., Kolesnykov, N., Lilja, P., Mani, R., Rayner, T., Sharma, A., William, E., Sarkans, U., Brazma, A.: ArrayExpress – a pcublic database of microarray experiments and gene expression profiles. Nucleic Acids Res. 35(DB issue), D747–750 (2007)
Galperin, M.Y.: The Molecular Biology Database Collection: 2007 update. Nucleic Acids Res. 35, D3–D4 (2007)
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Wheeler, D.L.: GenBank. Nucleic Acids Res. 36 (January 2008) (Database issue)
Sugawara, H., Ogasawara, O., Okubo, K., Gojobori, T., Tateno, Y.: DDBJ with new system and face. Nucleic Acids Res. 36 (January 2008) (Database issue)
Olivier, M., Eeles, R., Hollstein, M., Khan, M.A., Harris, C.C., Hainaut, P.: The IARC TP53 database: new online mutation analysis and recommendation to users. Hum. Mutat. 19(6), 607–614 (2002)
Hamroun, D., Kato, S., Ishioka, C., Claustres, M., Béroud, C., Soussi, T.: The UMD TP53 database and website: update and revisions. Hum. Mutat. 27(1), 14–20 (2006)
Forbes, S.A., Bharma, G., Bamford, S., Dawson, E., Kok, C., Clements, J., Menzies, A., Teague, J.W., Futreal, P.A., Stratton, M.R.: The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet. 2008, ch. 10: Unit 10.11 (April 2008)
The UniProt Consortium: The Universal Protein Resource (UniProt). Nucleic Acids Res. 36, D190–D195 (2008)
Peters, B., Sidney, J., Bourne, P., Bui, H.H., Buus, S., Doh, G., Fieri, W., Kronenberg, M., Kubo, R., Lund, O., Nemazee, D., Ponomarenko, J.V., Sathiamurthy, M.S., Choenberger, S., Stewart, S., Surko, P., Way, S., Wilson, S., Sette, A.: The immune epitope database and analysis resource: from vision to blueprint. PloS Biol. 3(3), 91 (2005)
Karp, P.D., Christos, A., Ouzounis, A., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Ahrén, D., Tsoka, S., Darzentas, N., Kunin, V., Lopez-Bigas, N.: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33(19), 6083–6089 (2005)
Paley, S.M., Karp, P.D.: The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res. 34(13), 3771–3778 (2006)
Krummenacker, M., Paley, S., Mueller, L., Yan, T., Karp, P.D.: Querying and computing with BioCyc databases. Bioinformatics 21(16), 3454–3455 (2005)
Romero, P., Wagg, J., Green, M.L., Kaiser, D., Krummenacker, M., Karp, P.D.: Computational prediction of human metabolic pathways from the complete human genome. Genome Biology 6, R2 (2004)
Vastrik, I., D’Eustachio, P., Schmidt, E., Joshi-Tope, G., Gopinath, G., Croft, D., de Bono, B., Gillespie, M., Jassal, B., Lewis, S., Matthews, L., Wu, G., Birney, E., Stein, L.: Reactome: a knowledge base of biologic pathways and processes. Genome Biology 8, R39 (2007)
Hucka, M., Finney, A., Sauro, H., Bolouri, H., Doyle, J., Kitano, H., Arkin, A., Bornstein, B., Bray, D., Cornish-Bowden, A., Cuellar, A.A., Dronov, S., Gilles, E.D., Ginkel, M., Gor, V., Goryanin, I.I., Hedley, W.J., Hodgman, T.C., Hofmeyr, J.H., Hunter, P.J., Juty, N.S., Kasberger, J.L., Kremling, A., Kummer, U., Le Novère, N., Loew, L.M., Lucio, D., Mendes, P., Minch, E., Mjolsness, E.D., Nakayama, Y., Nelson, M.R., Nielsen, P.F., Sakurada, T., Schaff, J.C., Shapiro, B.E., Shimizu, T.S., Spence, H.D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J., Wang, J.: SBML Forum: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4), 524–531 (2003)
Le Novère, N., Borsntein, B., Broicher, A., Courtout, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, J.L., Hucka, M.: BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, D689–D691 (2006)
LSR: Life Sciences Identifiers RFP Response, http://www.omg.org/docs/lifesci/03-12-02.pdf
Clark, T., Martin, S., Liefeld, T.: Globally distributed object identification for biological knowledgebases. Briefings in Bioinformatics 5, 59–70 (2004)
Etzold, T., Ulyanov, A., Argos, P.: SRS: information retrieval system for molecular biology data banks. Meth. Enzymol. 266, 114–128 (1996)
Mons, B., Ashburner, M., Chichester, C., van Mulligen, E., Weeber, M., den Dunnen, J., van Ommen, G.-J., Musen, M., Cockerill, M., Hermjakob, H., Mons, A., Packer, A., Pacheco, R., Lewis, S., Berkeley, A., Melton, W., Barris, N., Wales, J., Meijssen, G., Moeller, E., Roes, P.J., Borner, K., Bairoch, A.: Calling on a million minds for community annotation in WikiProteins. Genome Biology 9, R89 (2008)
Salzberg, S.L.: Genome re-annotation: a wiki solution? Genome Biology 8, 102 (2007)
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25(1), 25–29 (2000)
Gene Ontology Consortium. The Gene Ontology project in 2008. Nucleic Acids Res. 36(Database issue), D440–444 (January 2008)
Mungall, C.J.: Obol: integrating language and meaning in bio-ontologies. Comp. Funct. Genomics 5, 509–520 (2004)
Moreira, D.A., Musen, M.A.: OBO to OWL: a protege OWL tab to read/save OBO ontologies. Bioinformatics 23(14), 1868–1870 (2007)
Aranguren, M.E., Bechhofer, S., Lord, P., Sattler, U., Stevens, R.: Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL. BMC Bioinformatics 8, 57 (2007)
Khatri, P., Drăghici, S.: Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21(18), 3587–3595 (2005)
Lord, P.W., Stevens, R.D., Brass, A., Goble, C.A.: Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19(10), 1275–1283 (2003)
Côté, R.G., Jones, P., Apweiler, R., Hermjakob, H.: The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 7, 97 (2006)
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, J., Ceusters, W., Goldberg, J.L., Eilbeck, K., Ireland, A., Mungall, C.J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S.A., Scheuermann, R.H., Shah, N., Whetzel, P.L., Lewis, S.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25, 1251–1255 (2007)
Bada, M., Hunter, L.: Enrichment of OBO ontologies. J. Biomed. Inform. 40(3), 300–315 (2007)
Myhre, S., Tveit, H., Mollestad, T., Laegreid, A.: Additional gene ontology structure for improved biological reasoning. Bioinformatics 22(16), 2020–2027 (2006)
Smith, B., Ceusters, W., Klagges, B., Köhler, J., Kumar, A., Lomax, J., Mungall, C., Neuhaus, F., Rector, A.L., Rosse, C.: Relations in biomedical ontologies. Genome Biol. 6(5), R46 (2005)
Cheung, K.-H., Qi, P., Tuck, D., Krauthammer, M.: A semantic web approach to biological pathway data reasoning and integration. Web Semantics: Science, Services and Agents on the World Wide Web (Journal of Web Semantics) 4, 207–215 (2006)
Chen, H., Doherty, D., Forsberg, K., Gao, Y., Kashyap, V., Kinoshita, J., Luciano, J., Marshall, M.S., Ogbuji, C., Rees, J., Stephens, S., Wong, G.T., Wu, E., Zaccagnini, D., Hongsermeier, T., Neumann, E., Herman, I., Cheung, K.-H.: Advancing translational research with the Semantic Web. BMC Bioinformatics 8(suppl. 3), S2 (2007)
Splendiani, A.: RDFScape: Semantic Web meets Systems Biology. BMC Bioinformatics 9(suppl. 4), S6 (2008)
Chatraryamontri, A., Ceol, A., Palazzi, L.M., Nardelli, G., Schneider, M.V., Castagnoli, L., Cesareni, G.: MINT: the Molecular INTeraction database. Nucleic Acids Res. 35, D572–D574 (2007)
Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., Gaasterland, T., Glenisson, P., Holstege, F.C., Kim, I.F., Markowitz, V., Matese, J.C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., Vingron, M.: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 29(4), 365–371 (2001)
Ball, C.A., Brazma, A.: MGED standards: work in progress. OMICS 10(2), 138–144 (2006)
Soldatova, L.N., King, R.D.: Are the current ontologies in biology good ontologies? Nat. Biotechnol. 23(9), 1095–1098 (2005)
Le Novère, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D., Wanner, B.L.: Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 23(12), 1509–1515 (2005)
Whetzel, P.L., Brinkman, R.R., Causton, H.C., Fan, L., Field, D., Fostel, J., Fragoso, G., Gray, T., Heiskanen, M., Hernandez-Boussard, T., Morrison, N., Parkinson, H., Rocca-Serra, P., Sansone, S.A., Schober, D., Smith, B., Stevens, R., Stoeckert, C.J.: FuGO Working Group.: Development of FuGO: an ontology for functional genomics investigations. OMICS 10(2), 199–204 (2006) (review)
Wilkinson, M.D., Links, M.: BioMOBY: an open-source biological web services proposal. Briefings in Bioinformatics 3, 331–341 (2002)
Wroe, C., Stevens, R., Goble, C., Roberts, A., Greenwod, M.: A suite of DAML+OIL ontologies to describe bioinformatics web services and data. International Journal of Cooperative Information Systems – Special issue on Bioinformatics 12, 197–224 (2003)
Romano, P.: Automation of in-silico data analysis processes through workflow management systems. Briefings in Bioinformatics 9(1), 57–68 (2008)
Mahoui, M., Ben-Miled, Z., Srinivasan, S., Dippold, M., Yang, B., Li, N.: SIBIOS Ontology: a robust package for the integration and pipelining of bioinformatics services. In: Leser, U., Naumann, F., Eckman, B. (eds.) DILS 2006. LNCS (LNBI), vol. 4075. Springer, Heidelberg (2006)
Leser, U.: A query language for biological networks. Bioinformatics 21(suppl. 2), 33–39 (2005)
Ruttenberg, A., Rees, J., Zucker, J.: What BioPAX communicates and how to extend OWL to help it. In: Proceeding of OWLed (2006), http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-216/
Karp, P.D., Paley, S.: Automated drawing of metabolic pathways. In: Lim, H., Cantor, C., Robbins, R. (eds.) Proceedings of the Third International Conference on Bioinformatics and Genome Research. Florida State Conference Center, pp. 225–238. Tallahassee, Florida (1994)
Good, B.M., Wilkinson, M.D.: The Life Sciences Semantic Web is full of creeps. Brief Bioinform. 7(3), 275–286 (2006)
Cannata, N., Merelli, E., Altman, R.B.: Time to Organize the Bioinformatics Resourceome. PLoS Computational Biology 1(7), 76 (2007)
Cannata, N., Corradini, F., Gabrielli, S., Leoni, L., Merelli, E., Piersigilli, F., Vito, L.: Intuitive and machine understandable representation of the bioinformatics domain and of related resources with Resourceomes. In: Felicioli, C., Romano, P., Marangoni, R. (eds.) Proc. of the 7th International Workshop NETTAB 2007 on A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications, Pisa, June 12-15, 2007, pp. 35–46 (2007)
Dinov, I.D., Rubin, D., Lorensen, W., Dugan, J., Ma, J., Murphy, S., Kirschner, B., Bug, W., Sherman, M., Floratos, A., Kennedy, D., Jagadish, H.V., Schmidt, J., Athey, B., Califano, A., Musen, A., Altman, R., Kikinis, R., Kohane, I., Delp, S., Parker, D.S., Toga, A.W.: iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources. PLoS ONE 3(5), 2265 (2008)
Schröder, M., Burger, A., Kostkova, P., Stevens, R., Habermann, B., Dieng-Kuntz, R.: From a Services-based eScience Infrastructure to a Semantic Web for the Life Sciences: The Sealife Project. In: NETTAB 2006, Santa Margherita di Pula, CA, July 10-13 (2006)
Alexopoulou, D., Wachter, T., Pickersgill, L., Eyre, C., Schroeder, M.: Terminologies for text-mining; an experiment in the lipoprotein metabolism domain. BMC Bioinformatics 9(Suppl. 4), S2 (2008)
Neumann, E.K., Quan, D.: BioDash: a Semantic Web dashboard for drug development. In: Proc. Pacific Symposium Biocomputing (PSB 2006), pp. 176–187 (2006)
HCLS Charter, http://www.w3.org/2008/05/HCLSIGCharter
A Prototype Knowledge Base for the Life Sciences, W3C Interest Group Note (June 4, 2008), http://www.w3.org/TR/hcls-kb/
Lam, H.Y.K., Marenco, L., Clark, T., Gao, Y., Kinoshita, J., Shepherd, G., Miller, P., Wu, E., Wong, G.T., Liu, N., Crasto, C., Morse, T., Stephens, S., Cheung, K.-H.: AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics 8(suppl. 3), S4 (2007)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Romano, P., Splendiani, A. (2008). Applications of Semantic Web Methodologies and Techniques to Biology and Bioinformatics. In: Baroglio, C., Bonatti, P.A., Małuszyński, J., Marchiori, M., Polleres, A., Schaffert, S. (eds) Reasoning Web. Lecture Notes in Computer Science, vol 5224. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85658-0_6
Download citation
DOI: https://doi.org/10.1007/978-3-540-85658-0_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-85656-6
Online ISBN: 978-3-540-85658-0
eBook Packages: Computer ScienceComputer Science (R0)