research-article

Bioqueries: a social community sharing experiences while querying biological linked data

Authors:

María Jesús García-Godoy,

Ismael Navas-Delgado,

José Aldana-MontesAuthors Info & Claims

SWAT4LS '11: Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences

Pages 24 - 31

https://doi.org/10.1145/2166896.2166906

Published: 07 December 2011 Publication History

Abstract

Life Sciences have emerged as a key domain in the Linked Data community because of the diversity of data semantics and formats available by means of a great variety of databases and web technologies. Thus, it has been used as the perfect domain for applications in the Web of Data. Unfortunately, on the one hand, bioinformaticians are not exploiting the full potential of this already available technology and, on the other hand, the experts in Life Sciences have real problems to discover, understand and devise how to take advantage of these interlinked (integrated) data. In this paper, we present Bioqueries, a wiki-based portal that is aimed at community building around Biological Linked Data. This public space offers several services and a collaborative infrastructure with the objective of stimulating the generation of activity in the consumption of Biological Linked Data and therefore contributing to the deployment of the benefits of the Web of Data in this domain. This tool is not only designed to aid bioinformaticians when designing SPARQL queries to access biological databases exposed as Linked Data but also aid biologists to gain a deeper insight into the potential use of this technology. These queries published in the portal are also described and commented on natural language, to enable their use by experts in the domain but with less expertise in semantic technologies. The Bioqueries portal is accessible at http://bioqueries.uma.es

References

[1]

Klyne, G., Carroll, J. (2004). Resource Description Framework: Concepts and Abstract Syntax. W3C Recommendation. Technical report, World Wide Web Consortium

[2]

Bizer, C., Heath, T., Berners-Lee, T. 2008. Linked Data: Principles and state of art. In Proceedings 17^th International

[3]

World Wide Web conference, Beijing China 23--24 April (WWW2008)

[4]

Bizer, C., Heath, T., Berners-Lee, T. 2009. Linked Data - The Story so Far-. International Journal on Semantic Web and Information Systems 5, 3 1--22

[5]

W3C. 2008. SPARQL Query Language for RDF. W3C Recommendation. Technical Report, World Wide Web Consortium

[6]

Heath T., Berners-Lee, T. 2011. Linked Data: Evolving the Web into a Global Data Space., ACM Press, New York

Digital Library

[7]

Berrueta, D., Phipps, J. 2009. Best Practices Recipes for Publishing RDF Vocabularies. Technical report, World Wide Web Consortium

[8]

Isele, R., Jentzesch, Anja, Bizer, C. 2010. Silk Server -- Adding missing Links while consuming Linked Data. In: First International Workshosp on Consuming Linked Data (Shangai, China, November 7--11, 2010)

[9]

Berrueta, D., Fernández, S., Frade, I. 2008. Cooking HTTP content negotiation with Vapour. In: Proceedings of 4th workshop on Scripting for the Semantic Web 2008 (SFSW2008) co-located with ESWC2008 (Tenerife, Spain, June) DOI=10.1.1.142.8172

[10]

Berners-Lee, T., Chen T., Chilton, L., Connolly, D., Dhanaraj, R., Hollenbach, J., Lerer, A.,Sheets, D. 2006. Tabulator: Exploring and Analyzing Linked Data on the Semantic Web. In: Proceedings of the 3^rd International Semantic Web User Interaction Workshop. DOI=10.1.1.97.950

[11]

D'Aquin, M., Motta, E., Sabou, M., Angeleton, S., Gridinoc, L., Lopez, V., Guidi, D. 2008. Towards a New Generation of Semantic Web Applications. IEEE Intelligent Systems, 23: 20--28 DOI=10.1109/MIS.2008.54

Digital Library

[12]

Marshal, C. C., Shirpan, F. M. 2003. Which semantic web?. In: Proceedings of the 14^th ACM conference on Hypertext and Hypermedia (HYPERTEXT '03). ACM, New York, NY, USA, 57--66 DOI=10.1145/900051.900063

Digital Library

[13]

Belleau, F., Nolin, M. A., Tourigny, N., Rigault, P., Morisette, J. 2008. Bio2RDF: Towards a Mushup to Build Bioinformatics Knowledge Systems. Journal of Biomedical Informatics 41, 5 (Oct, 2008), 706--717 DOI=10.1016/j.jbi.2008.03.004

Digital Library

[14]

Jain E., Bairoch A., Duvaud S., Phan I., Redaschi N., Suzek B. E., Martin M. J., McGarvey P., Gasteiger E. 2009. Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics 10, 136 DOI=10.1186/1471-2105-10-136

[15]

Humish, A., Scott, A. F., Amberger, J. S., Bocchini, C. A., McKusick, V. A.: Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders Nucleic Acid Res 1, 33 (Jan, 2005), 514--517. DOI= 10.1093/nar/gki033

[16]

Kanehisa, M., G, S., Kawashima, S., Okuno, Y., Hattori, M. 2004. The KEGG Resource for Deciphering the Genome. Nucleic Acid Research 32, 1(Jan, 2004) 277--280 DOI = 10.1093/nar/gkh063.

[17]

Joshi-Tope G., Vastrik I., Gopinathrao G., Matthews L., Schmidt E., Gillespie M., D'Eustachio P., Jassal B., Lewis S., Wu G., Birney E., and Stein L. 2003. The Genome Knowledgebase: A Resource for Biologists and Bioinformaticists. Cold Spring Harb Symp Quant Biol. 68, 237--243 DOI=

[18]

Momtchev. V., Peychev, D., Primov, T., Georgiev, G. 2009. Expanding the Pathway and Interaction Knowledge in Linked Life Data. In: 8^th Proceedings of International Semantic Web Challenge (Washington, EEUU, October 25--29, 2008).

[19]

Kiryakov, A., O., Damyan, O., Manov, D. 2005. OWLIM - A Pragmatic Semantic Repository for OWL. Lecture Notes of Computing Science 3807, 182--192

Digital Library

[20]

Disco Hyper Data Vrowser: http://www4.wiwiss.fu-berlin.de/bizer/ng4j/disco/

[21]

Oinn, T et al. (2006). Taverna: lessons in creating a workflow environment for the life sciences. Concurrency and Computation: Practice & Experience 18, 1067--1100.

Digital Library

[22]

Goble, C. A., De Roure, D. C. 2007. myExperiment: social networking for workflow-using e-scientists. In Proceedings of the 2nd workshop on Workflows in support of large-scale science (Monterey, California, USA, 2007) DOI = http://doi.acm.org/10.1145/1273360.1273361

Digital Library

[23]

Ankolekar, A., Krotzsh, Tran, T., Vrandecic, V. 2007. The two cultures: mashing up web 2.0 and the semantic web. In: Proceedings of the 16th international conference on World Wide Web (WWW'07) ACM, New York, NY, USA, 825--834, DOI=10.1145/1242572.1242684

Digital Library

[24]

Leuf, B., Cunningham, W. 2001. The Wiki Way: Quick Collaboration on the Web. Addison-Wesley Professional.

Digital Library

[25]

Parker, K. R., Chao, J. T. 2007. Wiki as a Teaching Tool, International Journal of Instructional Technology and Distance Learning 4, 1(Jan, 2007), 57--72

[26]

Majchrzak, A., Wagner, C., Yates, D. Corporate wiki users: results of a Survey. 2006. In: Proceedings of the 2006 international symposium on Wikis ACM, Odense, Denmark 99--104 DOI=10.1145/1149453.1149472

Digital Library

[27]

Voss, J. 2005. Measuring Wikipedia. In: 10th International Conference of the International Society for Scientometrics and Infrometrics (Stochholm, Sweden, 24--27, 2005) DOI= 10.1.1.133.1456

[28]

Augar, N., Raitman, R., Zhou, W. 2004. Teaching and Learning Online with Wikis. In: Proceedings of the 21st Australasian Society for Computers in Learning in Tertiary Education Conference (ASCILITE, Perth, Australia, 2006) 95--104

[29]

Zinn, C. 2006. Bootstrapping a semantic wiki application for learning mathematics. In: International Conference on Semantics (Vienna, Austria, 2006) DOI=10.1.1.100.3540

[30]

Salzberg, S. L. 2007. Genome Re-Annotation: a Wiki Solution? Genome Biol, 8 1 (February, 2007) 102 DOI= 10.1186/gb-2007-8-1-102

[31]

Waldrop, M. 2008. Big data: Wikiomics. Nature 455, 22--25 DOI=10.1038/455022a

[32]

Pico, A. R., Kelder, T., Van Iersel M. P., Hanspers, K., Conklin, B. R., Evelo, C. 2008 WikiPathways: pathway editing for the people. Plos Biol 6, 7 (Jul,2008) 184 DOI=10.1371/journal.pbio.0060184

[33]

Dennis, A., Benson, I., Karsch-Mizrachi, D., Lipman, J., Ostell, J., Wheeler, D. L. 2005. GenBank Nucleic Acids Res 34, 1 (Jan, 2005) 34--38 DOI=10.1093/nar/gki063

[34]

Altintas, I., Berkley, C., Jaeger, E., Jones, M.; Ludascher, B.; Mock, S. 2004. Kepler: an extensible system for design and execution of scientific workflows, In: Scientific and Statistical Database Management, 2004. Proceedings. 16th International Conference on (21--23 June 2004, Santorini, Greece) 423--424

Digital Library

[35]

Taylor, S. I., Matthew, Wang, I., Harrison, A. 2007. The Triana Workflow Environment: Architecture and Applications. Taylor, Ian J. and Deelman, Ewa and Gannon, Dennis B. and Shields, Matthew, eds. Springer London, United Kingdom 320--339

[36]

VanDyk, J. K., Westage, M. 2008. Pro Drupal Development.

Digital Library

[37]

Cerami, E., Gross B. E., Demir, E., Rodchenkov. I., Babur, O., Anwar, N., Schultz, N., Bader G. D., Sander, C. 2010. Pathway Commons, a web resource for biological pathway data Nucleic Acids Research 39, 1(Nov, 2010), 685--690.

[38]

Demir et al. 2010. BioPAX community standard for pathway data sharing Nature Biotechnology 28, 935--942

[39]

Heim, P., Hellmann, S., Lehmann, J., Lohmann, S. Stegemann, T., Ziegler, J. 2010. The RelFinder User Interface: Interactive Exploration of Relationships between Objects of Interest. In: Proceedings of the 14th International Conference on Intelligent User Interfaces (New York, NY, USA, 2010) 421--422

Digital Library

Cited By

Arsić BÐokić-Petrović MSpalević PMilentijević IRančić DŽivanović M(2019)SpecINT: A framework for data integration over cheminformatics and bioinformatics RDF repositoriesSemantic Web10.3233/SW-18032710:4(795-813)Online publication date: 23-May-2019
https://doi.org/10.3233/SW-180327
Sima AMendes de Farias TZbinden EAnisimova MGil MStockinger HStockinger KRobinson-Rechavi MDessimoz C(2019)Enabling semantic queries across federated bioinformatics databasesDatabase10.1093/database/baz1062019Online publication date: 7-Nov-2019
https://doi.org/10.1093/database/baz106
Djokic-Petrovic MCvjetkovic VYang JZivanovic MWild D(2017)PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasetsJournal of Biomedical Semantics10.1186/s13326-017-0151-z8:1Online publication date: 20-Sep-2017
https://doi.org/10.1186/s13326-017-0151-z
Show More Cited By

Index Terms

Bioqueries: a social community sharing experiences while querying biological linked data
1. Applied computing
  1. Life and medical sciences

Recommendations

A semantic web approach to biological pathway data reasoning and integration

This paper describes the use of semantic web technology and Description Logic (DL) for facilitating the integration of molecular pathway data, which is illustrated by an Web Ontology Language (OWL)-based transformation of a more complex pathway ...
Mapping the central LOD ontologies to PROTON upper-level ontology
OM'10: Proceedings of the 5th International Conference on Ontology Matching - Volume 689

Linking Open Data (LOD) facilitates the emergence of a web of linked data by publishing and interlinking open data on the web in RDF. One can explore linked data across servers by following the links in the graph. The LOD cloud has 203 datasets and more ...
OntoWiki: community-driven ontology engineering and ontology usage based on Wikis
WikiSym '06: Proceedings of the 2006 international symposium on Wikis

Ontologies are consensual representations of a domain of discourse and the backbone of the future Semantic Web. Currently, however, only a fraction of Web users can take part in the process of building ontologies. In this paper, we show that standard ...

Comments

Please enable JavaScript to view thecomments powered by Disqus.

Information & Contributors

Information

Published In

cover image ACM Other conferences

SWAT4LS '11: Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences

December 2011

139 pages

ISBN:9781450310765

DOI:10.1145/2166896

Conference Chairs:
Adrian Paschke
Freie Universitaet Berlin, Germany
,
Albert Burger
Heriot-Watt University, and Medical Research Council, Edinburgh, Scotland, United Kingdom
,
Paolo Romano
IST National Cancer Research Institute, Genova, Italy
,
M. Scott Marshall
University of Amsterdam, The Netherlands
,
Andrea Splendiani
Rothamsted Research, UK

Copyright © 2011 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

Sponsors

Ontotext
Corporate Semantic Web: Corporate Semantic Web
BBRC: Biotechnology and Biological Sciences Research Council
NCBO: National Center for BioMedical Ontology
BioMed Central: BioMed Central

In-Cooperation

SIGBio: ACM Special Interest Group on Bioinformatics
IW3C2: International World Wide Web Conference Committee

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 07 December 2011

Permissions

Request permissions for this article.

Request Permissions

Check for updates

Author Tags

Qualifiers

Research-article

Funding Sources

Conference

SWAT4LS '11

Sponsor:

Corporate Semantic Web
BBRC
NCBO
BioMed Central

SWAT4LS '11: 4th Int. Workshop on Semantic Web Applications and Tools for Life Sciences

December 7 - 9, 2011

London, United Kingdom

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

4
Total Citations
View Citations
142
Total Downloads

Downloads (Last 12 months)0
Downloads (Last 6 weeks)0

Reflects downloads up to 29 Sep 2024

Other Metrics

View Author Metrics

Citations

Cited By

Arsić BÐokić-Petrović MSpalević PMilentijević IRančić DŽivanović M(2019)SpecINT: A framework for data integration over cheminformatics and bioinformatics RDF repositoriesSemantic Web10.3233/SW-18032710:4(795-813)Online publication date: 23-May-2019
https://doi.org/10.3233/SW-180327
Sima AMendes de Farias TZbinden EAnisimova MGil MStockinger HStockinger KRobinson-Rechavi MDessimoz C(2019)Enabling semantic queries across federated bioinformatics databasesDatabase10.1093/database/baz1062019Online publication date: 7-Nov-2019
https://doi.org/10.1093/database/baz106
Djokic-Petrovic MCvjetkovic VYang JZivanovic MWild D(2017)PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasetsJournal of Biomedical Semantics10.1186/s13326-017-0151-z8:1Online publication date: 20-Sep-2017
https://doi.org/10.1186/s13326-017-0151-z
Bertel-Paternina LCastillo LIsaza GGaitán-Bustamente A(2014)Towards a Linked Open Data Model for Coffee Functional RelationshipsAdvances in Computational Biology10.1007/978-3-319-01568-2_18(121-126)Online publication date: 2014
https://doi.org/10.1007/978-3-319-01568-2_18

View Options

Get Access

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Full Access

Get this Publication

View options

PDF

View or Download as a PDF file.

eReader

View online with eReader.

Media

Figures

Other

Tables

View Table of Contents