Mark D Wilkinson

Publications of Mark D Wilkinson

• The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

  Authors: Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano [......] Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi

  Journal of biomedical semantics. 08/2011; 2:4.

  ABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperabilityABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.

• The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

  Authors: Mark D Wilkinson, Benjamin Vandervalk, Luke McCarthy

  Journal of biomedical semantics. 01/2011; 2(1):8.

  ABSTRACT: The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards andABSTRACT: The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies.

• OWL2Perl: creating Perl modules from OWL class definitions.

  Authors: Edward Kawas, Mark D Wilkinson

  Bioinformatics (Oxford, England). 09/2010; 26(18):2357-8.

  Support for utilizing OWL ontologies in Perl is extremely limited, despite the growing importance of the Semantic Web in Healthcare and Life Sciences. Here, we present a Perl framework that generatesSupport for utilizing OWL ontologies in Perl is extremely limited, despite the growing importance of the Semantic Web in Healthcare and Life Sciences. Here, we present a Perl framework that generates Perl modules based on OWL Class definitions. These modules can then be used by other software applications to create resource description framework (RDF) data compliant with these OWL models. AVAILABILITY: OWL2Perl is available for download from CPAN, under the module name OWL2Perl. It is released under the new BSD license.

• OWL2Perl: creating Perl modules from OWL class definitions.

  Authors: Edward A. Kawas, Mark D. Wilkinson

  Bioinformatics. 01/2010; 26:2357-2358.

• Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins.

  Authors: David Withers, Edward A. Kawas, E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson

  Leveraging Applications of Formal Methods, Verification, and Validation - 4th International Symposium on Leveraging Applications, ISoLA 2010, Heraklion, Crete, Greece, October 18-21, 2010, Proceedings, Part I; 01/2010

• SADI, SHARE, and the in silico scientific method.

  Authors: Mark D Wilkinson, Luke McCarthy, Benjamin Vandervalk, David Withers, Edward Kawas, Soroush Samadian

  BMC bioinformatics. 01/2010; 11 Suppl 12:S7.

  The emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are alreadyThe emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are already becoming first-class objects in "the new way", and serve as explicit, shareable, referenceable representations of how an experiment was done. In turn, Semantic Web Service projects aim to facilitate workflow construction by biological domain-experts such that workflows can be edited, re-purposed, and re-published by non-informaticians. However the aspects of the scientific method relating to explicit discourse, disagreement, and hypothesis generation have remained relatively impervious to new technologies. Here we present SADI and SHARE - a novel Semantic Web Service framework, and a reference implementation of its client libraries. Together, SADI and SHARE allow the semi- or fully-automatic discovery and pipelining of Semantic Web Services in response to ad hoc user queries. The semantic behaviours exhibited by SADI and SHARE extend the functionalities provided by Description Logic Reasoners such that novel assertions can be automatically added to a data-set without logical reasoning, but rather by analytical or annotative services. This behaviour might be applied to achieve the "semantification" of those aspects of the in silico scientific method that are not yet supported by Semantic Web technologies. We support this suggestion using an example in the clinical research space.

• The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

  Authors: Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts [......] Daron M Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A Vos, Mark D Wilkinson, William York, Christian M Zmasek, Kiyoshi Asai, Toshihisa Takagi

  Journal of biomedical semantics. 01/2010; 1(1):8.

  Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands forWeb services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

• Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics.

  Authors: Benjamin M. Good, Joseph T. Tennis, Mark D. Wilkinson

  BMC Bioinformatics. 01/2009; 10:313.

• Interoperability with Moby 1.0--it's better than sharing your toothbrush!

  Authors: Mark D Wilkinson, Martin Senger, Edward Kawas, Richard Bruskiewich, Jerome Gouzy, Celine Noirot, Philippe Bardou, Ambrose Ng, Dirk Haase, Enrique de Andres Saiz [......] Antonio J Pérez, Jose Aldana, M Mar Rojano, Raul Fernandez-Santa Cruz, Ismael Navas, Gary Schiltz, Andrew Farmer, Damian Gessler, Heiko Schoof, Andreas Groscurth

  Briefings in bioinformatics. 06/2008; 9(3):220-31.

  The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analyticalThe BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. The standard, client software, and supporting code libraries are all freely available at http://www.biomoby.org/.

• DataBiNS-Viz: A Web-Based Tool for Visualization of Non-Synonymous SNP Data

  Authors: Fong Chun Chan, Edward A Kawas, Mark D Wilkinson, Scott J Tebbutt

  Journal of Proteomics & Bioinformatics. 01/2008;

  Here we describe DataBiNS-Viz – a visualization and exploration environment for non-synonymous coding single nucleotide polymorphisms (nsSNPs) data gathered by the BioMoby-based DataBiNS workflow.Here we describe DataBiNS-Viz – a visualization and exploration environment for non-synonymous coding single nucleotide polymorphisms (nsSNPs) data gathered by the BioMoby-based DataBiNS workflow. DataBiNSViz enables execution of the DataBiNS workflow on proteins described by KEGG, PubMed, or OMIM identifiers, followed by manual exploration of the integrated structure/function and pathway data for those proteins, with a particular focus on nsSNP data in-context. The tool can be freely accessed at http://bioinfo.icapture.ubc.ca:8090/ DataBiNS (please use the Firefox or Safari web browsers). Examples of the retrieved data are given under the“Help on inputs” option. Detailed documentation can be accessed at: http://bioinfo.icapture.ubc.ca/mywiki/ DataBiNS.

• DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs.

  Authors: Young C Song, Edward Kawas, Ben M Good, Mark D Wilkinson, Scott J Tebbutt

  Bioinformatics (Oxford, England). 04/2007; 23(6):780-2.

  DataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for theDataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow services. The use of an automated BioMoby workflow, rather than manual 'surfing', to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMoby Services enables fine-grained reusing of each service in other workflows, thus reducing the effort required to achieve similar investigations in the future. AVAILABILITY: The workflow is freely available as a Taverna SCUFL XML document at the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml.

• DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs.

  Authors: Young C. Song, Edward A. Kawas, Benjamin M. Good, Mark D. Wilkinson, Scott J. Tebbutt

  Bioinformatics. 01/2007; 23:780-782.

• Tag clouds for summarizing web search results.

  Authors: Byron Yu-Lin Kuo, Thomas Hentrich, Benjamin M. Good, Mark D. Wilkinson

  Proceedings of the 16th International Conference on World Wide Web, WWW 2007, Banff, Alberta, Canada, May 8-12, 2007; 01/2007

• Ontology engineering using volunteer labor.

  Authors: Benjamin M. Good, Mark D. Wilkinson

  Proceedings of the 16th International Conference on World Wide Web, WWW 2007, Banff, Alberta, Canada, May 8-12, 2007; 01/2007

• Using a Novel Data Transformation Technique to Provide the EMBOSS Software Suite as Semantic Web Services.

  Authors: Paul M. K. Gordon, Edward A. Kawas, Mark D. Wilkinson, Christoph W. Sensen

  Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007, Silicon Valley, CA, USA, November 2-4, 2007; 01/2007

• The Life Sciences Semantic Web is full of creeps!

  Authors: Benjamin M Good, Mark D Wilkinson

  Briefings in bioinformatics. 10/2006; 7(3):275-86.

  The Semantic Web for the Life Sciences (SWLS), when realized, will dramatically improve our ability to conduct bioinformatics analyses using the vast and growing stores of web-accessible resources.The Semantic Web for the Life Sciences (SWLS), when realized, will dramatically improve our ability to conduct bioinformatics analyses using the vast and growing stores of web-accessible resources. This ability will be achieved through the widespread acceptance and application of standards for naming, representing, describing and accessing biological information. The W3C-led Semantic Web initiative has established most, if not all, of the standards and technologies needed to achieve a unified, global SWLS. Unfortunately, the bioinformatics community has, thus far, appeared reluctant to fully adopt them. Rather, we are seeing what could be described as 'semantic creep'-timid, piecemeal and ad hoc adoption of parts of standards by groups that should be stridently taking a leadership role for the community. We suggest that, at this point, the primary hindrances to the creation of the SWLS may be social rather than technological in nature, and that, like the original Web, the establishment of the SWLS will depend primarily on the will and participation of its consumers.

• Fast, cheap and out of control: a zero curation model for ontology development.

  Authors: Benjamin M Good, Erin M Tranfield, Poh C Tan, Marlene Shehata, Gurpreet K Singhera, John Gosselink, Elena B Okon, Mark D Wilkinson

  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 02/2006;

  During two days at a conference focused on circulatory and respiratory health, 68 volunteers untrained in knowledge engineering participated in an experimental knowledge capture exercise. TheseDuring two days at a conference focused on circulatory and respiratory health, 68 volunteers untrained in knowledge engineering participated in an experimental knowledge capture exercise. These volunteers created a shared vocabulary of 661 terms, linking these terms to each other and to a pre-existing upper ontology by adding 245 hyponym relationships and 340 synonym relationships. While ontology-building has proved to be an expensive and labor-intensive process using most existing methodologies, the rudimentary ontology constructed in this study was composed in only two days at a cost of only 3 t-shirts, 4 coffee mugs, and one chocolate moose. The protocol used to create and evaluate this ontology involved a targeted, web-based interface. The design and implementation of this protocol is discussed along with quantitative and qualitative assessments of the constructed ontology.

• BioMoby extensions to the Taverna workflow management and enactment software.

  Authors: Edward Kawas, Martin Senger, Mark D Wilkinson

  BMC bioinformatics. 02/2006; 7:523.

  BACKGROUND: As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in theirBACKGROUND: As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface. RESULTS: The exposed BioMoby functionality aids in the design of "sensible" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s) that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate. CONCLUSION: With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional Web Services.

• iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website.

  Authors: Benjamin M Good, Edward A Kawas, Byron Yu-Lin Kuo, Mark D Wilkinson

  BMC bioinformatics. 02/2006; 7:534.

  BACKGROUND: User-scripts are programs stored in Web browsers that can manipulate the content of websites prior to display in the browser. They provide a novel mechanism by which users canBACKGROUND: User-scripts are programs stored in Web browsers that can manipulate the content of websites prior to display in the browser. They provide a novel mechanism by which users can conveniently gain increased control over the content and the display of the information presented to them on the Web. As the Web is the primary medium by which scientists retrieve biological information, any improvements in the mechanisms that govern the utility or accessibility of this information may have profound effects. GreaseMonkey is a Mozilla Firefox extension that facilitates the development and deployment of user-scripts for the Firefox web-browser. We utilize this to enhance the content and the presentation of the iHOP (information Hyperlinked Over Proteins) website. RESULTS: The iHOPerator is a GreaseMonkey user-script that augments the gene-centred pages on iHOP by providing a compact, configurable visualization of the defining information for each gene and by enabling additional data, such as biochemical pathway diagrams, to be collected automatically from third party resources and displayed in the same browsing context. CONCLUSION: This open-source script provides an extension to the iHOP website, demonstrating how user-scripts can personalize and enhance the Web browsing experience in a relevant biological setting. The novel, user-driven controls over the content and the display of Web resources made possible by user-scripts, such as the iHOPerator, herald the beginning of a transition from a resource-centric to a user-centric Web experience. We believe that this transition is a necessary step in the development of Web technology that will eventually result in profound improvements in the way life scientists interact with information.

• Applying Semantic Web Services to

  Authors: Phillip Lord, Sean Bechhofer, Mark D Wilkinson, Damian Gessler, Carole Goble, Lincoln Stein

  08/2004;

  We have seen an increasing amount of interest in the application of Semantic Web technologies to Web services. The aim is to support automated discovery and composition of the services allowingWe have seen an increasing amount of interest in the application of Semantic Web technologies to Web services. The aim is to support automated discovery and composition of the services allowing seamless and transparent interoperability. In this paper we discuss three projects that are applying such technologies to bioinformatics: MOBY-Services and Semantic-MOBY. Through an examination of the di#erences and similarities between the solutions produced, we highlight some of the practical di#culties in developing Semantic Web services and suggest that the experiences with these projects have implications for the development of Semantic Web services as a whole.