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ABSTRACT: The wide-scale development of ontologies in the bioinformatics domain facilitates their use in the creation of scientific workflows. To speed up the design of workflows, a Service Suggestion Engine is interfaced to the Galaxy Tool Integration and Workflow Platform. This enables users to ask for suggestions (e.g., what operation should go next) while designing workflows with the Galaxy user interface. The Service Suggest Engine utilizes semantic annotations to suggest appropriate Web service operations to plug into the workflow under design. The enriched Ontology for Biomedical Investigation (OBI) is used as a target for the annotations. The effectiveness of the suggestions provided is evaluated against a consensus of domain experts.
Proceedings of the 7th International Conference on Formal Ontology in Information Systems (FOIS'12), Graz, Austria; 07/2012
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ABSTRACT: Several fields have created ontologies for their subdomains. For example, the biological sciences have developed extensive ontologies such as the Gene Ontology, which is considered a great success. Ontologies could provide similar advantages to the Modeling and Simulation community. They provide a way to establish common vocabularies and capture knowledge about a particular domain with community-wide agreement. Ontologies can support significantly improved (semantic) search and browsing, integration of heterogeneous information sources, and improved knowledge discovery capabilities. This paper discusses the design and development of an ontology for Modeling and Simulation called the Discrete-event Modeling Ontology (DeMO), and it presents prototype applications that demonstrate various uses and benefits that such an ontology may provide to the Modeling and Simulation community.
Simulation 09/2011; 87(9):747-773. · 0.79 Impact Factor
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Simulation. 01/2011; 87:747-773.
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ABSTRACT: This paper presents a semi-automatic Web service composition approach. This approach ranks all available candidate Web service operations based on semantic annotations and suggests service operations to a human designer during the process of Web service composition. The ranking scores are based on data mediation, functionality and formal service specifications. A formal graph model, an IODAG, is defined to formalize an input/output schema of a Web service operation. Three data mediation algorithms are developed to handle the data heterogeneities arising during Web service composition. The data mediation algorithms analyze the schemas of the inputs and outputs of service operations and consider the structures of the schemas. A typed representation for our data mediation approach, which formalizes the data mediation problem as a subtype-checking problem, is presented. An evaluation is performed to study the effectiveness of different data mediation and service suggestion algorithms used to assist designers composing Web services.
Services (SERVICES), 2011 IEEE World Congress on; 01/2011
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01/2010
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Cristina Aurrecoechea,
John Brestelli,
Brian P. Brunk,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Gregory R. Grant,
Omar S. Harb,
Mark Heiges, [......],
Vishal Nayak,
Cary Pennington,
Deborah F. Pinney,
David S. Roos,
Chris Ross,
Ganesh Srinivasamoorthy,
Christian J. Stoeckert Jr,
Ryan Thibodeau,
Charles Treatman,
Haiming Wang
Nucleic Acids Research. 01/2010; 38:415-419.
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Martin Aslett,
Cristina Aurrecoechea,
Matthew Berriman,
John Brestelli,
Brian P. Brunk,
Mark Carrington,
Daniel P. Depledge,
Steve Fischer,
Bindu Gajria,
Xin Gao, [......],
Dhileep Sivam,
Deborah F. Smith,
Ganesh Srinivasamoorthy,
Christian J. Stoeckert Jr,
Sandhya Subramanian,
Ryan Thibodeau,
Adrian Tivey,
Charles Treatman,
Giles Velarde,
Haiming Wang
Nucleic Acids Research. 01/2010; 38:457-462.
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Cristina Aurrecoechea,
John Brestelli,
Brian P Brunk,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Greg Grant,
Omar S Harb,
Mark Heiges, [......],
Vishal Nayak,
Cary Pennington,
Deborah F Pinney,
David S Roos,
Chris Ross,
Ganesh Srinivasamoorthy,
Christian J Stoeckert,
Ryan Thibodeau,
Charles Treatman,
Haiming Wang
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ABSTRACT: EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. The most recent release of EuPathDB includes updates and changes affecting data content, infrastructure and the user interface, improving data access and enhancing the user experience. EuPathDB currently supports more than 80 searches and the recently-implemented 'search strategy' system enables users to construct complex multi-step searches via a graphical interface. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.
Nucleic Acids Research 11/2009; 38(Database issue):D415-9. · 8.03 Impact Factor
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Martin Aslett,
Cristina Aurrecoechea,
Matthew Berriman,
John Brestelli,
Brian P Brunk,
Mark Carrington,
Daniel P Depledge,
Steve Fischer,
Bindu Gajria,
Xin Gao, [......],
Dhileep Sivam,
Deborah F Smith,
Ganesh Srinivasamoorthy,
Christian J Stoeckert,
Sandhya Subramanian,
Ryan Thibodeau,
Adrian Tivey,
Charles Treatman,
Giles Velarde,
Haiming Wang
[show abstract]
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ABSTRACT: TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.
Nucleic Acids Research 10/2009; 38(Database issue):D457-62. · 8.03 Impact Factor
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JITR. 01/2009; 2:42-64.
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Cristina Aurrecoechea,
John Brestelli,
Brian P. Brunk,
Jennifer Dommer,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Gregory R. Grant,
Omar S. Harb, [......],
Wei Li, John A. Miller,
Vishal Nayak,
Cary Pennington,
Deborah F. Pinney,
David S. Roos,
Chris Ross,
Christian J. Stoeckert Jr,
Charles Treatman,
Haiming Wang
Nucleic Acids Research. 01/2009; 37:539-543.
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Cristina Aurrecoechea,
John Brestelli,
Brian P. Brunk,
Jane M. Carlton,
Jennifer Dommer,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Gregory R. Grant, [......],
Hilary G. Morrison,
Vishal Nayak,
Cary Pennington,
Deborah F. Pinney,
David S. Roos,
Chris Ross,
Christian J. Stoeckert Jr,
Steven Sullivan,
Charles Treatman,
Haiming Wang
Nucleic Acids Research. 01/2009; 37:526-530.
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ABSTRACT: As the availability of Web services for the biological domain increases, the need emerges for a Web service composition designer that is easy for biologists to use. Our work focuses on providing biologists and bioinformaticians with an online, semantic Web service composition tool. We adapt a bioinformatics tool called Galaxy, to support semantic Web service composition. A semi-automatic approach for semantic Web service composition is implemented. An easy to use online interface is provided.
Services - I, 2009 World Conference on; 01/2009
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Cristina Aurrecoechea,
John Brestelli,
Brian P Brunk,
Jennifer Dommer,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Greg Grant,
Omar S Harb, [......],
Wei Li, John A Miller,
Vishal Nayak,
Cary Pennington,
Deborah F Pinney,
David S Roos,
Chris Ross,
Christian J Stoeckert,
Charles Treatman,
Haiming Wang
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ABSTRACT: PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.
Nucleic Acids Research 11/2008; 37(Database issue):D539-43. · 8.03 Impact Factor
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Cristina Aurrecoechea,
John Brestelli,
Brian P Brunk,
Jane M Carlton,
Jennifer Dommer,
Steve Fischer,
Bindu Gajria,
Xin Gao,
Alan Gingle,
Greg Grant, [......],
Hilary G Morrison,
Vishal Nayak,
Cary Pennington,
Deborah F Pinney,
David S Roos,
Chris Ross,
Christian J Stoeckert,
Steven Sullivan,
Charles Treatman,
Haiming Wang
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ABSTRACT: GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.
Nucleic Acids Research 10/2008; 37(Database issue):D526-30. · 8.03 Impact Factor
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Reasoning Web, 4th International Summer School 2008, Venice, Italy, September 7-11, 2008, Tutorial Lectures; 01/2008
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Int. J. Web Service Res. 01/2007; 4:104-126.
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International Conference on Bioinformatics & Computational Biology, BIOCOMP 2007, Volume II, June 25-28, 2007, Las Vegas Nevada, USA; 01/2007
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ICEIS 2007 - Proceedings of the Ninth International Conference on Enterprise Information Systems, Volume SAIC, Funchal, Madeira, Portugal, June 12-16, 2007; 01/2007
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Proceedings of the Winter Simulation Conference WSC 2006, Monterey, California, USA, December 3-6, 2006; 01/2006
