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TalksThis page contains links to the slides of some talks I have presented. Note that these are slides, not notes. You are welcomed to use these slides but you must indicate where they come from.
In Spanish: Consultas federadas basadas en ontologías sobre datos de cáncer
Presentación en el Departamento de Computación; Facultad de Ciencias Exactas, Ingeniería y Agrimensura; Universidad Nacional de Rosario; Argentina; 2 de diciembre 2011.
GIATE and ConQueSt
Invited talk in the NCI/NCRI Joint Conference 2011. Tools and Technologies Theme. 13th-14th June 2011.
Ontology-based queries over cancer data
Presented at the EBI Industry Workshop on Biomedical Data and Model Interoperability, 28-29 March 2011, Hinxton, UK
Ontology-based queries over cancer data.
Alejandra González Beltrán, joint work with Ben Tagger and Anthony Finkelstein
Presented at the 3rd International Workshop on Semantic Web Applications and Tools for Life Sciences on December 10, 2010 in Berlin, Germany.
Best paper award
[Show pdf];[Show paper]; [Show Abstract ]
The ever-increasing amount of data in biomedical research, and in cancer research in particular, needs to be managed to support efficient data access, exchange and integration. Existing software infrastructures, such caGrid, support access to distributed information annotated with a domain ontology. However, caGrid's current querying functionality depends on the structure of individual data resources without exploiting the semantic annotations. In this paper, we present the design and development of an ontology-based querying functionality that consists of: the generation of OWL2 ontologies from the underlying data resources’ metadata and a query rewriting and translation process based on reasoning, which converts a query at the domain ontology level into queries at the software infrastructure level. We present a detailed analysis of our approach as well as an extensive performance evaluation. While the implementation and evaluation was performed for the caGrid infrastructure, the approach could be applicable to other model and metadata-driven environments for data sharing.
Guidelines for Information About Therapy Experiments (GIATE)
Alejandra González Beltrán, joint work with May Yong and Richard Begent
Presented at the 2nd MIBBI Workshop on December 1st-2nd, 2010 in Ruedesheim/Rhein, Germany.
[Show slides]; [Show Abstract ]
This presentation introduces GIATE, its scope, level of implementation, status, contributors and funding.
Exposing caGrid data services as Linked Data.
Joshua Phillips and Alejandra González Beltrán and Jyoti Pathak
Presented at the Joint Architecture and VCDE Workspace F2F Meeting on October 20-22, 2009 in Atlanta, USA.
[Show pdf]; [Show Abstract ]
The goal of the Linked Data community is to publish open data sets on the Web using Resource Description Framework (RDF) and create links among those data sets, also using RDF, thereby creating a Web of machine processable data. The Linked Data approach has recently gained momentum as institutions like the U.S. Library of Congress have begun to publish their data in this way. Within the health care and life sciences community, the Linked Open Drug Data (LODD) and Bio2RDF projects have published data sets that link clinical trials, drugs, gene expression and many more different types of heterogeneous data. As of May 2009, there are at least 4.7 billion records published as linked data on the Web. We feel there is great potential for benefit to the cancer research community by publishing caBIG data sets as linked data. These benefits include enabling researchers to easily browse relationships among data sets and to formulate queries that consider vast amounts of data from multiple omics modalities, or enabling semantic search engines to index cancer research data sets and provide semantics-driven search capabilities. In this presentation, we will describe how recent work on using Semantic Web technologies for data integration in caBIG and the caGrid Identifier Framework could be leveraged to publish caBIG data sets as linked data. Our initial technical approach attempts to use code artifacts produced by the caCORE SDK to create a data service plug-in that would provide Linked Data and SPARQL interfaces for caGrid data services have been constructed using the SDK. Our goal is to make existing caGrid data services become Linked Data-enabled without requiring any re-engineering by the data source providers.
Towards ontology-driven querying and integration of cancer-research data.
Alejandra González Beltrán and Joshua Phillips
Presented at the NCI/NCRI Joint Conference - Biomedical Informatics Without Borders: From Collaboration to Implementation on September 10-11, 2009 in London, UK.
[Show pdf];[Listen to podcast] [Show Abstract ]
Biomedical data sets are usually presented in diverse formats, stored in distributed locations and expressed using different terminologies. To share these data sets and to use them effectively, it is crucial that data owners provide unambiguous meaning through semantic annotations. The caBIG® initiative offers a service-based infrastructure - caGrid - and metadata services supporting sharing and discovery of semantically-rich distributed data sources.
The current caGrid infrastructure allows for discovery and navigation of data sets, their structure, syntax and semantics. However, more sophisticated functionality, such as queries based on the relationships between entities or data integration based on their semantic descriptions, is currently not supported.
In this talk, we will present the collaborative efforts between the National Cancer Research Institute Informatics Initiative and the National Cancer Institute caBIG® programme towards supporting ontology-driven querying and data integration of cancer-research data. The proposed approach combines Semantic Web technologies with the caGrid infrastructure.
Domain Concept-Based Queries for Cancer Research Data Sources.
Presented at the 22nd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2009) on August 3-4, 2009 in Albuquerque, NM, USA.
Semantic concept-based queries in ONIX - caGrid case.
Presented at the caBIG Architecture/Vocabularies and Common Data Elements Face-to-Face Meeting that was held on May 11-13, 2009 in Cambridge, MA, USA.
ONIX Semantic Federated Query Infrastructure - Data Service Ontologies Engineering.
Presented at the caBIG Architecture/Vocabularies and Common Data Elements Face-to-Face Meeting that was held on October 27-29, 2008 in Evanston, Illinois, USA.
ONIX Semantic Federated Query Infrastructure.
Biomedical Informatics Without Borders: Enabling Collaboration to Strengthen Research and Care. September 2-3, 2008. Bethesda, MD, USA.
More details coming soon!