<b>Copyright information:</b>Taken from "AlzPharm: integration of neurodegeneration data using RDF"http://www.biomedcentral.com/1471-2105/8/S3/S4BMC Bioinformatics 2007;8(Suppl 3):S4-S4.Published online 9 May... more
<b>Copyright information:</b>Taken from "AlzPharm: integration of neurodegeneration data using RDF"http://www.biomedcentral.com/1471-2105/8/S3/S4BMC Bioinformatics 2007;8(Suppl 3):S4-S4.Published online 9 May 2007PMCID:PMC1892101.ered Database.
Systems biology is frequently defined as the study of all of the elements in a biological system and their relationship to one another in response to perturbation. Advances in science and technology are enabling the development of this... more
Systems biology is frequently defined as the study of all of the elements in a biological system and their relationship to one another in response to perturbation. Advances in science and technology are enabling the development of this emerging and cross-disciplinary field by allowing researchers to explore how biological components function as a network in cells, tissues and organisms. Recently, pharmaceutical companies have begun to embrace systems approaches in an effort to better understand physiology, pathogenic processes and pharmacological responses. This review focuses on recent advances within three core areas of systems biology: data collection, data analysis, and the integration and sharing of data.
Research Interests:
There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical trials. These data are typically... more
There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical trials. These data are typically not connected together, which reduces the ease with which insights can be gained. Linking Open Drug Data (LODD) is a task force within the World Wide Web Consortium’s (W3C) Health Care and Life Sciences Interest Group (HCLS IG). LODD has surveyed publicly available data about drugs, created Linked Data representations of the data sets, and identified interesting scientific and business questions that can be answered once the data sets are connected. The task force provides recommendations for the best practices of exposing data in a Linked Data representation. In this paper, we present past and ongoing work of LODD and discuss the growing importance of Linked Data as a foundation for pharmaceutical R&D data sharing. Findings Pharmaceutical research...
The Semantic Web for Health Care and Life Sciences Workshop will be held in Beijing, China, on April 22, 2008. The goal of the workshop is to foster the development and advancement in the use of Semantic Web technologies to facilitate... more
The Semantic Web for Health Care and Life Sciences Workshop will be held in Beijing, China, on April 22, 2008. The goal of the workshop is to foster the development and advancement in the use of Semantic Web technologies to facilitate collaboration, research and development, and innovation adoption in the domains of Health Care and Life Sciences, We also encourage the participation of all research communities in this event, with enhanced participation from Asia due to the location of the event. The workshop consists of two invited keynote talks, eight peerreviewed presentations, and one panel discussion.
doi:10.1186/1471-2105-8-S3-S4 This article is available from:
Research Interests:
textabstractBackground A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical... more
textabstractBackground A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of are...
Research Interests:
Logic based systems typically use a collection of Condition -> Action rules to encode the behaviour and response of the system to a specific set of events. These systems function by having a working memory of facts. By adding, removing... more
Logic based systems typically use a collection of Condition -> Action rules to encode the behaviour and response of the system to a specific set of events. These systems function by having a working memory of facts. By adding, removing or changing facts in the working memory, the rules system can see which (if any) rules need triggering. If the effect of a rule changes a state in the working memory then rules will be re-evaluated.
Research Interests:
Presently, neuroscientists have access to a wide range of neuroscience databases through the Internet. However, most of these databases are neither integrated nor interoperating, which creates a barrier in answering complex neuroscience... more
Presently, neuroscientists have access to a wide range of neuroscience databases through the Internet. However, most of these databases are neither integrated nor interoperating, which creates a barrier in answering complex neuroscience research questions. Agreement upon a domain ontology is typically useful for querying diverse data sets, but is insufficient for integrating neuroscience data spanning multiple domains. To this end, eNeuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of diverse types and levels of neuroscience data. We present a Semantic Web approach to building this e-Neuroscience data integration framework, which involves using RDF as a standard data model to facilitate representation and integration of data. We have converted a subset of the BrainPharm database into RDF and integrated it with SWAN hypothesis and publication data extracted from Alzforum and made available in RDF as the upp...
Research Interests:
Research Interests:
New technologies have been developed in the life sciences that allow researchers to study biological systems in rich detail. These advances have resulted in an abundance of data that describes the relations between the fundamental... more
New technologies have been developed in the life sciences that allow researchers to study biological systems in rich detail. These advances have resulted in an abundance of data that describes the relations between the fundamental components of biological systems, such as genes, proteins, and metabolites. The network of relations between the components holds insights as to how biological systems function, and consequently can help researchers understand the mechanisms behind disease. Biological networks are commonly managed and analyzed in a graph representation. Oracle Database 10g has the functionality to model data as a graph, and thereby has the potential to greatly facilitate research. In this paper we describe the Oracle implementation and provide case studies from the life sciences.
Research Interests:
Abstract. Motivation: To support translational research and external innovation, we are evaluating the potential of the Semantic Web to integrate data from discovery research through to the clinical environment. This paper describes our... more
Abstract. Motivation: To support translational research and external innovation, we are evaluating the potential of the Semantic Web to integrate data from discovery research through to the clinical environment. This paper describes our experiences in mapping relational databases to RDF for data sets relating to neuroscience. Implementation: We describe how classes were identified in the original data sets and mapped to RDF, and how connections were made to public ontologies. Special attention was paid to the mapping of experimental measures to RDF and how it was impacted by the relational schemata. Results: Mapping from relational databases to RDF can benefit from techniques borrowed from dimensional modeling. However, current tools like D2R are still evolving. Nevertheless, mapping data in RDF, if done properly and consistently, facilitates data integration efforts. 1.
Abstract Performing sequence homology searches against DNA or protein sequence databases is an essential bioinformatics task. Past research efforts have been primarily concerned with the development of sensitive and fast sequence homology... more
Abstract Performing sequence homology searches against DNA or protein sequence databases is an essential bioinformatics task. Past research efforts have been primarily concerned with the development of sensitive and fast sequence homology search algorithms outside of the relational database management system (RDBMS). Oracle Data Mining (ODM) BLAST enables BLAST to be performed in a RDBMS. ODM BLAST relieves the burden of moving data out of the RDBMS, eliminates the need to parse data files, and ...
Research Interests:
Research Interests:
The recent trend towards enhanced functionality on the Web through rich internet applications has the ability to fundamentally change how people interact with each other. The most commonly used new applications include user-generated... more
The recent trend towards enhanced functionality on the Web through rich internet applications has the ability to fundamentally change how people interact with each other. The most commonly used new applications include user-generated content, collaboration tools, shared bookmarks and social networks. Once the power of the Semantic Web is added to this environment, it will enable the currently isolated applications
Research Interests:
... http://www.w3.org/TR/2004/REC-xml-20040204/ 7. Cheung, K., H., Yip, K., Y., Smith, A., deKnikker, R., Masiar A., Gerstein, M. (2005) YeastHub: a semantic web use case for integrating data in the life sciences domain. Bioin-formatics... more
... http://www.w3.org/TR/2004/REC-xml-20040204/ 7. Cheung, K., H., Yip, K., Y., Smith, A., deKnikker, R., Masiar A., Gerstein, M. (2005) YeastHub: a semantic web use case for integrating data in the life sciences domain. Bioin-formatics 21, i85-i96. ...
Research Interests:
Systems biology is frequently defined as the study of all of the elements in a biological system and their relationship to one another in response to perturbation. Advances in science and technology are enabling the development of this... more
Systems biology is frequently defined as the study of all of the elements in a biological system and their relationship to one another in response to perturbation. Advances in science and technology are enabling the development of this emerging and cross-disciplinary field by allowing researchers to explore how biological components function as a network in cells, tissues and organisms. Recently, pharmaceutical companies have begun to embrace systems approaches in an effort to better understand physiology, pathogenic processes and pharmacological responses. This review focuses on recent advances within three core areas of systems biology: data collection, data analysis, and the integration and sharing of data.
Research Interests:
... identify the candidates they believe would be the best match for the role, rather than having to engage in a back-and-forth dialogue about ... Going forward there are many reasons why the hiring company may decide to extend its... more
... identify the candidates they believe would be the best match for the role, rather than having to engage in a back-and-forth dialogue about ... Going forward there are many reasons why the hiring company may decide to extend its Semantic Web infrastructure to include OWL. ...
Research Interests:
New technologies have been developed in the life sciences that allow researchers to study biological sys- tems in rich detail. These advances have resulted in an abundance of data that describes the relations between the fundamental... more
New technologies have been developed in the life sciences that allow researchers to study biological sys- tems in rich detail. These advances have resulted in an abundance of data that describes the relations between the fundamental components of biological systems, such as genes, proteins, and metabolites. The network of relations between the components holds insights as to how biological systems
Research Interests:
Research Interests: Kinetics, Plant Biology, Phylogeny, Sequence alignment, Female, and 14 moreAnimals, Plant, Polymerase Chain Reaction, Membrane transport proteins, Molecular cloning, Phenylalanine, Seeds, Xenopus laevis, Protein Conformation, Amino Acid Sequence, Oocytes, Recombinant Proteins, PLANT PROTEINS, and Molecular Sequence Data
... is becoming increasingly widespread, one barrier to the adoption of such models has been ... However, IP is actually the currency of open innovation, and open innovation relies on the fact ... Proactive IP management looks to identify... more
... is becoming increasingly widespread, one barrier to the adoption of such models has been ... However, IP is actually the currency of open innovation, and open innovation relies on the fact ... Proactive IP management looks to identify opportunities for sharing IP to create real value. ...
Research Interests:
Research Interests:
ABSTRACT
Research Interests:
Research Interests: Semantic Web and Ruleml
The prototype we describe is a biomedical knowledge base, constructed for a demonstration at Banff WWW2007 , that integrates 15 distinct data sources using currently available Semantic Web technologies such as the W3C standard Web... more
The prototype we describe is a biomedical knowledge base, constructed for a demonstration at Banff WWW2007 , that integrates 15 distinct data sources using currently available Semantic Web technologies such as the W3C standard Web Ontology Language [OWL] and Resource Description Framework [RDF]. This report outlines which resources were integrated, how the knowledge base was constructed using free and open source triple store technology, how it can be queried using the W3C Recommended RDF query language SPARQL [SPARQL], and what resources and inferences are involved in answering complex queries. While the utility of the knowledge base is illustrated by identifying a set of genes involved in Alzheimer's Disease, the approach described here can be applied to any use case that integrates data from multiple domains.
The Resource Description Framework (RDF) is a language for representing information about resources in the World Wide Web. To describe information in RDF, statements are essentially broken into triples: {subject/resource,... more
The Resource Description Framework (RDF) is a language for representing information about resources in the World Wide Web. To describe information in RDF, statements are essentially broken into triples: {subject/resource, predicate/property, object/value}. Each triple is a ...
As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life... more
As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html.
Research Interests:
Finding the most relevant data sources for answering translational research questions represents a significant challenge in a global and highly decentralized research organization. This challenge is only likely to increase as more data... more
Finding the most relevant data sources for answering translational research questions represents a significant challenge in a global and highly decentralized research organization. This challenge is only likely to increase as more data becomes available from external collaborations. This paper presents an approach to enabling scientists to find data source of interest, and to then query and visualize the data. The solution consists of knowIT, a semantic wiki that provides a foundation for capturing explicit knowledge about sources of data in a collaborative fashion. As the metadata about the data sources is exposed as Resource Description Framework (RDF), knowIT is able to provide knowledge of the biomedical resources to other applications as part of a Linked Data framework. Illustrations are provided as to how the solution can be used for search and visualization of the biomedical data landscape.
Research Interests:
Performing sequence homology searches against DNA or protein sequence databases is an essential bioinformatics task. Past research efforts have been primarily concerned with the development of sen- sitive and fast sequence homology search... more
Performing sequence homology searches against DNA or protein sequence databases is an essential bioinformatics task. Past research efforts have been primarily concerned with the development of sen- sitive and fast sequence homology search algorithms outside of the relational database management system (RDBMS). Oracle Data Mining (ODM) BLAST enables BLAST to be performed in a RDBMS. ODM BLAST relieves the burden
Research Interests:
There are many daunting challenges for companies who wish to bring novel drugs to market. The information complexity around potential drug targets has increased greatly with the introduction of microarrays, high-throughput screening and... more
There are many daunting challenges for companies who wish to bring novel drugs to market. The information complexity around potential drug targets has increased greatly with the introduction of microarrays, high-throughput screening and other technological advances over the past decade, but has not yet fundamentally increased our understanding of how to modify a disease with pharmaceuticals. Further, the bar has been raised in getting a successful drug to market as just being new is no longer enough: the drug must demonstrate improved performance compared with the ever increasing generic pharmacopeia to gain support from payers and government authorities. In addition, partly as a consequence of a climate of concern regarding the safety of drugs, regulatory authorities have approved fewer new molecular entities compared to historical norms over the past few years. To overcome these challenges, the pharmaceutical industry must fully embrace information technology to bring better under...
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
A composition for detecting the presence and concentration of a substance, such as uranyl, comprises an organohalide covalently bonded to an indicator for said substance. The composition has at least one active OH site for forming a... more
A composition for detecting the presence and concentration of a substance, such as uranyl, comprises an organohalide covalently bonded to an indicator for said substance. The composition has at least one active OH site for forming a complex with the substance to be detected. The composition is made by reacting equimolar amounts of the indicator and the organohalide in a polar organic solvent. The absorbance spectrum of the composition-uranyl complex is shifted with respect to the absorbance spectrum of the indicator-uranyl complex, to provide better spectral resolution for detecting uranyl. 6 figs.
Research Interests:
Research Interests:
Research Interests:
There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical trials. These data are typically... more
There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical trials. These data are typically not connected together, which reduces the ease with which insights can be gained. Linking Open Drug Data (LODD) is a task force within the World Wide Web Consortium's (W3C) Health Care and Life Sciences Interest Group (HCLS IG). LODD has surveyed publicly available data about drugs, created Linked Data representations of the data sets, and identified interesting scientific and business questions that can be answered once the data sets are connected. The task force provides recommendations for the best practices of exposing data in a Linked Data representation. In this paper, we present past and ongoing work of LODD and discuss the growing importance of Linked Data as a foundation for pharmaceutical R&D data sharing.
Research Interests:
There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical trials. These data are typically... more
There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical trials. These data are typically not connected together, which reduces the ease with which insights can be gained. Linking Open Drug Data (LODD) is a task force within the World Wide Web Consortium's (W3C) Health Care and Life Sciences Interest Group (HCLS IG). LODD has surveyed publicly available data about drugs, created Linked Data representations of the data sets, and identified interesting scientific and business questions that can be answered once the data sets are connected. The task force provides recommendations for the best practices of exposing data in a Linked Data representation. In this paper, we present past and ongoing work of LODD and discuss the growing importance of Linked Data as a foundation for pharmaceutical R&D data sharing.