Biodash: A Semantic Web Dashboard for Drug Development

Neumann, Eric; Quan, Dennis

doi:10.1142/9789812701626_0017

Cited by 43 publications

(30 citation statements)

References 7 publications

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“…Philippi and Köhler [24], [25] discuss the many problems impeding the semantic integration of these life science databases and ontologies. Asking the question, " A life science semantic web: Are we there yet?," Neumann [26] and Neumann and Quan [27] provide another perspective featuring the Life Science Identifier (LSID) proposed standard [28], the Haystack semantic browser [29], and other initiatives such as the W3C Semantic web Health Care and Life Sciences Interest Group [30]. These influences have shaped the development of his prototype semantic web application BioDash [27] for drug discovery in pharmacogenomics and personalized medicine.…”

Section: Life Sciences Web and Gridmentioning

confidence: 99%

DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing

Taswell

2008

IEEE Trans. Inform. Technol. Biomed.

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Abstract-The semantic web remains in the early stages of development. It has not yet achieved the goals envisioned by its founders as a pervasive web of distributed knowledge and intelligence. Success will be attained when a dynamic synergism can be created between people and a sufficient number of infrastructure systems and tools for the semantic web in analogy with those for the original web. The domain name system (DNS), web browsers, and the benefits of publishing web pages motivated many people to register domain names and publish web sites on the original web. An analogous resource label system, semantic search applications, and the benefits of collaborative semantic networks will motivate people to register resource labels and publish resource descriptions on the semantic web. The Domain Ontology Oriented Resource System (DOORS) and Problem Oriented Registry of Tags and Labels (PORTAL) are proposed as infrastructure systems for resource metadata within a paradigm that can serve as a bridge between the original web and the semantic web. Registers domain names while DNS publishes domain addresses with mapping of names to addresses for the original web. Analogously, POR-TAL registers resource labels and tags while DOORS publishes resource locations and descriptions with mapping of labels to locations for the semantic web. BioPORT is proposed as a prototype PORTAL registry specific for the problem domain of biomedical computing.

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Section: Life Sciences Web and Gridmentioning

confidence: 99%

DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing

Taswell

2008

IEEE Trans. Inform. Technol. Biomed.

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“…While some of these graph based frameworks can be found in commercial products such as VTT (Gopalacharyulu, et al, 2005), ChipInspector / Bibliosphere Pathway Edition (from Genomatix), Phylosopher (from Genedata), ExPlain (from BIOBASE) and PathwayStudio (Nikitin, et al, 2003) (from Ariadne Genomics), some non-commercial systems are also available free of charge such as PathSys (Baitaluk, et al, 2006), BN++ (Küntzer, et al, 2006) and the ONDEX system (Köhler, et al, 2006;. Several projects have also followed a similar approach using the principles established for the semantic web such as SWEDI (Post, et al, 2007) or BioDASH (Neumann and Quan, 2006).…”

Section: Approaches To Data Integrationmentioning

confidence: 99%

Graph-based sequence annotation using a data integration approach

Pesch

Lysenko

Hindle

et al. 2008

Journal of Integrative Bioinformatics

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SummaryThe automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database AraCyc) which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation. The methods and algorithms presented in this publication are an integral part of the ON-DEX system which is freely available from http://ondex.sf.net/.

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“…Their approach uses ontologies and web services; however, this approach does not propose the use of rules to supplement domain knowledge to compensate for the limitations of OWL. BioDASH [2] is a Semantic Web prototype of a Drug Development Dashboard that associates disease, compounds, drug progression stages, molecular biology, and pathway knowledge for a team of users. This work mentions use of rule-based processing using off-the-shelf RDF inference engines, and the use of rules to filter and merge data.…”

Section: Related Workmentioning

confidence: 99%

Active Semantic Electronic Medical Record

Sheth

Agrawal

Lathem

et al. 2006

Lecture Notes in Computer Science

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Abstract. The healthcare industry is rapidly advancing towards the widespread use of electronic medical records systems to manage the increasingly large amount of patient data and reduce medical errors. In addition to patient data there is a large amount of data describing procedures, treatments, diagnoses, drugs, insurance plans, coverage, formularies and the relationships between these data sets. While practices have benefited from the use of EMRs, infusing these essential programs with rich domain knowledge and rules can greatly enhance their performance and ability to support clinical decisions. Active Semantic Electronic Medical Record (ASEMR) application discussed here uses Semantic Web technologies to reduce medical errors, improve physician efficiency with accurate completion of patient charts, improve patient safety and satisfaction in medical practice, and improve billing due to more accurate coding. This results in practice efficiency and growth by enabling physicians to see more patients with improved care. ASEMR has been deployed and in daily use for managing all patient records at the Athens Heart Center since December 2005. This showcases an application of Semantic Web in health care, especially small clinics.

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Biodash: A Semantic Web Dashboard for Drug Development

Cited by 43 publications

References 7 publications

DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing

DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing

Graph-based sequence annotation using a data integration approach

Active Semantic Electronic Medical Record

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