Posts Tagged ‘drug discovery’

Cognition Network Technology: Taking On Cancer By Repositioning Knowledge In A Semantic Network

rsz_defThis week saw Frost & Sullivan award its 2013 Company of the Year to Definiens, a provider of image analysis solutions and data mining solutions for life science, tissue diagnostics, and clinical digital pathology. Definiens’ gaining of the title owes much to its work around tissue datafication that’s leveraging its Definiens Cognition Network Technology, which the company says mimics the human mind’s cognitive powers to reposition knowledge within a semantic network.

“What we do essentially is look at ways to be able to better diagnose cancer and develop therapies,” says Merrilyn Datta, CMO at Definiens. The company looks to extract data from tumor images, historically available as slides from biopsies, datafying the tissues involved to create digital images and then using its Cognition Network Technology to extract all the different relevant objects in that image and correlate them to patient outcomes. “That can be extremely, extremely powerful,” says Datta.

The image analysis technology was developed by Physics Nobel Laureate Gerd Binning, and includes a set of principles aimed at emulating the human mind’s cognitive powers, which are defined by the ability to intuitively aggregate pixels into ‘objects’ and understand the context and relationships between those objects rather than the computer’s normal way of just examining images pixel by pixel. These principles include:  context, which is established and utilized through the technology’s creation of a hierarchical network of pixel clusters representing nested structures within the image; navigation, for supporting efficient navigation inside the network in order to enable specific local processing and addressing of specific contexts; and evolution of the network, in which the individual stages of segmentation and classification are alternated and the structures represented within the network are created and constantly improved in a series of loops, whereby each classification can be enhanced with local context and specific expert knowledge.

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In Search Of Apps To Leverage Public BioMolecular Data In RDF Platform

rsz_rdfpfThe European Molecular Biology Laboratory (EMBL) and the European Bioinformatics Institute (EBI) that is part of Europe’s leading life sciences laboratory this fall launched a new RDF platform hosting data from six of the public database archives it maintains. That includes peer-reviewed and published data, submitted through large-scale experiments, from databases covering genes and gene expression, proteins (with SIB), pathways, samples, biomodels and molecules with drug-like properties. And next week, during a competition at SWAT4LS in Edinburgh, it’s hoping to draw developers with innovative use case ideas for life-sciences apps that can leverage that data to the benefit of bioinformaticians or bench biologists.

“We need developers to build apps on top of the platform, to build apps to pull in data from these and other sources,” explains Andy Jenkinson, Technical Project Manager at EMBL-EBI. “There is the potential using semantic technology to build those apps more rapidly,” he says, as it streamlines integrating biological data, which is a huge challenge given the data’s complexity and variety. And such apps will be a great help for lab scientists who don’t know anything about working directly with RDF data and SPARQL queries.

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New Paper on Semantics and Drug Discovery Research

A new paper has been published entitled “Systems Chemical Biology and the Semantic Web: What They Mean for the Future of Drug Discovery Research.” The paper was written by David Wild, Ying Ding, Amit Sheth, Lee Harland, Eric Gifford, and Michael Lajiness. It can be downloaded for a fee of $27.95. According to the abstract, “Systems chemical biology, the integration of chemistry, biology and computation to generate understanding about the way small molecules affect biological systems as a whole, as well as related fields such as chemogenomics, are central to emerging new paradigms of drug discovery such as drug repurposing and personalized medicine.” Read more

Semantic Drug Discovery with Open PHACTS

A new article reports that a consortium of European organizations has united “to support next generation drug discovery by providing a single view across data sources, bringing the semantic web to drug discovery. The Open PHACTS consortium, funded by the Innovative Medicines Initiative, will reduce the barriers to drug discovery by applying semantic technologies to available data resources, creating an Open Pharmacological Space.” Read more

Dr. Babak Nemati to Lead Development of Life Science Applications with ai-oneâ„¢ Technology

La Jolla CA | Zurich Switzerland June 17 2010 – ai-one inc., a provider of software development technology (SDK) for semantic associative search and semiotic analysis, signed Dr. Nemati and his firm Strategic Intelligence as subject matter experts for life science applications. Dr. Nemati’s firm will provide scientific and industry domain expertise for the development of applications in medical imaging, drug discovery research tools and genomic sequencing…

Advancing Drug Discovery With Research Informatics – PharmExec.com

Advancing Drug Discovery With Research Informatics
PharmExec.com
Using semantic technologies, researchers and program directors can discover relationships that enable them to make better and faster decisions about disease

The Search for New Drugs – GenomeWeb Daily News

The Search for New Drugs
GenomeWeb Daily News
Clearly, the drug discovery process has been modernized since then, with advances including high-content screening and the advent of semantic Web tools,

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Semantic Chemistry


Executive Summary

Chemistry is an important and high-value vertical in the modern world and the "semantification" of chemistry will be crucial for further rapid innovation not only in the discipline itself, but also in related areas such as drug discovery, medicine and materials design. This article provides a short overview over the current technological state of the art in semantic chemistry and also discusses some obstancles, which have, so far, impeded the widespread uptake of chemistry in the domain.

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