Health Care / Life Sciences

Velichka Dimitrova of the Open Knowledge Foundation has called attention to an open data project that is trying to reduce animal testing by improving collaborative scientific research. She writes, “Effectopedia is a project of the International QSAR Foundation. Effectopedia itself is an open knowledge aggregation and collaboration tool that provides a means of describing adverse outcome pathways (AOPs) in an encyclopedic manner. Effectopedia defines internal organizational space which helps scientist with different backgrounds to know exactly where their knowledge belongs and aids them in identifying both the larger context of their research and the individual experts who might be actively interested in it.” Read more

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A new report from the Institute for Global Futures, Global Futures Forecast 2012, lays out the top trends that it believes will shape the coming year. It’s looking ahead to a future that it says may be characterized by complex trends, accelerated change, hyper-competition, disruption, innovation and uncertainty, and that will demand a new way of operating.

It recommends continuing investment in innovation in the U.S., as that is the central driver of US and global competitive advantage, and a requirement for achieving more stable growth. And it advises that organizations’ leaders need to do a better job becoming long-range thinkers given that the accelerated pace of change means that the future is coming at us faster than ever before, and with change comes risk.

What do such things have to do with the Semantic Web and semantic technologies? Apparently, quite a lot.

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Digital Reasoning, developers of the Synthesys platform for discovering the meaning in unstructured data at scale, has on the roadmap exposing to and packaging up for its customers a simplified version of its internal technology for teaching the system new grammatical structures so that it can quickly understand custom or otherwise specific data sets.

The company has quickly added support for new languages such as Arabic, traditional and simplified Chinese, Farsi and Urdu (with more languages on the way) to Synthesys using the tool. The tool gets the software up to speed on each one in just a few weeks by teaching it the grammatical structure and then letting it go off and figure out what the words mean for its work of transforming unstructured (and structured) data into the underlying facts, entities, relationships, and associated terms.

“In the same way we teach it languages you may have a data set that is highly scientific, for example, and this tool essentially makes it easier for our customers to make Synthesys even more accurate for that specific set of data,” says Dave Danielson, VP of marketing.

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The Semantic Web Journal has issued a call for papers on the topic of linked data for health care and the life sciences. According to the post, “Due to their descriptive nature and ongoing need to integrate large amounts of heterogeneous data, the areas of health care and the life sciences have long been used as a test-bed for the feasibility of Semantic Web technologies. Large scale integration projects like Bio2RDF, Chem2Bio2RDF, and the W3C HCLS’s (Health Care and Life Sciences) Linked Open Drug Data (LODD) have not only significantly contributed to the development of the Semantic Web’s Linked Data effort, but have also made social and technical contributions towards data integration, knowledge management, and knowledge discovery.” Read more

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

Researchers from the University Hospitals of Geneva, Switzerland, have published a new paper entitled Interoperability Driven Integration of Biomedical Data Sources. The paper, published in Studies in Health Technology and Informatics, introduces “a data integration methodology that promotes technical, syntactic and semantic interoperability for operational healthcare data sources. ETL processes provide access to different operational databases at the technical level.” Read more

Elsevier has acquired Ariadne Genomics, a company providing pathway analysis tools and semantic technologies to life science researchers. According to Alexander van Boetzelaer of Elsevier, “Ariadne Genomics’ pathway analysis tools and semantic technologies integrate research findings from across multiple content sources providing a deeper understanding of biological pathways and disease progression. Ariadne’s products improve research productivity and outcomes for life science researchers by delivering new insights for potential interventions, therapies and cures… Ariadne brings to Elsevier an information offering in the biology domain and a passionate and dedicated team of life science professionals. Ariadne’s team and offerings are a powerful complement to our chemistry, pre-clinical and clinical workflow solutions.” Read more

Bioinformatics software provider IO Informatics recently released its free Knowledge Explorer Personal Edition. Version 3.6 of the Personal Edition can handle most of what Knowledge Explorer Professional 3.6, launched in October, can, but it does all its work in memory without direct connectivity to a back-end database.

“In particular, a lot of the strengths of Knowledge Explorer have to do with modeling data as RDF and then testing queries, visualizing and browsing the data to see that you have the ontologies and data mappings you need for your integration and application requirements.” says Robert Stanley, IO Informatics president and CEO. The Personal version is aimed at academic experts focused on data integration and semantic data modeling, as well as personal power users in life sciences and other data-intensive industries, or anyone who wants to learn the tool in anticipation of leveraging their enterprise data sets for collaboration and integration projects.

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WebLib LLC has released NLMplus, “a semantic search and knowledge discovery application that utilizes a variety of semantic resources and natural language processing tools to produce improved search results from the vast collection of biomedical data and services of the National Library of Medicine (NLM).”

According to the article, “The NLMplus app combines a number of leading-edge semantic knowledge resources and technologies, such as a biomedical knowledge base, a semantic search engine, a distributed search engine, and a variety of smart content analysis and discovery services. Read more

West Shell, CEO of Healthline is turning to the semantic web to compete with internet health giants like WebMD. Wade Roush reports, “Shell says 170 million Americans turn to the Internet every month for help managing their health. And Healthline, the 130-employee company he’s been leading since 2005, captures a huge portion of them: roughly 100 million per month, spread across the many Web properties, such as Yahoo Health, AARP.com, and DoctorOz.com, that use the company’s search tools and medical content. It’s one of the three largest U.S. providers of consumer health information on the Web, the others being WebMD and Everyday Health.” Read more