Health Care / Life Sciences

Introducing SPARQLGraph, a Platform for Querying Biological Semantic Web Databases

sgDominik Schweiger, Zlatko Trajanoski and Stephan Pabinger recently wrote, “Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way.  Results: SPARQLGraph offers an intuitive drag &drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers.” Read more

Syapse Selects SYSTAP’s Bigdata® as Semantic Database for Precision Medicine Data Platform

Syapse and BigData logosFor immediate release: 8/19/2014

WASHINGTON, D.C. – SYSTAP, LLC. today announced that Syapse, the leading provider of software for enabling precision medicine, has selected Bigdata® as its backend semantic database. Syapse, which launched the Precision Medicine Data Platform in 2011, will use the Bigdata® database as a key element of their semantic platform. The Syapse Precision Medicine Data Platform integrates medical data, omics data, and biomedical knowledge for use in the clinic. Syapse software is delivered as a cloud-based SaaS, enabling access from anywhere with an internet connection, regular software updates and new features, and online collaboration and delivery of results, with minimal IT resources required. Syapse applications comply with HIPAA/HITECH, and data in the Syapse platform are protected according to industry standards.

Syapse’s Precision Medicine Data Platform features a semantic layer that provides powerful data modeling, query, and integration functionality. According to Syapse CTO and Co-Founder, Tony Loeser, Ph.D., “We have adopted SYSTAP’s graph database, Bigdata®, as our RDF store. Bigdata’s exceptional scalability, query performance, and high-availability architecture make it an enterprise-class foundation for our semantic technology stack.”

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Modern Science Must Be Open Science

3515348126_4315caf417Peter Murray-Rust of OpenSource.com recently wrote, “Open is about sharing and collaboration. It’s the idea that ‘we’ is more powerful, more rewarding and fulfilling than ‘I’. I can’t promise jobs, but I do know that openis becoming very big. Governments and funders are pushing the open agenda, even though academics are generally uninterested or seriously self-interested. Some governments and some companies recognize the value of teams; academia and academics generally don’t. The false values of impact factor and the false values of academic publishing mean that open access is a poor reflection of open, or what you may recognize as the open source way.” Read more

Cancer Researcher Using Machine Learning to Fight Cervical Cancer

14239805875_d25785a6f8A recent article in Medical Xpress reports, “Machine learning has been improved by Dr Thomas Wilhelm of the Institute of Food Research, which is strategically funded by the Biotechnology and Biological Sciences Research Council. Instead of developing one model from the training data, his technique involves developing hundreds of diverse models, and applying these to independent, unseen data, and seeing which models work best in their ability to predict outcomes. This avoids ‘overfitting’ of a model to a specific training data set. The new technique can be applied to many different situations, but Dr Wilhelm applied it to epigenetic data on cervical cancer.” Read more

Semantically Aligned Design Principles At Core of Australian Electronic Health Records Platform

site-header-10th-blog-304x200At the upcoming Semantic Technology & Business Conference in San Jose, Dr. Terry Roach, principal of  CAPSICUM Business Architects, and Dr. Dean Allemang, principal consultant at Working Ontologist, will host a session on A Semantic Model for an Electronic Health Record (EHR). It will focus on Australia’s electronic-Health-As-A-Service  (eHaas) national platform for personal electronic health records, provided by the CAPSICUM semantic framework for strategically aligned business architectures.

Roach and Allemang participated in an email interview with The Semantic Web Blog to preview the topic:

The Semantic Web Blog: Can you put the work you are doing on the semantic EHR model in context: How does what Australia is doing with its semantic framework compare with how other countries are approaching EHRs and healthcare information exchange?

Roach and Allemang: The eHaaS project that we have been working on has been an initiative of Telstra, a large, traditional telecommunications provider in Australia. Its Telstra Health division, which is focused on health-related software investments, for the past two years has embarked on a set of strategic investments in the electronic health space. Since early 2013 it has acquired and/or established strategic partnerships with a number of local and international healthcare software providers ranging from hospital information systems [to] mobile health applications [to] remote patient monitoring systems to personal health records [to] integration platforms and health analytics suites.

At the core of these investments is a strategy to develop a platform that captures and maintains diverse health-related interactions in a consolidated lifetime health record for individuals. The eHaaS platform facilitates interoperability and integration of several health service components over a common secure authentication service, data model, infrastructure, and platform. Starting from a base of stand-alone, vertical applications that manage fragmented information across the health spectrum, the eHaaS platform will establish an integrated, continuously improving, shared healthcare data platform that will aggregate information from a number of vertical applications, as well as an external gateway for standards-based eHealth messages, to present a unified picture of an individual’s health care profile and history.

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Healthcare IT Needs Better Search Tools (Enter Semantic Search!)

6322734819_a6c9748c49Megan Williams of Business Solutions recently wrote, “It’s a simple fact of the current state of healthcare that most providers are not using the data they gather via EHRs as best they could. The case of missed technological opportunities is nothing new to healthcare, but in the case of search engines, not employing them to mine existing information could be costing your clients, and their patients, unnecessary tests, wasted time, and missed information that would have been helpful in achieving desired patient outcomes.”

Williams goes on, “A study published by the Journal Of The American College Of Radiology titled “Optimizing Emergency Department Imaging Utilization Through Advanced Health Record Technology” addresses the application of search functions to clinical environments, specifically the emergency department (ED). This department presents special challenges because of the nature of the work involving evaluating complex patients while under time pressure. These challenges are made worse by the incomplete medical history that typically comes with patients who enter the department.”

She adds, “The study covers QPID, which is a programmable health record intelligence system that adds semantic search and knowledge management layers to an EHR system. QPID works as an extension of its data repository, facilitating extraction from it. While most EHR systems do include databases that handle rudimentary data retrieval, QPID allows users to pull data by topic-related ‘packages’ of data and concepts in saved, operable queries that can be used on both structured and unstructured data sources.”

Read more here.

Image: Courtesy Flickr/ Yann Ropars

Health Language Selected by Holy Name Medical Center to Improve Problem and Diagnosis Search

Wolterskluwer_new

July 7, 2014 – Wolters Kluwer Health, a leading global provider of information for healthcare professionals and students, announced today that Holy Name Medical Center (HNMC) has selected Health Language® to improve problem and diagnosis searches within its electronic health record (EHR). HNMC will use the Health Language Workflow-Enhancing Search solution to support encoding its problem lists in SNOMED-CT® for Stage 2 Meaningful Use and the transition to ICD-10. Read more

IBM Watson Group CTO Discusses Cognitive Computing, Content Curation For Healthcare Market

robhighThe role that cognitive computing can play in healthcare was explored last week in this story published at The Semantic Web Blog’s sister site Dataversity.net. That article looked at how Modernizing Medicine is leveraging IBM Watson for its new schEMA tablet app that helps doctors use the wealth of published medical research from highly reputable sources, such as the Journal of the American Medical Association (JAMA) and New England Journal of Medicine, to answer their questions.

Today, we’re complementing that article to further explore such aspects of the health care and cognitive computing connection based on an email conversation with IBM Watson Group CTO Robert High. “IBM Watson is transforming the patient experience and healthcare delivery system by helping physicians make sense of the enormous amount of data generated by an increasingly connected healthcare environment,” High writes.

“Content curation is a critical part of the solution delivery process. Without reputable and reliable sources of medical literature, therapy choices offered by Watson may not have the supporting evidence needed to inform clinicians in the use of those treatments. We work with the top clinicians at our partners to collect their feedback on supporting evidence and cull inappropriate information from their sources.” IBM, along with its solutions partners, works with a variety of content providers based on the relevance of their materials to treatment options, he adds.

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Detecting Pneumonia in ICU Patients with Natural Language Processing

76765412_618a458105Greg Goth of Health Data Management reports, “Researchers at the University of Washington and Microsoft have developed technology that uses natural language processing and machine learning to speed up the diagnosis of pneumonia in ICU patients. Bioinformatics professor Meliha Yetisgen and her colleagues at the university teamed up with Microsoft researcher Lucy Vanderwende on the project, called deCIPHER, using the Microsoft Research Statistical Parsing and Linguistic Analysis Toolkit (Splat).” Read more

Klappo Hopes to Improve Health with Its Semantic Platform for Ingredients

klappo

Jasper Hamill of Forbes recently wrote, “Perhaps the diet sector may soon be looking very emaciated indeed, due to the tasty-looking emerging market in health, wellness and nutrition apps… One of the companies hoping to join in this feeding frenzy is Klappo, a London-based startup which describes itself as a ‘semantic platform for ingredients’. I went to visit this fledgling firm at its Shoreditch headquarters to get a sense of what sort of dish it intends to serve this growing industry. ‘Food is our focus,’ explains the firm’s Italian founder and CEO Massimiliano Del Vita. ‘We want to feed proper data to all the companies who want to innovate and give them access to a huge knowledge base about recipes, products and foods so they can build the best apps possible’.” Read more

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