Posts Tagged ‘SPARQL’

Retrieving and Using Taxonomy Data from DBpedia

DBpedia logo on a halloween jack-o-lanternDBpedia, as described in the recent semanticweb.com article DBpedia 2014 Announced, is “a crowd-sourced community effort to extract structured information from Wikipedia and make this information available on the Web.” It currently has over 3 billion triples (that is, facts stored using the W3C standard RDF data model) available for use by applications, making it a cornerstone of the semantic web.

A surprising amount of this data is expressed using the SKOS vocabulary, the W3C standard model for taxonomies used by the Library of Congress, the New York Times, and many other organizations to publish their taxonomies and subject headers. (semanticweb.com has covered SKOS many times in the past.) DBpedia has data about over a million SKOS concepts, arranged hierarchically and ready for you to pull down with simple queries so that you can use them in your RDF applications to add value to your own content and other data.

Where is this taxonomy data in DBpedia?

Many people think of DBpedia as mostly storing the fielded “infobox” information that you see in the gray boxes on the right side of Wikipedia pages—for example, the names of the founders and the net income figures that you see on the right side of the Wikipedia page for IBM. If you scroll to the bottom of that page, you’ll also see the categories that have been assigned to IBM in Wikipedia such as “Companies listed on the New York Stock Exchange” and “Computer hardware companies.” The Wikipedia page for Computer hardware companies lists companies that fall into this category, as well as two other interesting sets of information: subcategories (or, in taxonomist parlance, narrower categories) such as “Computer storage companies” and “Fabless semiconductor companies,” and then, at the bottom of the page, categories that are broader than “Computer hardware companies” such as “Computer companies” and “Electronics companies.”

How does DBpedia store this categorization information? The DBpedia page for IBM shows that DBpedia includes triples saying that IBM has Dublin Core subject values such as category:Companies_listed_on_the_New_York_Stock_Exchange and category:Computer_hardware_companies. The DBpedia page for the category Computer_hardware_companies shows that is a SKOS concept with values for the two key properties of a SKOS concept: a preferred label and broader values. The category:Computer_hardware_companies concept is itself the broader value of several other concepts such as category:Fabless_semiconductor_companies. Because it’s the broader value of other concepts and has its own broader values, it can be both a parent node and a child node in a tree of taxonomic terms, so DBpedia has the data that lets you build a taxonomy hierarchy around any of its categories.

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Metreeca Offers Easier Interaction With Semantic Knowledge Bases

griverAccessing an enterprise’s semantic knowledge base has its challenges for the business’ general population. Perhaps development teams already have integrated specific SPARQL queries inside a customer app or custom dashboard or otherwise accommodated some very task-oriented activities and searches, but that has its limits for non-technical users who want to explore outside the box. All the same, these users aren’t likely to write new SPARQL queries on their own — but nor do they necessarily want to wait for their IT departments to pull that together for them. Interactive query builders are options but some may find these still a little too-technically oriented.

This is a problem that Metreeca is looking to solve with Graph Rover, a self-service search and analysis tool that enables non technical users to interact visually with semantic knowledge bases. It has just released the latest beta update of the product, which lets users build queries using a graphical interface, but Graph Rover has been in development for two years while the company was in stealth mode, and tech lead Alessandro Bollini says it is already a mature solution that should be available commercially in the first quarter of 2015.

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Linked Data LEAPS To More Sustainable Energy Sources

leapspixAt the IESD14 (Intelligent Exploration of Semantic Data) challenge at this week’s ISWC 2014, the award was handed out to LEAPS: A Semantic Web and Linked Data Framework for the Algal Biomass Domain. The application is the work of Monika Solanki, while at the Knowledge-Based Engineering Lab at Birmingham City University in the UK.

The motivation, according to slides about the project, relates to the idea that algae biomass-based biofuels could serve as a naturally viable and sustainable energy source alternative to fossil fuels. While many companies, governments and non-profit agencies have been researching the idea, knowledge gathered exists in diverse formats and proprietary databases. What’s lacking has been a knowledge level infrastructure that is equipped with the capabilities to provide semantic grounding to the datasets for algal biomass, the slides note.

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Introducing GEMS, a Multilayer Software System for Graph Databases

gemsThe Pacific Northwest National Laboratory recently reported on Phys.org, “As computing tools and expertise used in conducting scientific research continue to expand, so have the enormity and diversity of the data being collected. Developed at Pacific Northwest National Laboratory, the Graph Engine for Multithreaded Systems, or GEMS, is a multilayer software system for semantic graph databases. In their work, scientists from PNNL and NVIDIA Research examined how GEMS answered queries on science metadata and compared its scaling performance against generated benchmark data sets. They showed that GEMS could answer queries over science metadata in seconds and scaled well to larger quantities of data.” Read more

Symplectic Takes Another Step In Helping Universities Engage In Research Collaboration And Discovery

sympintThis summer, Symplectic Limited become the first DuraSpace Registered Service Provider (RSP) for the VIVO Project, an open-source, open-ontology, open-process platform for hosting semantically structured information about the interests, activities and accomplishments of scientists and scholars. (See our coverage here.) “Universities want to capture all that their researchers do, collaborate and reuse the data the research brings out,” says Sabih Ali, head of brand at Symplectic. “A lot of them are looking to be a part of something like VIVO and join the whole semantic web technology movement, but they don’t have the capacity to do it themselves.”

Symplectic brings that to the table with its role as a services provider and the expertise in data quality, organization and transfer that it has thanks to being a developer of Elements, software that captures, collects and showcases institutional research, and which is used by many leading universities including Cambridge and Oxford. It also offers an open-source VIVO harvester for clients allows the ingestion of information into VIVO profiles using the rich data that Elements captures.

More recently, Symplectic has taken on the role of authorized services provider for Profiles Research Networking Software, as well. Profiles RNS is an NIH-funded open source tool to speed the process of finding researchers with specific areas of expertise for collaboration and professional networking. It’s based on the VIVO 1.4 ontology, with support for RDF, SPARQL, and Linked Open Data.

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eXframe Platform Demos Power Of The Semantic Web For Biology

sccommonsA Drupal ++ platform for semantic web biomedical data – that’s how Sudeshna Das describes eXframe, a reusable framework for creating online repositories of genomics experiments. Das – who among other titles is affiliate faculty of the Harvard Stem Cell Institute – is one of the developers of eXframe, which leverages Stéphane Corlosquet’s RDF module for Drupal to produce, index (into an RDF store powered by the ARC2 PHP library) and publish semantic web data in the second generation version of the platform.

“We used the RDF modules to turn eXframe into a semantic web platform,” says Das. “That was key for us because it hid all the complexities of semantic technology.”

One instance of the platform today can be found in the repository for stem cell data as part of the Stem Cell Commons, the Harvard Stem Cell Institute’s community for stem cell bioinformatics. But Das notes the importance of the reusability aspect of the software platform to build genomics repositories that automatically produce Linked Data as well as a SPARQL endpoint, is that it becomes easy to build new repository instances with much less effort. Working off Drupal as its base, eXframe has been customized to support biomedical data and to integrate biomedical ontologies and knowledge bases.

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Semantic Web Job: Software Engineer

elevada logoElevada is looking for a software engineer. The job description states: “Elevada is a data management company seeking a skilled Software Engineer with 4+ years of professional development experience. This is an opportunity to get in early (employee number < 5) at a real company with a strong product vision + enterprise customers, real revenue, and a strong sales pipeline. Compensation will be a mix of cash and equity at the end of a trial contract. Below are parameters for the position. We will tailor responsibilities to suit the individual who best fits our culture and goals. Candidate responsibilities:

  • Web-based front-end development in Java+GWT, transitioning to a JavaScript framework in the future.
  • Develop/package/wrap JavaScript libraries for GWT integration via JSNI (and eventually into the new framework).
  • Server-side development using Java, Spring Framework, JPA, Hibernate.
  • Help maintain development and deployment infrastructure in Linux environments.”

Skills requirements include:

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XSB and SemanticWeb.Com Partner In App Developer Challenge To Help Build The Industrial Semantic Web

Semantic Web Developer Challenge - sponsored by XSB and SemanticWeb.comAn invitation was issued to developers at last week’s Semantic Technology and Business Conference: XSB and SemanticWeb.com have joined to sponsor the Semantic Web Developer Challenge, which asks participants to build sourcing and product life cycle management applications leveraging XSB’s PartLink Data Model.

XSB is developing PartLink as a project for the Department of Defense Rapid Innovation Fund. It uses semantic web technology to create a coherent Linked Data model for all part information in the Department of Defense’s supply chain – some 40 million parts strong.

“XSB recognized the opportunity to standardize and link together information about the parts, manufacturers, suppliers, materials, [and] technical characteristics using semantic technologies. The parts ontology is deep and detailed with 10,000 parts categories and 1,000 standard attributes defined,” says Alberto Cassola, vp sales and marketing at XSB, a leading provider of master data management solutions to large commercial and government entities. PartLink’s Linked Data model, he says, “will serve as the foundation for building the industrial semantic web.”

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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

SPARQL City’s Benchmark Results Showcase New Possibilities in Enterprise Graph Analytics

Solution demonstrates 10x+ the performance while running on 100x the data

Enterprise meet Graph Analysis - SPARQLcity.comNoSQL Now 2014 & SemTechBiz 2014

San Diego – August 20, 2014 – SPARQL City, which introduced its scalable graph analytic engine to market earlier this year, today announced that it has successfully run the SP2 SPARQL benchmark on 100 times the data volume as other graph solution providers, while still delivering an order of magnitude better performance on average compared to published results.

SPARQL City ran the SP2 Benchmark against 2.5 billion triples/edges on a sixteen node cluster on Amazon EC2. Average query response time for the set of seventeen queries was about 6 seconds, with query 4, the most data intensive query involving the entire dataset taking approximately 34 seconds to run. By comparison, the best reported query 4 result by other graph solution providers has been around 15 seconds, but this is when running against 25 million triples/edges, or 1/100th of the data volume in SPARQL City’s benchmark test. This level of performance, combined with the ability to easily scale out the solution on a cluster when required, makes easy to use interactive graph analytics on very large datasets possible for the first time. Detailed benchmark results can be found on our website.

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