Timothy Lebo

TWC LOGD: A portal for linked open government data ecosystems

International open government initiatives are releasing an increasing volume of raw government datasets directly to citizens via the Web. The transparency resulting from these releases not only creates new application opportunities but also imposes new burdens inherent to large-scale distributed data integration, collaborative data manipulation and transparent data consumption. The Tetherless World Constellation (TWC) at Rensselaer Polytechnic Institute (RPI) has developed the Semantic Web-based TWC LOGD portal to support the deployment of linked open government data (LOGD). The portal is both an open source infrastructure supporting linked open government data production and consumption and a vibrant community portal that educates and serves the growing international open government community of developers, data curators and end users. This paper motivates and introduces the TWC LOGD Portal and highlights innovative aspects and lessons learned.

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside

BackgroundTranslational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery.ResultsWe developed the Translational Medicine Ontology (TMO) as a unifying ontology to integrate chemical, genomic and proteomic data with disease, treatment, and electronic health records. We demonstrate the use of Semantic Web technologies in the integration of patient and biomedical data, and reveal how such a knowledge base can aid physicians in providing tailored patient care and facilitate the recruitment of patients into active clinical trials. Thus, patients, physicians and researchers may explore the knowledge base to better understand therapeutic options, efficacy, and mechanisms of action.ConclusionsThis work takes an important step in using Semantic Web technologies to facilitate integration of relevant, distributed, external sources and progress towards a computational platform to support personalized medicine.AvailabilityTMO can be downloaded from http://code.google.com/p/translationalmedicineontology and TMKB can be accessed at http://tm.semanticscience.org/sparql.

Converting governmental datasets into linked data

Linked Data provide many benefits to data consumers, but many publicly available datasets are still released in the Comma Separated Values (CSV) format, a ubiquitous common denominator. We introduce a methodology to transform such datasets into Linked Data. Our design is based on requirements identified while surveying existing governmental datasets released by data.gov. We present an implementation-independent RDF vocabulary to describe how a CSV dataset should be promoted into Linked Data, and use a Java-based converter to produce 5.3 billion RDF triples from 312 data.gov datasets.

Producing and Using Linked Open Government Data in the TWC LOGD Portal

As open government initiatives around the world publish an increasing number of raw datasets, citizens and communities face daunting challenges when organizing, understanding, and associating disparate data related to their interests. Immediate and incremental solutions are needed to integrate, collaboratively manipulate, and transparently consume large-scale distributed data. The Tetherless World Constellation (TWC) at Rensselaer Polytechnic Institute (RPI) has developed the TWC LOGD Portal based on Semantic Web principles to support the deployment of Linked Open Government Data. The portal is not only an open source infrastructure supporting Linked Open Government Data production and consumption, but also serves to educate the developers, data curators, managers, and end users that form the growing international open government community. This chapter introduces the informatic challenges faced while developing the portal over the past two years, describes the current design solutions employed by the portal’s LOGD production infrastructure, and concludes with lessons learned and future work.

The Web is My Back-end: Creating Mashups with Linked Open Government Data

Governments around the world have been releasing raw data to their citizens at an increased pace. The mixing and linking of these datasets by a community of users enhances their value and makes new insights possible. The use of mashups — digital works in which data from one or more sources is combined and presented in innovative ways — is a great way to expose this value. Mashups enable end users to explore data that has a real tangible meaning in their lives. Although there are many approaches to publishing and using data to create mashups, we believe Linked Data and Semantic Web technologies solve many of the true challenges in open government data and can lower the cost and complexity of developing these applications. In this chapter we discuss why Linked Data is a better model and how it can be used to build useful mashups.

A semantic portal for next generation monitoring systems

We present a semantic technology-based approach to emerging monitoring systems based on our linked data approach in the Tetherless World Constellation Semantic Ecology and Environment Portal (SemantEco). Our integration scheme uses an upper level monitoring ontology and mid-level monitoring-relevant domain ontologies. The initial domain ontologies focus on water and air quality. We then integrate domain data from different authoritative sources and multiple regulation ontologies (capturing federal as well as state guidelines) to enable pollution detection and monitoring. An OWL-based reasoning scheme identifies pollution events relative to user chosen regulations. Our approach captures and leverages provenance to enable transparency. In addition, SemantEco features provenance-based facet generation, query answering, and validation over the integrated data via SPARQL. We introduce the general SemantEco approach, describe the implementation which has been built out substantially in the water domain creating the SemantAqua portal, and highlight some of the potential impacts for the future of semantically-enabled monitoring systems.

Parallel Identities for Managing Open Government Data

Data consumers must be able to trust the datas provenance. A descriptive model enables consumers to make informed choices about data sources.

Provenance-Based Strategies to Develop Trust in Semantic Web Applications

Linked data and Semantic Web technologies enable people to navigate across heterogeneous sources of data thus making it easier for them to explore and develop multiple perspectives for use in making decisions and solving problems. While the Semantic Web offers benefits for developers and users, several new challenges are emerging that may negatively impact users’ trust in Web-based collaborative systems.

Towards Semantically Enabled Next Generation Community Health Information Portals: The PopSciGrid Pilot

We describe an approach to developing next generation health information portals. This prototype portal was developed to address two complementary goals (1) design and create a site where people can explore potential relationships between selected health-related behaviors, policies, and demographic data (2) explore semantic web technologies and linked data as enabling technologies for next generation health informatics portals. Our multidisciplinary team includes population and behavioral scientists, social network scientists, statisticians, and computer scientists focused on creating innovative proof of concept applications that integrate complex health data in understandable and usable ways. Our semantic-web based framework allowed us to design exemplar community health portal applications, with an initial focus on tobacco-related health data such as smoking prevalence and tobacco policies (taxation and smoking bans). We describe our approach, two semantically-enabled tobacco-related applications, and discuss how this approach can be used in a broad spectrum of community health applications.

Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications

To encourage data sharing in the life sciences, supporting tools need to minimize effort and maximize incentives. We have created infrastructure that makes it easy to create portals that supports dataset sharing and simplified publishing of the datasets as high quality linked data. We report here on our infrastructure and its use in the creation of a melanoma dataset portal. This portal is based on the Comprehensive Knowledge Archive Network (CKAN) and Prizms, an infrastructure to acquire, integrate, and publish data using Linked Data principles. In addition, we introduce an extension to CKAN that makes it easy for others to cite datasets from within both publications and subsequently-derived datasets using the emerging nanopublication and World Wide Web Consortium provenance standards.