ReDD-Observatory: Using the Web of Data for Evaluating the Research-Disease Disparity

The ReDD-Observatory is a project to evaluate the disparity between active areas of biomedical research and the global burden of disease using Linked Data and data-driven discovery.

Background

It is widely accepted that there is a large disparity between the availability of treatment options and the prevalence of diseases in the world, thus placing individuals in danger. This disparity is partially caused by the restricted access to information that would allow health- care and research policy makers to formulate more appropriate measures to mitigate this disparity. Specifically, this shortage of information is caused by the difficulty in reliably obtaining and integrating data regarding the disease burden for a given nation and the respective research investments.

In response to these challenges, the Linked Data paradigm provides a simple mechanism for publishing and interlinking structured information on the Web. In conjunction with the ever increasing data on diseases and healthcare research available as Linked Data, an opportunity is created to reduce this information gap that would allow for better policy in response to these disparities.

We present the ReDD-Observatory, an approach for evaluating the Research-Disease Disparity based on the interlinking and integrating of various biomedical data sources.

Methodology

The figure below provides a birds eye-view of the methodology involved in the ReDD-Observatory.

We first identified relevant datasets to be included that provided relevant information to evaluate the disparity. We not only consider the datasets already present as RDF but also those that are present in unstructured formats. These datasets are:

  1. LinkedCT - the RDF representation of ClinicalTrials.gov, which is the database of all clinical trials around the world.
  2. Bio2RDF's PubMed - the RDF representation of PubMed, which is a service of the US National Library of Medicine that includes bibliographic information and abstracts of over 19 million publications from MEDLINE and other life science journals.
  3. WHO's Global Health Observatory (GHO), which contains statistical information regarding the mortality and burden of disease classified according to the death and DALY (disability-adjusted life year) estimates grouped by countries and regions. However, since GHO is not available as Linked Data, as the next step we devised a method for representing unstructured data as RDF. We devised a plug-in in OntoWiki to represent statistical data from GHO as RDF. We used the Data Cube Vocabulary for this conversion. More information is present here. In order to ensure the completeness, conciseness and consistency for the selected datasets our next step is to assess the data quality of the datasets. The next challenging step is to interlink the datasets for a number of concepts such as (a) countries, (b) diseases and (c) publications. The assessment of the disparity is then performed with a number of parametrized SPARQL queries. We evaluate the results wrt. information quality and interlinking precision. As a consequence, we are, for the first time, able to provide reliable indicators for the extent of the research-disease disparity around the world in an semi- automated fashion, thus enabling healthcare professionals and policy makers to make more informed decisions.

Further Information

Project Team

Publications

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News

ASKW Colloquium, 24 August, 3pm, Lucene, SOLR, FEASIBLE ( 2015-08-24T13:40:58+02:00 by Dr. Amrapali Zaveri)

2015-08-24T13:40:58+02:00 by Dr. Amrapali Zaveri

In this colloquium, first, Kay Müller and Nilesh Chakraborty will give an overview of Lucene and SOLR and how they can be used in information retrieval scenarios, along with a short peek into ElasticSearch, introducing a few recent features, their … Continue reading → Read more about "ASKW Colloquium, 24 August, 3pm, Lucene, SOLR, FEASIBLE"

AKSW has 10 accepted publications in Semantics’2015 conference ( 2015-08-18T13:37:02+02:00 by Ivan Ermilov)

2015-08-18T13:37:02+02:00 by Ivan Ermilov

The Semantics‘2015 conference will take place in Vienna, Austria on September 15-17, 2015. AKSW is happy to announce 10 accepted publications: 6 for research track and 4 for demos/posters track. Read more about "AKSW has 10 accepted publications in Semantics’2015 conference"

AKSW Colloquium, 17-08-2015, Relational Machine Learning for Knowledge Graphs, Zoo Keeper, Apache Mesos ( 2015-08-17T10:58:54+02:00 by Patrick Westphal)

2015-08-17T10:58:54+02:00 by Patrick Westphal

Relational Machine Learning for Knowledge Graphs In this colloquium Patrick Westphal will present the paper “A Review of Relational Machine Learning for Knowledge Graphs” by Nickel, Murphy, Tresp and Gabrilovich. Read more about "AKSW Colloquium, 17-08-2015, Relational Machine Learning for Knowledge Graphs, Zoo Keeper, Apache Mesos"

18 AKSW Papers at ISWC 2015 ( 2015-08-12T03:16:15+02:00 by Muhammad Saleem)

2015-08-12T03:16:15+02:00 by Muhammad Saleem

We are very pleased to announce that AKSW will be presenting 18 papers in the upcoming International Semantic Web Conference (ISWC) 2015. Read more about "18 AKSW Papers at ISWC 2015"

Michael Röder at AKSW Colloquium, Monday, 10th August 2015, 3pm ( 2015-08-06T14:17:57+02:00 Michael Roeder)

2015-08-06T14:17:57+02:00 Michael Roeder

Crawling the Linked Open Data Cloud by Michael Röder In the recent years the Linked Open Data Cloud matured to support various applications, e.g., question answering, knowledge inference or database enrichment. Read more about "Michael Röder at AKSW Colloquium, Monday, 10th August 2015, 3pm"