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

DBpedia @ Google Summer of Code – GSoC 2017 ( 2017-03-13T11:12:50+01:00 Christopher Schulz)

2017-03-13T11:12:50+01:00 Christopher Schulz

DBpedia, one of InfAI’s community projects, will be part of the 5th Google Summer of Code program. The GsoC has the goal to bring students from all over the globe into open source software development. Read more about "DBpedia @ Google Summer of Code – GSoC 2017"

New GERBIL release v1.2.5 – Benchmarking entity annotation systems ( 2017-03-10T11:49:51+01:00 by Ricardo Usbeck)

2017-03-10T11:49:51+01:00 by Ricardo Usbeck

Dear all, the Smart Data Management competence center at AKSW is happy to announce GERBIL 1.2.5. Read more about "New GERBIL release v1.2.5 – Benchmarking entity annotation systems"

DBpedia Open Text Extraction Challenge – TextExt ( 2017-03-09T12:15:57+01:00 Christopher Schulz)

2017-03-09T12:15:57+01:00 Christopher Schulz

DBpedia, a community project affiliated with the Institute for Applied Informatics (InfAI) e.V., extract structured information from Wikipedia & Wikidata. Now DBpedia started the DBpedia Open Text Extraction Challenge – TextExt. Read more about "DBpedia Open Text Extraction Challenge – TextExt"

The USPTO Linked Patent Dataset release ( 2017-02-24T17:18:51+01:00 by Mofeed Hassan)

2017-02-24T17:18:51+01:00 by Mofeed Hassan

Dear all, We are happy to announce USPTO Linked Patent Dataset release. Patents are widely used to protect intellectual property and a measure of innovation output. Read more about "The USPTO Linked Patent Dataset release"

Two accepted papers in ESWC 2017 ( 2017-02-22T17:43:38+01:00 by Dr. Mohamed Ahmed Sherif)

2017-02-22T17:43:38+01:00 by Dr. Mohamed Ahmed Sherif

Hello Community! We are very pleased to announce the acceptance of two papers in ESWC 2017 research track. The ESWC 2017 is to be held in Portoroz, Slovenia from 28th of May to the 1st of June. Read more about "Two accepted papers in ESWC 2017"