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

AKSW Colloquium, 18.07.2016, AEGLE and node2vec ( 2016-07-18T14:56:44+02:00 TommasoSoru)

2016-07-18T14:56:44+02:00 TommasoSoru

On Monday 18.07.2016, Kleanthi Georgala will give her Colloquium presentation for her paper “An Efficient Approach for the Generation of Allen Relations”, that was accepted at the European Conference on Artificial Intelligence (ECAI) 2016. Read more about "AKSW Colloquium, 18.07.2016, AEGLE and node2vec"

AKSW Colloquium, 04.07.2016. Big Data, Code Quality. ( 2016-06-29T12:34:35+02:00 by Ivan Ermilov)

2016-06-29T12:34:35+02:00 by Ivan Ermilov

On the upcoming Monday (04.07.2016), AKSW group will discuss topics related to Semantic Web and Big Data as well as programming languages and code quality. Read more about "AKSW Colloquium, 04.07.2016. Big Data, Code Quality."

Accepted Papers of AKSW Members @ Semantics 2016 ( 2016-06-27T12:50:01+02:00 by Sandra Bartsch)

2016-06-27T12:50:01+02:00 by Sandra Bartsch

This year’s SEMANTiCS conference which is taking place between September 12 – 15, 2016 in Leipzig recently invited for the submission of research papers on semantic technologies. Read more about "Accepted Papers of AKSW Members @ Semantics 2016"

AKSW Colloquium, 27.06.2016, When owl:sameAs isn’t the Same + Towards Versioning for Arbitrary RDF Data ( 2016-06-26T15:46:24+02:00 by Marvin Frommhold)

2016-06-26T15:46:24+02:00 by Marvin Frommhold

In the next Colloquium, June the 27th at 3 PM, two papers will be presented: When owl:sameAs isn’t the Same: An Analysis of Identity in Linked Data André Valdestilhas will present the paper “When owl:sameAs isn’t the Same: An Analysis of Identity … Continue reading → Read more about "AKSW Colloquium, 27.06.2016, When owl:sameAs isn’t the Same + Towards Versioning for Arbitrary RDF Data"

Should I publish my dataset under an open license? ( 2016-06-22T11:41:28+02:00 by Dr.-Ing. Sebastian Hellmann)

2016-06-22T11:41:28+02:00 by Dr.-Ing. Sebastian Hellmann

Undecided, stand back we know flowcharts:   Taken from my slides for my keynote  at TKE: Linguistic Linked Open Data, Challenges, Approaches, Future Work from Sebastian Hellmann Read more about "Should I publish my dataset under an open license?"