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

by (Editors: ) [BibTex of ]

News

AKSW Colloquium, 23.05.2016, Instance Matching and RDF Dataset Similarity ( 2016-05-23T14:24:06+02:00 Michael Roeder)

2016-05-23T14:24:06+02:00 Michael Roeder

In the incoming colloquium, Mofeed Hassan will present the paper “Semi-supervised Instance Matching Using Boosted Classifiers” from Kejriwal et al., published in the proceedings of ESWC 2015 [PDF]. Read more about "AKSW Colloquium, 23.05.2016, Instance Matching and RDF Dataset Similarity"

AKSW Colloquium, 09.05.2016: Hebrew MMoOn inventory, federated SPARQL query processing ( 2016-05-03T13:57:03+02:00 by Bettina Klimek)

2016-05-03T13:57:03+02:00 by Bettina Klimek

In this week’s colloquium Bettina Klimek will give a practice talk of the paper ‘Creating Linked Data Morphological Language Resources with MMoOn – The Hebrew Morpheme Inventory‘, which she will present at the LREC conference 2016, 23-28 May 2016, Slovenia, … Continue reading → Read more about "AKSW Colloquium, 09.05.2016: Hebrew MMoOn inventory, federated SPARQL query processing"

AKSW Colloquium, 25.04.2016, DISPONTE, Workbench for Big Data Dev ( 2016-04-22T16:05:08+02:00 by Mohamed Sherif)

2016-04-22T16:05:08+02:00 by Mohamed Sherif

In this colloquium, Frank Nietzsche will present his master thesis titled “Game Theory- distributed solving” Game theory analyzes the behavior of individuals in complex situations. One popular game in Europe and North America with such a complex situation is Skat. Read more about "AKSW Colloquium, 25.04.2016, DISPONTE, Workbench for Big Data Dev"

AKSW Colloquium, 18.04.2016, DISPONTE, Workbench for Big Data Dev ( 2016-04-18T10:17:10+02:00 by Patrick Westphal)

2016-04-18T10:17:10+02:00 by Patrick Westphal

In this week’s Colloquium, today 18th of April at 3 PM, Patrick Westphal will present the paper ‘Probabilistic Description Logics under the Distribution Semantics‘ by Riguzzi et. al. Abstract Representing uncertain information is crucial for modeling real world domains. Read more about "AKSW Colloquium, 18.04.2016, DISPONTE, Workbench for Big Data Dev"

AKSW Colloquium, 11.04.2016, METEOR with DBnary ( 2016-04-11T09:07:18+02:00 by Ricardo Usbeck)

2016-04-11T09:07:18+02:00 by Ricardo Usbeck

In this week’s Colloquium, today 11th of April at 3 PM, Diego Moussallem will present the paper by Zied Elloumi et al. titled “METEOR for Multiple Target Languages using DBnary.” [PDF]. Read more about "AKSW Colloquium, 11.04.2016, METEOR with DBnary"