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, 01.02.2016, Co-evolution of RDF Datasets ( 2016-02-01T15:53:23+01:00 by Natanael Arndt)

2016-02-01T15:53:23+01:00 by Natanael Arndt

At the todays colloquium, Natanael Arndt will discuss the the paper “Co-evolution of RDF Dataset” by Sidra Faisal, Kemele M. Endris, Saeedeh Shekarpour and Sören Auer (2016, available on arXiv) Link: http://arxiv.org/abs/1601. Read more about "AKSW Colloquium, 01.02.2016, Co-evolution of RDF Datasets"

Holographic Embeddings of Knowledge Graphs ( 2016-02-01T14:32:03+01:00 by Johannes Frey)

2016-02-01T14:32:03+01:00 by Johannes Frey

During the upcoming colloquium, Nilesh Chakraborty will give a short introduction on factorising RDF tensors and present a paper on “Holographic Embeddings of Knowledge Graphs”: Holographic Embeddings of Knowledge Graphs Authors: Maximilian Nickel, Lorenzo Rosasco, Tomaso Poggio Abstract: Learning embeddings … Continue reading → Read more about "Holographic Embeddings of Knowledge Graphs"

AKSW Colloquium, 25.01.2016, LargeRDFBench and Introduction To The Docker Ecosystem ( 2016-01-25T14:39:49+01:00 by Ivan Ermilov)

2016-01-25T14:39:49+01:00 by Ivan Ermilov

On the upcoming colloquium, Muhammad Saleem will present his paper “LargeRDFBench: A Billion Triples Benchmark for SPARQL Endpoint Federation” about the benchmarking of federated SPARQL endpoints. The other talk will be an introduction to the Docker ecosystem by Tim Ermilov. Read more about "AKSW Colloquium, 25.01.2016, LargeRDFBench and Introduction To The Docker Ecosystem"

HOBBIT project kick-off ( 2016-01-22T14:52:43+01:00 Sandra Bartsch)

2016-01-22T14:52:43+01:00 Sandra Bartsch

HOBBIT, a new InfAI project within the EU’s “Horizon 2020″ framework program kicked-off in Luxembourg on 18 and 19 january in 2016. Read more about "HOBBIT project kick-off"

AKSW Colloquium, 18.01.2016, Natural Language Processing and Question Answering ( 2016-01-14T10:25:22+01:00 by Ivan Ermilov)

2016-01-14T10:25:22+01:00 by Ivan Ermilov

On the upcoming colloquium, Ivan Ermilov and Konrad Höffner, members of AKSW, will present two papers from the natural language processing (NLP) and Question Answering (QA) research areas. ClausIE: Clause-Based Open Information Extraction Authors. Del Corro, Luciano, and Rainer Gemulla. Read more about "AKSW Colloquium, 18.01.2016, Natural Language Processing and Question Answering"