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

Current Team

Publications

by (Editors: ) [BibTex of ]

News

AKSW Colloquium “Knowledge Extraction and Presentation” on Monday, July 28, 3.00 p.m. in Room P702 ( 2014-07-24T11:55:13+02:00 by Konrad Höffner)

2014-07-24T11:55:13+02:00 by Konrad Höffner

Knowledge Extraction and Presentation On Monday, July 28,  in room P702 at 3.00 p.m., Edgard Marx proposes a question answering system. He has a computer science background (BSc. and MSc. in Computer Science/PUC-Rio) and is a member of AKSW (Agile Knowledge Engineering and Semantic Web). Read more about "AKSW Colloquium “Knowledge Extraction and Presentation” on Monday, July 28, 3.00 p.m. in Room P702"

[CfP] Semantic Web Journal: Special Issue on Question Answering over Linked Data ( 2014-07-14T16:58:46+02:00 by Dr. Axel-C. Ngonga Ngomo)

2014-07-14T16:58:46+02:00 by Dr. Axel-C. Ngonga Ngomo

Dear all, The Semantic Web Journal is launching a special issue on Question Answering over Linked Data, soliciting original papers that * address the challenges involved in question answering over linked data, * present resources and tools to support question answering over linked data, or * describe question answering systems and applications. Read more about "[CfP] Semantic Web Journal: Special Issue on Question Answering over Linked Data"

New Version of FOX ( 2014-07-14T16:57:11+02:00 by Dr. Axel-C. Ngonga Ngomo)

2014-07-14T16:57:11+02:00 by Dr. Axel-C. Ngonga Ngomo

Dear all, We are very pleased to announce a new version of FOX [1]. Several improvements have been carried out: (1) We have fixed minor issues in the code. In addition, we have updated several libraries. (2) As a result, the FOX output parameters have changed minimally. Read more about "New Version of FOX"

AKSW Colloquium “Combination of Topic Modeling and Semantic Web” on Monday, June 30 ( 2014-06-26T10:12:50+02:00 by Konrad Höffner)

2014-06-26T10:12:50+02:00 by Konrad Höffner

Combination of Topic Modeling and Semantic Web On Monday, June 30, at 3.00 p.m. in room Paulinum 702, Michael Röder will present his yearly PhD progress report “Combination of Topic Modeling and Semantic Web”. The presentation addresses the usage of Topic Modeling in the area of Semantic Web. Read more about "AKSW Colloquium “Combination of Topic Modeling and Semantic Web” on Monday, June 30"

AKSW Colloquium Guest Talk “SWeeT Web of Heritage” on Wednesday, July 2 ( 2014-06-26T10:03:13+02:00 by Konrad Höffner)

2014-06-26T10:03:13+02:00 by Konrad Höffner

SWeeT Web of Heritage On Wednesday, July 2, at 1.30 p.m. in room P702, T B Dinesh from Janastu, a non-profit organisation providing free open source software, will present the SWeeT Web of Heritage. Read more about "AKSW Colloquium Guest Talk “SWeeT Web of Heritage” on Wednesday, July 2"