Inferring Cuisine – Drug Interactions Using the Linked Data Approach

Inferring Cuisine – Drug Interactions Using the Linked Data Approach

Milos Jovanovik, M.Sc.

Faculty of Computer Science and Engineering

Milos Jovanovik, M.Sc.Faculty of Computer Science and Engineering

Why am I here?

Milos Jovanovik

T&R assistant @ FCSE

PhD candidate

Linked Data, Open Data, Semantic Web

WP Lead

“Fusepool P3: Publish, Process, Perform”, EU Project for building a state-of-the-art Linked Open Data platform, http://p3.fusepool.eu/

Contact info

Web: http://about.me/milosjovanovik

Twitter: @ymilosy

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Latest Research

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http://go.nature.com/rnPO91


Focus on Two Aspects

1. Negative interactions between drugs from a given category and recipes from a given cuisine

2. Ingredients’ impact on the negative food - drug interactions in different parts of the world

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Two Patterns of Food – Drug Interactions

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Food Interactions of Blood Drugs in ‰

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http://viz.linkeddata.finki.ukim.mk/


Food Interactions of Antibiotics in ‰

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Two Main Ingredients Responsible for the Negative Food – Drug Interactions in the World

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Milk is the ‘problem’ in the Western World, Garlicin South Europe, Asia, Africa, Latin America

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The Global Impact of Milk in %

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The Global Impact of Garlic in %

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How Did We Make the Analysis?

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Recipe DataDrug Data


Data Quality: 5 Star Open Data

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http://5stardata.info/


The Drugs Dataset

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2 star data → 5 star dataData and Web Science RG, University of Mannheim


The Recipes Dataset

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1 star data → 3 star dataYong-Yeol Ahn et al., “Flavor Network and the Principles of Food Pairing”


Linking the Datasets

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RDF StoreVirtuoso Universal Server

3 star data → 5 star data

5 star data

5 star data


Linking the Datasets

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4 Star and 5 Star Data

Using RDF and Linked Data to increase data quality


Describing Data in RDF

The problem with the data in the figure is that without more information from the person who created it, you really don’t know what it means.

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This would be the information we want associated with the spreadsheet:

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What is Linked Data?

Linked Data is the next step in the Semantic Web –interconnecting the data

Data in traditional DB systems are in ‘silos’

Accessible only via APIs, web services, etc.

The Semantic Web + Linked Data allow data manipulation across distributed datasets, using one set of W3C standards:

RDF – to represent the data,

RDFS – to model the data,

OWL – to model the data and support reasoning,

SPARQL – to query the data.

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The Linked Data Principles

Linked Data is separated from RDF by the four Linked Data principles:

1. Use URIs as names for things. http://wifo5-04.informatik.uni-mannheim.de/drugbank/page/drugs/DB00046

2. Use HTTP URIs so that people can look up those names. http://wifo5-04.informatik.uni-mannheim.de/drugbank/page/drugs/DB00046

3. When someone looks up a URI, provide useful information, using the standards (RDF, SPARQL).

4. Include links to other URIs, so people can discover more things.

owl:sameAs <http://dbpedia.org/resource/Insulin_lispro>

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Using Dereferenceable URIs

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Using Dereferenceable URIs

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Using SPARQL to Retrieve the Data

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The Linking Open Data (LOD) Project

The LOD project is a community activity started in 2007 by W3C.

The project’s stated goal is to “make data freely available to everyone.”

The collection of Linked Data published on the Web is referred to as the LOD cloud.

More info about the LOD cloud is available at http://lod-cloud.net/.

The latest (2014) statistics are available here.

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http://lod-cloud.net/

http://linkeddatacatalog.dws.informatik.uni-mannheim.de/state/



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Other R&D Projects

Selected Linked Open Data Projects of our Research Team


Crime Map for Macedonia

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http://crimemap.finki.ukim.mk/


Crime Map for Macedonia

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http://crimemap.finki.ukim.mk/


Linked Open Drug Data from HIFM

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Linked Open Drug Data from MDB

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Linked Open Data for Drug Availability

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Linked Music Data from Global Charts

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Summary and Further Reading

Additional Resources


Summary

Linked Data is a set of techniques for publishing and consuming structured data on the Web.

Uses RDF as a data model and RDF syntax to express data representations.

It can be used for better data integration for:

Business ideas

Application development

Data analysis

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Further Reading & Resources

“Inferring Cuisine - Drug Interactions Using the Linked Data Approach” http://www.nature.com/srep/2015/150320/srep09346/full/srep09346.html

http://www.nature.com/srep/2015/150320/srep09346/pdf/srep09346.pdf

Contact:

web: http://about.me/milosjovanovik

publications: http://bit.ly/mj-publications

twitter: @ymilosy

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Q&A Session

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Data & Analytics

Inferring Cuisine – Drug Interactions Using the Linked Data Approach