Food Safety Challenge

Dr. Charalampos Thanopoulos

Agro-Know, Greece

supported by:

Future Food Hack 2015(in conjunction with GODAN 2nd Workshop)

The Food Safety Challenge

The issue

• According to WHO foodborne & waterborne diseases kill an estimated 2.2M people annually, most of whom are children

• In Europe 1.2M cases of foodborne diseases are reported annually, that lead to 350,000 hospitalisation and 5,000 deaths

• The foodborne diseases problem is not focused at the national level but also at international level as outbreaks, involving multiple countries are becoming more common with the ever-increasing global movement of food and people

The issue

• The early detection of the outbreaks and the extraction of conclusions from the analysis of the alerts has become a major challenge in the area

• Currently, decision makers both at the public and private sector, food scientists, microbiologists and epidemiologists that work on food safety topics cannot take full advantage of all the existing data for foodborne diseases mainly for two reasons – part of the information remains unstructured and still

closed in internal databases and – the information is stored in custom and non-standard

schemas and thus it is not shared globally in aninteroperable way.

The challenge

How to help

• researchers

• food scientists

• microbiologists

• epidimiologists

that work on food safety topics to take fulladvantage of all the existing data forfoodborne diseases, discover & access theresources they need?

Lots of Open Data

The Challenge’s Data Sources

SemaGrow SPARQL Endpoint API (1/2)

• SPARQL endpoint: http://143.233.226.42:8080/SemaGrow

• Included datasets in the SemaGrow SPARQL Endpoint:– AGRIS

– VOA3R

– Organic Edunet

– ARIADNE

– Europeana

– Natural Europe

– Trees for future

• User guide of the annotation tool can be found at http://wiki.agroknow.gr/agroknow/images/a/a8/Eleon_user_guide.pdf

• How to install a linux package distribution of the SemaGrowStack? http://semagrow.semantic-web.at/docs/semagrow-stack-assembly/1.0.0/installation.html#Debian

SemaGrow SPARQL endpoint API (2/2)

• SemaGrow provides access to numerous Linked Data sources: AGRIS, Ariadne, Europeana, Organic Edunet, Natural Europe, IFPRI, RASFF and AGROVOC.

• Developers can access the SemaGrow interface online (http://143.233.226.42:8080/SemaGrow/) or query it via a standard HTTP GET method.

• For example, to get results from this basic query:

SELECT * WHERE {?s ?p ?o

} LIMIT 20

one would have to apply HTTP GET to this URL: http://143.233.226.42:8080/SemaGrow/sparql?output=json&query=SELECT ?s ?p ?o WHERE { ?s ?p ?o } LIMIT 10

Green Learning Network (GLN)

GLN Search API (agINFRA-powered)

• Green Learning Network (GLN) is a data pool of high quality educational resources related to agriculture and biodiversity: – big variety of collections

– dataset is organized per collection

– access the GLN data pool APIhttp://api.greenlearningnetwork.com/documentation/

– focus on the akif data type http://api.greenlearningnetwork.com/search-api/v1/akif?q=*

– REST-based queries over harmonised information (result of metadata processing)

ABN Search API (agINFRA-powered)

• Agriculture Bibliographic Network (ABN) APIcurrently provides access to a small subset of AGRIS data pool that totally contains million bibliographic references on agricultural research and technology:

– access the AGRIS API http://api.greenlearningnetwork.com/search-api/

– focus on the agrif data type http://api.greenlearningnetwork.com/search-api/v1/agrif?q=*

– REST-based queries over aggregated metadata

Search options

• Simple search– http://domain/search-api/v1/akif/?q=tomato

• Searching within specific fields– http://BASE_URL/search-

api/v1/akif/?languageBlocks.en.description=tomato

• Temporal– http://BASE_URL/search-api/v1/akif/?creationDate=2013-04-16

• Fetching specific item– http://BASE_URL/search-api/v1/akif/COLLECTION/20296

Managing results

• Sorting results– e.g ?q=*&sort_by=creationDate&sort_order=desc

• Facets– e.g ?facets=set&facet_size=3

• Pagination– e.g ?q=sea&page_size=25&page=3

Resources related to food safety risk analysis:

http://api.greenlearningnetwork.com/

search-api/v1/akif/?q=risk?analysis

&set=aglrfaocdx,optunesco,faocapacityportal,oeorganiceprints,oeintute

The Food Safety Data

• Available in various types, formats and sources

– Application programming interface (API)

– Dump files (e.g. XML)

– SPARQL endpoints

– Harvesting from services (OAI-PMH)

– HTML / data scraping

– Crawling

– …combination of the above

• Documentation: – http://dev.socrata.com/docs/formats/rdf-xml.html

European Food Safety Authority

• URL: http://www.efsa.europa.eu

• Data types: Publications, reports, classification and monitoring data

Rapid Alert System for Food & Feed System

• URL: http://ec.europa.eu/food/safety/rasff/index_en.htm

• Data portal: https://webgate.ec.europa.eu/rasff-window/portal/

– andhttps://webgate.ec.europa.eu/rasff-window/portal/?event=SearchForm&cleanSearch=1

• Data types: historical data about food alerts, recalls and measures taken by the national authorities

EC Health & Consumers’ Open Data

• A knowledge base of the European Commission Health and Consumers Directorate General public data

• SPARQL endpoint: http://ec.europa.eu/semantic_webgate/query

Center of Science in the Public Interest

• URL: http://www.cspinet.org

• Database: http://www.cspinet.org/foodsafety/outbreak/pathogen.php

• Data types: Reports from foodborne illness outbreaks in US since 1997

• Database of outbreaks reports: http://cspinet.org/foodsafety/outbreak_report.html

Centers for Disease Control and Prevention

• URL: http://www.cdc.gov

• Database on foodborne illnesses: http://www.cdc.gov/foodborneburden/estimates-overview.html

• RSS feed of combined Food Safety information: http://www2c.cdc.gov/podcasts/createrss.asp?c=146

• Data types: food-borne outbreaks reports

International Food Policy Research Institute (IFPRI)

• URL: http://www.ifpri.org

• Database: http://data.ifpri.org

• SPARQL endpoint: http://data.ifpri.org/sparql

• Data types: statistical data, reports, maps

The Food Security Portal

• URL: http://www.foodsecurityportal.org

• API: http://www.foodsecurityportal.org/api/about

Social media / search engines

• Twitter: info related to to the identification of foodborne disease incidents reported directly by food consumers– http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785982

– Twitter API: https://dev.twitter.com

• Search engines: Data about search queries related to food safety incidents from search engines like Google and Yahoo – http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785982

thank you!

Charalampos Thanopoulos

Agro-Know

cthanopoulos@agroknow.gr

info@agroknow.gr