reflections on making efsa an open science organisation
TRANSCRIPT
background
An extraordinary company that captures, organizes and adds value to the rich information available in agricultural and biodiversity sciences, in order to
make it universally accessible, useful and meaningful.
http://www.agroknow.gr
Unorganized Content in local and remote sites
Widgets
Authoring services
Data Discovery Services
Analytics services
Data Platform
Ingestion Translation Publication
Harvesting BlossomCultivation
Organized and structured Content in local and remote
DBs
Educational
Bibliographic
Other
Enrichment
Aggregate data from diverse sources
Works with different type
of data
Prepare data for
meaningful services
Educational
Bibliographic
data aggregation & sharing solutions
indicative partners & clients• Food and Agriculture Organization (FAO)• Global Forum on Agricultural Research (GFAR)• International Fund for Agricultural Development (IFAD)• World Bank Group• UK’s Dept for International Development (DFID)• Michigan State University (MSU)• Wageningen University & Research (WUR)• French Institute of Agricultural Research (INRA)• International Centre for Research in Organic Food
Systems (ICROFS)
advocates of open
• CIARD.net: a global movement dedicated to open agricultural knowledge
• Global Open Data for Agriculture and Nutrition (GODAN): make agricultural and nutritionally relevant data available, accessible, and usable for unrestricted use worldwide
making different systems work together
• Agricultural Interoperability Interest Group (IG), Research Data Alliance (RDA)
• Knowledge & Learning Systems WG, Global Food Safety Partnership (GFSP)
large scale data-related projects• agINFRA: a data infrastructure to support agricultural scientific
communities (2011 - 2015)– 12 partners (incl. FAO); tech coordinator, evaluation, sustainability– in G8 Open Data in Agriculture Action Plan for Europe
• SemaGrow: Data intensive techniques to boost the real-time performance of global agricultural data infrastructures (2012 - 2015)– 8 partners (incl. FAO, WUR); tech, evaluation, sustainability– in G8 Open Data in Agriculture Action Plan for Europe
• OpenMinTeD: Open Mining INfrastructure for TExt and Data (2015- 2018)– 15 partners (incl. UoA, EBI, INRA); tech+data, requirements & evaluation
• Big Data Europe: Integrating Big Data, Software and Communities for Addressing Europe’s Societal Challenges (2015-2018)– 12 partners (incl. FAO); agri-food community & use cases
(my) understanding of the context
• vision: “Society engages in EFSA’s scientific work and gains trust in the EU food safety system”– increase openness & transparency– openness to meaningful contributions
levels of reflection
a) on a data e-infrastructure for EFSA operations
b) on positioning EFSA within a food safety data ecosystem
c) on “data need”-oriented innovation services for EFSA stakeholders
a data e-infrastructure for EFSA operations
example: agINFRA.eu
open & federated architecture
agINFRA automated metadata aggregation workflows
Publications
CIARD RING registry
Federated information providers
Data sets
CIARD RING registry
Educational
CIARD RING registry
…etc
catalogue of data sources/sets
published & linked vocabularies
complex, automated data ingestion
Metadata harvester
Filtering component
Stores
File system (DC, IEEE LOM, MODS XML)
File system (DC, IEEE LOM, MODS XML)
Stores
Identification and de-duplication component
MySQL
Duplicates
Stores
Transformation component ( to AKIF)
Store metadata in JSON (Internal Format)
Link checking component
PostProcessing/Enrichment component
File system (XMLs)
Get unique ID
Records with
Broken Links
Indexing mechanismAPI
big data technologies
data customer service
how could this look like for EFSA?
EFSA’s data & information hub
Toxicity testing methods
Registry
Various data providers, of various scientific data sources/formats
Pesticide outputs
Registry
Foodborne disease outbreaks
Registry
…etc
positioning EFSA within a food safety data ecosystem
example: AGRIS (http://agris.fao.org)
AGRIS central data processing
a collaborating aggregator (e.g. USDA’s AGRICOLA)AGRIS data
providers
the AGRIS ecosystem looks simple…
AGRIS search page
AGRIS central data processing
USDA’s AGRICOLA
EU institutions
…but it is a bit more complex
AGRIS search page
CGIAR harvester
CG centers
CGIAR Open
USDA’s repository
OpenAIRE PubAg search pageOpenAIRE search page
CAAS abstractsCAAS search page
EFSA central data processing?
INFOSAN network
EU food agencies
How does the EFSA data ecosystem look like?
EFSA data portal?
SAFE consortium
EU research institutions
SAFE web site
INFOSAN repository
GFSP WHO web siteGFSP search page
CDC databases
FOOD tool
need-oriented innovation services for EFSA stakeholders
example: CSPI• the organized voice of the American public on
nutrition, food safety, health and other issues– “improve food safety laws and reduce the incidence of
foodborne illness” • has tracked foodborne illness outbreaks since 1997
– events where two or more people become ill from eating the same food
– outbreaks where both the food and pathogen can be identified
US Outbreak Alert Database (until 2011)
http://cspinet.org/foodsafety/outbreak/pathogen.php
US Outbreak Report (after 2011)
http://cspinet.org/foodsafety/outbreak_report.html
stakeholder with very specific challenges
a) time-consuming & laborious primary data identification and documentation (by hand)
b) not complete coverage: incomplete & problematic data collection and sharing
c) multiple & outdated databases for secondary/processed data storage and curation
d) time-consuming & expensive processed data visualization & publication
advanced data organisation & classification
auto extract structured data from text
include & link to food recall data
add more (relevant) data sources
allow users to customize data reports
provide multi-channel access to data
Challenges of EFSA stakeholders?• each decision maker has own data needs
– Which information is critical for their work?– What is the main challenge in finding, managing
or disseminating this information?
and what’s next?
Separate Independent (variably linked) actions
Collective and Cohesive Approach(More Collaboration, Coordination, Communication, Connection)
harmonising & linking scientific outputs?
EFSA’s Data & Information Hub
Context-specific Data & Information Hubs
Source diagram from Open Models concept paper: http://bit.ly/1p729Jm
can openness be addictive?
