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Reflections on making EFSA an
open science organisation
Nikos Manouselis, CEO Agro-Know
nikosm@agroknow.gr
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
Dupli
cates
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 mechanism
API
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)
Reflections on making EFSA an open science organisation
the AGRIS ecosystem looks simple…
…but it is a bit more complex
How does the EFSA data ecosystem look like?
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?
thank you!
nikosm@agroknow.gr
www.agroknow.gr

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Reflections on making EFSA an open science organisation

  • 1. Reflections on making EFSA an open science organisation Nikos Manouselis, CEO Agro-Know nikosm@agroknow.gr
  • 3. 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
  • 4. 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
  • 5. 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)
  • 6. 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
  • 7. making different systems work together • Agricultural Interoperability Interest Group (IG), Research Data Alliance (RDA) • Knowledge & Learning Systems WG, Global Food Safety Partnership (GFSP)
  • 8. 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
  • 9. (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
  • 10. 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
  • 11. a data e-infrastructure for EFSA operations
  • 13. 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
  • 14. catalogue of data sources/sets
  • 15. published & linked vocabularies
  • 16. 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 Dupli cates 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 mechanism API
  • 19. 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
  • 20. positioning EFSA within a food safety data ecosystem
  • 23. the AGRIS ecosystem looks simple…
  • 24. …but it is a bit more complex
  • 25. How does the EFSA data ecosystem look like?
  • 27. 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
  • 28. US Outbreak Alert Database (until 2011) http://cspinet.org/foodsafety/outbreak/pathogen.php
  • 29. US Outbreak Report (after 2011) http://cspinet.org/foodsafety/outbreak_report.html
  • 30. 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
  • 31. advanced data organisation & classification
  • 32. auto extract structured data from text
  • 33. include & link to food recall data
  • 34. add more (relevant) data sources
  • 35. allow users to customize data reports
  • 37. 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?
  • 39. Separate Independent (variably linked) actions Collective and Cohesive Approach (More Collaboration, Coordination, Communication, Connection) harmonising & linking scientific outputs?
  • 40. 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?