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Ontology-Based Services and Knowledge Management in the Agricultural Domain, by Pierre Larmande

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Agricultural Data Interest Group (IGAD)
Pre-Meeting Agenda
Research Data Alliance
21st to 22nd September 2015
INRA, Paris (France)

Published in: Science
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Ontology-Based Services and Knowledge Management in the Agricultural Domain, by Pierre Larmande

  1. 1.  Ontology-­‐based   services  and  knowledge  management  in  the   Agronomic  Domain   Pierre  Larmande   Ins-tute  of  Research  for  Development  (IRD)   Head  of  data  integra-on  group  at  the  Ins-tute  of  Computa-onal  Biology   pierre.larmande@ird.fr    
  2. 2. Outline •  Data integration challenges in the Life Sciences •  Ontologies/ Semantic Web Technologies •  AgroPortal a proposition for ontology-based services in the agronomic domain •  Agronomic Linked Data project
  3. 3. Data landscape in the Life Sciences •  The availability of biological data has increased •  Advancements in: •  computational biology •  genome sequencing •  high-throughput technologies •  Integrative approaches are necessary to understand the functioning of biological systems
  4. 4. •  Lack of effective approaches to integrate data that has created a gap between data and knowledge •  Need for an effective method to bridge gap between data and underlying meaning •  Harvest the power of overlaying different data sets Data integration challenges
  5. 5. Semantic Web Technology •  An extension of the current Web technologies. •  Enables navigation and meaningful use of digital resources. •  Support aggregation and integration of information from diverse sources. •  Based on common and standard formats.
  6. 6. Resource Description Framework (RDF) •  Framework for representing information about resources on the Web •  Provides a labeled connection between two resources •  Uses Unique Resource Identifiers (URI) •  Statements take the form of triples: 
 Subject   Predicate   Object   <Gene_A>   <codes_for>   <Protein_A>   RDF  Triple  
  7. 7. •  Combining the triples results in a directed, labeled graph. <Gene_A>   <Protein_A>   <has_funcFon>   <BP_A>   <MF_A>   <Gene_X>   <regulates>   7  
  8. 8. AgroPortal    a  proposi(on  for  ontology-­‐based   services  in  the  agronomic  domain   Clément  Jonquet,     Esther  Dzalé-­‐Yeumo,    Elizabeth  Arnaud,    Pierre  Larmande    
  9. 9. ObjecFves  of  AgroPortal  project   •  Develop  and  support  a  reference  ontology  repository   for  the  agronomic  domain   –  One-­‐stop-­‐shop  for  plant/agronomic  related  ontologies     –  Primary  focus  on  the  agronomic  &  plant  domain   •  Reusing  the  NCBO  BioPortal  technology   –  Avoid  to  re-­‐implement  what  has  been  done   –  Facilitate  interoperability   –  Reusing  the  scien-fic  outcomes,  experience  &  methods   of  the  biomedical  domain     •  Enable  straighUorward  use  of  agronomic  related   ontologies   –  Respect  the  requirements  of  the  agronomic  community     –  Fully  seman-c  web  compliant  infrastructure   9  
  10. 10. HOW  DOES  IT  LOOKS?   10  
  11. 11. 11  
  12. 12. 12  
  13. 13. Available  ontologies   •  Already  29  ontologies…  and  we  expect  around  40  soon.   –  (half  are  not  included  in  the  NCBO  BioPortal)   •  Ontologies  are  organized  in  Groups  and  Categories   13  
  14. 14. 14  
  15. 15. 15  
  16. 16. Recommender   16  
  17. 17. Mappings   17  
  18. 18. Community  based  func-onali-es   Atelier  InOvive  2015  –  Rennes  –  29  juin   2015   18  
  19. 19. REST  Web  Service  API:   hhp://data.agroportal.lirmm.fr/documenta-on     Atelier  InOvive  2015  –  Rennes  –  29  juin   2015   19  
  20. 20. SPARQL  endpoint:   hhp://sparql.agroportal.lirmm.fr     20  
  21. 21. AN  ONTOLOGY  REPOSITORY…   WHO’S  GONNA  USE  IT?   21  
  22. 22. 4  Driving  Agronomic  Use  Cases   •  IBC  Rice  Genomics   –  data  integra-on  and  knowledge  management   related  to  rice     •  RDA  Wheat  Data  Interoperability  working  group   –  common  framework  for  describing,  represen-ng,   linking  and  publishing  wheat  data  with  respect  to   open  standards   •  INRA  Linked  Open  Vocabularies,  LovInra   –  publish  vocabularies  produced  or  co-­‐produced  by   INRA  scien-sts  and  foster  their  reuse  beyond  the   original  researchers   •  The  Crop  Ontology  project   –  publishes  ontologies  required  for  describing  crop   germplasm,  traits  and  evalua-on  trials.   22  
  23. 23. Each  use  case  has  a  specific  group  in   AgroPortal   •  Feature  to  come:  slices   – Specific  “entry”  in  the  AgroPortal   23  
  24. 24. AgroLD    The  Agronomic Linked Data project Aravind  Venkatensan,   Gildas  Tagny,   Nordine  El  Hassouni,   Manuel  Ruiz,    Pierre  Larmande    
  25. 25. Agronomic Linked Data (AgroLD) •  Semantic web based system that integrates data from South Green Bioinformatics node •  Aim: •  Capability to answer complex real life questions •  Efficient information integration / retrieval. •  Easy extensibility. •  Aid in holistic understanding of domain
  26. 26. AgroLD •  AgroLD will be developed in phases – •  Website: www.agrold.org •  Phase I: includes data on: •  Rice (Oryza spp). •  Oryza barthi •  Oryza brachyantha •  Oryza Sativa •  Oryza glaberimma •  Arabidopsis thaliana •  Sorghum (Sorghum bicolor) •  Maize/Corn (Zea mays) •  Wheat •  Triticum astivum •  Triticum urartu
  27. 27. Data  sources  in  AgroLD  
  28. 28. Ontologies  in  AgroLD  
  29. 29. Knowledge in AgroLD AgroLD   Ontologies  
  30. 30. www.agrold.org
  31. 31. Search  and  browse  AgroLD   Plant  height  
  32. 32. Sparql  query  editor  
  33. 33. Sparql  query  editor  
  34. 34. Results  are  annotated  with  evidence_code     hhp://geneontology.org/page/guide-­‐go-­‐evidence-­‐codes  
  35. 35. VisualisaFon  of  queries  
  36. 36. Advanced  form-­‐based  search  
  37. 37. Results  are  combined  with  external  services    
  38. 38. Please  send  us  your  Feedback!   Your  answers  will  help  us  to   improve  the  applicaton  
  39. 39. Acknowledgements   Elizabeth  Arnaud,     Leo  Valee,     Marie-­‐Angelique  Laporte,     Julian  Pietragalla   Manuel  Ruiz,   Nordine  El  Hassouni   Aravind  Venkatesan,   Gildas  Tagny   Esther  Dzalé-­‐Yeumo,   Cyril  Pommier   Patrick  Valduriez   Clement  Jonquet   Pierre  Larmande   Contact:  pierre.larmande@ird.fr  

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