1. Rice Data Interoperability Working Group Updates
Pierre Larmande, IRD Shaik Meera, IIRR Ramil Mauleon, IRRI
RDA9 Plenary 5 April 2017 In collaboration with GODAN

2. Rice Discussion Group (IGAD) 29th February 2016, Tokyo, Japan
12 people
CGIAR (IRRI/Bioversity)
Ramil P. Mauleon
Elizabeth Arnaud
India
Devika Madalli
Shaik N Meera
Japan
Emi Kameoka
Takuji Kiura
Akane takezaki
Kento Nishibori
Seishi Ninomiya
Thailand
Rathachai Chawuthai
Suchada Ujjin
Asanee Kawtrakul

3. Case statement accepted…

4. Rice Data Interoperability
Working Group Deliverables:
A survey/report on the existing resources (vocabularies, ontologies, data formats, metadata standards).
update : we have a draft survey
Update: we have additional institute members (IRIC, Africarice, PhilRice)
A cookbook intended for the Rice data managers community: guidelines on metadata, vocabularies and ontologies plus a decision tree based on data and metadata description recommendations and file format recommendations.
Repository of controlled vocabularies and ontologies compliant with the Linked Data standards
Update: we are linked to the CGIAR Big Data Platform ontology working group
A prototype of Rice-specific data registry
Update: we have a prototype data analysis workflow (Galaxy) publishing method using RDA Data Type Registry and RDA Persistent Identifier WG outputs
Good practices/method(s) for digitization of rice legacy data

5. The methodology Surveys
Landscape of Rice related standards and their use by the community
Comprehensive overview of Rice related ontologies and vocabularies
Workshops
Recommendations
Mappings between different data formats
Actions to conduct in order to improve the current level of Rice related data interoperability
Define Interoperability use cases
Implementation
Interactive cookbook: recommendations + guidelines
A repository of Rice related linked vocabularies
Implement Interoperability use cases
Prototype on Rice-specific data registry

6. Phenotype Data
Experiments : RBD, Split, Factorial , Screening Genotypes for pests/diseases, POS, FLDs
Disciplines: Plant Breeding, Agronomy, Soil Science, Physiology, Pathology, Entomology, FLDs
Locations: Funded, Public, Private + Voluntary centers
Parameters- Grain Yield, Plant Height, No. of Panicles, pest /disease intensity etc (Parameter list)
Many parameters – tested across locations

7. Update - Vocabulary
Which of the following vocabularies are you familiar with?
AGROVOC
Biorefinery
CAB Thesaurus (CABT)
Cell Ontology (CL)
Chemical Entities of Biological Interest (ChEBI)
Crop Ontology (CO)
Crop Research Ontology – part of Crop Ontology (CO_715)
Environment Ontology (ENVO)
Experimental Factor Ontology (EFO)
Feature Annotation Location Description Ontology (FALDO)
NAL Thesaurus (NALT)
Phenotype And Trait Ontology (PATO)
Plant Experimental Conditions Ontology (Plant Environment Ontology, EO, may be changing to PECO)
Plant Ontology (PO)
Plant Trait Ontology (TO)
Population and Community Ontology (PCO)
Protein Ontology (PRO)
Sequence Ontology (SO)
Variation Ontology (VariO)
Agronomy Ontology (CGIAR) – OBO Foundry

8. Update – Repositories
Which of the following repository are you familiar with?
RicePedia (CGIAR) :
Wide range of Tools & Databases (IRRI):
International Rice Informatics Consortium (IRIC):
RiceVarMap (China) :
Rice Genome & Genetics at South Green (France) : (Tropgene, OrygenesDB, Oryzatagline, Greenphyl,
Rice Knowledge Management Portal (India): _
Rice databases at Japan: Oryzabase- ; QTARO -
RiceGeneTresher (Thailand):
Rice Diversity Project (USA) -
Gramene (USA) -

9. Update - membership Join us ! INSTITUTIONS (10)
IRRI (CGIAR Center - CC)
IRD (France)
Bioversity (CC)
NARO (Japan)
IIRR (India)
CIRAD (France)
CIAT (CC)
FAO of the UN
INRA (France)
PHILRICE (Philippines)
IRIC – approved by Advisory Committee during PAGXXV
CAAS (China)
PEOPLE (18)
Alexandre Guitton
Devika Madalli
Imma Subirats Coll
N Meera Shaik
Pierre Larmande
Ramil Mauleon
Sridhar Gutam
Manuel Ruiz
Laurel Cooper
Elizabeth Arnaud
Vessela Ensberg
Giovanna Zappa
Jeffrey Detras
Muhammad Naveed Tahir
Terry Lee
Vassilis Protonotarios
Xavier Greg I. Caguiat
Ibnou Dieng
Xuefu Zhang
Join us !

10. IGAD 2017 pre-meeting updates on RDI activities / deliverables
Improve/expand membership
remind everyone to register to RDI website (listed members)
introduction letter to be sent to prospective members
Set up a survey
finish draft survey (D1) end of May (all in WG),
we need to pattern our survey questions based on the outline of the proposed cookbook
include AfricaRice and IRRI -- list of respondents:
design of online survey form (web-based, on-line editing - ask Esther's help - May )
Open survey from June - Aug
Work on the cookbook
(D2) look at the template of cookbook from Wheat WG
Use cases, FAQ
contain other output deliverables (D3, D4, )

11. RDI activities / deliverables
Evaluation of a prototype on Rice specific data registry
(D3) - End September (data – survey existing, eg. Dryad, CKAN/DKAN , Dataverse, institutional repositories; analysis method publication - Galaxy, RDA DTR ,PID) ...
Recommendations for ontologies appropriate for managing rice data
(D4) - structured list of which ontologies appropriate to rice are categorized by different fields of study (concept map to -> appropriate ontologies)
-- post shared list in RDI portal
Good practices/method(s) for digitization of rice legacy data
Digitization: -- few cases in India, Thailand, Japan, need to present the best cases and write up these best practices
-- people / services (manual transcription/encoding): guidelines how to properly do this (QC..)

12. Thank you! Questions ?