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ISSUE #5  /  29 May,  2019                                                                                                  NEWSLETTER


Welcome to the May 2019 Module 1 Newsletter.

You are receiving this email because you are a valued collaborator of Module 1 Organize of the CGIAR Platform for Big Data in Agriculture. We use MailChimp to provide updates on Module 1 activities, and with the recent changes of the EU GDPR, we would like to remind you that you can at any time update your preferences or unsubscribe from this list by following the links included at the bottom of the Newsletter.

Happy reading!

What we've been working on
We are proud to announce an updated identity for GARDIAN, which includes a new logo, and some new functionalities -- which will continue to grow and improve. The aim of the redesign was to offer a better look and easier navigation, as well as to introduce new functionalities. We invite you to visit the website at: A section is now devoted to analytics with clear guidelines on FAIR metrics to see how FAIR scores are calculated, and how you could improve these.
AgroFIMS (Agronomy Field Information Management System) 
AgroFIMS draws fully on ontologies, particularly the Agronomy Ontology and the Crop Ontology. It consists of modules that represent the typical cycle of operations in agronomic trial management and enables the creation of data collection templates resulting in  semantically described data variables. Digital data collection is available via the KDSmart mobile application developed by Diversity Arrays Technology, with other platforms to be enabled this year. 

Two user-testing workshops were organized in September 2018 and in March 2019, with participants including agronomists, crop modelers and developers from CGIAR centers (CIP, IITA, CIMMYT, Bioversity International, IFPRI), the University of Florida, and Rothamsted Research. The feedback collected during these meetings is helping us fine-tune a beta version that will be field-tested in summer 2019.
Other activities 
The Module 1 team is delighted to be able to turn to tasks not related to POWBs, Annual Reports, and budgets/PPAs -- which occupied a substantial part of our time early in the year! Thank you for your efforts and patience with this process, and most importantly, for your hard work on various Module 1 fronts. If you have not seen it already, please have a look at the Platform's overall Annual Report, much of which your efforts helped realize. Apart from spearheading tool development, we have been working on several other activities in the first half of this year, a few of which are highlighted below: 
  • Development of use cases for data analysis pipelines with the University of Florida (crop modeling) and the University of California, Davis (spatial analysis).
  • Iterative tests of the COPO tool to ease metadata entry (CG Core v.2.0) and data annotation with ontology terms.
  • Development of a joint convening with Chatham House and Cloudera Foundation, provisionally entitled "Harnessing AI and Big Data for Smallholders in Developing Countries" and slated for July 30-31.

Big Data Convention & DIM COP Annual Meeting

This year’s convention will be held in Hyderabad, India, 16-18 October, and hosted by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). To learn more about the event, visit the Convention 2019 web page.

The DIM COP annual meeting: Stay tuned for more information on this!

Working Groups (WGs) are intended to be a forum for cooperation and participation, with members sharing with each other what information, knowledge and expertise they have to help sort issues that are common to benefit all. Your active participation ensures that we move ahead cooperatively and efficiently, so big THANK YOU for your time and dedication!
Data & Information Management Community of Practice: new group created! 
During the DMTF & OAWG annual meeting in Naivasha in late October, it was proposed that both groups work together in the future as the Data and Information Management Community of Practice (DIM CoP). This includes the Metadata, Dataverse, Ontology and Open Access Working Groups; members of the former DMTF are automatically part of the DIM COP. You will soon receive notification of your membership to the DIM COP - please help us improve this collaboration space and send your comments/suggestions to Michelle Fotsy.
CGIAR PII Interest Group 
The CGIAR PII Interest Group was formed at the end of 2018. It is a virtual meeting place for the exchange of ideas, information and resources related to privacy, ethics, confidentiality, data protection, IT security & pro-privacy tools/services. 

The CGIAR PII-IG has been set up by the CGIAR Big Data Platform to facilitate multi-disciplinary interaction and knowledge sharing across CGIAR on issues relevant to the handling of personally-identifiable information (PII) in the Research Project Data Lifecycle. Active participation is sought from CGIAR researchers across all disciplines as well as specialists with information management, IT, IRB/ethics, policy, legal and IT expertise.

A webinar on 19 December 2018 discussed efforts by USAID and the CGIAR’s Big Data Platform to provide practical guidance on privacy protection and ethics in research. The Platform’s Responsible Data Guidelines: Managing PII in the Research Project Data Lifecycle released in advance of the webinar have been updated to incorporate feedback and released with complimentary resources focusing on:
  • Privacy Protection and Ethics: Key Concepts
  • PII & Data Management Plans
  • PII & Location Data
  • PII & Privacy Impact Assessments
  • PII Data Sharing

These resources are available via the CGIAR PII Interest Group SharePoint site which is accessible to all CGIAR staff. USAID will be invited to present a webinar once their Guidelines and Case Studies are released in Q1, 2019.  

From the Open Access Working Group (OAWG)
At the Joint DMTF-OAWG meeting held in Naivasha, Kenya, Ryan Miller from IFPRI was nominated as the lead of the Open Access Working Group. Since Naivasha the OAWG has welcomed new members and has met virtually every month. Discussions have been focused on sharing information on changes in the world of scholarly publishing related to Open Access, and other issues related to OA like copyright. The group is working on a white paper to document the collected experience of the CGIAR and its implementation of the OA policy, the value of that policy for our audience, and the challenges of full implementation within the changing scholarly publishing environment. So, watch this space for new developments!
From the Dataverse WG
The Dataverse Working group has been focusing on two main areas of work:
(1) Agriculture metadata block for CG-Specific fields: Working alongside the Metadata Working Group, the Dataverse Working Group are working with Harvard Dataverse Team to add fields for CG-specific metadata. Once completed this will result in the CGIAR Dataverse repositories being CG Core v. 2.0 compliant. (2) Creating a CGIAR Dataverse on Harvard: This effort will basically bring all the Dataverse from the CG centers collectively under one umbrella “CGIAR.” However, it will only cover the data repository from the centers that are already on Harvard. It will add more visibility to the datasets collectively as CGIAR while the centers are still able to maintain their independence. For more information contact either Nilam Prasai or Leroy Mwanzia.

From the Metadata WG
The Metadata WG has been busy finalizing the new version of the CG Core. In order to facilitate communication on the application profile, a GitHub repository has been created with guidelines and examples. The idea is to open the CG Core for feedback using GitHub during the next month before releasing officially the new version.

The CG Core has been implemented in the COPO tool to facilitate and harmonize the description of the information products by Information Specialist and researchers. Currently, COPO can be used to push metadata to institutional repositories such as Dataverse, CKAN or CGSpace.

From the Ontology WG & CoP
The Ontologies CoP is expanding the ontologies we maintain on a regular basis. The Agronomy Ontology (AgrO) is integrating terms on crop rotation. The Crop Ontology (CO) has added traits from Participatory Evaluation of varieties for Roots, Tubers and Bananas. The household module of the Socio-economic Ontology (SociO!) is in stand-by while the 100 core Questions for household surveys are finalized.

A webinar on ontologies for WorldFish was organized by Jacqueline Muliro to sensitize data managers and scientists on the importance of using controlled vocabularies and ontologies. The result is the creation by WorldFish of working groups on ontologies for Small Fisheries and Aquaculture.

On the communication side, the Ontologies CoP greatly improved the communications channels
thanks to the active support of Celine Aubert and Aman Sidhu. All webinars and PhenoHarmonIS2018 keynotes presentations are available on the new YouTube channel 'Ontologies in Agriculture' and an Ontologies LinkedIn group was created to share news and comments. The content of the CoP Ontologies web page was expanded with information on the working groups: Plant Phenotypes Ontologies, Socio Economic Ontology, Agronomy Ontology and soon Fish Ontology. Anyone interested can subscribe to the working group using the online form. A section provides information on tools recommended to use ontologies, the criteria indicated by ontology experts to select an ontology of reference to annotate data. 

The CoP launched a series of webinars to debate with experts, share knowledge and advance our thinking on selected topics. The first webinar held with an expert panel last February was on the 'criteria that make an ontology a reference for data annotation'. The next webinar planned on 12 June, 3:00pm CEST will aim to answer the question: 'Can Machine Learning technologies be useful to create or complete ontologies in agriculture?'. (

A feasibility study has started with Pier Luigi Buttigieg, Alfred Wegener Institute, Bremen, Germany, on the mapping and annotation of the CGIAR Strategic Research Framework with the Interface Ontology of the Sustainable Development Goals (SDG) to assess the potential for accessing CGIAR Data through the SDG interface, and thus display CGIAR's contribution to SDGs.

What's coming up
Upcoming webinars - stay tuned!

June 12, 2019: Machine Learning and Ontology [Webinar organized by the Ontologies COP] 
[Date TBD]: GARDIAN FAIR compliance - How to improve FAIRness of resources.


Past webinars

We host webinars designed to facilitate exchange among our members and support capacity building. Click on the links below to access recordings. Please note that some events are facilitated through the CGIAR Big Data course Platform and are internal to CGIAR for open learning and conversation within CGIAR specifically. You will need to register to to access those.

February 9, 2017: BMGF OA Policy presented by Ashley Farley [Associate Officer, Knowledge and Research Services of the Open Access Team, Bill & Melinda Gates Foundation].

July 10, 2017: An introduction to FAIR Data Stewardship presented by Erik Schultes [FAIR Data Scientific Projects Lead at the Dutch Techcentre for Life Sciences and at the Human Genetics Department at the Leiden University Medical Center].

September 11, 2017: An Introduction to the Concept and Use of Ontologies in Science presented by Elizabeth Arnaud & Marie-Angelique Laporte [Bioversity International].

October 5, 2017: Ontology Applications - A Use Case, presented by Medha Devare [CGIAR Big Data Module 1 Lead], Marie-Angelique Laporte & Elizabeth Arnaud [Bioversity International]. Link to presentation available upon request. 

November 23, 2017: An overview of RHoMIS (Rural Household Multiple Indicator Survey), presented by Mark van Wijk [Senior Scientist at ILRI].  

March 6, 2018: Text Mining and Semantic Resources for Agriculture & Food Science, presented by Sophie Aubin & Robert Bossy [INRA, the French National Institute for Agricultural Research].

May 7, 2018: Describing community data: consequences & opportunities for knowledge workers, presented by Dr. Chris Baker [CEO, IPSNP Computing Inc.].

Sept 19, 2018: Digital Strategy and CGIAR, presented by Brian King and Medha Devare [CGIAR Platform for Big Data in Agriculture].

Oct 30, 2018: Open data, privacy protection and ethics clearance: Tensions in a fragmented compliance landscape, presented by Rodrigo Sara [for the CGIAR Platform for Big Data in Agriculture] and a panel of experts.

Nov 30, 2018: The General Data Protection Regulation, Capacities and Implications for Compliance against CGIAR, presented by Rodrigo Sara [for the CGIAR Platform for Big Data in Agriculture].

Dec 19, 2018: Responsible Data Guidelines, presented by Rodrigo Sara [for the CGIAR Platform for Big Data in Agriculture].  

Jan 23, 2019: Managing Research Data with Globus, presented by Greg Nawrocki [Director of Customer Engagement of the Globus Department at the University of Chicago].

Feb 28, 2019: What makes an ontology a reference for data annotation? webinar organized by the Ontologies COP and presented by a panel of experts. 

April 10, 2019: A tale of two platforms – Gardian and GEMS: Platforms for discovering, sharing and storing datasets and tools,
webinar organized by the Crop Modeling Community of Practice and presented by Medha Devare [CGIAR Big Data Module 1 Lead], Philip Pardey and Kevin Silverstein [University of Minnesota]. 

May 29, 2019: Demo of early prototype of an ontology annotation tool, presented by Medha Devare [CGIAR Big Data Module 1 Lead]. Link to presentation will be made available. 

Useful resources

Questions/Concerns? Here's how you can get in touch:
Medha Devare
Michelle Fotsy
Copyright © 2019 CGIAR Platform for Big Data in Agriculture, All rights reserved.

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