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ISSUE #4 / June 29, 2018 NEWSLETTER
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Greetings!
Welcome to the June 2018 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 be in touch with you and 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.
The Module 1 team so far has largely been Michelle Fotsy and Medha Devare; we are pleased to announce that Sandra Perez (IFPRI; s.perez@cgiar.org) will be providing support as a Program Manager. We anticipate that Maria Garruccio will soon be lending her domain expertise to Module 1 one day each week, and Martin Mueller will be working for about a month on finalizing a draft CG Core Metadata Schema v.2.0. for the Metadata Working Group to provide input. Rodrigo Sara should also be working shortly for about a month to help guide us on data ethics and privacy issues. Welcome, Sandra, Maria, Martin, and Rodrigo!
Happy reading!
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What we've been working on
GARDIAN (http://gardian.bigdata.cgiar.org/)
CeRes has been improved and re-branded as the Global Agricultural Research Data Innovation and Acceleration Network (GARDIAN). The Big Data Platform is working to make improvements to GARDIAN this year, focusing on efforts such as: optimization of search and algorithms enabling linking of related publications and datasets; making resources FAIRer by semantically linking heterogeneous data; enhancing syntactic interoperability; exploring harvesting from more repositories; providing Centers an overview and mapping of licenses and exploring the possibility of rendering them machine readable and downloadable (e.g. with datasets). More details are available in the Agroknow workplan. If you have feedback on GARDIAN, please send it to Sandra Perez (s.perez@cgiar.org), who will ensure follow-up.
AgroFIMS (Agronomy Field Information Management System)
The Big Data Platform is facilitating the development of an ontology-based agronomy field information management system (field book template creator that includes CG Core metadata, variable descriptions, possibility for statistical analyses, quick data quality checks, one-click upload to institutional repositories, and more). This work is intended to ensure that agronomic trial data collected using the AgroFIMS will be standardized and harmonized to the extent possible at collection, and be available for semantic exploration. This effort is being led by a team of developers at CIP and the ontology team at Bioversity. An early prototype was demonstrated at agronomy breakout sessions during the May 2018 PhenoHarmonis workshop, with valuable feedback obtained from the agronomist, modeler, ontology, and developer participants from across CGIAR, academic institutions, and private sector. Current work on AgroFIMS is focused on making the system responsive to this user feedback, enhancing functionalities, and exploring digital data collection platforms, including proprietary and open source efforts for maximum user flexibility.
Other activities
Efforts are ongoing to assess how annotations for legacy data might be improved and/or standardized, to enable reuse. The results of a small pilot led by Wageningen University and Research aimed to assess the possibility of data curation by students, in conjunction with machines; this work is likely to be built on in 2018. Planned and envisioned collaborations with other Big Data partners (the University of Florida, the University of California - Davis, Oregon State University, the University of Minnesota, Syngenta, Rothamsted Research, Earlham Institute, INRA, CIRAD, Spatial Dev Inc. and others) will help develop/contribute to synergies in the development of analytical approaches and tools to more easily leverage CGIAR data discoverable through GARDIAN.
Big Data Platform - Management & Meetings
The Big Data Platform had a Management Team retreat on Feb 27 and 28 at CIMMYT to discuss progress, priorities, and Center POWBs. A high-level view of Module 1 priorities is available here. Please note that we will be trying to set up calls in August/September with data and information specialists as well as Big Data Focal Points at each Center to discuss progress on the POWBs and to try and provide support as needed.
Big Data Convention & OAWG/DMTF Meetings
CGIAR Big Data Convention 2018
3-5 October, Nairobi, Kenya
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OAWG & DMTF Annual Meetings
7-9 October, Naivasha, Kenya
We are pleased to announce that, based on the results of the brief survey to plan for our face-to-face meeting, we are making arrangements to have the 2018 DMTF & OAWG annual meetings in conjunction with the Big Data Convention. We hope to move DMTF and OAWG members from Nairobi to the beautiful (and cost-effective!) Lake Naivasha area on Friday evening or Saturday morning (October 5 or 6) for a day of rest & relaxation. These meetings will start on Sunday, October 7, and run through Tuesday, October 9 afternoon. Please plan accordingly. Both meetings will be held in parallel with joint breakout sessions and plenaries envisioned. More detailed information will follow shortly; in the meantime, please save the dates in your calendars!
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WORKING GROUPS
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!
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From the Ontology WG & CoP
 14-18 May, Montpellier, France
PhenoHarmonIS 2018 was co-organized by the CGIAR Big Data Platform, RTB, CGIAR Excellence in Breeding Platform, GOBii, CIRAD, INRA, CGIAR Excellence in Breeding Platform, EU project Phenome, NSF project Planteome and Digitag.
The workshop addressed priority topics of the Ontology CoP of Big Data and focused on harmonization of germplasm, plant phenotypic and agronomic data. It offered a forum for 110 attendees from 29 countries and 41 public institutions, universities and companies. Participants discussed ontologies and metadata standards relevant to crop phenotyping and agronomy. International speakers discussed fieldbooks to analytical pipelines and multidisciplinary platforms, addressing solutions and challenges for data harmonization, interoperability, sharing and re-use. Data included several scientific domains: conservation, breeding, gender-sensitive participatory varietal selection, agronomy and agroecology. Hands-on sessions explored the use of ontologies and standards (e.g. Minimum Information on Plant Phenotypic Experimentation - MIAPPE) and annotation tools (e.g. COPO). Several sessions focused on the agronomy fieldbook developed by CGIAR (AgroFIMS) and its ontology (AgrO). The feedback survey indicates that participants thought the workshop high level and successful. A call will be issued for hosting the next meeting.
The Socioeconomic Ontology (SociO) group made progress on creating basic concepts using existing ontologies such as the Basic Formal Ontology (BFO) , Information Artifact Ontology (IAO), Sustainable Development Goals Interface Ontology (SDGIO), and the Agronomy Ontology (AgrO). This group collaborates closely with other working groups, and together with the '100 questions‘ and CAPI working groups, hosted a May 15 webinar entitled “The 100 Questions activity within the Big Data in Agriculture platform: can we define a common core for household survey instruments?” The webinar focused on defining a core set of questions that are commonly used in household surveys, and researchers provided valuable comments related to gender/tenure, demographics, land use, crop production and incomes, crop intensification measure, livestock produce and income, etc. We plan to arrange another meeting soon to discuss more intensively. In June, the working group participated in a meeting hosted by the University of Minnesota which is developing an agroinformatics data discovery and analysis platform dubbed G.E.M.S™. Big Data Platform’s Module 1 representatives were already in attendance to assess the possibility of collaboration around ontologies. The discussion for this session focused on the scope, methodology, and best practices to build the links between existing ontologies (SociO, AgrO, SDGIO, and others).
From the Metadata WG
For the past year, Martin Mueller has done a great job leading the Metadata WG, and we would like to thank him for his commitment and efforts in supporting the review of the CG core metadata schema. Martin has left IITA for new adventures, but has kindly agreed to continue his work for about a month to develop a draft version 2.0. of the CG Core for review by the Metadata Working Group at the next meeting scheduled for 24 July 2018. We wish Martin all best in his new endeavors, and extend a warm welcome to Marie-Angélique Laporte as she takes over as Chair of the Metadata Working Group.
From the Dataverse CoP
Due to other work obligations, Kate Dreher is stepping down from being a co-chair of the Dataverse group. We take this opportunity to thank Kate for her excellent contributions to and leadership of this community over the past two years. She will participate in the meetings as a member, and Leroy will continue to lead the community as a co-chair with a new partner. The next meeting is scheduled for 19 July, and we will call for colleagues interested in helping chair this group.
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What's coming up
Upcoming webinars - stay tuned!
Blockchain in Agriculture Research Data [TBC]
Data Privacy & Ethics [TBC]
Upcoming events
November 5-8, 2018: SciDataCon - International Data Week 2018, Lusaka, Zambia. If you're interested, conference abstracts should be submitted here.
November 5, 2018: RDA 12th Plenary Meeting - part of the International Data Week 2018, Gaborone, Botswana.
Past webinars
We host webinars designed to facilitate exchange among our members and support capacity building. Click on the links below to access recordings.
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 at 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.].
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Questions/Concerns? Here's how you can get in touch:
Medha Devare m.devare@cgiar.org
Michelle Fotsy m.fotsy@cgiar.org
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