ALBERT

Description: Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture and agrifood systems requires quality data labeling or annotation in order to be interoperable. As recommended by the FAIR principles, data, labels, and metadata must use controlled vocabularies and ontologies that are popular in the knowledge domain and commonly used by the community. Despite the existence of robust ontologies in the Life Sciences, there is currently no comprehensive full set of ontologies recommended for data annotation across agricultural research disciplines. In this paper, we discuss the added value of the Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture for harnessing relevant expertise in ontology development and identifying innovative solutions that support quality data annotation. The Ontologies CoP stimulates knowledge sharing among stakeholders, such as researchers, data managers, domain experts, experts in ontology design, and platform development teams. Digital technology use in agriculture and agrifood systems research accelerates the production of multidisciplinary data, which spans genetics, environment, agroecology, biology, and socio-economics. Quality labeling of data secures its online findability, reusability, interoperability, and reliable interpretation, through controlled vocabularies organized into meaningful and computer-readable knowledge domains called ontologies. There is currently no full set of recommended ontologies for agricultural research, so data scientists, data managers, and database developers struggle to find validated terminology. The Ontologies Community of Practice of the CGIAR Platform for Big Data in Agriculture harnesses international expertise in knowledge representation and ontology development to produce missing ontologies, identifies best practices, and guides data labeling by teams managing multidisciplinary information platforms to release the FAIR data underpinning the evidence of research impact. The deployment of digital technology in Agriculture and Food Science accelerates the production of large quantities of multidisciplinary data. The Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture harnesses the international ontology expertise that can guide teams managing multidisciplinary agricultural information platforms to increase the data interoperability and reusability. The CoP develops and promotes ontologies to support quality data labeling across domains, e.g., Agronomy Ontology, Crop Ontology, Environment Ontology, Plant Ontology, and Socio-Economic Ontology.

Description: Four years after the Genomic Observatories Network was formally established as a collaboration between the Group on Earth Observations Biodiversity Observation Network and the Genomic Standards Consortium, we review the development of the network. Considering institutional infrastructure, we note the growing role of omic observation in active and increasingly interlinked marine networks, with examples such as EMBRC/ASSEMBLE, International Long Term Ecological Research Network, AtlantOS, National Association of Marine Labs, Smithsonian MarineGEO, and Partnership on Observation of the Global Oceans. We also note some key human elements essential to meeting the networks' goals, address how the community is evolving, and why performing seemingly simple tasks within a broadly distributed community presents significant challenges even among those who have agreed to use standards. From the perspectives above, we review lessons learned from use cases that leverage Genomic Observatories Network, such as the Autonomous Reef Monitoring Structures (ARMS), Ocean Sampling Day (OSD) and myOSD, which included experiences with citizen science. Looking forward, we survey 1) promising new technologies for in situ biological observation (e.g., cheap 3D printed omics samplers), 2) progress towards adoption of omics methods in marine policy and conservation programs, and 3) opportunities that a Genomic Observatory brings, alone or embedded in a network, to address novel scientific questions and support Essential Biodiversity Variables, Essential Ocean Variables, and indices such as the Ocean Health Index. Given the data intensive nature of omics investigation, we note emerging cyberinfrastructure solutions, such as the Genomic Observatories Metadatabase (GeOMe), an open-access repository for geographic and ecological metadata associated with biosamples, and predictive modeling efforts, such as those of the Island Digital Ecosystem Avatar (IDEA) Consortium. Finally, we explore the potential of Genomic Observatories as components of high-resolution calibration sites. Such observatories would provide super-contextualized "data trusts" for machine learning and artificial intelligence applications that draw on multi-omic observation.

Description: Essential Biodiversity Variables (EBV) are fundamental variables that can be used for assessing biodiversity change over time, for determining adherence to biodiversity policy, for monitoring progress towards sustainable development goals, and for tracking biodiversity responses to disturbances and management interventions. Data from observations or models that provide measured or estimated EBV values, which we refer to as EBV data products, can help to capture the above processes and trends and can serve as a coherent framework for documenting trends in biodiversity. Using primary biodiversity records and other raw data as sources to produce EBV data products depends on cooperation and interoperability among multiple stakeholders, including those collecting and mobilising data for EBVs and those producing, publishing and preserving EBV data products. Here, we encapsulate ten principles for the current best practice in EBV-focused biodiversity informatics as ‘The Bari Manifesto’, serving as implementation guidelines for data and research infrastructure providers to support the emerging EBV operational framework based on trans-national and cross-infrastructure scientific workflows. The principles provide guidance on how to contribute towards the production of EBV data products that are globally oriented, while remaining appropriate to the producer's own mission, vision and goals. These ten principles cover: data management planning; data structure; metadata; services; data quality; workflows; provenance; ontologies/vocabularies; data preservation; and accessibility. For each principle, desired outcomes and goals have been formulated. Some specific actions related to fulfilling the Bari Manifesto principles are highlighted in the context of each of four groups of organizations contributing to enabling data interoperability - data standards bodies, research data infrastructures, the pertinent research communities, and funders. The Bari Manifesto provides a roadmap enabling support for routine generation of EBV data products, and increases the likelihood of success for a global EBV framework.

Description: Climate change and sustainable use of natural capital demand increased collaboration across the sciences. The first steps for effective collaboration often focus on improving interoperability between observation and analyses methodologies. This is traditionally done through a combination of standards and best practices. The ocean observation community and observing infrastructures - with regionally diverse members working in physics, chemistry, biology and engineering - is looking toward a dynamic consensus-building approach to match the rapid pace of technological evolution. This is an essential part of the long-term cooperation among ocean observing infrastructures. In the last 12 months, the ocean observing community has implemented an Ocean Best Practices System (OBPS). This System was recently adopted by the Intergovernmental Ocean Commission as an international project under GOOS and IODE. The System consists of a permanent OBPS repository hosted by IODE with state-of-the-art semantic discovery and metadata indexing for improved access to best practices and, eventually, to the data associated with them. There have been discussions to understand how to deal with differing best practices and standards on the same observation or analyses objective and other issues that arise from a comprehensive ocean best practices system. A recent survey, to be described, offers options on alternative approaches. Further, we have created a forum, in “Frontiers in Marine Science” for discussion of best practices and their applications. This presentation will cover options for evolving and sustaining ocean best practices across infrastructures. The recommendations build upon the community survey, the OGC experience, the outcomes of the OceanObs’19 conference as well as inputs from the Decade for Ocean Sciences community meetings. The extension of this work to other communities will also be examined.

Description: Target audience: All ocean scientists who wish to share or discover best practice documents in their domain. Background: A working group convened under the AtlantOS project and including partners from ODIP, IODE, JCOMM, IEEE, and AWI is currently developing new technologies and approaches for handling best practices (BPs) across ocean science. The goal of the working group is to create a sustained repository for BPs, to ease their propagation and adoption. Goals: After briefly describing its work, the BP working group will engage town hall participants in a discussion on 1) how best to find and centrally archive BPs in participants' disciplines and 2) what capacities a central archive of BPs would need to help participants create, discover, share, and archive their BPs. The participant input gathered will be used to further the development of a multidisciplinary repository for BPs and better harmonise ocean observation.