COPO: a metadata platform for brokering FAIR data in the life sciences

Abstract

Scientific innovation is increasingly reliant on data and computational resources. Much of today’s life science research involves generating, processing, and reusing heterogeneous datasets that are growing exponentially in size. Demand for technical experts (data scientists and bioinformaticians) to process these data is at an all-time high, but these are not typically trained in good data management practices. That said, we have come a long way in the last decade, with funders, publishers, and researchers themselves making the case for open, interoperable data as a key component of an open science philosophy. In response, recognition of the FAIR Principles (that data should be Findable, Accessible, Interoperable and Reusable) has become commonplace. However, both technical and cultural challenges for the implementation of these principles still exist when storing, managing, analysing and disseminating both legacy and new data. COPO is a computational system that attempts to address some of these challenges by enabling scientists to describe their research objects (raw or processed data, publications, samples, images, etc.) using community-sanctioned metadata sets and vocabularies, and then use public or institutional repositories to share them with the wider scientific community. COPO encourages data generators to adhere to appropriate metadata standards when publishing research objects, using semantic terms to add meaning to them and specify relationships between them. This allows data consumers, be they people or machines, to find, aggregate, and analyse data which would otherwise be private or invisible, building upon existing standards to push the state of the art in scientific data dissemination whilst minimising the burden of data publication and sharing.

ISA API: An open platform for interoperable life science experimental metadata

“…The Collaborative Open Omics (COPO) platform [ 70 ] supports ISA-JSON as one of its metadata formats and uses ISA API's SRA exporter to allow COPO users to publish studies directly to the European Nucleotide Archive. COPO configures its back end and front end for brokering various data types, including omics data, through consuming ISA configurations.…”

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems

“…The CoP members have identified and are testing COPO (collaborative open plant omics) ( https://copo-project.org/ ), a promising tool currently being developed by the Earlham Institute, which provides metadata and ontology annotation capabilities, thus offering a platform for researchers to publish their research assets. 37 COPO uses the EBI OLS to perform real-time look-up of ontology concepts when a user enters a term. The COPO tool goes further than simply adding keywords to metadata by supporting the tagging of column headings of data files where values of variables are stored, thus increasing the interoperability of the data.…”

Data management challenges for artificial intelligence in plant and agricultural research

“…7 (Rife & Poland 2014) and the Grassroots information infrastructure of the BBSRC Designing Future Wheat programme. Efforts such as the COPO platform also implement semantic standards, including MIAPPE, in user interfaces to aid data brokering which underpins the availability of well-described datasets that can in turn power AI/ML studies (Shaw et al, 2020).…”