Eoghan Ó Carragáin, Carole Goble, Peter Sefton, Stian Soiland-Reyes (2019):
RO-Crate: A lightweight approach to research object data packaging.
RO-15 at Workshop on Research Objects (RO 2019), IEEE eScience 2019, 2019-09-24, San Diego, CA, USA.
RO-Crate, a lightweight approach to Research Object data packaging
Eoghan Ó Carragáin¹, Carole Goble², Peter Sefton³, Stian Soiland-Reyes²⁴
¹ University College Cork, Ireland
² The University of Manchester, UK
³ University of Technology Sydney, Australia
⁴ University of Amsterdam, Amsterdam, Netherlands
- License: Creative Commons Attribution License (CC BY 4.0).
- Modifications: Formatting as Markdown; reference in s11 house style; reference author lists completed; Gigascience citation updated.
A Research Object (RO) provides a machine-readable mechanism to communicate the diverse set of digital and real-world resources that contribute to an item of research. The aim of an RO is to replace traditional academic publications of static PDFs, to rather provide a complete and structured archive of the items (such as people, organisations, funding, equipment, software etc) that contributed to the research outcome, including their identifiers, provenance, relations and annotations. This is increasingly important as researchers now rely heavily on computational analysis, yet we are facing a reproducibility crisis  as key components are often not sufficiently tracked, archived or reported.
We are developing Research Object Crate (or RO-Crate for short), a lightweight approach to package research data with their structured metadata, based on schema.org annotations in a formalized JSON-LD format that can be used independent of infrastructure to encourage FAIR sharing of reproducible datasets and analytical methods.
Earlier work introduced the notion of Research Objects . Their formalization combines existing Linked Data standards: W3C RDF, JSON-LD, OAI-ORE, W3C Web Annotations, PROV, Dublin Core Terms, ORCID. The RO ontologies  combined these to describe ROs, but do not themselves formalize how ROs are saved or transmitted. Multiple formats have since been realized: the portal RO Hub  use RDF REST resources; while workflow provenance make RO Bundle ZIP files  or Big Data BagIt archives (BDBag)  . Each of these require RO support in the packaging infrastructure.
Multiple data packaging initiatives have recently emerged, within Research Data Alliance, Force11, DataOne and elsewhere; like Frictionless data  for table-like files, BioCompute Objects for regulatory science , CodeMeta for software, Psych-DS for psychology studies, and DataCrate  for datasets. RDA has surveyed a large variety of data packaging formats across different domains.
Common among these is structured metadata, e.g. with a single JSON file that refer to neighbouring data files and scripts maintained and published together, e.g. in GitHub. Many of these initiatives use schema.org  as basis for common metadata. With JSON-LD this offers a developer-friendly experience and interoperability with web conventions outside of the research domain.
Data packaging principles
At an RDA meeting on data packaging we concluded that many initiatives arrive at similar principles: simple folder structure; JSON-LD manifest; schema.org for core metadata; BagIt for fixity; OAI-ORE for aggregation. This points to: a) appetite for general package/folder-oriented approach in different contexts; b) a generic solution won’t work for all and needs to be domain-extensible; c) a tendency to re-invent the wheel, leading to sub-optimal interoperability and duplication of effort.
We have identified a gap for a solid base format for data packaging that also allow communities to build domain-specific solutions. Frictionless data  could arguably fill this gap, with mature specifications and a strong design philosophy, however as an independent JSON format it does not fully apply Linked Data principles, and would be harder to use in FAIR integrations and extensions.
Our proposal is to build on DataCrate  to evolve RO-Crate, based around these principles: a) metadata as Linked Data, using schema.org as much as possible; b) extensible for different domains; c) retain the core Research Object principles Identity, Aggregation, Annotation; d) inferred metadata rather than repetition; e) “just-enough” provenance; f) layered validation; g) archivable with BagIt; h) hooks to reuse existing domain formats; i) lightweight programmatic generation and consumption.
Similar to the approach of BioSchemas, rather than building new specifications from scratch, we aim to build best-practice guides and validatable profiles for building rich research data packages with existing standards, without requiring expert knowledge for developing producers and consumers.
In the desire to make a lightweight approach that is also generally applicable we have focused primarily on RO-Crate as a way to capture and describe a dataset of neighbouring files, for instance maintained in a GitHub repository, while also describing external resources and provenance.
A goal of RO-Crate is to simplify the creation and maintenance of metadata, supporting both a manual or programmatic manner, with a set of opinionated profiles for describing common resource types such as tables, organizations, equipment, software, workflows, places. One design challenge is the pressure between explicit and implicit. For instance, should the creator be repeated for every file they also made, or can the creator of the research object be a reasonable default? Do all files in a directory need to be listed in the RO-Crate metadata, or is it sufficient to describe the directory or a filename glob pattern?
Recognising this challenge, our vision is a separation of concern between packaging and description. By letting
ro-crate-metadata.jsonld be used in any file-or web-based approach at a root directory, we can rely on BDBag  when the RO-Crate needs to be shipped, archived or deposited. At this point the Research Object would be “completed” to generate a full “classical” Research Object manifest, integrating the BagIt checksums and file list with metadata implied from the RO-Crate metadata. We are developing this tooling for this completion step, which should also perform validation against the declared profile, might include snapshotting remote resources and minting of RO identifiers using MinId . Although an RO-Crate is in a sense a recipe for making full Research Objects, RO-Crate metadata can also be consumed “as-is” as JSON-LD if discovered in the wild, or updated programmatically based on the profile and other schema.org markup.
Building community consensus
RO-Crate is a fresh initiative, bringing together data archive and repository maintainers with existing Research Object, workflow and provenance communities. Starting as a small cross-domain group, organically formed to build the core principles and first sketches of their use, we are now expanding to collect use cases and reaching out to other packaging initiatives to build common ground.
One emerging use of RO-Crate is for capturing workflows and tools in a federated workflow repository being built in EOSC-Life, a large European Open Science Cloud project across 13 research infrastructures in the life science domain. However RO-Crate is also aiming to be usable by individual scientists with no particular infrastructure beyond Jupyter notebook, who may not have the time or motivation to use a cascade of metadata vocabularies and research data management tools .
RO-Crate development and discussion is done openly in a GitHub repository by volunteers, with monthly telcons to synchronize the effort. Anyone can join to help form the RO-Crate approach.
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An earlier version of this abstract was accepted for BOSC 2019, see https://doi.org/10.5281/zenodo.3250687.