Research Object. Enabling reproducible, transparent research

Research Object Crate

RO-Crate has been developed as a schema.org-based JSON lightweight approach to the next generation Research Object serialization.

2019-11-05: The specification RO-Crate 1.0 has been released. Join the community to help further develop RO-Crate!

Workshop on Research Objects (RO2019)

The RO2019 workshop was at IEEE eScience Conference 2019 in San Diego, US. This successful workshop followed the initial RO2018. Proceedings of accepted papers and talks are available, along with links to slides and posters.

Researchobject.org aims to map the landscape of initiatives and activity in the development of Research Objects, an emerging approach to the publication, and exchange of scholarly information on the Web. Research Objects aim to improve reuse and reproducibility by:

  • Supporting the publication of more than just PDFs, making data, code, and other resources first class citizens of scholarship
  • Recognizing that there is often a need to publish collections of these resources together as one shareable, cite-able resource.
  • Enriching these resources and collections with any and all additional information required to make research reusable, and reproducible!

Research objects are not just data, not just collections, but any digital resource that aims to go beyond the PDF for scholarly publishing!

Going beyond the PDF

Science advances on a foundation of trusted discoveries. Reproducing an experiment is one important approach that scientists use to gain confidence in their conclusions.

  • Marcia McNutt, Editor-in-Chief of Science

The reuse and reproduction of scientific experiments as they are described in publications can be hard. Often it requires additional information, data, tooling or support beyond that provided in the text of a traditional publication.

As part of one research investigation you might for example have:

  • Slides hosted on slideshare,
  • Code in a github repository,
  • Data in figshare,
  • Data in ArrayExpress.

A growing number of activities are developing new mechanisms, or repurposing existing mechanisms in order to describe and associate resources like this together, in a machine-readable manner, so that they can be more easily shared, and exchanged.

The goal of research objects is to improve the potential for understanding and reuse of research by making sure that the information that is needed to make a published resource useful is associated with it, and shared as a whole.

How?

aggregation

There are a growing number of, individuals, groups, and initiatives – all trying to improve the state of scholarly publication. These range from domain specific to general, and from the practical and immediately actionable, to the more visionary and experimental.

What is emerging from these activities is a common set of goals and principles – features that are required required to support research that is Findable, Accessible, Interoperable, and Reusable (FAIR).

To understand more about the principles, goals of the Research Object approach, head over to the Overview page.

To discover the range of on going activities, and mechanisms that can be used to build research objects, check out the RO Initiatives & Resources page.

Get Involved!

ResearchObject.org is a community site aimed at gathering information, ideas, and interest around the topic of modernizing scholarly publication. You can contribute using GitHub issues or pull requests.

Most of the current RO activities are happening as part of the RO-Crate community which you are welcome to join!

Unless otherwise noted, the documentation and images on this website is Open Source and licensed as Apache License, version 2.0:

  • Copyright © 2013-2014 University of Oxford, UK
  • Copyright © 2013-2020 The University of Manchester, UK

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0</a</small>

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Please see the file NOTICE for required attributions.

2018-10-29 Workshop on Research Objects

The Workshop on Research Objects (RO2018) has been announced as part of IEEE eScience Conference 2018. The RO2018 workshop takes place on 2018-10-29 in Amsterdam, Netherlands. The Call for Papers is out, which particularly encourages to submit in a FAIR research data packing format.
Tags: escience, ro2018, workshop

2017-12-05 FAIRy Stories for Christmas

On 2017-12-05, Carole Goble presented the keynote FAIRy Stories for Christmas at the 10th International Semantic Web Applications and Tools for Healthcare and Life Sciences Conference (SWAT4LS): [Read More]
Tags: fair

2017-11-27 BioCompute Objects

BioCompute Objects (BCO) is a community-driven project backed by the FDA (US Food and Drug Administration) and George Washington University to standardize exchange of High-Throughput-Sequencing workflows for regulatory submissions between FDA, pharma, bioinformatics platform providers and researchers. Members of the Research Object team (Carole Goble, Stian Soiland-Reyes, Michael R Crusoe)... [Read More]
Tags: bagit, bco, cwl, fda

2017-10-24 Revamped ROHub portal officially released

The completely renovated ROHub portal, developed by the EVER-EST project, includes a new and modern design, improved performance, plus a set of new features focused on improving the user experience. The ROHub was also presented at IEEE eScience Conference, described in the paper Towards a Human-Machine Scientific Partnership Based on... [Read More]
Tags: ever-est, rohub, Tooling

2017-10-21 Keynote at SemSci ISWC 2017

Carole Goble presented the keynote The Rhetoric of Research Objects at the First Workshop on Enabling Open Semantic Science (SemSci2017), co-located with the 16th International Semantic Web Conference (ISWC 2017). [Read More]
Tags: semantic web

2017-09-27 eLife Reproducible Portable Publications

On 2017-09-27 I met with Naomi Penfold and Giuliano Maciocci from the journal eLife, Oliver Buchtala and Michael Aufreiter working on Substance, and Nokome Bentley doing Stencila. Our topic was the eLife/Substance/Stencila collaboration for a Reproducible Document Stack, and how that can relate to Research Objects and other Scholarly HTML... [Read More]
Tags: markdown, Packaging, publication, Reproducibility

2016-05-18 Make Research Reproducible Again

On 2016-05-18, Stian Soiland-Reyes presented Make Research Reproducible Again at the ELIXIR organized hackathon Tools, Workflow and Workbenches at Institut Pasteur in Paris. The hackathon had a very strong focus and presence for both bio.tools and Common Workflow Language, one of the activities was to explore how CWL metadata profile could... [Read More]
Tags: cwl, elixir, hackathon

2016-01-28 ROHub

On 2016-01-28, Raul Palma presented ROHub at the Dagstuhl Seminar 16041 Reproducibility of Data-Oriented Experiments in e-Science: [Read More]
Tags: Dagstuhl

BagIt for transferring and archiving Research Objects

BagIt is an Internet Draft that specifies a file system structure for transferring and archiving a collection of files, including their checksums and brief metadata. BagIt is commonly used by digital library communities for archival purposes, and is mandated by the Library of Congress for digital preservation. Research Object bundles... [Read More]
Tags: Archive, bagit, Containers, Exchange, Packaging, RO Bundle, specification, ZIP

Research Objects at BOSC

Norman Morrison presented Research Objects at BOSC including work on ‘Research Objects in the wild’, where Research Objects supported a reproducibility case study that was recently publish in PLOS One. This work was also presented at BOSC by Alejandra González-Beltrán from the ISA-team and you can get the slides here. You... [Read More]

Research Objects bioCADDIE webinar

On June 11th 2015, Carole Goble presented The Research Object Initiative: Frameworks and Use Cases as part of the bioCADDIE webinar series.

Why publish and be so damned hard to find?

Chris Parr from Times Higher Education Interviewed Prof Carole Goble at JISC Digifest. You can read and listen to Carole’s views on the lack of transparency about academic research methods by clicking on the links below. “Outdated practices and lack of simplicity result in ‘unfindable’ work, Carole Goble tells Jisc Digital Festival” [Read More]

JISC Digifest Keynote

Carole Goble gave a thought provoking keynote presentation at the JISC Digital Festival where she talked about www.researchobject.org. It was great to see that the TARDIS (Time and Relative Dimensions in Scholarship) analogy was picked up by Chris Parr from Times Higher Education. You can find the talk live on the JISC... [Read More]
Tags: JISC

Combining Docker & R for Reproducible Research

Interesting preprint posted to arxiv by Carl Boettiger from UC Santa Cruz, describing an example of an increasing trend to use Docker to package up investigations as reproducible research: Carl Boettiger, An introduction to Docker for reproducible research, with examples from the R environment

Example of Encoding an RO using RDF-a

As an example of encoding a Research Object using RDF-a is now available to the community, see the “Parameter Optimization of an Ecological Niche Modeling Workflow”. The page represents a Research Object representing the optimizations made on the AUC output parameter of the ENM workflow using Support Vector Machines (SVM). The optimizations are performed using... [Read More]

The Launch of Research Object Creator Tool (Give it a try!)

 Research Object Creator Tool is a very lightweight RO creation tool built by Daniel Garijo of UPM. The tool takes as input a LaTeX file and extracts its title and abstract to create an annotated page in RDF-a. It also produces a structure of the contents to reference, so users only... [Read More]

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

Wf4Ever member Daniel Garijo of UPM published an article, titled “Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome” in the world-leading Computational Biology journal PLOS ONE, with researchers from 5 other institutions. The article quantifies the cost of reproducing computational research in computational biology by using an... [Read More]

10th International Conference on Preservation of Digital Objects

  Half day tutorial: From Preserving Data to Preserving Research: Curation of Process and Context at iPres 2013. The video presented at the tutorial shows the process of building a research object from the music research experiment, with the purpose of sharing and preserving the experiment and its context, in order to facilitate... [Read More]

From Preserving Data to Preserving Research:Curation of Process and Context

The TIMBUS and Wf4Ever projects are offering a half-day tutorial at the International Conference on Theory and Practice of Digital Libraries (TPDL) 2013, in Valletta, Malta on September 22, 2013. http://tpdl2013.upatras.gr/tut-pdpr.php ABSTRACT In the domain of eScience, investigations are increasingly collaborative. Most scientific and engineering domains benefit from building on... [Read More]

Wf4Ever in ISMB/ECCB 2013

Wf4Ever members are going to host a workshop on “What Bioinformaticians need to know about digital publishing beyond the PDF”, together with Dr Scott Edmund of GigaScience, at ISMB/ECCB 2013, Berlin, Germany. July 19th – 23rd, 2013 in Berlin, Germany – More info

10th ESWC 2013 Semantics and Big Data

The ESWC is a major venue for discussing the latest scientific results and technology innovations around semantic technologies. May 26th – 30th, 2013 in Montpellier, France – More info