ro2019
Workshop on Research Objects 2019
Peer Review of RO-11
- Author: Anita de Waard, Marina Soares E Silva
- Title: Research Object Composer: A Tool for Publishing Complex Data Objects in the Cloud
- Submission: https://doi.org/10.5281/zenodo.3382263
- Submitted as: RO2019 abstract
- Decision: accept talk (accepted for oral presentation)
Review 1
- Reviewer: (anonymous)
Quality of Writing
Is the text easy to follow? Are core concepts defined or referenced? Is it clear what is the author’s contribution?
- fair
The writing style is clear, and the overall thread of the abstract is easy to follow. The overall topic, mapping the growing demand for data commons in bioinformatics, the need for persistent identification of research data inputs/outputs, and the need to be able to aggregate and describe complex research objects, is certainly relevant to topics outlined in the call for papers.
However, better referencing would be useful in understanding the unique contribution of this project and make the authors’ contribution clearer. For example:
-
The second paragraph opens with “In earlier work, we developed an open source tool that allows users to mint a dataset DOI in an open data repository (Mendeley Data, http://data.mendeley.com), through an API that can be accessed from a proprietary cloud-based bioinformatics workflow tool [5]”. No link/reference is given for the “open source tool”.
I was able to find a github repo https://github.com/elsevierlabs-os/nih-guid-broker containing a yaml configuration file but no source code of a tool which actually interacts with Mendeley data to mint the DOI.
The reference provided to the “proprietary cloud-based bioinformatics workflow tool” links to smart-api.info, the code of which is available on github under and MIT license. The “open source tool” should be properly referenced and the authors contribution clarified.
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No link or reference is provided for the Research Object Composer (ROC) tool, despite the fact that some relevant code appears to be available here https://github.com/ResearchObject/research-object-composer/blob/master/NOTICE.txt
Research Object / Zenodo
URL for a Research Object or Zenodo record provided? Guidelines followed? Open format (e.g. HTML)? Sufficient metadata, e.g. links to software? Some form of Data Package provided? Add text below if you need to clarify your score.
- none (e.g. only abstract in easychair/github)
I could not find a record for this in the Zenodo research object community or on the github repo. The abstract is submitted as *.odt format to easychair.
Overall evaluation
Please provide a brief review, including a justification for your scores. Both score and review text are required.
- weak accept
As noted, the abstract itself could use some clarification and the preferred/recommended submission guidelines were not followed.
Nevertheless, the abstract is relevant to the topics outlined in the call for papers. The availability of a “research object composer” tool will be of interest to audience participants, as will the discussion of the motivation to develop such a tool and the choice to adopt the “Research Object” standard in doing so.
Review 2
- Reviewer: (anonymous)
Quality of Writing
Is the text easy to follow? Are core concepts defined or referenced? Is it clear what is the author’s contribution?
- good
very short abstract
Research Object / Zenodo
URL for a Research Object or Zenodo record provided? Guidelines followed? Open format (e.g. HTML)? Sufficient metadata, e.g. links to software? Some form of Data Package provided? Add text below if you need to clarify your score.
- none (e.g. only abstract in easychair/github)
Overall evaluation
Please provide a brief review, including a justification for your scores. Both score and review text are required.
- accept
This abstract introduces the research object composer tool, which allows the generation of a Research Object from a workflow and set of inputs.
Although no further hints on the implementation are provided, e.g., types of workflows supported, types of relations and annotations created, license, etc., it sounds quite interesting and in line with the workshop goal. Also unfortunately there was no link to any implementation to try it out.
Review 3
- Reviewer: (anonymous)
Quality of Writing
Is the text easy to follow? Are core concepts defined or referenced? Is it clear what is the author’s contribution?
- excellent
Research Object / Zenodo
URL for a Research Object or Zenodo record provided? Guidelines followed? Open format (e.g. HTML)? Sufficient metadata, e.g. links to software? Some form of Data Package provided? Add text below if you need to clarify your score.
- none (e.g. only abstract in easychair/github)
Overall evaluation
Please provide a brief review, including a justification for your scores. Both score and review text are required.
- strong accept
The authors will Research Object Composer that can generate a Research Object from a workflow and set of inputs. This is going to be extremely useful for interoperability and can account for the heterogeneity of inputs and outputs in biomedical research data.