Open Data to Support CANCER Science—A Bioinformatics Perspective on Glioma Research
Round 1
Reviewer 1 Report
I thank authors for addressing my comment appropriately.
Author Response
I thank authors for addressing my comment appropriately.
We thank you for your time. We have again included minor revisions from another reviewer.
Reviewer 2 Report
This is an "Opinion" article. Therefore, the scientific merit related to the manuscript is difficult to assess. However, the authors have adequately responded to my previous concerns and modified the manuscript accordingly.
Author Response
We thank you for your time. We have included minor revisions from another reviewer and hope our manuscript will serve the scientific community.
Reviewer 3 Report
The article ‘Open Data to support Cancer Science – a Bioinformatics perspective on Glioma research’ has been improved during the first round of revision, however still some mistakes have to be corrected. That is why I suggest minor revision.
Line 12 – brackets not needed
Line 14-18 – consider splitting the long sentence into several shorter questions
Line 18 – are being raised
Line 24 – DNA methylation (no hyphen)
Line 57 – in 2008
Line 58 – In 2014
Line 60 - …and together global corporations throughout the world… - the sentence is grammatically incorrect; verb missing?
Line 81-92 and other - one sentence does not make a paragraph. Join the separate micro-fragments into bigger ones (do not start each sentence, two sentences with a new line).
Line 85 – worldwide (capital letter unnecessary)
Line 107 – 500,000 or 50,000?
Line 143 - while meanwhile
Line 191 - explainable AI, change into abbreviation xAI
Line 261 - to to a lesser extent
Author Response
We thank you again for another detailed look at the revised manuscript. We incorporated corrections for all mentioned issues.
Line 12 – brackets not needed
- removed
Line 14-18 – consider splitting the long sentence into several shorter questions
- We changed subphrases into independent interrogative sentences as suggested
Line 18 – are being raised
- added
Line 24 – DNA methylation (no hyphen)
- removed
Line 57 – in 2008
- added
Line 58 – In 2014
- added
Line 60 - …and together global corporations throughout the world… - the sentence is grammatically incorrect; verb missing?
- inserted “joined” and split sentence in two for better comprehensibility
Line 81-92 and other - one sentence does not make a paragraph. Join the separate micro-fragments into bigger ones (do not start each sentence, two sentences with a new line).
- page layout has been changed as suggested
Line 85 – worldwide (capital letter unnecessary)
- changed
Line 107 – 500,000 or 50,000?
- typing mistake corrected
Line 143 - while meanwhile
- we removed the complicated and unnecessary phrase
Line 191 - explainable AI, change into abbreviation xAI
- changed
Line 261 - to to a lesser extent
- “to” deleted
This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.
Round 1
Reviewer 1 Report
The article ‘Open Data to support Cancer Research – a Bioinformatics perspective at Glioma’ presents how open data can be used for cancer research (in particular glioma research), pointing out the available resources and tools helpful in biomedicine.
The idea of such a paper is really good, as it collects a large portion of knowledge regarding the available tools/platforms/resources in the biomedicine research. This article can be very helpful for young researchers, but even the more experienced ones can find interesting data there. Thus I suggest the article should be published in Onco, however major revision must be done first.
The tools could be described in more detail, because sometimes the text is hard to read, as subsequent tools/resources are introduced one by one. I suggest introducing a tool/platform, and defining the abbreviation and the general use in the first sentence and then giving some details in the following 3-4 sentences. This would make the ‘flow’ of the text better and the paper would be more informative to the readers.
Please also refer to the sentence from the abstract: ‘For example, how targeted therapies can be made more precise, or general and much more fundamental questions, such as how apoptosis or migration can be influenced’, in the main body of the manuscript, as some readers being attracted by this sentence may want to find some more tips of how to/where to find data related to the mentioned apoptosis, migration. Or change the sentence from the Abstract to be more general. Besides, the fragment: ‘how targeted therapies can be made more precise, or general’ needs rewording. Maybe use ‘more effective’, and erase ‘or general’ etc.
A Table summarizing the tools with the short description, and link would be much helpful.
Minor comments:
Title: Bioinformatics perspective at Glioma sounds strange. ‘For glioma’, or ‘in glioma’ wouldn’t be better?
Please make sure all abbreviations are defined when they are first used.
Line 16 which overall survival can be predicted --> how overall survival…
Line 17 certain subtypes --> certain cancer subtypes
Line 18 for certain variations --> genomic variations?
Figure captions PMC --> PubMed Central
Line 43: Nasa --> should be NASA
Line 44 --> In 1995
Line 54 with the goal to unlock genomic silos --> bit informal
Line 237 radiomic studies of ?
Line 241 Imagine openness across institutes --> consider changing imperative into indicative mood
Author Response
We thank you for your support and valuable comments. We have reviewed the entire contribution, revised its readability, and we have reorganized and expanded the description of resources. In addition, we have added a summary table, additional abbreviations and other details.
Thank you for pointing out that we should stay more general if a detailed direction to some given example would be beyond the scope of this manuscript. We therefore adapted the exemplary questions that will further avoid distracting the readers attention.
Regarding your minor comments:
title changed,
went over the manuscript again to define abbreviations at first use,
replaced,
inserted,
inserted,
changed,
changed,
inserted,
changed,
deleted,
changed,
still more imperative than indicative but more friendly!
Thank you for your careful review of our texts. We have changed the listed wordings and have gone through the entire text of the manuscript again.
Reviewer 2 Report
This "Opinion" article reads like an updated to the previous publication of the authors in Int J Mol Sc in 2020 (Jean-Quartier et al., Open Data for Differential Network Analysis in Glioma, Int J Mol Sci. 2020 Jan; 21(2): 547). Although there are some qualitative differences, the overall emphasis appears to be quite similar. While a compendium listing the databases that can utilized in Glioma research would have been helpful, too much of verbose with no defined conclusion does not fit with the scope of the journal. This will be a good fit for a journal that focuses on scientific policies or data management.
Author Response
Thank you for your valuable comments which we have carefully incorporated into our manuscript. We have now made much clearer the difference between the older contributions in the examples section so that readers know exactly what they will find in each contribution. We have also improved the focus now and added an overview table and subsection headings to increase readability. In addition, we have reorganized and expanded the description of tools. Bioinformatics is a hot topic in precision medicine and therefore particularly important for cancer research. Since data management is an integral part of bioinformatics, we have included details on this topic in this work. We also focus on the example of glioma, a cancer subdisease, since it falls within our area of expertise and where we already have experience. Our recent work on open data for differential network analysis in glioma is not an opinion piece, and constitutes a research article providing guidance on the use of various tools for differential network analysis on only a select group of open gene expression data. In the current manuscript, we go far beyond this and show different types of data and possible methods to use them, also pointing out cutting-edge approaches for glioma research as added value.
Reviewer 3 Report
This opinion manuscript addresses well the need and future direction of open data for bioinformatics research including artificial intelligence study. It also describes a comprehensive list of open databases of multi-omics data that will be very helpful and beneficial for readers who are seeking the data for a secondary analysis or confirmatory validation of findings from their own experimental data. Overall, this is a very well written opinion paper and I have one minor comment as below.
Line 208: I suggest authors elaborating a bit more about what communication data indicates.
Author Response
We are grateful for the reviewer's positive analysis, which also echoes our intention to help other researchers and thereby facilitate research in the common fight against cancer. Cancer can only be defeated in a joint effort cross-domain and cross-disciplinary. Thank you also for pointing out our carelessness regarding the term "communication" in the source review, which we now explain in more detail.
