The paper provides a very nice overview of research on integration and matching of radiology images from different modalities, in terms of two methodologies: ontology based approach through spatial relationships, and image processing based approach through fiducial points. The paper covers a comprehensive survey of literature in the field, and is technically sound. One major concern for the paper is that it has to be adjusted for the audience with compelling use cases for applicability of the research related to biology research, and be major-revised for presentation.

Major Compulsory Revisions

1. While the paper is a nice review paper, the current presentation and content makes it difficult for readers of the journal to appreciate the paper. In practice, radiology images in healthcare are used for different studies in radiology and they are handled by experts from different domains. While mapping different image modalities together sound interesting, the authors have not presented any driving use cases that could take advantage of such mapping and integration, i.e., use cases relevant to “life and biomedical sciences”. This seems critical to stimulate interest of audience.

2. While the paper covers many papers, and similar work, there is no metrics defined, and the comparison is very high level. It could make the review more interesting if the authors could present different work with some metrics.

Minor Essential Revisions

1. The wording of the paper has to be significantly improved. There are numerous syntax errors and wording problems. For example, the authors have difficulty to use singular and plural terms correctly.

Level of interest: An article whose findings are important to those with closely related research interests

Quality of written English: Needs some language corrections before being published

Statistical review: No, the manuscript does not need to be seen by a statistician.

Declaration of competing interests: N/A

Bedoya-Reina et al report on a set of tools that have been integrated into Galaxy for performing analyses on genetic variation within species. How these tools can be used to analyse nucleotide and amino acid polymorphisms is exemplified by the authors in a number of use cases using published polymorphism data sets from a range of organisms including canine, pig, lemur and human. The authors state that a major reason for integrating these tools into Galaxy is to enhance the reproducibility of analyses of genetic polymorphisms.

The set of tools described by the authors is comprehensive in nature. There are tools allowing users to pre-process polymorphism data once it is loaded into a Galaxy server before tools are used to analyze population structure and how this is related to the differences in genotype within species. Finally, tools using data from KEGG and the Gene Ontology have been wrapped into Galaxy to enable hypotheses to be made about the possible biological outcomes caused by the polymorphisms in genes in species.

The range of use cases demonstrated by the authors is impressive and are well described in the text. It appears that the authors have been thorough in showing that by using various combinations of their tools, it is possible to recapitulate published results in addition to producing new data derived from the initial input polymorphism data for follow-on studies.

Major Compulsory Revisions

1. The data for in the use cases are available within a data library in the main Galaxy sever. However, I think it is important that there is a Galaxy server which provides users with access to the tools, workflows and histories associated with the use cases to complement this manuscript before it can be accepted for publication. It is currently stated in the manuscript that these resources are not yet available. Please provide the location of the server in the URLs section of the manuscript when this has been done.

Minor Essential Revisions

There seems to be a number of typos in the manuscript:

1. Abstract: There are typos in the Conclusions section. “…that addresses the needs of a growing community of biologists who are attempting to reap the rewards of high-throughput genome sequencing to study intra-species diversity. This project provides a model for the development of a Galaxy tool set to meet the needs of a particular community of biologists”?

2. Tools for analyzing SNV tables – page 19. “Principal component analysis (tool #12) is performed by smartpca”

3. KEGG and Gene Ontology – page 19. “To do so,each gene is associated to a GO term following the Ensembl annotation (Flicek et al. 2013).”

4. KEGG and Gene Ontology – page 20. “In addition, the Get Pathways tool (#19) maps KEGG genes and pathways to Ensembl codes, while the Pathway Image tool (#21) plots KEGG pathways highlighting genes of interest respectively (e.g. Figure 2).”

Level of interest: An article of importance in its field

Quality of written English: Acceptable

Statistical review: No, the manuscript does not need to be seen by a statistician.

Declaration of competing interests: I declare that I have no competing interests.