Ficus Genome Database: A Comprehensive Genomics and Transcriptomics Research Platform
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsFicus DB is a portal that consolidates data for the Ficus species. This approach has proven to be relevant for multiple communities. The technological choices are overall relevant, building on Drupal/Tripal tools. I particularly like the synteny block system with the circus, which is a nice addition. Ficus DB can be a valuable resource for its research community. However, I have some comments mostly on the website that should be addressed. There is still some work for better tool integration and some description or data should be added.
Here is a list of proposed modifications to improve user experience.
Website
· For each species page, it would be good to have a description of each species like here http://www.ficusgd.com/organism/289928 and to not have aonly link for file download.
· There should be more tracks on Jbrowse as only the reference sequence is available. Please add at least the gene annotations. Transcriptomics data could be added too if BAM file are available. A convenient method is also to use liftoff between genomes and add their correspondence in different tracks for comparative genomics.
· Is it intended to register on the website? If so, there is an issue with this link (http://www.ficusgd.com/user/register) (You are not authorized to access this page). Either fix the issue or hide the link if not appropriate.
· All websites with www2 are not in Drupal and are externa resources. The level of integration low since this is just a link redirection. I would recommend looking for iframe integration in Drupal as this is done with other Drupal portals. It would give a much better user experience.
· Tripal has developed a Jbrowse module allowing better integration in the portal. It could be tested as this is not optimal at the moment.
· Data download: It is important to indicate the genome version. So if there is a new one, the users can easily see the version they used. The same should be done for annotations. The date and version of the databases used (UniProt, GO) should be indicated. If there is no update for many years, the users should be able to see that the data are obsolete as those databases are regularly making updates.
· I noticed this publication https://www.sciencedirect.com/science/article/pii/S2589004222013724 . Are those genomes relevant to the portal? Are the authors planning to integrate public data from the literature?
· There is no Term of use for the database. It would be relevant to clarify this for visitors.
· How can the Analysis Search be used? Without examples it is difficult to test it. What type of keywords are expected? Same for gene search.
· The organism search may not bring much added value compared to the menu on species. Should it be provided?
Manuscript
· L61: Two examples of species portal are cited but it is not clear why those ones were selected and why focusing only on recent ones. It would have been more relevant to list well established ones using Tripal technology.
· Table 1: HTML is not really a data type. Please specify the type of data.
· The legend of figure 1 could be improved as well as the figure which is not very appealing.
· For figure 2: Is it always the same gene or region visualized? Or just a random juxtaposition of screenshots? It would be good to have a concrete use case to show what can be achieved using a characterized gene for Ficus. Then, this information would be better reflected in the legend.
· L336: It is not obvious why there is a focus on TPS gene family and only this one. Could it be elaborated?
· Aknowledgement section looks not complete: Acknowledgments: The authors thank Lei Yang, Jinghong Wei, Han Su etc
· This part does not look appropriate for Ficus species: Informed Consent Statement: Written informed consent has been obtained from the patient(s) to publish this paper.
Comments on the Quality of English LanguageI did not spend a lot of time checking the quality of English but it reads pretty well, although sometimes too concise. Some legends could be elaborated.
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThe authors present a database on Ficus. This is more like a technical paper so I am not sure t fits the purpose of the journal. Further on I have some specific comments to make
The paragraph starting from line 75 is part of the results, so it should be moved to the results section.
General comment for the different software they used: they need to mention If they used the default or modified parameters. They do mention that for some software, not all of them
In line 148, section 2.4, they mention they used a reference genome but they do not provide details as to the version of the Reference genome and whether that genome was the Ficus genome or something else.
In line 176, section 2.6, the authors talk about the Pathway Tools software with reference 34. I think they need to be more specific about what tool this is and mention the parameters used, as I indicated earlier under a general comment I made for software they have used.
Authors are talking about the Expression heatmap in line 274, what are the underlying software and pipelines to come up with expression analysis for the genes of interest? Do they perform e.g. Differential expression analysis? They need to be more clear on that. However the display of a heatmap is nice.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsThank you for addressing my comments. As a final suggestion, I would advise to add in the species page a link to the publication of the study that generated the resources. This is important to give proper credit to data generator.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
