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Variants submitted to the EVA have been determined by a number of different algorithms and software packages. As a result, the VCF files generated by these differing methodologies describe variants in a number of different ways. The primary processing step of the EVA is to normalise variant representation following two basic rules:Each variant is shifted to be left-aligned
The Start and End positions represent exactly the range where the variation occurs (which could, in the case of insertions, result in the reference allele being recorded as 'empty')
Representing variant data in a spreadsheet can be convenient when you have a small number of variants to report. This file can be used as an example or template: spreadsheet_to_vcf.xlsx (you will need to create a copy). When reporting a large number of variants, the use of specialised software may be a better approach.
The reviewers point out issues that remain with both the manuscript and the ontology it describes, as well as raise some new issues. I have attempted to clearly state the required revisions based only on issues raised in the first round, and to leave any other responses as optional. If the authors would be so kind as to address this list, I will make an editorial decision without further consulting the reviewers.1. The introduction sets out no hypothesis. This is still true, but I leave it to the author's discretion how they wish to state their goal, as long as they do so (see point 3).2. \"Generic Feature and Genomic Variation File Formats\" section is awkward. This is still true, but I leave this matter of style to the authors' discretion.3. The authors fail to state the central objective of modeling genomic features in a computable manner using RDF. This is a valid criticism, and I believe the reviewers have pointed out in various ways that the implication in the abstract that GFVO provideds a single \"unifying solution to genomic data representation\" is overstated given what is reported in the paper. The authors must justify and state their objective more clearly and narrowly.4. Missing external references to well-defined ontologies, e.g. SIO:cell (SIO_010001). This is valid, though not a flaw in the manuscript, per se. While I recognize that SIO is published separately, the authors may optionally wish to point out where further mappings in GVFO or SIO may be needed, where known.5. One of the reviewers raises questions about a large number of modeling decisions that were revealed by inspection of the examples. I leave it to the authors' discretion to decide which to correct, which to explain in the manuscript, and which to leave unanswered.6. \"The background and/or discussion still lacks depth with respect to making the case for, and demonstrating the utility of, the new ontology, and a Semantic Web based approach in general\" and \"don't just provide lots of examples of how genomic variation data can be represented with RDF and GFVO, also show the reader what this is actually good for.\" This is still valid and closely related to point 3. The authors must add content, however they choose to do so, to rectify this weakness in the manuscript. The authors will likely find it economical to address points 3 and 6 together. 7. \"The article skates over and does not mention some of the non-trivial drawbacks of a Semantic Web based approach\". This is true, but as this was not raised in the original review, I will leave it to the authors discretion to address or not as they see fit.8. Inclusion of a Results section (from Editor's comments on prior version). This is still required. Note that the preprint referenced in the authors' response was subsequently published the in the Journal of Biomedical Semantics, not PeerJ, and so not relevant to the requirements of this journal. 076b4e4f54