Peer Review of Ontological Annotation of Data

This is a peer review of Ontological Annotation Of Data.

Overall, this is a very useful resource for people learning about how ontological annotations can be applied to data. There are just a few points below which, when addressed, should improve the overall clarity of the article.

As (strictly) Ontogenesis contains articles rather than blog posts, I suggest modifying the first sentence by removing the word “blogged”. I would also agree with the other reviewer that the links to articles should be replaced by DOIs before final publishing.

At the end of the last paragraph in the first section, you have the following large sentence: “When we consider the phenotype of the human from which samples were taken and the purpose of the study, and results generated by the study there are two axes of annotation to consider – that which relate to what is being assayed – the genetic content of the individual where the genes are, and what they may do, and the meta data about the individual: age, sex, physical characteristics, diseases they may have, and what was actually sampled – e.g. diseased or normal tissue, or peipheral blood.”

This sentence is a little long, and would be clearer with some changes. Perhaps making into two sentences, something like: “There are two axes of annotation when considering assays relating to the phenotype of the human from which samples were taken and the purpose of the study. The first axis is the genetic content of the individual, and what those genes may do. Secondly, annotation concerning the meta data about the individual: age, sex, physical characteristics, diseases they may have, and what was actually sampled – e.g. diseased or normal tissue, or peipheral blood.” This may need further re-wording to capture exactly what was meant.

When you describe GO, you have a note to yourself about a reference to GO: this needs to be added.

In the “Why do we do it” section, I would change “More or less specific annotation…” to “more specific or less specific annotation…” as the meaning is more clear that way. At the end of this same paragraph is the following sentence: “Annotations change over time  on the basis of emerging biological knowledge, and the content of the GO also changes as terms are added, or removed, annotations are therefore updated periodically.” In this case, the last bit of the sentence is difficult to understand. Perhaps change to something like “Annotations change over time on the basis of emerging biological knowledge. As a consequence, the annotation content of the GO is updated periodically as terms are added, or removed.”

Finally, to match how other articles are written, I don’t think you need to number your headings, especially as they aren’t all numbered in the first place. However, each heading should be a real HTML heading, e.g. <h2></h2> in order for the automated Table of Contents to be generated, as a TOC would be very useful in this type of article, which covers many topics.