I have added attributes to the database in a more significant way. This page is to document those attributes and ways to access/modify them. The page has two sections, a non-technical section for general discussion and overview, and a technical section for behind-the-scenes type information.
Most people should read the first section and ignore the second section.
A comment on nomenclature: I use the term tag/value pairs and attributes interchangeably. Something can have an attribute, and you have to say what that is and what its value is. We also have an idea that an attribute can be a URL, and if so, it should be presented as a URL. So we actually have tag, value, value. You will see this in action. The third element is called URL, but we always check and make sure that it begins http before turning it into a URL, and so we reserve the option of renaming this and making it something else. That will be mentioned here.
We have extended the notion of tag/value pairs beyond things associated with a peg and into the arena of anything. Any feature such as peg, prophage, rna, insertion element, and so on, can have a tag value pair associated with it. In addition, genomes have tag/value pairs associated with them. In this sense, we can annotate the organisms from which the genomes were derived and begin to ask complex questions of the type "show me all organisms that are motile but don't have any flagellar genes". We are working on this interface.
Try the following exercises to see key/value pairs in action:
The rules that apply here are:
Rightly or wrongly I moved some of the methods in FIG.pm associated with attributes. I also renamed a couple of them. The old names are still valid, they are just pointers to the new routines. Apparently nothing breaks, but let me know if it does.
There are now four base methods for handling attributes:
In addition, there are some methods that make specific calls I am using: