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Revision 1.3 - (download) (as text) (annotate)
Sat Mar 12 20:30:39 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
CVS Tags: Root-bobdev_news, merge-trunktag-bobdev_news-1, merge-bobdev_news-2, merge-bobdev_news-1, merge-trunktag-bobdev_news-2
Branch point for: Branch-bobdev_news
Changes since 1.2: +23 -7 lines
Changed Subsystems to allow selection of active_subsetR (rows) based on tag/value pairs

<h1 style="text-align: center">Attributes</h1>

<p>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.</p>

<p>Most people should read the first section and ignore the second section.</p>

<p>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.</p>

<h2>Non-technical Section</h2>

<p>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, <em>genomes</em> 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.<p>

<p>Try the following exercises to see key/value pairs in action:</p>

<ul>
<li>Choose an organism from the FIG search page and select statistics to see the list. There is an option at the bottom of the page to edit the key/value pairs, and this will pull up a table where you can enter the information for an organim.
</li>

<li>Open the <a href="http://localhost/FIG/subsys.cgi?user=&ssa_name=Flagellum&request=show_ssa&can_alter=">Flagellum subsytem</a>, and scroll to the checkboxes/buttons at the bottom. There are two pulldown lists, from the first one (labeled "color rows by each organism's attribute" choose MOTILE), and click show spreadsheet. The sheet is now highlighted with motile and non-motile organisms that have flagella. This view is also helped by decresing the text size from the view menu. There is a key at the bottom just above the "show spreadsheet" button so you know which color is which, and in this case there is only motile and non-motile. This key is also an active link that will limit the display of the spreadsheet to just those particular organisms that you have highlighted.</li>

<li>Now choose WIDTH from the same pull down menu, and click show spreadsheet. Because width is a numeric variable, I grouped these key/value pairs in 1/10ths of the maximum. If you look at the Color Descriptions box you will see ranges (this is not perfect at the moment, but it is on the way).</li>

<li>Now reset the WIDTH pull-down menu to empty (the first option in the list), and choose PIRSF from the menu labelled "color columns by each PEGs attribute" and click show spreadsheet. This is the same as before, but hopefully we can add more tags here and color other things.</li>

<li>From one of the PEGs that is colored as having a PIRSF link click on the link to get to the protein page. There is the attributes box (as before), and a new "Edit Attributes" button. When you click this, you will get three fields, key, value, and URL. If you go to a protein that does not have any attributes yet, you still get the edit box to let you add some attributes.</li>

<ul><p>The rules that apply here are:</p>
<li>the text is free form and can be whatever you like.</li>
<li>the key is case insensitive (at the moment generally uppercase, but I may change this to Sentence Case)</li>
<li>if the URL is a webpage, the key/value pair will be visible on the protein page. The URL doesn't have to be a webpage, and as I mentioned before, will probably become a flag for many other things.</li>
<li>you can add, edit, or delete individual key/value pairs here.</li>
<li>if you have a lot of key value pairs, you can send them to me and I'll load them in batch.</li>
</ul>

</ul>


<h2>Technical stuff</h2>

<p>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.</p>

<p>There are now four base methods for handling attributes:</p>
<ol>
<li>add_attribute    - to add a new attribute to an object</li>
<li>delete_attribute - to remove an existing attribute from an object</li>
<li>change_attribute - to modify an existing attribute</li>
<li>get_attributes   - to get attributes for an object</li>
</ol>


<p>In addition, there are some methods that make specific calls I am using:</p>
<ol>
<li>get_tags   	     - get tags for either all known objects or a selected type of object (peg, rna, genome, etc)</li>
</ol>


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