Diving into standard protocols – First thoughts

To begin with, I want to present a simple approach to construct a XML based structure for biological protocols: To those of you that don’t know what XML is, you can refer to http://en.wikipedia.org/wiki/XML.

As I believe, based on my experience with several known molecular biology protocols, We can break almost every protocol to several different elements that can be thoroughly defined with standard properties.

I won’t show the elements type and properties I thought of yet, but instead show the general, abstract protocol structure.

The main structure of biological protocols:

<protocol>
      <element type=”…”/>
      <element type=”…”/>
      <element type=”…”/>
  …
</protocol>

Since every protocol have some “meta-data” like author, date, description etc. , I think the best thing will be to present this data in the header of the protocol:

for Example:

<protocol   name = “The protocol name”
                   Author =”Author name”
                   source =”…”>
    <element type=”…”/>
    <element type=”…”/>
    <element type=”…”/>
  …
</protocol>
 

And finally each element should include some properties that describe that describe the properties of the action done in the particular method’s element like:

<protocol   name= “The protocol name”
                   Author =”Author name”
                   source =”…”>
    <element type=”…”>
            <property type=”…”>
                   …property of the current element…
            </property>

    </element>
    <element type=”…”/>
  …
</protocol>

 

 This hierarchical structure will allow the computer a lot of freedom in understanding protocols:

1. The software will be able to decide what is the function of each protocol’s part and element: if it is a title, a description, a remark or action.
2. The computer can draw the relationship between different parts of the protocol.
3. Different protocols can be compared according to their structure and order, even without understanding the meaning of the words.
4. It is very easy to present this protocols according the the user preferences, in a way that every protocol is presented with the user recognizable template, a fact that can ease the way he can understand the protocol, and shorten the learning curve.

 

In the next posts, I get more deeply into this scheme and show some simple protocols that obey these standards, and the methods to present it.

Later on. I’ll keep building a small database of standard protocols and while doing so, I’ll try to develop my standards even more.

 

~ by drohilm on June 11, 2007.