Chapter 13. Protocols

Table of Contents

13.1. Protocol parameters

A protocol is a document describing some kind of process that is typically performed in the lab to create an item of some type (for example, how to create an extract from a sample). It can also represent a procedure for running software programs to extract measured data (for example, from a scanned microarray image). A protocol in the simplest form is just a name with an optional link to a file. The file may for example be a PDF or some other document with a more detailed description.

Protocols are typically added to a BASE server by an administrator and can be managed from AdministrateProtocols.

Figure 13.1. Protocol properties

Protocol properties

This tab allows users to enter essential information about a protocol.


The name of the protocol.


The protocol type of the protocol. The list may evolve depending on additions by the server administrator. Selecting the proper protocol type is important and enables BASE to automatically guess the most likely protocol when creating new items. See Chapter 12, Item subtypes for more information.

External ID

An ID identifying this protocol in an external database. The value does not have to be unique.


A document containing the protocol description, e.g. PDF documents from kit providers to the protocol. Use the Select button to select or upload a file.


A description of the protocol.

13.1. Protocol parameters

BASE users may declare parameters attached to a particular protocol. Parameters are selected from a list of annotation types which have been flagged as parameters. Annotation types which has been selected as parameters show up in the regular annotation dialog whenever the protocol is used for an item. For more information see Chapter 10, Annotations.

Figure 13.2. Protocol parameters

Protocol parameters

Annotation types

This list contains the annotation types selected as parameters for the protocol.

Add annotation types

Use this button to open a pop-up where you can select annotation type to use for parameters. The list only shows annotations types which has the Protocol parameter flag set.


Removes the selected annotation types from the list.

The Annotations tab allows BASE users to use annotation types to refine protocol description. More about annotating items can be read in Section 10.2, “Annotating items”.