16.3. Extracts

16.3.1. Create extract
16.3.2. Extract properties
16.3.3. Extract parents

Extract items should be used to describe the events that transform a sample material into an extract material. An extract can be created from one sample item or from one or more extract items. When an extract is created from several other extracts, a pooling event is performed.

During the transformation from samples to extracts, it is possible to provide information about the protocol used to perform this task. It is not enforced in BASE but it should serve as guidance when devising the granularity of the sample processing task. Also, it is good practice to provide protocol information.

Use Biomaterial LIMSExtracts to get to the list of extracts.

16.3.1. Create extract

Beside the common way, using the New… button, an extract can be created in one of the following ways:

from either sample list- or single view- page.

No matter how complex the extract processing phase is, at least one extract has to be anchored to a sample. Therefore, a natural way to create an extract is to click on in the Child extracts column for the sample that should be a parent of the extract. There is also a corresponding button, New child extract… in the toolbar when viewing a single sample.

from the extract list page

Child extracts can be created from a single parent by clicking on the icon in the Child extracts column. Pooled extract can be created by first selecting the parents from the list of extracts and then press Pool… in the toolbar. The selected extracts will be put into the parent property.

16.3.2. Extract properties

Figure 16.4. Extract properties

Extract properties

Name

A mandatory field for providing the extract name. BASE by default assigns names to extract (by suffixing e# when creating an extract from an existing sample or New extract otherwise) but it is possible to edit it at will.

Type

The subtype of the extract. The list may evolve depending on additions by the server administrator. Selecting the proper subtype is recommended and enables BASE to automatically guess the most likely subtype when creating child biomaterial and bioassays. See Chapter 12, Item subtypes for more information.

Tag

If the extract has been marked with a tag, select it here. Note that the subtype of the extract usually limits what kind of tag that can be used. For example, a labeled extract should be tagged with a label.

External ID

The extracts identification outside BASE

Original quantity

Holds information about the original mass of the created extract.

Created

The date when the extract was created. The information can be important when running quality controls on data and account for potential confounding factor (e.g. day effect)

Registered

This is automatically populated with a date at which the sample was entered in BASE system.

Protocol

The extraction protocol that was used to produce the extract.

Bioplate

The bioplate where this extract is located.

Biowell

Biowell that holds this extract. Bioplate has to be defined before biowell can be selected.

Description

A text field to report any information that not can be captured otherwise.

16.3.3. Extract parents

Figure 16.5. Extract parents

Extract parents

This is meant to keep track of the extract origin. BASE distinguishes between two cases which are controlled by the Parent type radio-button in the edit pop-up window.

  • If the parent is a sample the radio-button is set to Sample. Only a single sample can be used as the parent. This option is automatically selected if the user selects a sample with the Select sample button.

  • When the parent is one or several other extracts the radio-button is set to Extract. This option is automatically selected if the user add extracts with the Add extracts button.

For each parent item, it is possible to specify the amount used in micrograms. This will automatically update the remaining quantity of the parent.

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

This Inherited annotations tab contains a list of those annotations that are inherited from the extract's parents. Information about working with inherited annotations can be found in Section 10.2.1, “Inheriting annotations from other items”.