Table of Contents
Several of the main item types in BASE can be subclassified by subtypes and sub-categories. This includes for example, biosources, samples and extracts as well as protocols, hardware and software. One of the main reasons for subtypes is to group items together and allowing users to filter out items that are of no interest in the current context. For example, the protocol selection list when creating an extract is filtered to only show Extraction protocols.
The filtering can be even more fine-grained by linking subtypes to each other. For example, in a standard BASE installation there are two extract subtypes: Labeled extract and Library. The labeled extract subtype is linked with the Labeling protocol subtype and the library subtype is linked with the Library preparation protocol subtype. So by assigning the correct subtype to a protocol, BASE knows which one that should be used when creating a labeled extract and which one should be used when creating a library.
![[Tip]](../gfx/admonitions/tip.png) |
Project default items |
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This feature can be a real time-saver when used together with project default items (see Section 6.2.4, “Default items”). When creating new items (eg. a biomaterial) BASE will search among the default items in the active project for protocols, hardware, software, etc. and automatically select the best match based on the subtype of the new item. |
Subtypes and categories are also useful in list pages. All subtypes and categories will show up as a quick selection menu on the list page and allows the user to quickly switch between listings that has automatic filtering on the items matching the subtype and category. Also, the various options for configuring the table will take the current subtype and category into account. For example, annotation types that doesn't belong to the currently selected category are initially hidden making selection lists a lot less cluttered with irrelevant information.
Another important feature is that all list settings can be independently configured for each subtype and category and they are automatically saved between sessions. Switching between different subtypes and categories will automatically restore the settings that was used the last time with that subtype and category.
Subtypes are typically added to a BASE server by an administrator and can be managed from . Sub-categories are managed from .
- Name
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The name of the subtype.
- Main item type
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Select the main item type that the subtype can used on. This can't be changed later.
- Sub-categories
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Items with the same subtype may divided into sub-categories by using an annotation. The annotation must be an enumerated annotation type and it is only the annotation type that is selected here. This annotation type is matched against values that are specified in one or more Annotation type categories. See Section 12.3, “Annotation type category properties”.
- Description
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A optional description of the subtype.
- Related subtypes
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This section allows you to select other subtyps that are related to the current subtype. The possible options depend on the which the main item type is. For example, for biosource there are no other related subtypes, but a derived bioassay can have a related physical bioassay and extract as well as protocol, hardware and software subtypes.
If the main item type for a subtype is a derived bioassay (which has support for linking of data files) it is possible to select data file types (see Section 11.3, “Data file types”) that can be used for items of the given subtype. This is very similar to how the selected platform of a raw bioassay or array design dictates which files types that can be used.
- File types
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The list contains the file types that are currently associated with the item subtype.
- Required
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Mark this checkbox to indicate that the file is required for all items of the given subtype.
![[Note]](../gfx/admonitions/note.png)
Note The requried flag is not enforced when creating items. It is used for generating warnings when validating an experiment and can be checked by plug-ins that may need the file in order to run.
- Allow multiple files
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Mark this checkbox if it is possible to have more than one file of the given type. In most cases, a single file is used, but some subtypes, for example Scan, may generate multiple images.
- Add file types
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Click on this button to open a popup window for selecting more file types to associated with the item subtype.
- Remove
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Click on this button to remove the association with the selected file types.
- Name
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The name of the category.
- Short name
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A shorter name that can be used when listing categories that belong to the same subtype.
- Main category
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Select one subtype that this category belongs to.
- Sub-category
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If the subtype that is selected for the main category has specified an annotation type to use for sub-categories the possible values are listed here. Select one or more values that should belong to this category.
- Description
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A optional description of the category.