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Quick guide to understanding acedb tree displays

This page provides some information about how to understand the basic tree displays that acedb uses to display information. For more details about acedb in general, read the quick guide to acedb at the official acedb web site.

A tree display is the default method that acedb uses for showing the information concerning any object in a database. The layout of the display reflects the way in which the data is held in the database. Tree displays are so called because the data 'branches' out from one main 'tag' to several 'subtags' which contain the actual data associated with an object, and may additionally contain links to other objects. Tree displays are not for the display of phylogenetic data.

All objects in any acedb database can be represented using a tree display, though for many objects there will normally be more specialist ways of displaying the data, e.g. graphic displays for sequences and maps.

The following table shows a typical tree display for a Sequence object from the AGR database. The main features of the display are as follows:

The name of the 'object' (in this case 'EMBL:AL163812) always appears on the left.
In the next column are the names of the 'top level tags' e.g. 'DNA', 'Structure', 'Database_info' etc. These represent the primary 'branches' on the tree and can be thought of as the main category headings for this object.
Any top level tag can contain subtags, which in turn can contain more subtags and so on.
Tags and subtags coloured red indicate that they contain at least two subtags or pieces of data. Clicking on a red tag 'closes' that tag.
Tags coloured grey are tags that are 'closed'. If you click on a grey tag, it will 'open' to reveal its contents. If a tag contains over 7 subtags or pieces of data, they remain closed by default.
Final level subtags will usually (but not always) contain one or more associated pieces of data. E.g. 'AL163812.1' is the data associated with the subtag 'Version'. The data can be either a static piece of text, or a link to another object in the database (or even in another database).
Some subtags need no associated data and represent the end of that 'branch' in the tree. E.g. the subtag 'AGI_sequence' is a tag with no associated values.

EMBL:AL163812	DNA	EMBL:AL163812	103638
	Structure	Subsequence (23)
		5'_overlapping_sequence	EMBL:AL163814
		3'_overlapping_sequence	EMBL:AL133421
	Database_info	Database_name	EMBL
		EMBL_Identifier	ATF14F18
		Accession	AL163812
		Version	AL163812.1
		Database_date	13-APR-2000
		Complete_database_entry	EMBL:AL163812
	Origin	Species	Arabidopsis thaliana
	Visible	Title	Arabidopsis thaliana DNA chromosome 5, BAC clone F14F18 (ESSA project)
		Corresponding_protein (22)
		Clone	F14F18
		Locus	F14F18
		Chromosome	V
	Subclass	Arabidopsis_thaliana
		AGI_sequence
	EMBL_feature	Gene (23)
		misc_feature	1	8764
			99518	103593
	Homol	DNA_homol (88)

Page last modified: Wednesday, 14-Mar-2001 13:48:57 GMT

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