Introduction to ACEDB


The simplest way to access the GrainGenes and MaizeDB databases on AGIS is to browse them. The first screen presents a list of classes, and the number of objects in each class. Clicking on an individual class name presents a list (possibly collapsed) of all the objects in that class; clicking on an individual object name brings back the data stored in that object. This is the basic organization of data in ACEDB: everything is stored in an object. The objects belong to separate classes, which can contain different types of data. For an example, see Locus Adh. Here is the portion of the page relevant to the ACEDB data organization:

Locus : Adh


Type Gene 
Location Map Tt-Appels-4D Position 8.1 
Associated_gene Adh-D1 (Triticum) 
Data T.tauschii, Appels 
Each of the highlighted words is a link to another object in the database; for instance, this locus has been located on the Map Tt-Appels-4D. Clicking on this link returns the description of the map:

Map : Tt-Appels-4D

[Locus/position table|view graphic]

Mapping_data T.tauschii, Appels 
Display Centre 12 24 
        Default_view Default 
        View Default          
             SampleDB-full    
             SampleDB-default 
Contains Locus Adh          
               X7SGlob-a    
               X7SGlob-c    
               X7SGlob-d    
               XFbp         
               XGermin      
               XPot-t       
               XcsIH87      
               XcsIHA114-1a 
               XcsIHA114-1b 
               Xpsr101      
               Xpsr139      
               Xpsr163      
               Xpsr164-1    
               Xtag431      
               Xtag578      
               Xtam57b      
               Xtam57c      
               Xwg114       
Note how the data is arranged in a tree, or outline. With some exceptions, all of the data in ACEDB is arranged this way. The non-highlighted words in the tree are known as tags, and are used in the database to identify different branches of the tree. Sometimes, tags are used as data themselves- for instance, in Locus Adh above, 'Gene' (following 'Type') is a tag. To see all the potential tags and fields that can be present in a Locus object in GrainGenes, click the Locus model link at the bottom of the Locus Adh page. This will display the model of the Locus class:

Model: Locus

?Locus	Type	RFLP
		RAPD
		APPCR		
		Microsatellite
		STS
		Gene
		QTL
                Translocation_break_point
		Centromere
        Homoeology_name ?Locus	
        Other_name ?Locus XREF Correct_name ?Reference
        Correct_name ?Locus XREF Other_name ?Reference 
        Previous_name ?Locus ?Reference 
        Current_name ?Locus ?Reference 
        Location Chromosome ?Text	
		 Chromosome_arm ?Text	
		 Map ?Map XREF Locus #map_position
                 Main_Marker ?Map XREF Main_Marker
                 Inside Chrom_Band ?Chrom_Band XREF Locus
                 Rearrangement ?Rearrangement XREF Carries 
	Probe ?Probe XREF Locus ?Reference
	TABLE ?Text REPEAT 
	Mapped_bands ?Restriction Float ?Germplasm ?Text 
	Linked_QTL ?QTL XREF Nearest_marker
	Associated_gene ?Gene XREF Locus 
	Candidate_gene ?Gene XREF Candidate_locus 
	Image ?Image XREF Locus 
	Data	?Map_Data XREF Locus 
	Mapping_data Well_ordered 
               	     2_point ?2_Point_Data
        Rearrangement_data  Uncovered_by ?Rearrangement XREF Uncovers
                            Not_uncovered_by ?Rearrangement XREF Does_not_uncover
                            Carried_by ?Rearrangement XREF Carries
                            Not_carried_by ?Rearrangement XREF Does_not_carry
	Reference ?Reference XREF Locus
	Data_source ?Colleague Text 
	Remarks Text
        Candidate_orthology_group ?Locus XREF Possible_orthologues
	Possible_orthologues ?Locus XREF Candidate_orthology_group
        Gale_orthology_group ?Locus XREF Gale_orthologues
        Gale_orthologues ?Locus XREF Gale_orthology_group
This is a skeletal object, with all tags present, and with no data values filled in. Any object in the Locus class conforms to this model: some tags and data values may be missing, or there may be multiple values for an individual tag (just as the Map above has many Locus objects listed after the tag Locus). The tag does not indicate what data type can go in any individual field; this is instead shown as ?Map, ?Reference, ?Gene, etc., for classes in the database, and Float, Int, and Text for predefined types. In the model, the highlighted fields are linked to other models; thus, it is very easy to browse through the models of the database, to see how all the data is organized. This is true of any of the ACEDB databases on AGIS; by browsing the database and the models, one can learn where to find a particular datum.