Magic Tags
in Mappable and Map Data Objects

An object is mappable by virtue of its association with a map rather than because it is a member of a special class like "Gene" or "YAC". Its graphical behavior depends on whether it is a point or an interval (see documentation for Map Classes). Certain gMap features are supported by objects which are associated with mappable objects rather than directly with the maps themselves (2_point_data, Pos_neg_data, Multi_pt_data).

?Thing Map ?Map XREF Thing #Map_position
       Positive Hybridizes_to ?Clone XREF Positive_Thing
       Negative Does_not_hybridize_to ?Clone XREF Negative_Thing
       Positive_clone ?Clone XREF Positive_Thing ?Author
       Mapping_data     2_point ?2_point_data
                        Multi_point ?Multi_pt_data
                        Pos_neg_data ?Pos_neg_data
       Display  Dark
                NOR
                Centromere
                p_Telomere
                q_Telomere



?2_point_data   Point_1 UNIQUE Locus_1	UNIQUE ?Locus XREF 2_point
		Point_2 UNIQUE Locus_2	UNIQUE ?Locus XREF 2_point
		Calculation UNIQUE Full UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int
				   One_recombinant UNIQUE Int UNIQUE Int
				   Selected UNIQUE Int UNIQUE Int
				   One_all UNIQUE Int UNIQUE Int
				   Recs_all UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int
				   One_let UNIQUE Int UNIQUE Int
				   Tested UNIQUE Int UNIQUE Int
				   Selected_trans UNIQUE Int UNIQUE Int
				   Backcross UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int
				   Back_one UNIQUE Int UNIQUE Int
				   Sex_full UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int
				   Sex_one UNIQUE Int UNIQUE Int
				   Sex_cis UNIQUE Int UNIQUE Int
				   Dom_one UNIQUE Int UNIQUE Int
				   Dom_selected UNIQUE Int UNIQUE Int
				   Dom_semi UNIQUE Int UNIQUE Int
				   Dom_let UNIQUE Int UNIQUE Int
				   Direct UNIQUE Int UNIQUE Int
				   Complex_mixed UNIQUE Int UNIQUE Int
		Calc  Calc_distance UNIQUE Float
		      Calc_lower_conf UNIQUE Float
		      Calc_upper_conf UNIQUE Float
	        Simple_distance	Min      UNIQUE Float 
                                Distance UNIQUE Float
                                Max      UNIQUE Float
                                Error    UNIQUE Float
                                Linkage  UNIQUE Text

?Pos_neg_data	Item_1	UNIQUE	Locus_1	UNIQUE ?Locus XREF Pos_neg_data
		Item_2	UNIQUE	Locus_2	UNIQUE ?Locus XREF Pos_neg_data
		Calculation UNIQUE Positive
				   Negative


?Multi_pt_data	Results A_non_B #Multi_counts
			B_non_A	#Multi_counts
			Combined #Multi_counts

?Multi_counts	UNIQUE Locus UNIQUE ?Locus XREF Multi_point UNIQUE Int #Multi_counts
                       Allele UNIQUE ?Allele XREF Multi_point UNIQUE Int #Multi_counts
                       Rearrangement UNIQUE ?Rearrangement XREF Multi_point UNIQUE Int #Multi_counts

Map <Map> #Map_position

Associates an object with a map. The XREF must address a field in ?Map that "Contains" the object. Positional information (#Map_position) is required for the object to appear on the map graphic as either a point or interval. See documentation on Map Classes for additional information.

Warning: data containing timestamps is parsed with XREF disabled. This may interfere with map construction.

Positive <Tag> <Object>
Negative <Tag> <Object>

These "type 2" tags define an association between two mappable objects, a point and an interval. For example, a locus (fad) can have a positive relationship with two clones (lambda-5 and lambda-6). Whether this agrees with the map positions of fad and the clones is another issue; in fact, there may be a discrepancy which is displayed by the use of color. These colors are configurable in the Column Control. The default used below are:

---------------------------------------------------------
map coordinate     overlaps               doesn't overlap
---------------------------------------------------------
relationship
------------
positive           green                  red

negative           red                    light blue
---------------------------------------------------------
fad with positive relationship to clones lambda-5 and lambda-6:

alb with negative relationship to clones cosmid-1 and cosmid-2:

Positive_clone <Clone>

pMap, not gMap? check yellow contig column for effect

2_point <2_point_data>

Permits display of 2-point data and results of maximum likelihood calculations. The style depends heavily on exactly what data is available in the 2-point object. See documentation below on ?2_point_data for more information.

Multi_point <Multi_pt_data>

Pos_neg_data <Pos_neg_data>

Dark
NOR
Centromere
p_Telomere
q_Telomere

These tags are used to build chromosome diagrams. If the diagrams are viewed in the "Chromsome_picture" column, they will be of fixed size (i.e., not zoomable) and will be in a fixed choice of whites and greys. On the other hand, the "Interval_SRK" column allows zooming and arbitrary assignment of colors to the tags.

Interval       Tag
------------------
F              p_Telomere
G              Dark
H              Centromere
I              NOR
J              q_Telomere
The intervals must be listed two to the right of the Main_markers tag in ?Map. For example, if ?Chrom_Band is used to construct the diagram, then the models should include:

?Map  Main_Marker Band ?Chrom_Band
      Contains Chrom_Band ?Chrom_Band

?Chrom_Band Display Dark
                    NOR
                    Centromere
                    p_Telomere
                    q_Telomere
                    Map ?Map XREF Chrom_Band #Map_position
The Display tag is not needed but helps organize the ?Chrom_Band model. The data for interval F would be:

Map : aaa
Band F

Chrom_Band F
Map aaa Left 85
Map aaa Right 95
p_Telomere

Point_1 UNIQUE <Object1>
Point_2 UNIQUE <Object2>

Point_1 and Point_2 are tag 2 systems. <Object1> and <Object2> must be supplied and both must be mappable objects with coordinates. If these minimal criteria are met the map display can represent the 2_point_data object with a line drawn between the coordinates. The appearance of the graphic depends on column configuration.

For example, this data is sufficient to draw a line between ama-2 and dpy-11:

2_point_data : "4441"
Locus_1	 "dpy-11"
Locus_2	 "ama-2"

Locus : "ama-2"
Map	 "aaa" Position 26 Error 0.9

Locus : "dpy-11"
Map	 "aaa" Position 31 Error 0.6

Calculation UNIQUE <Tag> UNIQUE <Int1> UNIQUE <Int2>...

Calculation is required in order to use any of the registered genetic analysis functions. These allow ACEDB to perform full likelihood calculations on the fly from raw data (<Int>...). The functions themselves are named using <Tag>. A 2_point_data object can use at most one of them. It is possible to create new analysis functions but this requres modifying the ACEDB source code. Contact Richard Durbin for details. A list of available functions is provided as an appendix.

The example below includes all of the underlying data required to draw the graphic. The green bars are confidence limits. The blue histogram is a likelihood distribution.

Locus : "ama-2"
Map	 "aaa" Position 26 Error 0.9
2_point	 "3630"
2_point	 "4441"
2_point	 "4442"

Locus : "unc-76"
Map	 "aaa" Position 24 Error 0.3
2_point	 "3630"
2_point	 "4442"

Locus : "dpy-11"
Map	 "aaa" Position 31 Error 0.6
2_point	 "4441"

2_point_data : "3630"
Locus_1	 "ama-2"
Locus_2	 "unc-76"
One_recombinant	 2487 37

2_point_data : "4441"
Locus_1	 "dpy-11"
Locus_2	 "ama-2"
One_let	 97 2093

2_point_data : "4442"
Locus_1	 "ama-2"
Locus_2	 "unc-76"
One_let	 40 2093

Calc_distance UNIQUE <Float>
Calc_lower_conf UNIQUE <Float>
Calc_upper_conf UNIQUE <Float>

These fields are filled in by ACEDB (using the Calculation data described above) if the "Calc all 2pt" option in the "Gmap data..." menu of the Gmap window is selected.

Min UNIQUE <Float>
Distance UNIQUE <Float>
Max UNIQUE <Float>
Error UNIQUE <Float>

Used for drawing in the absence of Calculation data. The example below includes all of the underlying data required to draw the graphic. The green bars are confidence limits. The blue histogram is a likelihood distribution.

Locus : "ama-2"
Map	 "aaa" Position 26 Error 0.9
2_point	 "3630"
2_point	 "4441"
2_point	 "4442"

Locus : "unc-76"
Map	 "aaa" Position 24 Error 0.3
2_point	 "3630"
2_point	 "4442"

Locus : "dpy-11"
Map	 "aaa" Position 31 Error 0.6
2_point	 "4441"

2_point_data : "3630"
Locus_1	 "ama-2" "m323"
Locus_2	 "unc-76" "e911"
Min 1.5
Max 3
Distance	 2.200000
Error	 0.400000

2_point_data : "4441"
Locus_1	 "dpy-11" "e224"
Locus_2	 "ama-2" "m323"
Min 2.2
Max 8.6
Distance	 4.700000
Error	 0.600000

2_point_data : "4442"
Locus_1	 "ama-2" "m323"
Locus_2	 "unc-76" "e911"
Min .9
Max 3.6
Distance	 1.900000
Error	 0.400000

Item_1 UNIQUE <Tag1> UNIQUE <Object1>
Item_2 UNIQUE <Tag2> UNIQUE <Object2>

Used to establish a positive or negative relationship between two mappable objects. Item_1 and Item_2 are tag 2 systems. <Object1> and <Object2> must be supplied and both must be mappable objects with coordinates.

Positive
Negative

These provide the same functionality as the tag 2 Positive/Negative system used in mappable objects. The rationale for this duplication is that ?Pos_neg_data allows the creation of a seperate object for an experiment, including such details as author, date, and experimental conditions.

In the example below, locus dpy-11 has a positive relationship to clone a1259 and a negative relationship to a1260.

A_non_B <#Multi_counts>
B_non_A <#Multi_counts>
Combined <#Multi_counts>

?Multi_counts	UNIQUE Locus UNIQUE ?Locus XREF Multi_point UNIQUE Int #Multi_counts
                       Allele UNIQUE ?Allele XREF Multi_point UNIQUE Int #Multi_counts
                       Rearrangement UNIQUE ?Rearrangement XREF Multi_point UNIQUE Int #Multi_counts
?Multi_pt_data is designed to capture 4 point, 5 point, n-point experiments as well as 3 point. The presumption is that recombinants are selected between GeneA and GeneB, and one measures how many carry each additional marker. The magic tags identify the results expressed in terms of A_non_B recombinants, B_non_A recombinants, and combined results.

Genes and the number of recombination events between them are represented using the required #Multi-counts structure. The structure has no magic tags; the mappable class ?Foo could be substituted for ?Locus. The structure sets up a repeating unit consisting of a mappable object and number of recombinations. The first and last items must be the names of the selected markers. The results from a typical experiment might be:

  abc  5  def  14  ghi
which means that 5 recombinations occured between abc and def, and 14 between def and ghi, with abc and ghi being selected. Zero means there were no recombinants between two genes. Even in this case the selected markers must be the first and last items in the row.

[need graphic here]

--Multi-point data
Mapper: Hodgkin JA
Date: 1/82
Genotype: her-1(e224)/dpy-11(e1518) unc-42(e270)
GeneA: dpy-11
GeneB: unc-42
A_non_B_results: dpy-11 27 her-1 0 unc-42
B_non_A_results: dpy-11 31 her-1 2 unc-42
 
--Multi-point data
Mapper: Hodgkin JA
Date: 05/83
Genotype: mor-2(e1125)/unc-5(e53) him-8(e1489) dpy-20(e1282)
GeneA: unc-5
GeneB: dpy-20
Combined_results: unc-5 1 mor-2 7 him-8 2 dpy-20

 
--Multi-point data
Mapper: Other AN
Date: 12/97
Genotype: unc-5(e53) dpy-20(e1282)/eP2000 eP2001 eP2002 eP2003
GeneA: unc-5
GeneB: dpy-20
A_non_B_results: unc-5 0 eP2000 13 eP2003 0 eP2001 6 eP2002 1 dpy-20
Comment: polymorphism data

Locus

Allele

Rearrangement