Re: Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy

From: Rob <rmpsfdbs_at_gmail.com>
Date: 15 Dec 2006 08:36:44 -0800
Message-ID: <1166200604.769505.314740_at_t46g2000cwa.googlegroups.com>

Neo wrote:
> In recent thread titled "Generalised Approach to Storing Address
> Details" in cdt, the following argument was make against hierarchal
> interfaces (not hierarchal data model):
>
> "It has been proven in numerous research studies that menu's use is
> deletrious if nesting goes above two levels ... Very little in the
> world is hierarchical. Even the oft cited hierarchy of biological
> taxonomy, breaks down at several points."
>
> Does anyone have a link to web pages that shows the overall biological
> taxonomy in a manner where it would be relatively easy to enter into a
> database. I am searching but haven't found an appropriate one yet. I
> would like to enter some portion of the biological taxonomy in a db
> with a hierarchal interface. If someone would be willing to enter
> similar information in a relational db like MS Access, we can compare
> hierarchal vs non-hierarchal interfaces in above case.

I deal with hierarchies a lot. From a database perspective, attribute data clouds the structure issue, so I usually work only with names.

Can you parse this tree (from one of Celko's examples)?:

(Albert(Bert,Chuck(Donna,Eddie,Fred)))

If so, here is a Human Cytogenetic Map (i.e., of the bands in human chromosomes resulting from a widely-used diagnostic staining agent):

(HumanCytogeneticMap(1(1p(1p3(1p36(1p36.3(1p36.33,1p36.32,1p36.31),1p36.2(1p36.23,1p36.22,1p36.21),1p36.1(1p36.13,1p36.12,1p36.11)),1p35(1p35.3,1p35.2,1p35.1),1p34(1p34.3,1p34.2,1p34.1),1p33,1p32(1p32.3,1p32.2,1p32.1),1p31(1p31.3,1p31.2,1p31.1)),1p2(1p22(1p22.3,1p22.2,1p22.1),1p21(1p21.3,1p21.2,1p21.1)),1p1(1p13(1p13.3,1p13.2,1p13.1),1p12,1p11(1p11.2,1p11.1))),1q(1q1(1q11,1q12),1q2(1q21(1q21.1,1q21.2,1q21.3),1q22,1q23(1q23.1,1q23.2,1q23.3),1q24(1q24.1,1q24.2,1q24.3),1q25(1q25.1,1q25.2,1q25.3)),1q3(1q31(1q31.1,1q31.2,1q31.3),1q32(1q32.1,1q32.2,1q32.3)),1q4(1q41,1q42(1q42.1(1q42.11,1q42.12,1q42.13),1q42.2,1q42.3),1q43,1q44))),2(2p(2p2(2p25(2p25.3,2p25.2,2p25.1),2p24(2p24.3,2p24.2,2p24.1),2p23(2p23.3,2p23.2,2p23.1),2p22(2p22.3,2p22.2,2p22.1),2p21),2p1(2p16(2p16.3,2p16.2,2p16.1),2p15,2p14,2p13(2p13.3,2p13.2,2p13.1),2p12,2p11(2p11.2,2p11.1))),2q(2q1(2q11(2q11.1,2q11.2),2q12(2q12.1,2q12.2,2q12.3),2q13,2q14(2q14.1,2q14.2,2q14.3)),2q2(2q21(2q21.1,2q21.2,2q21.3),2q22(2q22.1,2q22.2,2q22.
3),2q23(2q23.1,2q23.2,2q23.3),2q24(2q24.1,2q24.2,2q24.3)),2q3(2q31(2q31.1,2q31.2,2q31.3),2q32(2q32.1,2q32.2,2q32.3),2q33(2q33.1,2q33.2,2q33.3),2q34,2q35,2q36(2q36.1,2q36.2,2q36.3),2q37(2q37.1,2q37.2,2q37.3)))),3(3p(3p2(3p26(3p26.3,3p26.2,3p26.1),3p25(3p25.3,3p25.2,3p25.1),3p24(3p24.3,3p24.2,3p24.1),3p23,3p22(3p22.3,3p22.2,3p22.1),3p21(3p21.3(3p21.33,3p21.32,3p21.31),3p21.2,3p21.1)),3p1(3p14(3p14.3,3p14.2,3p14.1),3p13,3p12(3p12.3,3p12.2,3p12.1),3p11(3p11.2,3p11.1))),3q(3q1(3q11(3q11.1,3q11.2),3q12(3q12.1,3q12.2,3q12.3),3q13(3q13.1(3q13.11,3q13.12,3q13.13),3q13.2,3q13.3(3q13.31,3q13.32,3q13.33))),3q2(3q21(3q21.1,3q21.2,3q21.3),3q22(3q22.1,3q22.2,3q22.3),3q23,3q24,3q25(3q25.1,3q25.2,3q25.3(3q25.31,3q25.32,3q25.33)),3q26(3q26.1,3q26.2,3q26.3(3q26.31,3q26.32,3q26.33)),3q27(3q27.1,3q27.2,3q27.3),3q28,3q29))),4(4p(4p1(4p16(4p16.3,4p16.2,4p16.1),4p15(4p15.3(4p15.33,4p15.32,4p15.31),4p15.2,4p15.1),4p14,4p13,4p12,4p11)),4q(4q1(4q11,4q12,4q13(4q13.1,4q13.2,4q13.3)),4q2(4q21(4q21.1,4q21.2
(4q21.21,4q21.22,4q21.23),4q21.3),4q22(4q22.1,4q22.2,4q22.3),4q23,4q24,4q25,4q26,4q27,4q28(4q28.1,4q28.2,4q28.3)),4q3(4q31(4q31.1,4q31.2(4q31.21,4q31.22,4q31.23),4q31.3),4q32(4q32.1,4q32.2,4q32.3),4q33,4q34(4q34.1,4q34.2,4q34.3),4q35(4q35.1,4q35.2)))),5(5p(5p1(5p15(5p15.3(5p15.33,5p15.32,5p15.31),5p15.2,5p15.1),5p14(5p14.3,5p14.2,5p14.1),5p13(5p13.3,5p13.2,5p13.1),5p12,5p11)),5q(5q1(5q11(5q11.1,5q11.2),5q12(5q12.1,5q12.2,5q12.3),5q13(5q13.1,5q13.2,5q13.3),5q14(5q14.1,5q14.2,5q14.3),5q15),5q2(5q21(5q21.1,5q21.2,5q21.3),5q22(5q22.1,5q22.2,5q22.3),5q23(5q23.1,5q23.2,5q23.3)),5q3(5q31(5q31.1,5q31.2,5q31.3),5q32,5q33(5q33.1,5q33.2,5q33.3),5q34,5q35(5q35.1,5q35.2,5q35.3)))),6(6p(6p2(6p25(6p25.3,6p25.2,6p25.1),6p24(6p24.3,6p24.2,6p24.1),6p23,6p22(6p22.3,6p22.2,6p22.1),6p21(6p21.3(6p21.33,6p21.32,6p21.31),6p21.2,6p21.1)),6p1(6p12(6p12.3,6p12.2,6p12.1),6p11(6p11.2,6p11.1))),6q(6q1(6q11(6q11.1,6q11.2),6q12,6q13,6q14(6q14.1,6q14.2,6q14.3),6q15,6q16(6q16.1,6q16.2,6q16.3)),6q2(6q21,6q22(6q
22.1,6q22.2,6q22.3(6q22.31,6q22.32,6q22.33)),6q23(6q23.1,6q23.2,6q23.3),6q24(6q24.1,6q24.2,6q24.3),6q25(6q25.1,6q25.2,6q25.3),6q26,6q27))),7(7p(7p2(7p22(7p22.3,7p22.2,7p22.1),7p21(7p21.3,7p21.2,7p21.1)),7p1(7p15(7p15.3,7p15.2,7p15.1),7p14(7p14.3,7p14.2,7p14.1),7p13,7p12(7p12.3,7p12.2,7p12.1),7p11(7p11.2,7p11.1))),7q(7q1(7q11(7q11.1,7q11.2(7q11.21,7q11.22,7q11.23))),7q2(7q21(7q21.1(7q21.11,7q21.12,7q21.13),7q21.2,7q21.3),7q22(7q22.1,7q22.2,7q22.3)),7q3(7q31(7q31.1,7q31.2,7q31.3(7q31.31,7q31.32,7q31.33)),7q32(7q32.1,7q32.2,7q32.3),7q33,7q34,7q35,7q36(7q36.1,7q36.2,7q36.3)))),8(8p(8p2(8p23(8p23.3,8p23.2,8p23.1),8p22,8p21(8p21.3,8p21.2,8p21.1)),8p1(8p12,8p11(8p11.2(8p11.23,8p11.22,8p11.21),8p11.1))),8q(8q1(8q11(8q11.1,8q11.2(8q11.21,8q11.22,8q11.23)),8q12(8q12.1,8q12.2,8q12.3),8q13(8q13.1,8q13.2,8q13.3)),8q2(8q21(8q21.1(8q21.11,8q21.12,8q21.13),8q21.2,8q21.3),8q22(8q22.1,8q22.2,8q22.3),8q23(8q23.1,8q23.2,8q23.3),8q24(8q24.1(8q24.11,8q24.12,8q24.13),8q24.2(8q24.21,8q24.22,8q24.23),
8q24.3)))),9(9p(9p2(9p24(9p24.3,9p24.2,9p24.1),9p23,9p22(9p22.3,9p22.2,9p22.1),9p21(9p21.3,9p21.2,9p21.1)),9p1(9p13(9p13.3,9p13.2,9p13.1),9p12,9p11(9p11.2,9p11.1))),9q(9q1(9q11,9q12,9q13),9q2(9q21(9q21.1(9q21.11,9q21.12,9q21.13),9q21.2,9q21.3(9q21.31,9q21.32,9q21.33)),9q22(9q22.1,9q22.2,9q22.3(9q22.31,9q22.32,9q22.33))),9q3(9q31(9q31.1,9q31.2,9q31.3),9q32,9q33(9q33.1,9q33.2,9q33.3),9q34(9q34.1(9q34.11,9q34.12,9q34.13),9q34.2,9q34.3)))),10(10p(10p1(10p15(10p15.3,10p15.2,10p15.1),10p14,10p13,10p12(10p12.3(10p12.33,10p12.32,10p12.31),10p12.2,10p12.1),10p11(10p11.2(10p11.23,10p11.22,10p11.21),10p11.1))),10q(10q1(10q11(10q11.1,10q11.2(10q11.21,10q11.22,10q11.23))),10q2(10q21(10q21.1,10q21.2,10q21.3),10q22(10q22.1,10q22.2,10q22.3),10q23(10q23.1,10q23.2,10q23.3(10q23.31,10q23.32,10q23.33)),10q24(10q24.1,10q24.2,10q24.3(10q24.31,10q24.32,10q24.33)),10q25(10q25.1,10q25.2,10q25.3),10q26(10q26.1(10q26.11,10q26.12,10q26.13),10q26.2,10q26.3)))),11(11p(11p1(11p15(11p15.5,11p15.4,11p15.3,11p
15.2,11p15.1),11p14(11p14.3,11p14.2,11p14.1),11p13,11p12,11p11(11p11.2,11p11.1(11p11.12,11p11.11)))),11q(11q1(11q11,11q12(11q12.1,11q12.2,11q12.3),11q13(11q13.1,11q13.2,11q13.3,11q13.4,11q13.5),11q14(11q14.1,11q14.2,11q14.3)),11q2(11q21,11q22(11q22.1,11q22.2,11q22.3),11q23(11q23.1,11q23.2,11q23.3),11q24(11q24.1,11q24.2,11q24.3),11q25))),12(12p(12p1(12p13(12p13.3(12p13.33,12p13.32,12p13.31),12p13.2,12p13.1),12p12(12p12.3,12p12.2,12p12.1),12p11(12p11.2(12p11.23,12p11.22,12p11.21),12p11.1))),12q(12q1(12q11,12q12,12q13(12q13.1(12q13.11,12q13.12,12q13.13),12q13.2,12q13.3),12q14(12q14.1,12q14.2,12q14.3),12q15),12q2(12q21(12q21.1,12q21.2,12q21.3(12q21.31,12q21.32,12q21.33)),12q22,12q23(12q23.1,12q23.2,12q23.3),12q24(12q24.1(12q24.11,12q24.12,12q24.13),12q24.2(12q24.21,12q24.22,12q24.23),12q24.3(12q24.31,12q24.32,12q24.33))))),13(13p(13p1(13p13,13p12,13p11(13p11.2,13p11.1))),13q(13q1(13q11,13q12(13q12.1(13q12.11,13q12.12,13q12.13),13q12.2,13q12.3),13q13(13q13.1,13q13.2,13q13.3),13q14(
13q14.1(13q14.11,13q14.12,13q14.13),13q14.2,13q14.3)),13q2(13q21(13q21.1,13q21.2,13q21.3(13q21.31,13q21.32,13q21.33)),13q22(13q22.1,13q22.2,13q22.3)),13q3(13q31(13q31.1,13q31.2,13q31.3),13q32(13q32.1,13q32.2,13q32.3),13q33(13q33.1,13q33.2,13q33.3),13q34))),14(14p(14p1(14p13,14p12,14p11(14p11.2,14p11.1))),14q(14q1(14q11(14q11.1,14q11.2),14q12,14q13(14q13.1,14q13.2,14q13.3)),14q2(14q21(14q21.1,14q21.2,14q21.3),14q22(14q22.1,14q22.2,14q22.3),14q23(14q23.1,14q23.2,14q23.3),14q24(14q24.1,14q24.2,14q24.3)),14q3(14q31(14q31.1,14q31.2,14q31.3),14q32(14q32.1(14q32.11,14q32.12,14q32.13),14q32.2,14q32.3(14q32.31,14q32.32,14q32.33))))),15(15p(15p1(15p13,15p12,15p11(15p11.2,15p11.1))),15q(15q1(15q11(15q11.1,15q11.2),15q12,15q13(15q13.1,15q13.2,15q13.3),15q14,15q15(15q15.1,15q15.2,15q15.3)),15q2(15q21(15q21.1,15q21.2,15q21.3),15q22(15q22.1,15q22.2,15q22.3(15q22.31,15q22.32,15q22.33)),15q23,15q24(15q24.1,15q24.2,15q24.3),15q25(15q25.1,15q25.2,15q25.3),15q26(15q26.1,15q26.2,15q26.3)))),16(16p

(16p1(16p13(16p13.3,16p13.2,16p13.1(16p13.13,16p13.12,16p13.11)),16p12(16p12.3,16p12.2,16p12.1),16p11(16p11.2,16p11.1))),16q(16q1(16q11(16q11.1,16q11.2),16q12(16q12.1,16q12.2),16q13),16q2(16q21,16q22(16q22.1,16q22.2,16q22.3),16q23(16q23.1,16q23.2,16q23.3),16q24(16q24.1,16q24.2,16q24.3)))),17(17p(17p1(17p13(17p13.3,17p13.2,17p13.1),17p12,17p11(17p11.2,17p11.1))),17q(17q1(17q11(17q11.1,17q11.2),17q12),17q2(17q21(17q21.1,17q21.2,17q21.3(17q21.31,17q21.32,17q21.33)),17q22,17q23(17q23.1,17q23.2,17q23.3),17q24(17q24.1,17q24.2,17q24.3),17q25(17q25.1,17q25.2,17q25.3)))),18(18p(18p1(18p11(18p11.3(18p11.32,18p11.31),18p11.2(18p11.23,18p11.22,18p11.21),18p11.1))),18q(18q1(18q11(18q11.1,18q11.2),18q12(18q12.1,18q12.2,18q12.3)),18q2(18q21(18q21.1,18q21.2,18q21.3(18q21.31,18q21.32,18q21.33)),18q22(18q22.1,18q22.2,18q22.3),18q23))),19(19p(19p1(19p13(19p13.3,19p13.2,19p13.1(19p13.13,19p13.12,19p13.11)),19p12,19p11)),19q(19q1(19q11,19q12,19q13(19q13.1(19q13.11,19q13.12,19q13.13),19q13.2,19q13. 3(19q13.31,19q13.32,19q13.33),19q13.4(19q13.41,19q13.42,19q13.43))))),20(20p(20p1(20p13,20p12(20p12.3,20p12.2,20p12.1),20p11(20p11.2(20p11.23,20p11.22,20p11.21),20p11.1))),20q(20q1(20q11(20q11.1,20q11.2(20q11.21,20q11.22,20q11.23)),20q12,20q13(20q13.1(20q13.11,20q13.12,20q13.13),20q13.2,20q13.3(20q13.31,20q13.32,20q13.33))))),21(21p(21p1(21p13,21p12,21p11(21p11.2,21p11.1))),21q(21q1(21q11(21q11.1,21q11.2)),21q2(21q21(21q21.1,21q21.2,21q21.3),21q22(21q22.1(21q22.11,21q22.12,21q22.13),21q22.2,21q22.3)))),22(22p(22p1(22p13,22p12,22p11(22p11.2,22p11.1))),22q(22q1(22q11(22q11.1,22q11.2(22q11.21,22q11.22,22q11.23)),22q12(22q12.1,22q12.2,22q12.3),22q13(22q13.1,22q13.2,22q13.3(22q13.31,22q13.32,22q13.33))))),X(Xp(Xp2(Xp22(Xp22.3(Xp22.33,Xp22.32,Xp22.31),Xp22.2,Xp22.1(Xp22.13,Xp22.12,Xp22.11)),Xp21(Xp21.3,Xp21.2,Xp21.1)),Xp1(Xp11(Xp11.4,Xp11.3,Xp11.2(Xp11.23,Xp11.22,Xp11.21),Xp11.1))),Xq(Xq1(Xq11(Xq11.1,Xq11.2),Xq12,Xq13(Xq13.1,Xq13.2,Xq13.3)),Xq2(Xq21(Xq21.1,Xq21.2,Xq21.3(Xq21.31,Xq21 .32,Xq21.33)),Xq22(Xq22.1,Xq22.2,Xq22.3),Xq23,Xq24,Xq25,Xq26(Xq26.1,Xq26.2,Xq26.3),Xq27(Xq27.1,Xq27.2,Xq27.3)))),Y))

These maps are used for laboratory diagnostics at the microscopic level, not the nucleotide level.

This will give you a large example to work with. The naming convention involves bilateral traversal along the p and q arms of each of 24 chromosomes (1-22,X,Y) starting at the centromere, but this enumeration is tree-like from the distal (telomere) end of the p arm of chromosome 1 to the distal end of the q arm of chromosome X to chromosome Y. Note that there are no details bands for the Y (last) chromosome in this map.

Good luck.

P.S. If your browser or newsreader incorrectly interprets this 9054 byte string, let me know and I'll send you the file as an email attachment. Received on Fri Dec 15 2006 - 17:36:44 CET