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.

Neo wrote:

Linnean or cladistic?

I'd start looking at the Tree of Life Project:

http://tolweb.org/tree/


Larry Coon
University of California

What is the main difference between the two? I could enter them both
but would like to start with that preferred by practicing taxanomists.

Thanks, I had breifly visited this site earlier, but dismissed it as
the trees diagrams are graphical instead of textual, thus preventing me
from easily gathering the data. But if this the definitive site on bio
taxonomy, I could go ahead and type in the major ones. The home page
makes it sound as if there are about 5000 entries? Is this
approximately correct?

Larry Coon wrote:

Which common bird is it that has three cohorts A, B and C where A and B
can interbreed, B and C can interbreed but A and C cannot? Is it the robin?

Neo wrote:
Then forget about taxonomy and jump onto the HOT! HOT! gene
wagon. Go here:

http://www.geneontology.org/

and download the ontology flat files (or better yet the HOT!
HOT! XML!). Spend a few months playing with all that network
(as in edges and nodes, ie a graph) data and who knows? You
might be able to contribute neo DB software to the project.

And they already have a mySQL file so when it comes time to
compare your queries to SQL or similar, the data is already
formatted for you.

Have fun!

Keith -- Fraud 6

Holy Jesus! It is the Mother of All Hierarchies!

I am already thinking of renaming it to GO Dummy GO

Thanks. Just for fun, I download the 10 MB text file that can viewed
with NotePad. I would have thought it would be much larger. Looks as
though I would have to write a custom parser to import the data into
dbd from this or any of the other downloadable formats.

You're still carrying the Badge that Cimode bestowed upon you?

Bob Badour <bbadour (AT) pei (DOT) sympatico.ca> wrote:



I used to study genetics, and there are several types of animal that
can do this - IIRC from my studies, there is a (super-)species of
American prairie dog that has three sub-species - Rocky, Plain and
Appallachian.

R and P can breed, and P and A can breed, but R and A cannot.


There is a point at which the genetic distance between two creatures
leads not to hybrid vigour but rather to infertility and/or sterility
of the resultant offspring (horse + donkey = mule).


Paul...


--

plinehan __at__ yahoo __dot__ __com__

XP Pro, SP 2,

Oracle, 9.2.0.1.0 (Enterprise Ed.)
Interbase 6.0.1.0;

When asking database related questions, please give other posters
some clues, like operating system, version of db being used and DDL.
The exact text and/or number of error messages is useful (!= "it didn't work!").
Thanks.

Furthermore, as a courtesy to those who spend
time analysing and attempting to help, please
do not top post.

Neo wrote:
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),1 p36.1(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(1q21.1,1q2 1.2,1q21.3),1q22,1q23(1q23.1,1q23.2,1q23.3),1q24(1 q24.1,1q24.2,1q24.3),1q25(1q25.1,1q25.2,1q25.3)),1 q3(1q31(1q31.1,1q31.2,1q31.3),1q32(1q32.1,1q32.2,1 q32.3)),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),2 p21),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(2q24.1,2q24.2,2 q24.3)),2q3(2q31(2q31.1,2q31.2,2q31.3),2q32(2q32.1 ,2q32.2,2q32.3),2q33(2q33.1,2q33.2,2q33.3),2q34,2q 35,2q36(2q36.1,2q36.2,2q36.3),2q37(2q37.1,2q37.2,2 q37.3)))),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(3p21.3 3,3p21.32,3p21.31),3p21.2,3p21.1)),3p1(3p14(3p14.3 ,3p14.2,3p14.1),3p13,3p12(3p12.3,3p12.2,3p12.1),3p 11(3p11.2,3p11.1))),3q(3q1(3q11(3q11.1,3q11.2),3q1 2(3q12.1,3q12.2,3q12.3),3q13(3q13.1(3q13.11,3q13.1 2,3q13.13),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(3q 26.31,3q26.32,3q26.33)),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(4q28.1,4q 28.2,4q28.3)),4q3(4q31(4q31.1,4q31.2(4q31.21,4q31. 22,4q31.23),4q31.3),4q32(4q32.1,4q32.2,4q32.3),4q3 3,4q34(4q34.1,4q34.2,4q34.3),4q35(4q35.1,4q35.2))) ),5(5p(5p1(5p15(5p15.3(5p15.33,5p15.32,5p15.31),5p 15.2,5p15.1),5p14(5p14.3,5p14.2,5p14.1),5p13(5p13. 3,5p13.2,5p13.1),5p12,5p11)),5q(5q1(5q11(5q11.1,5q 11.2),5q12(5q12.1,5q12.2,5q12.3),5q13(5q13.1,5q13. 2,5q13.3),5q14(5q14.1,5q14.2,5q14.3),5q15),5q2(5q2 1(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),5q34,5q3 5(5q35.1,5q35.2,5q35.3)))),6(6p(6p2(6p25(6p25.3,6p 25.2,6p25.1),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(6p12.3,6p12.2,6p 12.1),6p11(6p11.2,6p11.1))),6q(6q1(6q11(6q11.1,6q1 1.2),6q12,6q13,6q14(6q14.1,6q14.2,6q14.3),6q15,6q1 6(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),6 q25(6q25.1,6q25.2,6q25.3),6q26,6q27))),7(7p(7p2(7p 22(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(7p 11.2,7p11.1))),7q(7q1(7q11(7q11.1,7q11.2(7q11.21,7 q11.22,7q11.23))),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(7q31.31,7q31.32,7q 31.33)),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)),8 p1(8p12,8p11(8p11.2(8p11.23,8p11.22,8p11.21),8p11. 1))),8q(8q1(8q11(8q11.1,8q11.2(8q11.21,8q11.22,8q1 1.23)),8q12(8q12.1,8q12.2,8q12.3),8q13(8q13.1,8q13 .2,8q13.3)),8q2(8q21(8q21.1(8q21.11,8q21.12,8q21.1 3),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),9p2 3,9p22(9p22.3,9p22.2,9p22.1),9p21(9p21.3,9p21.2,9p 21.1)),9p1(9p13(9p13.3,9p13.2,9p13.1),9p12,9p11(9p 11.2,9p11.1))),9q(9q1(9q11,9q12,9q13),9q2(9q21(9q2 1.1(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(9q3 4.11,9q34.12,9q34.13),9q34.2,9q34.3)))),10(10p(10p 1(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),10p1 1.1))),10q(10q1(10q11(10q11.1,10q11.2(10q11.21,10q 11.22,10q11.23))),10q2(10q21(10q21.1,10q21.2,10q21 .3),10q22(10q22.1,10q22.2,10q22.3),10q23(10q23.1,1 0q23.2,10q23.3(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(10 q26.11,10q26.12,10q26.13),10q26.2,10q26.3)))),11(1 1p(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),11q 13(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),1 1q24(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(12p 11.2(12p11.23,12p11.22,12p11.21),12p11.1))),12q(12 q1(12q11,12q12,12q13(12q13.1(12q13.11,12q13.12,12q 13.13),12q13.2,12q13.3),12q14(12q14.1,12q14.2,12q1 4.3),12q15),12q2(12q21(12q21.1,12q21.2,12q21.3(12q 21.31,12q21.32,12q21.33)),12q22,12q23(12q23.1,12q2 3.2,12q23.3),12q24(12q24.1(12q24.11,12q24.12,12q24 .13),12q24.2(12q24.21,12q24.22,12q24.23),12q24.3(1 2q24.31,12q24.32,12q24.33))))),13(13p(13p1(13p13,1 3p12,13p11(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(13q21.31,13 q21.32,13q21.33)),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),13 q34))),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(1 4q23.1,14q23.2,14q23.3),14q24(14q24.1,14q24.2,14q2 4.3)),14q3(14q31(14q31.1,14q31.2,14q31.3),14q32(14 q32.1(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(15q1 1.1,15q11.2),15q12,15q13(15q13.1,15q13.2,15q13.3), 15q14,15q15(15q15.1,15q15.2,15q15.3)),15q2(15q21(1 5q21.1,15q21.2,15q21.3),15q22(15q22.1,15q22.2,15q2 2.3(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),16p1 1(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(16q23.1,16q23.2,16q 23.3),16q24(16q24.1,16q24.2,16q24.3)))),17(17p(17p 1(17p13(17p13.3,17p13.2,17p13.1),17p12,17p11(17p11 .2,17p11.1))),17q(17q1(17q11(17q11.1,17q11.2),17q1 2),17q2(17q21(17q21.1,17q21.2,17q21.3(17q21.31,17q 21.32,17q21.33)),17q22,17q23(17q23.1,17q23.2,17q23 .3),17q24(17q24.1,17q24.2,17q24.3),17q25(17q25.1,1 7q25.2,17q25.3)))),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(1 8q12.1,18q12.2,18q12.3)),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(19p 13.3,19p13.2,19p13.1(19p13.13,19p13.12,19p13.11)), 19p12,19p11)),19q(19q1(19q11,19q12,19q13(19q13.1(1 9q13.11,19q13.12,19q13.13),19q13.2,19q13.
3(19q13.31,19q13.32,19q13.33),19q13.4(19q13.41,19q 13.42,19q13.43))))),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(20q1 3.31,20q13.32,20q13.33))))),21(21p(21p1(21p13,21p1 2,21p11(21p11.2,21p11.1))),21q(21q1(21q11(21q11.1, 21q11.2)),21q2(21q21(21q21.1,21q21.2,21q21.3),21q2 2(21q22.1(21q22.11,21q22.12,21q22.13),21q22.2,21q2 2.3)))),22(22p(22p1(22p13,22p12,22p11(22p11.2,22p1 1.1))),22q(22q1(22q11(22q11.1,22q11.2(22q11.21,22q 11.22,22q11.23)),22q12(22q12.1,22q12.2,22q12.3),22 q13(22q13.1,22q13.2,22q13.3(22q13.31,22q13.32,22q1 3.33))))),X(Xp(Xp2(Xp22(Xp22.3(Xp22.33,Xp22.32,Xp2 2.31),Xp22.2,Xp22.1(Xp22.13,Xp22.12,Xp22.11)),Xp21 (Xp21.3,Xp21.2,Xp21.1)),Xp1(Xp11(Xp11.4,Xp11.3,Xp1 1.2(Xp11.23,Xp11.22,Xp11.21),Xp11.1))),Xq(Xq1(Xq11 (Xq11.1,Xq11.2),Xq12,Xq13(Xq13.1,Xq13.2,Xq13.3)),X q2(Xq21(Xq21.1,Xq21.2,Xq21.3(Xq21.31,Xq21
..32,Xq21.33)),Xq22(Xq22.1,Xq22.2,Xq22.3),Xq23,Xq2 4,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.

Looks interesting, I'll give it a shot. What is each "node"? A gene? A
chromosone? A Band? What would be an appropriate name for the
relationship between 1 and 1p? Can I treat 1p36.3 as one node or does
the decimal encode a relationship between nodes 1p36 and 3?

Could you email it to neo55592 (AT) hotmail (DOT) com , just incase? Thx

Is it equivalent to:

Albert
Bert
Chuck
Donna
Eddie
Fred

If so, below I parsed it manually. I have assumed a parent/child
relationship.

(new 'albert 'person)
(new 'bert 'person)
(new 'chuck 'person)
(new 'donna 'person)
(new 'eddie 'person)
(new 'fred 'person)

(; Create hierarchy consisting of alberts chlidren)
(; Note that child is part of system data)
(set albert child bert)
(set albert child chuck)
(set chuck child donna)
(set chuck child eddie)
(set chuck child fred)

(; Get chuck's children)
(; Gets donna, eddie and fred)
(get chuck child *)

(; Get albert's children)
(; Gets bert, chuck, donna, eddie, fred)
(getRel albert child *)

(; Get fred's parent)
(; Gets chuck)
(get * child fred)

(; Get fred's grand parent)
(; Get albert)
(get * child (get * child fred))

The above is similar to example www.dbfordummies.com/example/ex006.asp

Ok, I have imported the above data into dbd with a hastily coded
parser. Because the gene map data had lots of parentheses, just like
dbd's interface language, I selected it first. The executable with the
parser, a populated db, and the source map file are posted at
www.dbfordummies.com/example/ex700.asp To find the gene named Xq27.3,
type "(get Xq27.3)" in the input box and click the submit button. Or
simply browse the tree by clicking nodes.

Some questions? How many of these sequences would a db need to store?
Was the above sequence small/average/big in comparision to others? How
large is the biggest sequence? Each gene seems to only have one parent.
Is this always the case? Does each gene typcially have additional data
associated with it? What are some basic operations on such gene maps?