getting started with spatial extender

[Belinda]

Hi. I am just getting started with DB2's spatial extender and could
really use some help. Pointers to good docs or examples are welcome.
I am using DB2 version 8 on Sun. I have a database of genomic data
and believe the spatial extender will help in querying. I have to do
intersections, subtractions, proximity, etc of ranges in the
chromosomes. The database and even some tables include data on all
chromosomes of several species. I am not even sure what coordinate
system to use. From my reading (if I understand it correctly) the
multiline data type sounds good, if I can assign species/chromosome to
individual lines. If I sound confused it is because I am ;) Any
pointers to get me started would be greatly appreciated.

Thanks,
Belinda

[Belinda]

bm****@penn.com (Belinda) wrote in message news:<87**************************@posting.google. com>...

Hi. I am just getting started with DB2's spatial extender and could
really use some help. Pointers to good docs or examples are welcome.
I am using DB2 version 8 on Sun. I have a database of genomic data
and believe the spatial extender will help in querying. I have to do
intersections, subtractions, proximity, etc of ranges in the
chromosomes. The database and even some tables include data on all
chromosomes of several species. I am not even sure what coordinate
system to use. From my reading (if I understand it correctly) the
multiline data type sounds good, if I can assign species/chromosome to
individual lines. If I sound confused it is because I am ;)
pointers to get me started would be greatly appreciated.

Thanks,
Belinda

I have made some progress of sorts. I still have no idea whether I
made the right choice but have set up the human genome as
MuliLineString type and have the y axis be the chromosome and the x
axis be the nucleotides. I have created a test table and registered
the columns. I can enter data using insert statements but this isn't
practical for real data. The loader returns SQL3529N The "LOAD"
operation encountered the unsupported data type
"Structured Data Type" in column "10" so that obviously doesn't work.
From my reading what I need is a GeoCoder. There are references to
writing your own but no links to docs on how to do it, only how to
register after it is written.

For reference the most detailed docs I have found so far:
http://www-306.ibm.com/software/data/spatial/db2sb.pdf

Belinda

[Knut Stolze]

Belinda <bm****@penn.com> wrote:

bm****@penn.com (Belinda) wrote in message
news:<87**************************@posting.google. com>...

Hi. I am just getting started with DB2's spatial extender and could
really use some help. Pointers to good docs or examples are welcome.
I am using DB2 version 8 on Sun. I have a database of genomic data
and believe the spatial extender will help in querying. I have to do
intersections, subtractions, proximity, etc of ranges in the
chromosomes. The database and even some tables include data on all
chromosomes of several species. I am not even sure what coordinate
system to use. From my reading (if I understand it correctly) the
multiline data type sounds good, if I can assign species/chromosome to
individual lines. If I sound confused it is because I am ;)
pointers to get me started would be greatly appreciated.

I have made some progress of sorts. I still have no idea whether I
made the right choice but have set up the human genome as
MuliLineString type and have the y axis be the chromosome and the x
axis be the nucleotides.
First, I believe the Spatial Extender (SE) could indeed be used for your
purposes. However, I am not aware of a real world scenario where folks
have done so.

As for the exact data type I would recommend, I need to get a better
understanding if your scenario. For example, if you want to store a
chromosome (with its embedded nucleotides) as a single value, then
ST_LineString might be a good choice. It might also be that you consider a
part of a chromosome as a single value. Storing all chromosomes together
in a ST_MultiLineString doesn't seem to be an ideal approach to me, but as
I said - I don't know all the details to make that call.
Maybe we should take this discussion offline?
I have created a test table and registered
the columns. I can enter data using insert statements but this isn't
practical for real data. The loader returns SQL3529N The "LOAD"
operation encountered the unsupported data type
"Structured Data Type" in column "10" so that obviously doesn't work.
From my reading what I need is a GeoCoder. There are references to
writing your own but no links to docs on how to do it, only how to
register after it is written.
DB2's LOAD command does not yet support the loading of spatial data. What
we would need to know is the format in which your data is available, e.g.
somehow you have to represent the spatial information (your chromosome
information). Once we know that, we can see if:
(a) the spatial extender's import routines could be used, or
(b) we have to write a small tool that will import/load the data from your
format
For reference the most detailed docs I have found so far:
http://www-306.ibm.com/software/data/spatial/db2sb.pdf
This document is the Spatial Extender User's Guide and Reference and is the
most complete document that describes the various functions and features of
the extender. There are also some papers available at different places,
which cover more specialized requirements (like more examples for geocoding
or replication of spatial data) - I don't think you need those, at least
not at this time.

You might also want to read the news group at
news://news.software.ibm.com/ibm.sof...b2.udb.spatial It is dedicated
to discuss problems and questions regarding the DB2 Spatial Extender.

Belinda

--
Knut Stolze
Information Integration
IBM Germany / University of Jena