gmod-schema Mailing List for Generic Model Organism Database Project

The latest chado gadfly load, version 05, is available at
ftp://ftp.fruitfly.org/pub/people/cwiel/.
The release notes are below.
Cheers,
Colin
----------------------------------------
RELEASE NOTES
Gadfly Chado Load 0.5
Colin Wiel
4/30/03
This version of the Gadfly Chado load has the following fixes:
1. arm residue problem resolved - now using proper fasta files.
2. includes featureloc's for all accessions
3. removed assembly:path analysis
4. exons "partof", not "producedby" transcripts
----------------------------------------

In a message dated 4/23/2003 4:30:24 PM Eastern Daylight Time, ca...@cs... 
writes:
> So, as a proof of principle, I think I can call my gbrowse port to chado
> done (after how many months?). 
Congratulations and thanks!!
I have to wonder though if there is any
> 
> way to check the results of the update of the featureloc table other
> than randomly clicking and looking at the picture it creates. Any ideas?
> 
Sure -- you can write a query that verifies the property you just established 
--
find all alignment hits that do not have featurelocs whose coords are the 
mins
and maxes of their HSPs. If there are any something is wrong.
Cheers, -Stan

Hello all,
First, I wanted to announce that I've used SQL provided by Chris to add
alignment hits with locations to featureloc in the most recent port of
gadfly to chado (code I actually used below). And it appeared to work
correctly; that is, it executed without an error and the pictures that
it creates in gbrowse seem correct (ie, for the most part, the HSPs line
up under annotated exons). 
So, as a proof of principle, I think I can call my gbrowse port to chado
done (after how many months?). I have to wonder though if there is any
way to check the results of the update of the featureloc table other
than randomly clicking and looking at the picture it creates. Any ideas?
Here is the SQL I used (note that it uses fmin and fmax that I added to
speed up gbrowse)
INSERT INTO featureloc (feature_id, fmin, fmax, srcfeature_id)
 SELECT DISTINCT hit.feature_id,
 min(hsploc1.fmin), max(hsploc2.fmax),
 min(hsploc1.srcfeature_id)
 FROM
 feature AS hit
 INNER JOIN
 feature_relationship ON (hit.feature_id = objfeature_id)
 INNER JOIN
 featureloc AS hsploc1 ON (hsploc1.feature_id = subjfeature_id)
 INNER JOIN
 featureloc AS hsploc2 ON (hsploc2.feature_id = subjfeature_id)
 WHERE hit.type_id = 13
 AND hsploc1.rank = 0
 AND hsploc2.rank = 0
 GROUP BY hit.feature_id
Thanks,
Scott
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D. ca...@cs...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory

The latest chado gadfly load, version 04, is available at
ftp://ftp.fruitfly.org/pub/people/cwiel/.
The major changes are:
1. GO integration.
2. SO feature types.
3. Adherence to latest chado schema.
Release notes are below.
Cheers,
Colin
----------------------------------------
RELEASE NOTES
Gadfly Chado Load 0.4
Colin Wiel
4/14/03
This version of the Gadfly Chado load has the following changes:
1. GO Integration
The GO terms have been loaded as three CV's: cellular_component,
molecular_function, and biological_process. Each GO term is a cvterm,
and the isa and partof relationships are stored in cv_relationship. A
dbxref was created for each term, and associated in cvterm_dbxref. GO
associations are stored in feature_cvterm.
2. SO Feature Types
A CV called SO was created, with 30 terms. Almost all of these are in
the current version of SO, although a few are not yet in SO (e.g. arm,
and protein). These remaining terms will be resolved with SO in the
next few weeks, probably by adding these terms to SO. Each feature now
has a SO term as its type_id. In a future release, after SO has
stabilized, I will load all 800-ish SO terms, and will also load the
cv_relathionships, dbxrefs, and cvterm_dbxrefs.
3. Chado Schema 
The load uses the latest chado schema.
Note:
Relationship types "part of" and "produced by" have been changed to
"partof" and "producedby" to adhere to the GO protocol.
----------------------------------------

An ontology can be used to describe an organism, but can it be used to 
describe a disease? Not in clinical terms (controlled vocabularies in 
medicine are used) but in biochemical terms, a disease may be seen as a mal 
function in one or many metabolic processes. So considering only metabolic 
pathways a disease can be fully described, and because metabolic pathways 
involve proteins and genes then real integration is achieved. The in 
formation in metabolic pathways describing a disease is in a real context. 
Ontology in molecular biology have been used in order to describe the 
function of biological objects; and now they have been incorporated in to 
most existing databases as one of the items, but the relations that this 
objects have among them have been leaved behind (at least has not being 
really incorporated in to the databases that have GO as one of the items in 
entries). So my question is: if a real model of a disease were to be built, 
would not this model have to consider more than just descriptions of the 
different objects that outline it (the disease) and focus more on the 
relations of this objects and how the balance among this objects is being 
disturbed in order for a disease to be produced? The infectious process 
along with all the rest of the processes that the disease have are any way 
part of the disease it self, and for studying the system as such it must be 
at some degree isolated (?).
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