In order to judge the quality of a data model for Drools you should
have a fairly conclusive idea about the rules you are going to write.
(This isn't different from other applications: Storing the data in
some organisation may work fine, but fitness for access is a different
matter.)
The Lists may stand investigation. Is the order in the List important?
Is the List just a hidden set? Is an m:n relationship better expressed
by an entity of its own?
The relational data model of DBs is a good approach for being prepared
for a variety of requests and, therefore, rules.
-W
On 16/05/2014, lindenb plindenb...@yahoo.fr wrote:
Hi all,
I'm working in the field of bioinformatics where I study more a large
number
of variations (N 10E6) along the human genome among individuals affected
by a genetic disease. ( * )
my data looks like this (much simplified !)
#CHROMOSOME POSITION GENE PROPERTIES SAMPLE1 SAMPLE2
SAMPLE3
chr1 987 GENE1,GENE3 score=1 null A/A A/G
chr1 988 GENE3score=4;id=989 A/G null A/A
chr1 1988 null score=4;id=989 C/G null C/A
People in my lab have to filter those variation using different strategy,
they then extract the overlapping genes and then filter those genes to find
one or more gene that could explain the disease.
Currently they use knime.org to run those filters.
(http://www.myexperiment.org/workflows/2320.html )
But I've got the feeling that drools could be used to filter those
variations.
Users would 'just' have to write some rules, run the engine and get the
result.
Rules would be removed/switched to get the result for another strategy.
Question:
1) is drools a good choice here ?
2) how should I model my data ?
If I use this java model:
class Gene {
ListVariation getVariations();
}
class Variation {
String getChromosome();
int getPosition();
ListGene getGenes();
ListGenotype getGenotypes();
}
class Genotype{
Variation getVariation();
Sample getSample();
String getDNA();
}
it will create a large graph, can drools support it ?
3) Where in the documentation can I find how to easily set the state my
objects in order to filter them. E.g:
variations -[filters1]- [filter2]-[fiilter5] - result
`[filter3]-[filter4]--/
Thank you,
Pierre
(*)
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
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