[rules-users] Newbie: is my data model suitable for drools ?

[lindenb]

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       GENE3        score=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 {
List<Variation> getVariations();
}

class Variation {
String getChromosome();
int getPosition();
List<Gene> getGenes();
List<Genotype> 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



--
View this message in context: http://drools.46999.n3.nabble.com/Newbie-is-my-data-model-suitable-for-drools-tp4029590.html
Sent from the Drools: User forum mailing list archive at Nabble.com.