Approching substructure mining

With a simple query like the one below random compounds from kinases from the Tk family is collected. I would like to filter the standard value to be under a certain value but I have some problem with doing that in Bioclipse, via SPARQL endpoint I've managed to create this filter. Will work on it.

var allsmiles = " \
PREFIX onto: \
PREFIX blueobelisk: \
\
SELECT DISTINCT ?smiles \
WHERE { \
?target a onto:Target . \
?target onto:classL5 \"Tk\" . \
?target onto:classL6 ?L6 . \
?assay onto:hasTarget ?target . \
?activity onto:onAssay ?assay . \
?activity onto:standardValue ?st . \
?activity onto:forMolecule ?mol . \
?mol blueobelisk:smiles ?smiles . \
}LIMIT 20 \
";
var all = rdf.sparqlRemote("http://rdf.farmbio.uu.se/chembl/sparql", allsmiles)

var all now contains a list of molecules that I is saved in a file via the net.bioclipse.moss.business plug-in.

moss.saveMoss(String fileName, List all)
Will create a file that support moss(id, threshold value, description), not complete
0,0,Cc1nc(N)sc1c2ccnc(Nc3cccc(c3)[N+](=O)[O-])n2
1,0,COc1cc(Nc2c(cnc3cc(OCCC4CCN(C)CC4)c(OC)cc23)C#N)c(Cl)cc1Cl
2,0,CCOc1cc(Nc2c(cnc3cc(OCC4CCN(C)CC4)c(OC)cc23)C#N)c(Cl)cc1Cl
3,0,COc1ccc(C)c(Nc2c(cnc3cc(OCC4CCN(C)CC4)c(OC)cc23)C#N)c1
4,0,COc1ccc(Cl)c(Nc2c(cnc3cc(OCC4CCN(C)CC4)c(OC)cc23)C#N)c1
5,0,COc1cc2c(Nc3ccc(C)cc3C)c(cnc2cc1OCC4CCN(C)CC4)C#N
6,0,COc1cc(Nc2c(cnc3cc(OCC4CCN(C)CC4)c(OC)cc23)C#N)c(C)cc1C

This file now have to be initialized, add parameters for the run and when done simply run.

> moss.saveMoss("/Moss/Test/collected", all)
> moss.init("/Moss/Test/collected")
done
>moss.setLimits(10,2)
> moss.run("/Moss/Test/collectedOut", "/Moss/Test/collectedOutId")

Only two basic parameter settings work at the moment, this is something to be added as soon as possible. It will take time though since lots of parameters are set by combining flags which I remember to be a crucial thing to do.

To read about how MoSS works, how to understand the output files etc look at Christian Borgelt homepage, http://www.borgelt.net/doc/moss/moss.html.

Output file(not complete):
id,description,nodes,edges,s_abs,s_rel,c_abs,c_rel
1,n1:c2:c(:c(-N-c3:c(-Cl):c:c(-Cl):c(-O-C):c:3):c(-C#N):c:1):c:c(-O-C):c(-O-C-C1-C-C-N(-C-C-1)-C):c:2,34,37,2,10.0,0,0.0
2,n1:c2:c(:c(-N-c3:c(-Cl):c:c:c(-O-C):c:3):c(-C#N):c:1):c:c(-O-C):c(-O-C-C1-C-C-N(-C-C-1)-C):c:2,33,36,3,15.0,0,0.0
3,n1:c2:c(:c(-N-c3:c(-Cl):c:c(-Cl):c(-O-C):c:3):c(-C#N):c:1):c:c(-O-C):c(-O-C-C(-C-C)-C):c:2,31,33,3,15.0,0,0.0
4,n1:c2:c(:c(-N-c3:c(-Cl):c:c:c(-O-C):c:3):c(-C#N):c:1):c:c(-O-C):c(-O-C-C(-C-C)-C):c:2,30,32,4,20.0,0,0.0

Output file Id(not complete)
id:list
1:2,10
2:2,4,10
3:2,9,10
4:2,4,9,10
5:2,7,10
6:2,4,7,10

Want to be able to visualize the result in tables later on, perhaps together with the input and other information collected via SPARQL.