On this blog you are able to follow my degree project(master thesis in Bioinformatics) which have the title Pharmaceutical knowledge retrieval through reasoning of ChEMBL RDF.
My supervisor is Egon Willighagen, http://chem-bla-ics.blogspot.com/.


måndag 14 juni 2010

A small but wonderful add-on

Look at the following scenarios:


> var camk = chembl.MossGetProtFamilyCompAct("camk", "IC50")

> chembl.MoSSViewHistogram(camk)

> var camkBounds = chembl.MossSetActivityBound(camk, 1,1000000)

> camkBounds.getRowCount()


>chembl.MossSaveFormat("/ChEMBL-MoSS/Rapport/CAMKIC501", camk)


> var camk=chembl.MossGetProtFamilyCompActBounds("CAMK","IC50",1, 1000000)

> camk.getRowCount()


> chembl.MossSaveFormat("/ChEMBL-MoSS/Rapport/CAMKIC502", camk)

(a)+(b) Scripts taken from the context of retrieving molecules for molecular substructure mining. (a) Collects compounds that bind to proteins from the family CAMK with the activity IC50. The activities for the compounds are looked at in a histogram and the bound is later set to involve molecules within activities between 1-1000,000. Lastly saved out to a file that supports MoSS input file.

(b)Lets say you been working with this set a couple of times and know exactly your parameters then the script in (b) would reduce unnecessary steps in retrieving molecules by simply adding the upper and lower value to the query directly. At last saving into an input file of MoSS.

Small step but wonderful when you run scripts all day!

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