Department of Bioinformatics - BiGCaT 1

Using standards to gaininteroperability:Bioclipse-OpenTox scripting

Egon WillighagenBiGCaT - Maastricht University

17 May 2012

Department of Bioinformatics - BiGCaT 2

Managers: the vital organs of Bioclipse

Some theory● Make sure that things happen● They provide all domain-related functionality● All Bioclipse GUI is using managers in the background● Takes care of threading (background processes)● They are plugged into the system● Bioclipse dynamically discovers managers when booted● Extend the JavaScript Console (also Groovy)Spjuth, O., Alvarsson, J., Berg, A., Eklund, M., Kuhn, S., Mäsak, C., Torrance, G., Wagener, J., Willighagen, E. L., Steinbeck, C., Wikberg, J. E., Dec. 2009. Bioclipse 2: A scriptable integration platform for the life sciences. BMC Bioinformatics 10 (1), 397+.

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Many managers...

Core bioclipse: latex, ui, bioclipse, xml, js, balloon, cdk, rdf, inchi, cml, moltable, jcp, jcpprops

Additional libraries: bridgedb, metfrag, metware, joelib, oscar, opsin, r, pellet, specmol, spectrum, bibtex, owl, ds, qsar, ambit, structuredb

Online services: cir, opentox, google, gist, myexperiment, sadi, pubchem, pubmed, nmrshiftdb, twitter

… and more.

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JavaScript Console

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TAB TAB• Discover manager in the JavaScript

console with:1) TAB TAB (auto-completion)2) man

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man <manager>• Discover what functionality a

manager has

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Ctrl-N JavaScript editor→

• Ctrl-N JavaScript Wizard Editor → → Save As …→

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Running JavaScripts in the Editor• JavaScript Editor Run Action→ →

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Managers can be combined ...var alkanesIUPACNames = ["methane", "ethane", "propane", "butane"];

var alkanes = cdk.createMoleculeList()for (var i=0; i<alkanesIUPACNames.length; i++) { js.say("Adding: " + alkanesIUPACNames[i]); alkanes.add( opsin.parseIUPACName(alkanesIUPACNames[i]) );}

var filename = "/OpenTox/alkanes.sdf";cdk.saveSDFile(filename, alkanes);ui.open(filename);

Department of Bioinformatics - BiGCaT 10

OpenTox: downloading data sets

var service = "http://apps.ideaconsult.net:8080/ambit2/";

var datasets = opentox.listDataSets(service);for (set=0; set<5; set++) { var dataset = datasets.get(set); js.say("Downloading set: " + dataset); ui.open( opentox.downloadDataSetAsMDLSDfile( service, dataset, "/OpenTox/ambit/" + set + ".sdf" ) )}

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OpenTox: download-ed data sets

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OpenTox: authentication

opentox.getToken(); // return a null

// log in on the OpenTox networkopentox.login("user", "password")

opentox.getToken(); // returns the active token

// log out againopentox.logout()

opentox.getToken(); // return again

Department of Bioinformatics - BiGCaT 13

OpenTox: XLogP calculationmolecules = cdk.createMoleculeList();

molecules.add(cdk.fromSMILES("COC"));

molecules.add(cdk.fromSMILES("CNC"));

js.say(opentox.calculateDescriptor(service, descriptor, molecules));

js.say(opentox.calculateDescriptor(

service, descriptor,

cdk.fromSMILES("CCC")

));

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OpenTox: running models

models = opentox.listModels(ontologyService);

model = models.get(3); // third model

js.say(

opentox.predictWithModel(

service,

model,

molecules

)

);

Department of Bioinformatics - BiGCaT 15

Under the hood...

Internally, the opentox manager uses RDF and SPARQL for a lot of communication with the OpenTox network.

For this, it uses the rdf manager. For example, directly to the ontology server:1. rdf.sparqlRemote(String url, String SPARQL)

Or to a REST service:1. rdf.createInMemoryStore()2. rdf.importFromStream(IRDFStore store, InputStream stream, String format)3. rdf.sparql(IRDFStore store, String query)

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Where to get more scripts ...

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Future ...

• Continued development

• Computation without downloading data (pass by reference)

• More ontology development for further standardization

Pointers● Bug tracker: http://bugs.bioclipse.net/● Feature requests: http://wishes.bioclipse.net/

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OpenTox: public, private, local!

• AMBIT2 (IdeaConsult Ltd., Nina)

http://apps.ideaconsult.net:8080/ambit2/

• localhost:8080

• ambitserver

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Delivering Bioclipse plugins...