Using standards to gain interoperability:Bioclipse-OpenTox scripting

Egon Willighagen

http://egonw.github.com/

http://chem-bla-ics.blogspot.com/

IMM

Karolinska Institutet, Stockholm

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

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+.

3

JavaScript Console

4

TAB TAB

Discover manager in the JavaScript console with:

1) TAB TAB (auto-completion)

2) man

5

Many Managers

Cheminformatics1. cdk

2. opsin

3. jmol

4. balloon

General1. bioclipse

2. ui

3. rdf

Online1. chemspider

2. pubchem

3. gist

4. opentox

Many more can be installed via update sites...

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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);

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(if needed)

opentox.getToken(); // return a null

// log in on the OpenTox network

opentox.login("user", "password")

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

// log out again

opentox.logout()

opentox.getToken(); // return again

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OpenTox: searching data sets

var ontologyService = "http://apps.ideaconsult.net:8080/ontology/";

js.clear();

sets = opentox.searchDataSets(ontologyService, "EPA");

js.say(sets);

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OpenTox: finding descriptors

serviceSPARQL = "http://apps.ideaconsult.net:8080/ontology/";

stringMat = opentox.listDescriptors(serviceSPARQL);

stringMat.getColumn("algo"); // returns the descriptor services

stringMat.getColumn("desc"); // returns the descriptor ontology entries

js.say(stringMat);

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OpenTox: XLogP calculation

molecules = 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: searching descriptors(next release; a 5 min hack)

var ontologyService = "http://apps.ideaconsult.net:8080/ontology/";

js.clear();

descriptors = opentox.searchDescriptors(

ontologyService, "LogP"

);

js.say(descriptors);

17

OpenTox: searching models(next release; another 5 min hack)

var ontologyService = "http://apps.ideaconsult.net:8080/ontology/";

js.clear();

descriptors = opentox.searchModels(

ontologyService, "ToxTree"

);

js.say(descriptors);

18

OpenTox: running models

models = opentox.listModels(ontologyService);

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

js.say(

opentox.predictWithModel(

service,

model,

molecules

)

);

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Ontology development needed...

… just saying ...

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More OpenTox: man opentox

Or type: “opentox.” and hit TAB TAB ...

21

Under the hood...

Some more theory...

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/