Orange3 Example Add-on Documentation

124 Pages·2017·5.11 MB·English

Orange3 Example Add-on
Documentation
Release 2.6.21
Biolab
Apr 04, 2017

Contents
1 Widgets 3
2 ScriptingReference 49
3 Installation 101
4 SourceCodeandIssueTracker 103
5 Indicesandtables 105
Bibliography 107
PythonModuleIndex 109
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Orange3ExampleAdd-onDocumentation,Release2.6.21
OrangeBioinformaticsisanadd-onforOrangedataminingsoftwarepackage. ItextendsOrangebyprovidingfunc-
tionality for some elementary tasks in bioinformatics, like gene set analysis, enrichment, and access to pathway li-
braries. Includedarealsowidgetsforwithgraphicaluserinterfacefor,mainly,geneexpressionanalytics.
Orange Bioinformatics provides access to publicly available data, like GEO data sets, Biomart, GO, KEGG, Atlas,
ArrayExpress, and PIPAx database. As for the analytics, there is gene selection, quality control, scoring distances
betweenexperimentswithmultiplefactors. Allfeaturescanbecombinedwithpowerfulvisualization,networkexplo-
rationanddataminingtechniquesfromtheOrangedataminingframework.
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Orange3ExampleAdd-onDocumentation,Release2.6.21
2 Contents
1
CHAPTER
Widgets
BioMart
GivesaccesstoBioMartdatabases.
Signals
Inputs:
• None.
Outputs:
• Data
Dataset.
Description
BioMart is a widget for direct access to BioMart databases. It sources data from BioMart, filters it by categories
(gene, region, phenotype, gene ontology, etc.) and appends selected attributes in the output (IDs, sources, strains,
etc.). ReadmoreontheBioMartdatabaselibraryhere.
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Orange3ExampleAdd-onDocumentation,Release2.6.21
1. Clearcacheddata.
2. Selectthedatabasetosourceyourdatafrom.
3. Selectthedataset(organism)tosourceyourgenesfrom.
4. IfUniqueresultsonlyisticked,thewidgetwillpreventdataduplication. ClickGetresultstooutputthedata.
5. Settheoutput:
• inAttributesyousetthemetadatayouwishtooutput(e.g. IDs,sources,strains...).
• inFilteryoufilterthedatabygene,phenotype,ontology,proteindomains,etc.
Example
BioMartisagreatwidgetforappendingadditionalinformationtoyourdata. Weusedbrown-selecteddataintheFile
widget. Then we selected Ensembl genes 81 (Sanger UK) database to source our additional data from. We decided
toappendEnsemblGeneID,EnsemblTranscriptID,genetypeandPDBID.Wealsofilteredthedatatooutputonly
thosegenesthatcanbefoundonchromosomeI.Wegot9997instanceswith4metaattributes. ThenweusedMerge
Datawidgettoappendthesemetastoourdata. Wematchedthedatabygene/EnsemblegeneIDandintheendwegot
amergeddatatablewith5metaattributes.
4 Chapter1. Widgets
Orange3ExampleAdd-onDocumentation,Release2.6.21
Databases Update
Updateslocalsystemsbiologydatabases,likegeneontologies,annotations,genenames,proteininteractionnetworks,
andsimilar.
Signals
Inputs:
• None
Outputs:
• None
1.2. DatabasesUpdate 5
Orange3ExampleAdd-onDocumentation,Release2.6.21
Description
Withthebioinformaticsadd-onyoucanaccessseveraldatabasesdirectlyfromOrange. Thewidgetcanalsobeused
toupdateandmanagelocallystoreddatabases.
1. Findthedesireddatabase.
2. Alistofavailabledatabasesdescribedwithdatasource,updateavailability,dateofyourlastupdateandfilesize.
AlargeUpdatebuttonwillbedisplayednexttothedatabasethatneedstobeupdated.
3. Update All will update and Download All will download all the selected databases. Cancel will abort the
action.
4. SomedatasetsrequiretheAccesscode. Typeitintheprovidedfieldtoaccessthedatabase.
5. Informationontheselecteddatabases.
Togetamoredetailedinformationontheparticulardatabasehoveronitsname.
6 Chapter1. Widgets