Swertz bosc2010 molgenis

Morris A. Swertz

K Joeri van der Velde, Alexandros Kanterakis, Juha Muilu, Tomasz Adamusiak, Martijn Dijkstra, Gudmundur A. Thorisson, George Byelas, Danny Arends, Members of EU-GEN2PHEN, NL-NBIC, EU-CASIMIR, BBMRI-NL, EU-PANACEA, Anthony J. Brookes, Ritsert C. Jansen and Helen Parkinson

EBI

Outline

• MOLGENIS overview

• Demo movie

• Summary

Challenge

biologist

GUI

DB

bioinformatician

inbreed

100

10.000

1,000,000

100,000

10,000

10

10,000,00

QTL profiles

network

correlate

genomestrains

individuals

markers

expressions preprocess

probesmicroarrays

100

hybridize

100,000

genotype genotypes

norm exprs.

map

Logic

APIs

Exchange services

Etc

Use

Animal Observatory

NextGenSeq

Mutation database

Model organisms

Biologist needs Work very hard

Challenge multiplied by project

Needed alternative method

http://www.molgenis.orgSwertz & Jansen (2007) Nature Reviews Genetics 8, 235-243Swertz et al (2004) Bioinformatics 20(13), 2075-83 Your database at the push

of a buttonmolgenis.org

NextGenSeq

Mutation database

Model organisms

Model in DSL Use

Animal Observatory

Three steps

GeneratorGenerator

DSL – domain specific language

Use

Animal Observatory

NextGenSeq

Mutation database

Model organisms

Model in DSL

GeneratorGenerator

Reuse notwithstanding large variation

DSL – domain specific language

MOLGENIS: How does it work?

<link to movie>

Applications

etc.

etc.

11

XGAP for GWAS/GWL

FINDIS disease DB

Pheno-OM biobank

catalogue

SeqLIMS

MAGE-TAB microarray

AnimalDB

<add your project here>

Example models

eXtensible Genotype And Phenotype (XGAP)

DATA ELEMENT

TRAIT

SUBJECT

columns

rows

DIMENSIONELEMENT

PROBE-Name-Gene

-Chromosme-Locus

PROBE-Name-Gene

-Chromosme-Locus

MARKER-Name-Allele

-Chromosme-Locus

MARKER-Name-Allele

-Chromosme-Locus

MASSPEAK-Name

-MZ-RetentionTime

MASSPEAK-Name

-MZ-RetentionTime

Panel-Name

-Type: CSS, RIL..-Parent Panels

Panel-Name

-Type: CSS, RIL..-Parent Panels

INDIVIDUAL-Name-Strain

-Mother-Father

-Sex

INDIVIDUAL-Name-Strain

-Mother-Father

-Sex

SAMPLE-Name

-Individual-Tissue

SAMPLE-Name

-Individual-TissueAnd so on

…

And so on…

And so on…

And so on…

http://www.xgap.org Swertz, van der Velde et al (2010) Genome Biology 9;11(3): R27.

Data loading



Data exploration

Data analysis using cloud/cluster

See poster Q01: User friendly cluster computing for R/QTL analysis on XGAP

RDF + SPARQL

18

Panacea

GEN2PHENLifeLines

IOP

Deformed ears?

HPO:Abnormally shaped ears Auricular malformation

Deformed auricles

MP:Malformed auricles

Malformed ears Malformed external ears

etc

query expansion

See poster P05: OntoCAT – simple API for ontologies

Data integration using RDFLocal

ontologies

(OLW or OBO)

BioPortal

OLS

Summary

Result:

• Database-in-a-box

• Rich web GUI

• Standard deployment

• 10k writes/sec

• Interfaces for analysis• Java

• R

• REST

• SOAP

• RDF

Method:

• Rapid dev cycle

• Edit simple models

• Pair with biologists

• Discuss documentation

• Test on real data

• Generated junit tests

• Plugin system

• Matrix data backend

• Reuse!

Extensive manuals

AcknowledgementsMorris Swertz

Joeri van der Velde

Joris Lops

Danny Arends

Alex Kanterakis

Erik Roos

Richard Scheltema

Martijn Dijkstra

Rudi Alberts

Bruno M. Tesson

Gonzalo Vera Rodriguez

Tomasz Adamuziak

Juha Muilu

Gudmundur Thorisson

Damian Smedley

Katy Wolstencroft

Ritsert C. Jansen

Cisca Wijmenga

Carole Goble

John M. Hancock

Andrew R. Jones

Klaus Schughart

Paul Schofield

Anthony Brookes

Helen E. Parkinson

BBMRI-NL biobanking (Hs)

EU-GEN2PHEN consortium (Hs)

EU-PANACEA consortium (Ce)

NL Brassica Nutr. consortium (At)

EU-CASIMIR consortium (Mm)

NBIC/BioAssist consortium (bioinfo)

21

NLNLEBI

ISMB• E15 - MOLGENIS

• Q01 – QTL analysis

• E19 – MAGE-TAB

• P05 – OntoCAT

• TT36, Tuesday 12.15-12.40

Web • MOLGENIS: http://www.molgenis.org

• XGAP: http://www.xgap.org

• MAGETAB-OM: http://magetab-om.sourceforge.net/

• Pheno-OM: http://wwwdev.ebi.ac.uk/microarray-srv/pheno/

• FINDIS: http://www.findis.org/molgenis_findis/

• AnimalDB: http://www.animaldb.org

Pubmed• Swertz & Jansen (2007) Nature Reviews Genetics 8, 235-243

• Swertz et al (2004) Bioinformatics 20(13), 2075-83

• Swertz et al (2010) Genome Biology 9;11(3): R27.

Thank [email protected]

Model –> Generate –> UseModeling language

506 lines of XML code for Pheno-OM16 entities, 67 fields

Generates 150 files, 30k lines of Java, SQL and R code + docs

0 INFO [myFactory] working dir: D:\Development\Molgenis33Workspace\molgenis4phenotype78 INFO [myFactory] MOLGENIS version 3.3.0-testing94 INFO [myFactory] Using options:model_database = [pheno_db.xml] #File with data structure specification (in MOLGENIS DSL).model_userinterface = pheno_ui.xml #File with user interface specification (in MOLGENIS DSL). Can be same file as model_databaseoutput_src = generated/java #Output-directory for the generated project.output_hand = handwritten/java #Output-directory for the generated project.output_sql = generated/sql #Output-directory for the generated sql files.output_doc = WebContent/doc #Output-directory for the generated documentation.output_type = #Output type of the project, either war (for use in tomcat) or jar (standalone).output_web = WebContent #Output-directory for any generated web resourcesdb_driver = com.mysql.jdbc.Driver #Driver of database. Any JDBC compatible driver should work.db_user = molgenis #Username for database. db_password = xxxxxx #Password for database. db_uri = jdbc:mysql://localhost/pheno #Uri of the database. Default: localhostdb_filepath = attachedfiles #Path where the database should store file attachements. Default: nulldb_jndiname = jdbc/molgenisdb #Used to create a JDBC database resource for the applicationobject_relational_mapping = subclass_per_table #Expert option: Choosing OR strategy. Either 'class_per_table', 'subclass_per_table', 'hierarchy_per_table'. Default: class_per_tablemapper_implementation = multiquery #Expert option: Choosing wether multiquery is used instead of prepared statements. Default: falseexclude_system = true #Expert option: Whether system tables should be excluded from generation. Default: trueforce_molgenis_package = false #Expert option. Whether the generated package should be 'molgenis' or the name specified in the model. Default: falseauth_loginclass = org.molgenis.framework.security.SimpleSecurity #Expert option.verbose = true #This switch turns the verbose-mode on.compile = false #This switch makes the factory also compile (usefull outside IDE).mail_smtp_protocol = #Sets the email protocol, either smtp, smtps or null. Default: null meaning email disabledmail_smtp_hostname = localhost #SMTP host server. Default: localhostmail_smtp_port = 25 #SMTP host server port. Default: 25mail_smtp_user = #SMTP user for authenticated emailing. Default: null.mail_smtp_password = #SMTP user for authenticated emailing. Default: null.

110 INFO [MolgenisLanguage] parsing db-schema from [pheno_db.xml]780 WARN [Entity] [WARNING]: missing key 0 for entity Nameable780 WARN [Entity] [WARNING]: missing key 0 for entity Nameable780 WARN [Entity] [WARNING]: missing key 0 for entity Nameable780 WARN [Entity] [WARNING]: missing key 0 for entity Nameable780 WARN [Entity] [WARNING]: missing key 0 for entity Nameable797 WARN [Entity] [WARNING]: missing key 0 for entity Nameable797 WARN [Entity] [WARNING]: missing key 0 for entity Nameable844 INFO [MolgenisLanguage] parsing ui-schema937 INFO [main] generating ....1717 INFO [TableDocGen] generated WebContent\doc\tabledoc.html2076 INFO [EntityDocGen] generated WebContent\doc\objectmodel.html2436 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram.dot2545 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram-pheno.system.dot2748 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram-pheno.observation.dot2842 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram-pheno.target.dot2998 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram-pheno.variable.dot3138 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram-pheno.protocol.dot3997 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-minimal-diagram.dot4184 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-diagram-minimal-pheno.system.dot4388 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-diagram-minimal-pheno.observation.dot4606 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-diagram-minimal-pheno.target.dot4731 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-diagram-minimal-pheno.variable.dot4887 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-diagram-minimal-pheno.protocol.dot5184 INFO [ClassDocGen] generated WebContent\doc\classmodel.html5293 INFO [InMemoryDatabaseGen] generated generated\java\ui\data\InMemoryDatabase.java5609 INFO [MySqlCreateSubclassPerTableGen] generated generated\sql\create_tables.sql5671 INFO [JDBCDatabaseGen] generated generated\java\ui\JDBCDatabase.java5921 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Identifiable.java5921 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Nameable.java5968 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\OntologySource.java6014 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\OntologyTerm.java6030 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Investigation.java6061 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ObservableFeature.java6124 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ObservedValue.java6170 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ObservedRelationship.java6217 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\InferredValue.java6233 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ObservationTarget.java6280 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Individual.java6311 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Panel.java6326 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\CodeList.java6327 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Code.java6374 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Protocol.java6390 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ProtocolApplication.java6405 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ProtocolParameter.java6437 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ParameterValue.java6452 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\InferredValue_derivedFrom.java6468 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Panel_individuals.java6483 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Protocol_observableFeatures.java6499 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Protocol_protocolComponents.java6624 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\OntologySourceMapper.java6655 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\OntologyTermMapper.java6671 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\InvestigationMapper.java6702 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ObservableFeatureMapper.java6733 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ObservedValueMapper.java6780 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ObservedRelationshipMapper.java6827 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\InferredValueMapper.java6842 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ObservationTargetMapper.java6873 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\IndividualMapper.java6889 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\PanelMapper.java6905 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\CodeListMapper.java6936 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\CodeMapper.java6951 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ProtocolMapper.java6983 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ProtocolApplicationMapper.java6998 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ProtocolParameterMapper.java7029 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ParameterValueMapper.java7045 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\InferredValue_derivedFromMapper.java7061 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\Panel_individualsMapper.java7076 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\Protocol_observableFeaturesMapper.java7092 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\Protocol_protocolComponentsMapper.java7217 INFO [JDBCMetaDatabaseGen] generated generated\java\ui\JDBCMetaDatabase.java7263 INFO [CountPerEntityGen] generated generated\sql\count_per_entity.sql7310 INFO [CountPerTableGen] generated generated\sql\count_per_table.sql7341 INFO [FillMetadataTablesGen] generated generated\sql\insert_metadata.sql7405 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\OntologySourceCsvReader.java7420 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\OntologyTermCsvReader.java7420 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\InvestigationCsvReader.java7436 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ObservableFeatureCsvReader.java7452 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ObservedValueCsvReader.java7467 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ObservedRelationshipCsvReader.java7483 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\InferredValueCsvReader.java7498 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ObservationTargetCsvReader.java7514 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\IndividualCsvReader.java7514 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\PanelCsvReader.java7530 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\CodeListCsvReader.java7545 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\CodeCsvReader.java7545 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ProtocolCsvReader.java7561 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ProtocolApplicationCsvReader.java7561 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ProtocolParameterCsvReader.java7576 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ParameterValueCsvReader.java7576 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\InferredValue_derivedFromCsvReader.java7592 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\Panel_individualsCsvReader.java7608 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\Protocol_observableFeaturesCsvReader.java7608 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\Protocol_protocolComponentsCsvReader.java7748 INFO [REntityGen] generated generated\java\pheno\core\R\OntologySource.R7748 INFO [REntityGen] generated generated\java\pheno\core\R\OntologyTerm.R7764 INFO [REntityGen] generated generated\java\pheno\core\R\Investigation.R7779 INFO [REntityGen] generated generated\java\pheno\core\R\ObservableFeature.R7779 INFO [REntityGen] generated generated\java\pheno\core\R\ObservedValue.R7795 INFO [REntityGen] generated generated\java\pheno\core\R\ObservedRelationship.R7795 INFO [REntityGen] generated generated\java\pheno\core\R\InferredValue.R7810 INFO [REntityGen] generated generated\java\pheno\core\R\ObservationTarget.R7810 INFO [REntityGen] generated generated\java\pheno\core\R\Individual.R7826 INFO [REntityGen] generated generated\java\pheno\core\R\Panel.R7826 INFO [REntityGen] generated generated\java\pheno\core\R\CodeList.R7842 INFO [REntityGen] generated generated\java\pheno\core\R\Code.R7857 INFO [REntityGen] generated generated\java\pheno\core\R\Protocol.R7857 INFO [REntityGen] generated generated\java\pheno\core\R\ProtocolApplication.R7873 INFO [REntityGen] generated generated\java\pheno\core\R\ProtocolParameter.R7873 INFO [REntityGen] generated generated\java\pheno\core\R\ParameterValue.R7888 INFO [REntityGen] generated generated\java\pheno\core\R\InferredValue_derivedFrom.R7888 INFO [REntityGen] generated generated\java\pheno\core\R\Panel_individuals.R7888 INFO [REntityGen] generated generated\java\pheno\core\R\Protocol_observableFeatures.R7904 INFO [REntityGen] generated generated\java\pheno\core\R\Protocol_protocolComponents.R7998 INFO [RApi] generated generated\java\source.R8044 INFO [HtmlFormGen] generated generated\java\pheno\core\html\IdentifiableHtmlForm.java8044 INFO [HtmlFormGen] generated generated\java\pheno\core\html\NameableHtmlForm.java8044 INFO [HtmlFormGen] generated generated\java\pheno\core\html\OntologySourceHtmlForm.java8044 INFO [HtmlFormGen] generated generated\java\pheno\core\html\OntologyTermHtmlForm.java8060 INFO [HtmlFormGen] generated generated\java\pheno\core\html\InvestigationHtmlForm.java8060 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ObservableFeatureHtmlForm.java8076 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ObservedValueHtmlForm.java8076 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ObservedRelationshipHtmlForm.java8076 INFO [HtmlFormGen] generated generated\java\pheno\core\html\InferredValueHtmlForm.java8091 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ObservationTargetHtmlForm.java8091 INFO [HtmlFormGen] generated generated\java\pheno\core\html\IndividualHtmlForm.java8091 INFO [HtmlFormGen] generated generated\java\pheno\core\html\PanelHtmlForm.java8091 INFO [HtmlFormGen] generated generated\java\pheno\core\html\CodeListHtmlForm.java8107 INFO [HtmlFormGen] generated generated\java\pheno\core\html\CodeHtmlForm.java8107 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ProtocolHtmlForm.java8107 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ProtocolApplicationHtmlForm.java8107 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ProtocolParameterHtmlForm.java8122 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ParameterValueHtmlForm.java8122 INFO [HtmlFormGen] generated generated\java\pheno\core\html\InferredValue_derivedFromHtmlForm.java8122 INFO [HtmlFormGen] generated generated\java\pheno\core\html\Panel_individualsHtmlForm.java8122 INFO [HtmlFormGen] generated generated\java\pheno\core\html\Protocol_observableFeaturesHtmlForm.java8138 INFO [HtmlFormGen] generated generated\java\pheno\core\html\Protocol_protocolComponentsHtmlForm.java8138 INFO [MolgenisServletContextGen] generated WebContent\META-INF\context.xml8169 INFO [MolgenisContextListenerGen] generated generated\java\servlet\ContextListener.java8232 INFO [MolgenisServletGen] generated generated\java\MolgenisServlet.java8403 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\InvestigationsForm.java8560 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ObservableFeaturesForm.java8591 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\PanelsForm.java8654 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\Panels\IndividualsForm.java8701 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ObservedValuesForm.java8732 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ProtocolApplicationsForm.java8825 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ProtocolApplications\ProtocolApplicationMenu\ParameterValuesForm.java8857 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ProtocolApplications\ProtocolApplicationMenu\ObservedValuesForm.java8888 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ProtocolApplications\ProtocolApplicationMenu\InferredValuesForm.java9013 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\InferredValuesForm.java9044 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\ObservableFeaturesForm.java9137 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\ObservationTargets\IndividualsForm.java9169 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\ObservationTargets\PanelsForm.java9200 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\ProtocolsForm.java9293 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Protocols\ProtocolMenu\ParametersForm.java9325 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Protocols\ProtocolMenu\ProtocolComponentsForm.java9496 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Ontologies\OntologyTermsForm.java9528 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Ontologies\OntologySourcesForm.java9606 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Ontologies\OntologySources\OntologyTermsForm.java9638 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Ontologies\CodeListsForm.java9700 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Ontologies\CodeLists\CodesForm.java9965 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenuMenu.java10012 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\MainMenu.java10059 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenuMenu.java10152 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ProtocolApplications\ProtocolApplicationMenuMenu.java10230 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\Main\ObservationTargetsMenu.java10293 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\Main\Protocols\ProtocolMenuMenu.java10324 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\Main\OntologiesMenu.java11354 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\Main\ReportPlugin.java11557 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\Main\Ontologies\OntologyManagerPlugin.java11604 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\Model_documentationPlugin.java11604 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\RprojectApiPlugin.java11620 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\HttpApiPlugin.java11635 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\WebServicesApiPlugin.java11651 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\report\InvestigationOverview.ftl11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\OntologyBrowser\OntologyBrowserPlugin.ftl11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\DocumentationScreen.ftl11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\RprojectApiScreen.ftl11823 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\HttpAPiScreen.ftl11823 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\SoapApiScreen.ftl11854 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\report\InvestigationOverview.java12057 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\OntologyBrowser\OntologyBrowserPlugin.java12072 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\DocumentationScreen.java12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\RprojectApiScreen.java12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\HttpAPiScreen.java12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\SoapApiScreen.java12103 INFO [MolgenisServletContextGen] generated WebContent\META-INF\context.xml12259 INFO [SoapApiGen] generated generated\java\ui\SoapApi.java12353 INFO [CsvExportGen] generated generated\java\tools\CsvExport.java12431 INFO [CsvImportByNameGen] generated generated\java\tools\CsvImportByName.java12636 INFO [CopyMemoryToDatabaseGen] generated generated\java\ui\tools\CopyMemoryToDatabase.java

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Model –> Generate –> Use

26

26

Connect to R statisticsConnect to R statistics Workflow ready web-services

Workflow ready web-services

UML documentation of your model

UML documentation of your model

Edit & trace your dataEdit & trace your data

Import/export to ExcelImport/export to Excel

plugin your own scripts (OntBrowse)

plugin your own scripts (OntBrowse)

find.investigation()102 downloaded

obs<-find.observedvalue(43,920 downloaded

#some calculationadd.inferredvalue(res)36 added

Model –> Generate –> Use

Plugins

Swertz bosc2010 molgenis

Technology

Transcript of Swertz bosc2010 molgenis