The document describes MOLGENIS, an open-source software system that allows users to define data models and generate full-featured web applications and databases from those models. Key features include a graphical user interface, database integration, support for common data formats, and the ability to rapidly develop applications by editing simple domain-specific models. The system has been applied to build several genomic and biomedical databases.

1. 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

2. Outline MOLGENIS overview Demo movie Summary

3. Challenge biologist Etc GUI DB bioinformatician inbreed 100 10.000 1,000,000 100,000 10,000 10 10,000,00 QTL profiles network correlate genome strains individuals markers expressions preprocess probes microarrays 100 hybridize 100,000 genotype genotypes norm exprs. map Logic APIs Exchange services

4. Challenge multiplied by project Use Animal Observatory NextGenSeq Mutation database Model organisms Biologist needs Work very hard

5. Needed alternative method http://www.molgenis.org Swertz & Jansen (2007) Nature Reviews Genetics 8, 235-243 Swertz et al (2004) Bioinformatics 20(13), 2075-83

6. Three steps NextGenSeq Mutation database Model organisms Model in DSL DSL – domain specific language Use Animal Observatory Generator

7. Reuse notwithstanding large variation Use Animal Observatory NextGenSeq Mutation database Model organisms Model in DSL Generator DSL – domain specific language

8. MOLGENIS: How does it work? <link to movie>

9. Applications

10. etc. etc.

11. Example models XGAP for GWAS/GWL FINDIS disease DB Pheno-OM biobank catalogue SeqLIMS MAGE-TAB microarray AnimalDB <add your project here>

12. eXtensible Genotype And Phenotype (XGAP) DATA ELEMENT TRAIT SUBJECT PROBE Name Gene Chromosme Locus MARKER Name Allele Chromosme Locus MASSPEAK Name MZ RetentionTime Panel Name Type: CSS, RIL.. Parent Panels INDIVIDUAL Name Strain Mother Father Sex SAMPLE Name Individual Tissue And so on … And so on … http://www.xgap.org Swertz, van der Velde et al (2010) Genome Biology 9;11(3): R27. columns rows DIMENSION ELEMENT

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

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

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

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

17. Data analysis using cloud/cluster See poster Q01: User friendly cluster computing for R/QTL analysis on XGAP

18. Data integration using RDF RDF + SPARQL Panacea GEN2PHEN LifeLines 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 Local ontologies (OLW or OBO) BioPortal OLS

19. 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!

20. Extensive manuals

21. Acknowledgements Morris 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) EBI NL NL

22. 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 you! Questions? [email_address]

24. Model –> Generate –> Use Modeling language 506 lines of XML code for Pheno-OM 16 entities, 67 fields

25. Generates 150 files, 30k lines of Java, SQL and R code + docs 0 INFO [myFactory] working dir: D:\Development\Molgenis33Workspace\molgenis4phenotype 78 INFO [myFactory] MOLGENIS version 3.3.0-testing 94 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_database output_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 resources db_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: localhost db_filepath = attachedfiles #Path where the database should store file attachements. Default: null db_jndiname = jdbc/molgenisdb #Used to create a JDBC database resource for the application object_relational_mapping = subclass_per_table #Expert option: Choosing OR strategy. Either 'class_per_table', 'subclass_per_table', 'hierarchy_per_table'. Default: class_per_table mapper_implementation = multiquery #Expert option: Choosing wether multiquery is used instead of prepared statements. Default: false exclude_system = true #Expert option: Whether system tables should be excluded from generation. Default: true force_molgenis_package = false #Expert option. Whether the generated package should be 'molgenis' or the name specified in the model. Default: false auth_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 disabled mail_smtp_hostname = localhost #SMTP host server. Default: localhost mail_smtp_port = 25 #SMTP host server port. Default: 25 mail_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 Nameable 780 WARN [Entity] [WARNING]: missing key 0 for entity Nameable 780 WARN [Entity] [WARNING]: missing key 0 for entity Nameable 780 WARN [Entity] [WARNING]: missing key 0 for entity Nameable 780 WARN [Entity] [WARNING]: missing key 0 for entity Nameable 797 WARN [Entity] [WARNING]: missing key 0 for entity Nameable 797 WARN [Entity] [WARNING]: missing key 0 for entity Nameable 844 INFO [MolgenisLanguage] parsing ui-schema 937 INFO [main] generating .... 1717 INFO [TableDocGen] generated WebContent\doc\tabledoc.html 2076 INFO [EntityDocGen] generated WebContent\doc\objectmodel.html 2436 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram.dot 2545 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram-pheno.system.dot 2748 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram-pheno.observation.dot 2842 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram-pheno.target.dot 2998 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram-pheno.variable.dot 3138 INFO [DotDocGen] generated WebContent\doc\entity-uml-diagram-pheno.protocol.dot 3997 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-minimal-diagram.dot 4184 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-diagram-minimal-pheno.system.dot 4388 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-diagram-minimal-pheno.observation.dot 4606 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-diagram-minimal-pheno.target.dot 4731 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-diagram-minimal-pheno.variable.dot 4887 INFO [DotDocMinimalGen] generated WebContent\doc\entity-uml-diagram-minimal-pheno.protocol.dot 5184 INFO [ClassDocGen] generated WebContent\doc\classmodel.html 5293 INFO [InMemoryDatabaseGen] generated generated\java\ui\data\InMemoryDatabase.java 5609 INFO [MySqlCreateSubclassPerTableGen] generated generated\sql\create_tables.sql 5671 INFO [JDBCDatabaseGen] generated generated\java\ui\JDBCDatabase.java 5921 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Identifiable.java 5921 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Nameable.java 5968 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\OntologySource.java 6014 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\OntologyTerm.java 6030 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Investigation.java 6061 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ObservableFeature.java 6124 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ObservedValue.java 6170 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ObservedRelationship.java 6217 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\InferredValue.java 6233 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ObservationTarget.java 6280 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Individual.java 6311 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Panel.java 6326 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\CodeList.java 6327 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Code.java 6374 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Protocol.java 6390 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ProtocolApplication.java 6405 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ProtocolParameter.java 6437 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\ParameterValue.java 6452 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\InferredValue_derivedFrom.java 6468 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Panel_individuals.java 6483 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Protocol_observableFeatures.java 6499 INFO [DataTypeGen] generated generated\java\pheno\core\data\types\Protocol_protocolComponents.java 6624 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\OntologySourceMapper.java 6655 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\OntologyTermMapper.java 6671 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\InvestigationMapper.java 6702 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ObservableFeatureMapper.java 6733 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ObservedValueMapper.java 6780 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ObservedRelationshipMapper.java 6827 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\InferredValueMapper.java 6842 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ObservationTargetMapper.java 6873 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\IndividualMapper.java 6889 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\PanelMapper.java 6905 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\CodeListMapper.java 6936 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\CodeMapper.java 6951 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ProtocolMapper.java 6983 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ProtocolApplicationMapper.java 6998 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ProtocolParameterMapper.java 7029 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\ParameterValueMapper.java 7045 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\InferredValue_derivedFromMapper.java 7061 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\Panel_individualsMapper.java 7076 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\Protocol_observableFeaturesMapper.java 7092 INFO [MultiqueryMapperGen] generated generated\java\pheno\core\data\mappers\Protocol_protocolComponentsMapper.java 7217 INFO [JDBCMetaDatabaseGen] generated generated\java\ui\JDBCMetaDatabase.java 7263 INFO [CountPerEntityGen] generated generated\sql\count_per_entity.sql 7310 INFO [CountPerTableGen] generated generated\sql\count_per_table.sql 7341 INFO [FillMetadataTablesGen] generated generated\sql\insert_metadata.sql 7405 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\OntologySourceCsvReader.java 7420 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\OntologyTermCsvReader.java 7420 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\InvestigationCsvReader.java 7436 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ObservableFeatureCsvReader.java 7452 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ObservedValueCsvReader.java 7467 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ObservedRelationshipCsvReader.java 7483 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\InferredValueCsvReader.java 7498 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ObservationTargetCsvReader.java 7514 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\IndividualCsvReader.java 7514 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\PanelCsvReader.java 7530 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\CodeListCsvReader.java 7545 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\CodeCsvReader.java 7545 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ProtocolCsvReader.java 7561 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ProtocolApplicationCsvReader.java 7561 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ProtocolParameterCsvReader.java 7576 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\ParameterValueCsvReader.java 7576 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\InferredValue_derivedFromCsvReader.java 7592 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\Panel_individualsCsvReader.java 7608 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\Protocol_observableFeaturesCsvReader.java 7608 INFO [CsvReaderGen] generated generated\java\pheno\core\data\csv\Protocol_protocolComponentsCsvReader.java 7748 INFO [REntityGen] generated generated\java\pheno\core\R\OntologySource.R 7748 INFO [REntityGen] generated generated\java\pheno\core\R\OntologyTerm.R 7764 INFO [REntityGen] generated generated\java\pheno\core\R\Investigation.R 7779 INFO [REntityGen] generated generated\java\pheno\core\R\ObservableFeature.R 7779 INFO [REntityGen] generated generated\java\pheno\core\R\ObservedValue.R 7795 INFO [REntityGen] generated generated\java\pheno\core\R\ObservedRelationship.R 7795 INFO [REntityGen] generated generated\java\pheno\core\R\InferredValue.R 7810 INFO [REntityGen] generated generated\java\pheno\core\R\ObservationTarget.R 7810 INFO [REntityGen] generated generated\java\pheno\core\R\Individual.R 7826 INFO [REntityGen] generated generated\java\pheno\core\R\Panel.R 7826 INFO [REntityGen] generated generated\java\pheno\core\R\CodeList.R 7842 INFO [REntityGen] generated generated\java\pheno\core\R\Code.R 7857 INFO [REntityGen] generated generated\java\pheno\core\R\Protocol.R 7857 INFO [REntityGen] generated generated\java\pheno\core\R\ProtocolApplication.R 7873 INFO [REntityGen] generated generated\java\pheno\core\R\ProtocolParameter.R 7873 INFO [REntityGen] generated generated\java\pheno\core\R\ParameterValue.R 7888 INFO [REntityGen] generated generated\java\pheno\core\R\InferredValue_derivedFrom.R 7888 INFO [REntityGen] generated generated\java\pheno\core\R\Panel_individuals.R 7888 INFO [REntityGen] generated generated\java\pheno\core\R\Protocol_observableFeatures.R 7904 INFO [REntityGen] generated generated\java\pheno\core\R\Protocol_protocolComponents.R 7998 INFO [RApi] generated generated\java\source.R 8044 INFO [HtmlFormGen] generated generated\java\pheno\core\html\IdentifiableHtmlForm.java 8044 INFO [HtmlFormGen] generated generated\java\pheno\core\html\NameableHtmlForm.java 8044 INFO [HtmlFormGen] generated generated\java\pheno\core\html\OntologySourceHtmlForm.java 8044 INFO [HtmlFormGen] generated generated\java\pheno\core\html\OntologyTermHtmlForm.java 8060 INFO [HtmlFormGen] generated generated\java\pheno\core\html\InvestigationHtmlForm.java 8060 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ObservableFeatureHtmlForm.java 8076 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ObservedValueHtmlForm.java 8076 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ObservedRelationshipHtmlForm.java 8076 INFO [HtmlFormGen] generated generated\java\pheno\core\html\InferredValueHtmlForm.java 8091 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ObservationTargetHtmlForm.java 8091 INFO [HtmlFormGen] generated generated\java\pheno\core\html\IndividualHtmlForm.java 8091 INFO [HtmlFormGen] generated generated\java\pheno\core\html\PanelHtmlForm.java 8091 INFO [HtmlFormGen] generated generated\java\pheno\core\html\CodeListHtmlForm.java 8107 INFO [HtmlFormGen] generated generated\java\pheno\core\html\CodeHtmlForm.java 8107 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ProtocolHtmlForm.java 8107 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ProtocolApplicationHtmlForm.java 8107 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ProtocolParameterHtmlForm.java 8122 INFO [HtmlFormGen] generated generated\java\pheno\core\html\ParameterValueHtmlForm.java 8122 INFO [HtmlFormGen] generated generated\java\pheno\core\html\InferredValue_derivedFromHtmlForm.java 8122 INFO [HtmlFormGen] generated generated\java\pheno\core\html\Panel_individualsHtmlForm.java 8122 INFO [HtmlFormGen] generated generated\java\pheno\core\html\Protocol_observableFeaturesHtmlForm.java 8138 INFO [HtmlFormGen] generated generated\java\pheno\core\html\Protocol_protocolComponentsHtmlForm.java 8138 INFO [MolgenisServletContextGen] generated WebContent\META-INF\context.xml 8169 INFO [MolgenisContextListenerGen] generated generated\java\servlet\ContextListener.java 8232 INFO [MolgenisServletGen] generated generated\java\MolgenisServlet.java 8403 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\InvestigationsForm.java 8560 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ObservableFeaturesForm.java 8591 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\PanelsForm.java 8654 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\Panels\IndividualsForm.java 8701 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ObservedValuesForm.java 8732 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ProtocolApplicationsForm.java 8825 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ProtocolApplications\ProtocolApplicationMenu\ParameterValuesForm.java 8857 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ProtocolApplications\ProtocolApplicationMenu\ObservedValuesForm.java 8888 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ProtocolApplications\ProtocolApplicationMenu\InferredValuesForm.java 9013 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\InferredValuesForm.java 9044 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\ObservableFeaturesForm.java 9137 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\ObservationTargets\IndividualsForm.java 9169 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\ObservationTargets\PanelsForm.java 9200 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\ProtocolsForm.java 9293 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Protocols\ProtocolMenu\ParametersForm.java 9325 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Protocols\ProtocolMenu\ProtocolComponentsForm.java 9496 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Ontologies\OntologyTermsForm.java 9528 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Ontologies\OntologySourcesForm.java 9606 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Ontologies\OntologySources\OntologyTermsForm.java 9638 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Ontologies\CodeListsForm.java 9700 INFO [FormScreenGen] generated generated\java\ui\screen\TopMenu\Main\Ontologies\CodeLists\CodesForm.java 9965 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenuMenu.java 10012 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\MainMenu.java 10059 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenuMenu.java 10152 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\Main\Investigations\InvestigationMenu\ProtocolApplications\ProtocolApplicationMenuMenu.java 10230 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\Main\ObservationTargetsMenu.java 10293 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\Main\Protocols\ProtocolMenuMenu.java 10324 INFO [MenuScreenGen] generated generated\java\ui\screen\TopMenu\Main\OntologiesMenu.java 11354 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\Main\ReportPlugin.java 11557 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\Main\Ontologies\OntologyManagerPlugin.java 11604 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\Model_documentationPlugin.java 11604 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\RprojectApiPlugin.java 11620 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\HttpApiPlugin.java 11635 INFO [PluginScreenGen] generated Molgenis33Workspace\molgenis4phenotype\generated\java\ui\screen\TopMenu\WebServicesApiPlugin.java 11651 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\report\InvestigationOverview.ftl 11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\OntologyBrowser\OntologyBrowserPlugin.ftl 11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\DocumentationScreen.ftl 11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\RprojectApiScreen.ftl 11823 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\HttpAPiScreen.ftl 11823 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\SoapApiScreen.ftl 11854 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\report\InvestigationOverview.java 12057 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\OntologyBrowser\OntologyBrowserPlugin.java 12072 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\DocumentationScreen.java 12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\RprojectApiScreen.java 12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\HttpAPiScreen.java 12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwritten\java\plugin\topmenu\SoapApiScreen.java 12103 INFO [MolgenisServletContextGen] generated WebContent\META-INF\context.xml 12259 INFO [SoapApiGen] generated generated\java\ui\SoapApi.java 12353 INFO [CsvExportGen] generated generated\java\tools\CsvExport.java 12431 INFO [CsvImportByNameGen] generated generated\java\tools\CsvImportByName.java 12636 INFO [CopyMemoryToDatabaseGen] generated generated\java\ui\tools\CopyMemoryToDatabase.java Model –> Generate –> Use

26. Model –> Generate –> Use Connect to R statistics Workflow ready web-services UML documentation of your model Edit & trace your data Import/export to Excel plugin your own scripts (OntBrowse) Tech keywords: object oriented data models, multi-platform java, tomcat/glassfish web server, mysql/postgresql database, Eclipse/Netbeans IDE, Java API, WSDL/SOAP API, R-project API, MVC, freemarker templates and css for custom layout, open source. find.investigation() 102 downloaded obs<-find.observedvalue( 43,920 downloaded #some calculation add.inferredvalue(res) 36 added

27. Plugins