Morris A. Swertz K Joeri van der Velde, Alexandros Kanterakis, Juha Muilu, Tomasz Adamusiak, Martijn Dijkstra, Gudmundur A...
Outline <ul><li>MOLGENIS overview </li></ul><ul><li>Demo movie </li></ul><ul><li>Summary </li></ul>
Challenge biologist Etc GUI DB bioinformatician inbreed 100 10.000 1,000,000 100,000 10,000 10 10,000,00 QTL profiles netw...
Challenge multiplied by project Use Animal Observatory NextGenSeq Mutation database Model organisms Biologist needs Work v...
Needed alternative method http://www.molgenis.org Swertz & Jansen (2007)  Nature Reviews Genetics  8, 235-243 Swertz et al...
Three steps NextGenSeq Mutation database Model organisms Model in DSL DSL – domain specific language Use Animal Observator...
Reuse notwithstanding large variation Use Animal Observatory NextGenSeq Mutation database Model organisms Model in DSL Gen...
MOLGENIS: How does it work? <link to movie>
Applications
etc. etc.
Example models XGAP for GWAS/GWL FINDIS disease DB Pheno-OM biobank catalogue SeqLIMS MAGE-TAB microarray AnimalDB <add yo...
eXtensible Genotype And Phenotype (XGAP) DATA  ELEMENT TRAIT SUBJECT <ul><li>PROBE </li></ul><ul><li>Name </li></ul><ul><l...
http://www.xgap.org   Swertz, van der Velde et al (2010)  Genome Biology 9;11(3): R27.
Data loading http://www.xgap.org   Swertz, van der Velde et al (2010)  Genome Biology 9;11(3): R27.
Data loading http://www.xgap.org   Swertz, van der Velde et al (2010)  Genome Biology 9;11(3): R27.
Data exploration http://www.xgap.org   Swertz, van der Velde et al (2010)  Genome Biology 9;11(3): R27.
Data analysis using cloud/cluster See poster Q01:  User friendly cluster computing for R/QTL analysis on XGAP
Data integration using RDF RDF + SPARQL Panacea GEN2PHEN LifeLines IOP Deformed ears? HPO : Abnormally shaped ears  Auricu...
Summary <ul><li>Result: </li></ul><ul><li>Database-in-a-box </li></ul><ul><li>Rich web GUI </li></ul><ul><li>Standard depl...
Extensive manuals
Acknowledgements <ul><li>Morris Swertz </li></ul><ul><li>Joeri van der Velde </li></ul><ul><li>Joris Lops </li></ul><ul><l...
<ul><li>ISMB </li></ul><ul><li>E15 - MOLGENIS </li></ul><ul><li>Q01 – QTL analysis </li></ul><ul><li>E19 – MAGE-TAB </li><...
 
Model   –> Generate –> Use Modeling language 506 lines of XML code for Pheno-OM 16 entities, 67 fields
Generates 150 files, 30k lines of Java, SQL and R code + docs 0  INFO  [myFactory] working dir: D:DevelopmentMolgenis33Wor...
Model  –> Generate –>  Use Connect to R statistics Workflow ready web-services UML documentation of your model Edit & trac...
Plugins
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Swertz bosc2010 molgenis

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  • Development takes.. Fair amount of experts Fair amount of time Unfortunatly.. Life sciences is as flexible as life itself Maintaining and updating of systems takes Fair amount of experts Fair amount of time Therefore.. Life science data systems are created and kept running by large, dedicated teams
  • First, we initiated community consultation on phenotypic, high-throughput and locus specific data [3] in consultation with the Gen2Phen projects and representatives from P3G and the model organism community. We successfully tested this strategy in a series of systems: XGAP: an eXtensible Genotype And Phenotype data platform [5] to integrate systems genetics studies (GWAS, GWL) on gene expression, metabolomics and proteomics data. See http://www.xgap.org . MAGETAB-OM: a microarray experiment data platform based on the MAGE-TAB data format standard. See http://magetab-om.sourceforge.net/ Pheno-OM: a data platform to integrate phenotype data from locus specific annotations from LSDBs to rich clinical reports from cohort studies and model organism data. See http://wwwdev.ebi.ac.uk/microarray-srv/pheno/ FINDIS: a mutation database for monogenic diseases belonging to the Finnish disease heritage. See http://www.findis.org/molgenis_findis/ Each of the systems was created in a standard way by providing a MOLGENIS compatible model.
  • When looking in more detail at the spreadsheet-like data structure on the previous slide, you will notice it stores a combination of ‘Phenotype’ and ‘Individual’ just like the sheet with the eyes on it. We separate this ‘measured’ data from the annotations about these individuals and phenotypes because we consider the annotations to be constant, whereas measurements can or will always vary.
  • Import data Run on cluster View results
  • Swertz bosc2010 molgenis

    1. 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. 2. Outline <ul><li>MOLGENIS overview </li></ul><ul><li>Demo movie </li></ul><ul><li>Summary </li></ul>
    3. 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. 4. Challenge multiplied by project Use Animal Observatory NextGenSeq Mutation database Model organisms Biologist needs Work very hard
    5. 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. 6. Three steps NextGenSeq Mutation database Model organisms Model in DSL DSL – domain specific language Use Animal Observatory Generator
    7. 7. Reuse notwithstanding large variation Use Animal Observatory NextGenSeq Mutation database Model organisms Model in DSL Generator DSL – domain specific language
    8. 8. MOLGENIS: How does it work? <link to movie>
    9. 9. Applications
    10. 10. etc. etc.
    11. 11. Example models XGAP for GWAS/GWL FINDIS disease DB Pheno-OM biobank catalogue SeqLIMS MAGE-TAB microarray AnimalDB <add your project here>
    12. 12. eXtensible Genotype And Phenotype (XGAP) DATA ELEMENT TRAIT SUBJECT <ul><li>PROBE </li></ul><ul><li>Name </li></ul><ul><li>Gene </li></ul><ul><li>Chromosme </li></ul><ul><li>Locus </li></ul><ul><li>MARKER </li></ul><ul><li>Name </li></ul><ul><li>Allele </li></ul><ul><li>Chromosme </li></ul><ul><li>Locus </li></ul><ul><li>MASSPEAK </li></ul><ul><li>Name </li></ul><ul><li>MZ </li></ul><ul><li>RetentionTime </li></ul><ul><li>Panel </li></ul><ul><li>Name </li></ul><ul><li>Type: CSS, RIL.. </li></ul><ul><li>Parent Panels </li></ul><ul><li>INDIVIDUAL </li></ul><ul><li>Name </li></ul><ul><li>Strain </li></ul><ul><li>Mother </li></ul><ul><li>Father </li></ul><ul><li>Sex </li></ul><ul><li>SAMPLE </li></ul><ul><li>Name </li></ul><ul><li>Individual </li></ul><ul><li>Tissue </li></ul>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. 13. http://www.xgap.org Swertz, van der Velde et al (2010) Genome Biology 9;11(3): R27.
    14. 14. Data loading http://www.xgap.org Swertz, van der Velde et al (2010) Genome Biology 9;11(3): R27.
    15. 15. Data loading http://www.xgap.org Swertz, van der Velde et al (2010) Genome Biology 9;11(3): R27.
    16. 16. Data exploration http://www.xgap.org Swertz, van der Velde et al (2010) Genome Biology 9;11(3): R27.
    17. 17. Data analysis using cloud/cluster See poster Q01: User friendly cluster computing for R/QTL analysis on XGAP
    18. 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. 19. Summary <ul><li>Result: </li></ul><ul><li>Database-in-a-box </li></ul><ul><li>Rich web GUI </li></ul><ul><li>Standard deployment </li></ul><ul><li>10k writes/sec </li></ul><ul><li>Interfaces for analysis </li></ul><ul><ul><li>Java </li></ul></ul><ul><ul><li>R </li></ul></ul><ul><ul><li>REST </li></ul></ul><ul><ul><li>SOAP </li></ul></ul><ul><ul><li>RDF </li></ul></ul><ul><li>Method: </li></ul><ul><li>Rapid dev cycle </li></ul><ul><li>Edit simple models </li></ul><ul><li>Pair with biologists </li></ul><ul><li>Discuss documentation </li></ul><ul><li>Test on real data </li></ul><ul><li>Generated junit tests </li></ul><ul><li>Plugin system </li></ul><ul><li>Matrix data backend </li></ul><ul><li>Reuse! </li></ul>
    20. 20. Extensive manuals
    21. 21. Acknowledgements <ul><li>Morris Swertz </li></ul><ul><li>Joeri van der Velde </li></ul><ul><li>Joris Lops </li></ul><ul><li>Danny Arends </li></ul><ul><li>Alex Kanterakis </li></ul><ul><li>Erik Roos </li></ul><ul><li>Richard Scheltema </li></ul><ul><li>Martijn Dijkstra </li></ul><ul><li>Rudi Alberts </li></ul><ul><li>Bruno M. Tesson </li></ul><ul><li>Gonzalo Vera Rodriguez </li></ul><ul><li>Tomasz Adamuziak </li></ul><ul><li>Juha Muilu </li></ul><ul><li>Gudmundur Thorisson </li></ul><ul><li>Damian Smedley </li></ul><ul><li>Katy Wolstencroft </li></ul><ul><li>Ritsert C. Jansen </li></ul><ul><li>Cisca Wijmenga </li></ul><ul><li>Carole Goble </li></ul><ul><li>John M. Hancock </li></ul><ul><li>Andrew R. Jones </li></ul><ul><li>Klaus Schughart </li></ul><ul><li>Paul Schofield </li></ul><ul><li>Anthony Brookes </li></ul><ul><li>Helen E. Parkinson </li></ul><ul><li>BBMRI-NL biobanking (Hs) </li></ul><ul><li>EU-GEN2PHEN consortium (Hs) </li></ul><ul><li>EU-PANACEA consortium (Ce) </li></ul><ul><li>NL Brassica Nutr. consortium (At) </li></ul><ul><li>EU-CASIMIR consortium (Mm) </li></ul><ul><li>NBIC/BioAssist consortium (bioinfo) </li></ul>EBI NL NL
    22. 22. <ul><li>ISMB </li></ul><ul><li>E15 - MOLGENIS </li></ul><ul><li>Q01 – QTL analysis </li></ul><ul><li>E19 – MAGE-TAB </li></ul><ul><li>P05 – OntoCAT </li></ul><ul><li>TT36, Tuesday 12.15-12.40 </li></ul><ul><li>Web </li></ul><ul><li>MOLGENIS: http://www.molgenis.org </li></ul><ul><li>XGAP: http://www.xgap.org </li></ul><ul><li>MAGETAB-OM: http://magetab-om.sourceforge.net/ </li></ul><ul><li>Pheno-OM: http://wwwdev.ebi.ac.uk/microarray-srv/pheno/ </li></ul><ul><li>FINDIS: http://www.findis.org/molgenis_findis/ </li></ul><ul><li>AnimalDB: http://www.animaldb.org </li></ul><ul><li>Pubmed </li></ul><ul><li>Swertz & Jansen (2007) Nature Reviews Genetics 8, 235-243 </li></ul><ul><li>Swertz et al (2004) Bioinformatics 20(13), 2075-83 </li></ul><ul><li>Swertz et al (2010) Genome Biology 9;11(3): R27. </li></ul>Thank you! Questions? [email_address]
    23. 24. Model –> Generate –> Use Modeling language 506 lines of XML code for Pheno-OM 16 entities, 67 fields
    24. 25. Generates 150 files, 30k lines of Java, SQL and R code + docs 0 INFO [myFactory] working dir: D:DevelopmentMolgenis33Workspacemolgenis4phenotype 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 WebContentdoc abledoc.html 2076 INFO [EntityDocGen] generated WebContentdocobjectmodel.html 2436 INFO [DotDocGen] generated WebContentdocentity-uml-diagram.dot 2545 INFO [DotDocGen] generated WebContentdocentity-uml-diagram-pheno.system.dot 2748 INFO [DotDocGen] generated WebContentdocentity-uml-diagram-pheno.observation.dot 2842 INFO [DotDocGen] generated WebContentdocentity-uml-diagram-pheno.target.dot 2998 INFO [DotDocGen] generated WebContentdocentity-uml-diagram-pheno.variable.dot 3138 INFO [DotDocGen] generated WebContentdocentity-uml-diagram-pheno.protocol.dot 3997 INFO [DotDocMinimalGen] generated WebContentdocentity-uml-minimal-diagram.dot 4184 INFO [DotDocMinimalGen] generated WebContentdocentity-uml-diagram-minimal-pheno.system.dot 4388 INFO [DotDocMinimalGen] generated WebContentdocentity-uml-diagram-minimal-pheno.observation.dot 4606 INFO [DotDocMinimalGen] generated WebContentdocentity-uml-diagram-minimal-pheno.target.dot 4731 INFO [DotDocMinimalGen] generated WebContentdocentity-uml-diagram-minimal-pheno.variable.dot 4887 INFO [DotDocMinimalGen] generated WebContentdocentity-uml-diagram-minimal-pheno.protocol.dot 5184 INFO [ClassDocGen] generated WebContentdocclassmodel.html 5293 INFO [InMemoryDatabaseGen] generated generatedjavauidataInMemoryDatabase.java 5609 INFO [MySqlCreateSubclassPerTableGen] generated generatedsqlcreate_tables.sql 5671 INFO [JDBCDatabaseGen] generated generatedjavauiJDBCDatabase.java 5921 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesIdentifiable.java 5921 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesNameable.java 5968 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesOntologySource.java 6014 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesOntologyTerm.java 6030 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesInvestigation.java 6061 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesObservableFeature.java 6124 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesObservedValue.java 6170 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesObservedRelationship.java 6217 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesInferredValue.java 6233 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesObservationTarget.java 6280 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesIndividual.java 6311 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesPanel.java 6326 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesCodeList.java 6327 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesCode.java 6374 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesProtocol.java 6390 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesProtocolApplication.java 6405 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesProtocolParameter.java 6437 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesParameterValue.java 6452 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesInferredValue_derivedFrom.java 6468 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesPanel_individuals.java 6483 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesProtocol_observableFeatures.java 6499 INFO [DataTypeGen] generated generatedjavaphenocoredata ypesProtocol_protocolComponents.java 6624 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersOntologySourceMapper.java 6655 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersOntologyTermMapper.java 6671 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersInvestigationMapper.java 6702 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersObservableFeatureMapper.java 6733 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersObservedValueMapper.java 6780 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersObservedRelationshipMapper.java 6827 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersInferredValueMapper.java 6842 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersObservationTargetMapper.java 6873 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersIndividualMapper.java 6889 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersPanelMapper.java 6905 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersCodeListMapper.java 6936 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersCodeMapper.java 6951 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersProtocolMapper.java 6983 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersProtocolApplicationMapper.java 6998 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersProtocolParameterMapper.java 7029 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersParameterValueMapper.java 7045 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersInferredValue_derivedFromMapper.java 7061 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersPanel_individualsMapper.java 7076 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersProtocol_observableFeaturesMapper.java 7092 INFO [MultiqueryMapperGen] generated generatedjavaphenocoredatamappersProtocol_protocolComponentsMapper.java 7217 INFO [JDBCMetaDatabaseGen] generated generatedjavauiJDBCMetaDatabase.java 7263 INFO [CountPerEntityGen] generated generatedsqlcount_per_entity.sql 7310 INFO [CountPerTableGen] generated generatedsqlcount_per_table.sql 7341 INFO [FillMetadataTablesGen] generated generatedsqlinsert_metadata.sql 7405 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvOntologySourceCsvReader.java 7420 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvOntologyTermCsvReader.java 7420 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvInvestigationCsvReader.java 7436 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvObservableFeatureCsvReader.java 7452 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvObservedValueCsvReader.java 7467 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvObservedRelationshipCsvReader.java 7483 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvInferredValueCsvReader.java 7498 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvObservationTargetCsvReader.java 7514 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvIndividualCsvReader.java 7514 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvPanelCsvReader.java 7530 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvCodeListCsvReader.java 7545 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvCodeCsvReader.java 7545 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvProtocolCsvReader.java 7561 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvProtocolApplicationCsvReader.java 7561 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvProtocolParameterCsvReader.java 7576 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvParameterValueCsvReader.java 7576 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvInferredValue_derivedFromCsvReader.java 7592 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvPanel_individualsCsvReader.java 7608 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvProtocol_observableFeaturesCsvReader.java 7608 INFO [CsvReaderGen] generated generatedjavaphenocoredatacsvProtocol_protocolComponentsCsvReader.java 7748 INFO [REntityGen] generated generatedjavaphenocoreROntologySource.R 7748 INFO [REntityGen] generated generatedjavaphenocoreROntologyTerm.R 7764 INFO [REntityGen] generated generatedjavaphenocoreRInvestigation.R 7779 INFO [REntityGen] generated generatedjavaphenocoreRObservableFeature.R 7779 INFO [REntityGen] generated generatedjavaphenocoreRObservedValue.R 7795 INFO [REntityGen] generated generatedjavaphenocoreRObservedRelationship.R 7795 INFO [REntityGen] generated generatedjavaphenocoreRInferredValue.R 7810 INFO [REntityGen] generated generatedjavaphenocoreRObservationTarget.R 7810 INFO [REntityGen] generated generatedjavaphenocoreRIndividual.R 7826 INFO [REntityGen] generated generatedjavaphenocoreRPanel.R 7826 INFO [REntityGen] generated generatedjavaphenocoreRCodeList.R 7842 INFO [REntityGen] generated generatedjavaphenocoreRCode.R 7857 INFO [REntityGen] generated generatedjavaphenocoreRProtocol.R 7857 INFO [REntityGen] generated generatedjavaphenocoreRProtocolApplication.R 7873 INFO [REntityGen] generated generatedjavaphenocoreRProtocolParameter.R 7873 INFO [REntityGen] generated generatedjavaphenocoreRParameterValue.R 7888 INFO [REntityGen] generated generatedjavaphenocoreRInferredValue_derivedFrom.R 7888 INFO [REntityGen] generated generatedjavaphenocoreRPanel_individuals.R 7888 INFO [REntityGen] generated generatedjavaphenocoreRProtocol_observableFeatures.R 7904 INFO [REntityGen] generated generatedjavaphenocoreRProtocol_protocolComponents.R 7998 INFO [RApi] generated generatedjavasource.R 8044 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlIdentifiableHtmlForm.java 8044 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlNameableHtmlForm.java 8044 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlOntologySourceHtmlForm.java 8044 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlOntologyTermHtmlForm.java 8060 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlInvestigationHtmlForm.java 8060 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlObservableFeatureHtmlForm.java 8076 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlObservedValueHtmlForm.java 8076 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlObservedRelationshipHtmlForm.java 8076 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlInferredValueHtmlForm.java 8091 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlObservationTargetHtmlForm.java 8091 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlIndividualHtmlForm.java 8091 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlPanelHtmlForm.java 8091 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlCodeListHtmlForm.java 8107 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlCodeHtmlForm.java 8107 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlProtocolHtmlForm.java 8107 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlProtocolApplicationHtmlForm.java 8107 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlProtocolParameterHtmlForm.java 8122 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlParameterValueHtmlForm.java 8122 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlInferredValue_derivedFromHtmlForm.java 8122 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlPanel_individualsHtmlForm.java 8122 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlProtocol_observableFeaturesHtmlForm.java 8138 INFO [HtmlFormGen] generated generatedjavaphenocorehtmlProtocol_protocolComponentsHtmlForm.java 8138 INFO [MolgenisServletContextGen] generated WebContentMETA-INFcontext.xml 8169 INFO [MolgenisContextListenerGen] generated generatedjavaservletContextListener.java 8232 INFO [MolgenisServletGen] generated generatedjavaMolgenisServlet.java 8403 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsForm.java 8560 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuObservableFeaturesForm.java 8591 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuPanelsForm.java 8654 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuPanelsIndividualsForm.java 8701 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuObservedValuesForm.java 8732 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuProtocolApplicationsForm.java 8825 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuProtocolApplicationsProtocolApplicationMenuParameterValuesForm.java 8857 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuProtocolApplicationsProtocolApplicationMenuObservedValuesForm.java 8888 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuProtocolApplicationsProtocolApplicationMenuInferredValuesForm.java 9013 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuInferredValuesForm.java 9044 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainObservableFeaturesForm.java 9137 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainObservationTargetsIndividualsForm.java 9169 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainObservationTargetsPanelsForm.java 9200 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainProtocolsForm.java 9293 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainProtocolsProtocolMenuParametersForm.java 9325 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainProtocolsProtocolMenuProtocolComponentsForm.java 9496 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainOntologiesOntologyTermsForm.java 9528 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainOntologiesOntologySourcesForm.java 9606 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainOntologiesOntologySourcesOntologyTermsForm.java 9638 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainOntologiesCodeListsForm.java 9700 INFO [FormScreenGen] generated generatedjavauiscreenTopMenuMainOntologiesCodeListsCodesForm.java 9965 INFO [MenuScreenGen] generated generatedjavauiscreenTopMenuMenu.java 10012 INFO [MenuScreenGen] generated generatedjavauiscreenTopMenuMainMenu.java 10059 INFO [MenuScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuMenu.java 10152 INFO [MenuScreenGen] generated generatedjavauiscreenTopMenuMainInvestigationsInvestigationMenuProtocolApplicationsProtocolApplicationMenuMenu.java 10230 INFO [MenuScreenGen] generated generatedjavauiscreenTopMenuMainObservationTargetsMenu.java 10293 INFO [MenuScreenGen] generated generatedjavauiscreenTopMenuMainProtocolsProtocolMenuMenu.java 10324 INFO [MenuScreenGen] generated generatedjavauiscreenTopMenuMainOntologiesMenu.java 11354 INFO [PluginScreenGen] generated Molgenis33Workspacemolgenis4phenotypegeneratedjavauiscreenTopMenuMainReportPlugin.java 11557 INFO [PluginScreenGen] generated Molgenis33Workspacemolgenis4phenotypegeneratedjavauiscreenTopMenuMainOntologiesOntologyManagerPlugin.java 11604 INFO [PluginScreenGen] generated Molgenis33Workspacemolgenis4phenotypegeneratedjavauiscreenTopMenuModel_documentationPlugin.java 11604 INFO [PluginScreenGen] generated Molgenis33Workspacemolgenis4phenotypegeneratedjavauiscreenTopMenuRprojectApiPlugin.java 11620 INFO [PluginScreenGen] generated Molgenis33Workspacemolgenis4phenotypegeneratedjavauiscreenTopMenuHttpApiPlugin.java 11635 INFO [PluginScreenGen] generated Molgenis33Workspacemolgenis4phenotypegeneratedjavauiscreenTopMenuWebServicesApiPlugin.java 11651 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenjavaplugin eportInvestigationOverview.ftl 11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenjavapluginOntologyBrowserOntologyBrowserPlugin.ftl 11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenjavaplugin opmenuDocumentationScreen.ftl 11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenjavaplugin opmenuRprojectApiScreen.ftl 11823 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenjavaplugin opmenuHttpAPiScreen.ftl 11823 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenjavaplugin opmenuSoapApiScreen.ftl 11854 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenjavaplugin eportInvestigationOverview.java 12057 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenjavapluginOntologyBrowserOntologyBrowserPlugin.java 12072 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenjavaplugin opmenuDocumentationScreen.java 12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenjavaplugin opmenuRprojectApiScreen.java 12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenjavaplugin opmenuHttpAPiScreen.java 12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenjavaplugin opmenuSoapApiScreen.java 12103 INFO [MolgenisServletContextGen] generated WebContentMETA-INFcontext.xml 12259 INFO [SoapApiGen] generated generatedjavauiSoapApi.java 12353 INFO [CsvExportGen] generated generatedjava oolsCsvExport.java 12431 INFO [CsvImportByNameGen] generated generatedjava oolsCsvImportByName.java 12636 INFO [CopyMemoryToDatabaseGen] generated generatedjavaui oolsCopyMemoryToDatabase.java Model –> Generate –> Use
    25. 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
    26. 27. Plugins
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