Generative Artificial Intelligence: How generative AI works.pdf
Swertz bosc2010 molgenis
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
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
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:evelopmentolgenis33Workspaceolgenis4phenotype 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 WebContentocabledoc.html 2076 INFO [EntityDocGen] generated WebContentocbjectmodel.html 2436 INFO [DotDocGen] generated WebContentocntity-uml-diagram.dot 2545 INFO [DotDocGen] generated WebContentocntity-uml-diagram-pheno.system.dot 2748 INFO [DotDocGen] generated WebContentocntity-uml-diagram-pheno.observation.dot 2842 INFO [DotDocGen] generated WebContentocntity-uml-diagram-pheno.target.dot 2998 INFO [DotDocGen] generated WebContentocntity-uml-diagram-pheno.variable.dot 3138 INFO [DotDocGen] generated WebContentocntity-uml-diagram-pheno.protocol.dot 3997 INFO [DotDocMinimalGen] generated WebContentocntity-uml-minimal-diagram.dot 4184 INFO [DotDocMinimalGen] generated WebContentocntity-uml-diagram-minimal-pheno.system.dot 4388 INFO [DotDocMinimalGen] generated WebContentocntity-uml-diagram-minimal-pheno.observation.dot 4606 INFO [DotDocMinimalGen] generated WebContentocntity-uml-diagram-minimal-pheno.target.dot 4731 INFO [DotDocMinimalGen] generated WebContentocntity-uml-diagram-minimal-pheno.variable.dot 4887 INFO [DotDocMinimalGen] generated WebContentocntity-uml-diagram-minimal-pheno.protocol.dot 5184 INFO [ClassDocGen] generated WebContentoclassmodel.html 5293 INFO [InMemoryDatabaseGen] generated generatedavaiatanMemoryDatabase.java 5609 INFO [MySqlCreateSubclassPerTableGen] generated generatedqlreate_tables.sql 5671 INFO [JDBCDatabaseGen] generated generatedavaiDBCDatabase.java 5921 INFO [DataTypeGen] generated generatedavahenooreataypesdentifiable.java 5921 INFO [DataTypeGen] generated generatedavahenooreataypesameable.java 5968 INFO [DataTypeGen] generated generatedavahenooreataypesntologySource.java 6014 INFO [DataTypeGen] generated generatedavahenooreataypesntologyTerm.java 6030 INFO [DataTypeGen] generated generatedavahenooreataypesnvestigation.java 6061 INFO [DataTypeGen] generated generatedavahenooreataypesbservableFeature.java 6124 INFO [DataTypeGen] generated generatedavahenooreataypesbservedValue.java 6170 INFO [DataTypeGen] generated generatedavahenooreataypesbservedRelationship.java 6217 INFO [DataTypeGen] generated generatedavahenooreataypesnferredValue.java 6233 INFO [DataTypeGen] generated generatedavahenooreataypesbservationTarget.java 6280 INFO [DataTypeGen] generated generatedavahenooreataypesndividual.java 6311 INFO [DataTypeGen] generated generatedavahenooreataypesanel.java 6326 INFO [DataTypeGen] generated generatedavahenooreataypesodeList.java 6327 INFO [DataTypeGen] generated generatedavahenooreataypesode.java 6374 INFO [DataTypeGen] generated generatedavahenooreataypesrotocol.java 6390 INFO [DataTypeGen] generated generatedavahenooreataypesrotocolApplication.java 6405 INFO [DataTypeGen] generated generatedavahenooreataypesrotocolParameter.java 6437 INFO [DataTypeGen] generated generatedavahenooreataypesarameterValue.java 6452 INFO [DataTypeGen] generated generatedavahenooreataypesnferredValue_derivedFrom.java 6468 INFO [DataTypeGen] generated generatedavahenooreataypesanel_individuals.java 6483 INFO [DataTypeGen] generated generatedavahenooreataypesrotocol_observableFeatures.java 6499 INFO [DataTypeGen] generated generatedavahenooreataypesrotocol_protocolComponents.java 6624 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersntologySourceMapper.java 6655 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersntologyTermMapper.java 6671 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersnvestigationMapper.java 6702 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersbservableFeatureMapper.java 6733 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersbservedValueMapper.java 6780 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersbservedRelationshipMapper.java 6827 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersnferredValueMapper.java 6842 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersbservationTargetMapper.java 6873 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersndividualMapper.java 6889 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersanelMapper.java 6905 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersodeListMapper.java 6936 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersodeMapper.java 6951 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersrotocolMapper.java 6983 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersrotocolApplicationMapper.java 6998 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersrotocolParameterMapper.java 7029 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersarameterValueMapper.java 7045 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersnferredValue_derivedFromMapper.java 7061 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersanel_individualsMapper.java 7076 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersrotocol_observableFeaturesMapper.java 7092 INFO [MultiqueryMapperGen] generated generatedavahenooreataappersrotocol_protocolComponentsMapper.java 7217 INFO [JDBCMetaDatabaseGen] generated generatedavaiDBCMetaDatabase.java 7263 INFO [CountPerEntityGen] generated generatedqlount_per_entity.sql 7310 INFO [CountPerTableGen] generated generatedqlount_per_table.sql 7341 INFO [FillMetadataTablesGen] generated generatedqlnsert_metadata.sql 7405 INFO [CsvReaderGen] generated generatedavahenooreatasvntologySourceCsvReader.java 7420 INFO [CsvReaderGen] generated generatedavahenooreatasvntologyTermCsvReader.java 7420 INFO [CsvReaderGen] generated generatedavahenooreatasvnvestigationCsvReader.java 7436 INFO [CsvReaderGen] generated generatedavahenooreatasvbservableFeatureCsvReader.java 7452 INFO [CsvReaderGen] generated generatedavahenooreatasvbservedValueCsvReader.java 7467 INFO [CsvReaderGen] generated generatedavahenooreatasvbservedRelationshipCsvReader.java 7483 INFO [CsvReaderGen] generated generatedavahenooreatasvnferredValueCsvReader.java 7498 INFO [CsvReaderGen] generated generatedavahenooreatasvbservationTargetCsvReader.java 7514 INFO [CsvReaderGen] generated generatedavahenooreatasvndividualCsvReader.java 7514 INFO [CsvReaderGen] generated generatedavahenooreatasvanelCsvReader.java 7530 INFO [CsvReaderGen] generated generatedavahenooreatasvodeListCsvReader.java 7545 INFO [CsvReaderGen] generated generatedavahenooreatasvodeCsvReader.java 7545 INFO [CsvReaderGen] generated generatedavahenooreatasvrotocolCsvReader.java 7561 INFO [CsvReaderGen] generated generatedavahenooreatasvrotocolApplicationCsvReader.java 7561 INFO [CsvReaderGen] generated generatedavahenooreatasvrotocolParameterCsvReader.java 7576 INFO [CsvReaderGen] generated generatedavahenooreatasvarameterValueCsvReader.java 7576 INFO [CsvReaderGen] generated generatedavahenooreatasvnferredValue_derivedFromCsvReader.java 7592 INFO [CsvReaderGen] generated generatedavahenooreatasvanel_individualsCsvReader.java 7608 INFO [CsvReaderGen] generated generatedavahenooreatasvrotocol_observableFeaturesCsvReader.java 7608 INFO [CsvReaderGen] generated generatedavahenooreatasvrotocol_protocolComponentsCsvReader.java 7748 INFO [REntityGen] generated generatedavahenoorentologySource.R 7748 INFO [REntityGen] generated generatedavahenoorentologyTerm.R 7764 INFO [REntityGen] generated generatedavahenoorenvestigation.R 7779 INFO [REntityGen] generated generatedavahenoorebservableFeature.R 7779 INFO [REntityGen] generated generatedavahenoorebservedValue.R 7795 INFO [REntityGen] generated generatedavahenoorebservedRelationship.R 7795 INFO [REntityGen] generated generatedavahenoorenferredValue.R 7810 INFO [REntityGen] generated generatedavahenoorebservationTarget.R 7810 INFO [REntityGen] generated generatedavahenoorendividual.R 7826 INFO [REntityGen] generated generatedavahenooreanel.R 7826 INFO [REntityGen] generated generatedavahenooreodeList.R 7842 INFO [REntityGen] generated generatedavahenooreode.R 7857 INFO [REntityGen] generated generatedavahenoorerotocol.R 7857 INFO [REntityGen] generated generatedavahenoorerotocolApplication.R 7873 INFO [REntityGen] generated generatedavahenoorerotocolParameter.R 7873 INFO [REntityGen] generated generatedavahenoorearameterValue.R 7888 INFO [REntityGen] generated generatedavahenoorenferredValue_derivedFrom.R 7888 INFO [REntityGen] generated generatedavahenooreanel_individuals.R 7888 INFO [REntityGen] generated generatedavahenoorerotocol_observableFeatures.R 7904 INFO [REntityGen] generated generatedavahenoorerotocol_protocolComponents.R 7998 INFO [RApi] generated generatedavaource.R 8044 INFO [HtmlFormGen] generated generatedavahenooretmldentifiableHtmlForm.java 8044 INFO [HtmlFormGen] generated generatedavahenooretmlameableHtmlForm.java 8044 INFO [HtmlFormGen] generated generatedavahenooretmlntologySourceHtmlForm.java 8044 INFO [HtmlFormGen] generated generatedavahenooretmlntologyTermHtmlForm.java 8060 INFO [HtmlFormGen] generated generatedavahenooretmlnvestigationHtmlForm.java 8060 INFO [HtmlFormGen] generated generatedavahenooretmlbservableFeatureHtmlForm.java 8076 INFO [HtmlFormGen] generated generatedavahenooretmlbservedValueHtmlForm.java 8076 INFO [HtmlFormGen] generated generatedavahenooretmlbservedRelationshipHtmlForm.java 8076 INFO [HtmlFormGen] generated generatedavahenooretmlnferredValueHtmlForm.java 8091 INFO [HtmlFormGen] generated generatedavahenooretmlbservationTargetHtmlForm.java 8091 INFO [HtmlFormGen] generated generatedavahenooretmlndividualHtmlForm.java 8091 INFO [HtmlFormGen] generated generatedavahenooretmlanelHtmlForm.java 8091 INFO [HtmlFormGen] generated generatedavahenooretmlodeListHtmlForm.java 8107 INFO [HtmlFormGen] generated generatedavahenooretmlodeHtmlForm.java 8107 INFO [HtmlFormGen] generated generatedavahenooretmlrotocolHtmlForm.java 8107 INFO [HtmlFormGen] generated generatedavahenooretmlrotocolApplicationHtmlForm.java 8107 INFO [HtmlFormGen] generated generatedavahenooretmlrotocolParameterHtmlForm.java 8122 INFO [HtmlFormGen] generated generatedavahenooretmlarameterValueHtmlForm.java 8122 INFO [HtmlFormGen] generated generatedavahenooretmlnferredValue_derivedFromHtmlForm.java 8122 INFO [HtmlFormGen] generated generatedavahenooretmlanel_individualsHtmlForm.java 8122 INFO [HtmlFormGen] generated generatedavahenooretmlrotocol_observableFeaturesHtmlForm.java 8138 INFO [HtmlFormGen] generated generatedavahenooretmlrotocol_protocolComponentsHtmlForm.java 8138 INFO [MolgenisServletContextGen] generated WebContentETA-INFontext.xml 8169 INFO [MolgenisContextListenerGen] generated generatedavaervletontextListener.java 8232 INFO [MolgenisServletGen] generated generatedavaolgenisServlet.java 8403 INFO [FormScreenGen] generated generatedavaicreenopMenuainnvestigationsForm.java 8560 INFO [FormScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenubservableFeaturesForm.java 8591 INFO [FormScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenuanelsForm.java 8654 INFO [FormScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenuanelsndividualsForm.java 8701 INFO [FormScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenubservedValuesForm.java 8732 INFO [FormScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenurotocolApplicationsForm.java 8825 INFO [FormScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenurotocolApplicationsrotocolApplicationMenuarameterValuesForm.java 8857 INFO [FormScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenurotocolApplicationsrotocolApplicationMenubservedValuesForm.java 8888 INFO [FormScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenurotocolApplicationsrotocolApplicationMenunferredValuesForm.java 9013 INFO [FormScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenunferredValuesForm.java 9044 INFO [FormScreenGen] generated generatedavaicreenopMenuainbservableFeaturesForm.java 9137 INFO [FormScreenGen] generated generatedavaicreenopMenuainbservationTargetsndividualsForm.java 9169 INFO [FormScreenGen] generated generatedavaicreenopMenuainbservationTargetsanelsForm.java 9200 INFO [FormScreenGen] generated generatedavaicreenopMenuainrotocolsForm.java 9293 INFO [FormScreenGen] generated generatedavaicreenopMenuainrotocolsrotocolMenuarametersForm.java 9325 INFO [FormScreenGen] generated generatedavaicreenopMenuainrotocolsrotocolMenurotocolComponentsForm.java 9496 INFO [FormScreenGen] generated generatedavaicreenopMenuainntologiesntologyTermsForm.java 9528 INFO [FormScreenGen] generated generatedavaicreenopMenuainntologiesntologySourcesForm.java 9606 INFO [FormScreenGen] generated generatedavaicreenopMenuainntologiesntologySourcesntologyTermsForm.java 9638 INFO [FormScreenGen] generated generatedavaicreenopMenuainntologiesodeListsForm.java 9700 INFO [FormScreenGen] generated generatedavaicreenopMenuainntologiesodeListsodesForm.java 9965 INFO [MenuScreenGen] generated generatedavaicreenopMenuMenu.java 10012 INFO [MenuScreenGen] generated generatedavaicreenopMenuainMenu.java 10059 INFO [MenuScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenuMenu.java 10152 INFO [MenuScreenGen] generated generatedavaicreenopMenuainnvestigationsnvestigationMenurotocolApplicationsrotocolApplicationMenuMenu.java 10230 INFO [MenuScreenGen] generated generatedavaicreenopMenuainbservationTargetsMenu.java 10293 INFO [MenuScreenGen] generated generatedavaicreenopMenuainrotocolsrotocolMenuMenu.java 10324 INFO [MenuScreenGen] generated generatedavaicreenopMenuainntologiesMenu.java 11354 INFO [PluginScreenGen] generated Molgenis33Workspaceolgenis4phenotypeeneratedavaicreenopMenuaineportPlugin.java 11557 INFO [PluginScreenGen] generated Molgenis33Workspaceolgenis4phenotypeeneratedavaicreenopMenuainntologiesntologyManagerPlugin.java 11604 INFO [PluginScreenGen] generated Molgenis33Workspaceolgenis4phenotypeeneratedavaicreenopMenuodel_documentationPlugin.java 11604 INFO [PluginScreenGen] generated Molgenis33Workspaceolgenis4phenotypeeneratedavaicreenopMenuprojectApiPlugin.java 11620 INFO [PluginScreenGen] generated Molgenis33Workspaceolgenis4phenotypeeneratedavaicreenopMenuttpApiPlugin.java 11635 INFO [PluginScreenGen] generated Molgenis33Workspaceolgenis4phenotypeeneratedavaicreenopMenuebServicesApiPlugin.java 11651 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenavalugineportnvestigationOverview.ftl 11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenavaluginntologyBrowserntologyBrowserPlugin.ftl 11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenavaluginopmenuocumentationScreen.ftl 11807 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenavaluginopmenuprojectApiScreen.ftl 11823 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenavaluginopmenuttpAPiScreen.ftl 11823 WARN [PluginScreenFTLTemplateGen] Skipped because exists: handwrittenavaluginopmenuoapApiScreen.ftl 11854 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenavalugineportnvestigationOverview.java 12057 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenavaluginntologyBrowserntologyBrowserPlugin.java 12072 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenavaluginopmenuocumentationScreen.java 12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenavaluginopmenuprojectApiScreen.java 12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenavaluginopmenuttpAPiScreen.java 12088 WARN [PluginScreenJavaTemplateGen] Skipped because exists: handwrittenavaluginopmenuoapApiScreen.java 12103 INFO [MolgenisServletContextGen] generated WebContentETA-INFontext.xml 12259 INFO [SoapApiGen] generated generatedavaioapApi.java 12353 INFO [CsvExportGen] generated generatedavaoolssvExport.java 12431 INFO [CsvImportByNameGen] generated generatedavaoolssvImportByName.java 12636 INFO [CopyMemoryToDatabaseGen] generated generatedavaioolsopyMemoryToDatabase.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
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.
![Outline ,[object Object],[object Object],[object Object]](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)