ELIXIR . Technical Coordinator
•Download as PPTX, PDF•
0 likes•31 views
24 September 2013
Recommended
Recommended
More Related Content
What's hot
What's hot (20)
Similar to ELIXIR . Technical Coordinator
Similar to ELIXIR . Technical Coordinator (20)
More from Rafael C. Jimenez
More from Rafael C. Jimenez (20)
Recently uploaded
Recently uploaded (20)
ELIXIR . Technical Coordinator
- 1. ELIXIR Technical Coordinator Rafael C Jimenez 2013 - 09 - 24 “Before, no one cared about standards. Now, people are very aware of their importance, so everyone is developing their own” ELIXIR WP12 report - Preparatory phase.
- 2. Mission • Ensure implementation of services • Forge collaborative development • Execute the ELIXIR technical strategy
- 3. ELIXIR technical strategy Compute Data Standards Tools Access Search Analysis Formats Ontologies Guidelines Privacy Optimization Integration Storage Network Computing e-infrastructure for Biological data
- 4. How? Federative infrastructure based on collaboration and share resources National coordination
- 5. Specialization Task forces coordination • Database • Computational • Biological domain • Standards • Tools • Training Do what you do best!
- 6. Compute Data Standards Tools Technical coordination • Nodes • Task forces • Central management BioMedBridges Research Infrastructures Technological infrastructures EMBRC, INSTRUCT, Eurobioimagining, Infrafrontier, ERINHA, EUOpenScreen, EATRIS, BBMRI, ECRINm, LifeWatch, … EUDAT, PRACE, GEANT, EGI, JISC, …
- 7. Timeline2007 2008 2009 2010 2011 2012 2013 2018 2014 2015 2016 2017 CTO Permanent phaseConstruction phasePreparatory phase 2021 2019 2020 2022 When
- 9. Projects & experience Standards, reusability, data integration, discoverability, community development, open source.
- 10. More data coverage Consortiums for data exchange Nucleotide sequences INSDC ENA DDBJ NCBI Molecular interactions IMEx IntAct InnateDB DIP MINT … Protein indentifications ProteomeXchange PRIDE PeptideAtlas GPMDB Tranche … Replication Federation Centralization Proteomics data exchange and storage: the need for common standards and public repositories. Jiménez RC, Vizcaíno JA. Better data management Less redundancy Agreement on data standards and data integration Less inconsistency
- 11. Schema Interfaces Guidelines Ontologies Format Identifiers Data Definition Representation Access Federation PublishFind Registry DAS ClientsDAS Clients Clients PSICQUIC sources PSICQUIC sourcesServices query format DAS PSICQUIC Service Oriented Architecture Standards PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Aranda B, Jimenez RC, et all. Integrating biological data- -the Distributed Annotation System. Jenkinson AM, Jimenez RC, et all Teaching the fundamentals of biological data integration using classroom games. Schneider MV, Jimenez RC.
- 12. Components Web applications reuse share BioJS BioJS: an open source JavaScript framework for biological data visualization. Gómez J, García LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N, Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.
- 13. Biologists & Developer Design Requirements 13.12.2018 BioJS Best practices Developer BioJS component BioJS Coding Developer Registry Source code Release API doc Specification Guidelines & tutorials
- 14. Unifying components 13.12.2018 • Represent the same type of information in different projects using the same graphical component 1 2 3 Graphical representation Developer 1 2 3 * Type of representation Website Implementation a b c d
- 15. EMBL-EBI integration projects EBI search / S4 • Summaries from different sources • Links to the original data • “Just enough” just “in time” 13.12.2018 15 Biosapiens • Comparable annotations from different sources • Common control vocabulary • Links to the original data
- 16. Improving Links Between the Human Protein Atlas (HPA) and EMBL-EBI’s resources 13.12.2018 16 DASS4 HP-WSBioJS Summary data Details Standards
- 17. molecular interactions integration molecular interaction databases organellar proteomics datasets analysisorganellar interactomes interactome data visualization + interactome query PSICQUIC MISCORE MICLUSTER INTERACTOME BUILDER BIOJS PSICQUIC integrated resource Organellar interactomes Interactome context Cellular location evidence Stats/Analysis Proteomics interactome project + EMBL-EBI
- 18. PSICQUIC MISCORE MICLUSTER INTERACTOME BUILDER BIOJS PSICQUIC integrated resource Organellar interactomes Interactome context Cellular location evidence Stats/Analysis Services APID API WS WEB API WS DB API WEB API DB WEBWS WS FW API FW WEB EMBL-EBI
- 19. Publications PSICQUIC MISCORE MICLUSTER INTERACTOME BUILDER BIOJS PSICQUIC integrated resource Organellar interactomes Interactome context Cellular location evidence Stats/Analysis BioJS: An Open Source JavaScript Framework for Biological Data Visualization Apr 2013, 23435069 A New Reference Implementation of the PSICQUIC web service July 2013, 23671334 Clustering and scoring molecular interactions relying on community standards Aiming to submit in Sept Integration and visualization of protein interactions in context with organelle protein identifications. Aiming to submit before Dec EMBL-EBI
- 20. iAnn Curation Centralization Distribution Integration Registry Input form Web sites Visualization ModulesWeb services Editor Web services Viewer Open source community-driven platform for dissemination of life science events iAnn: an event sharing platform for the life sciences. Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M.
- 21. Format Ontology Minimum Information guideline Standards to exchange announcements among bioinformatics societies More data coverage, less redundancy, less inconsistency, better data management Integration Access Exchange Sharing Portability Interoperability Annotation Comparison Verification Reusability Representation
- 22. Conclusions • Be realistic about what you can achieve • Keep it simple • Open the project to external contributions • Let the community decide • Purpose-driven requirements • Fail early
- 24. Dasty3, a WEB framework for DAS Integration of Cardiac Proteome Biology and Medicine iAnn: an event sharing platform for the life sciences A new reference implementation of the PSICQUIC web service BioJS: an open source JavaScript framework for biological data visualization Best practices in bioinformatics training for life scientists Bioinformatics workflows and web services for experimentalists Proteomics data exchange and storage: common standards and public repositories. Teaching the fundamentals of biological data integration using classroom games. The IntAct molecular interaction database in 2012 myKaryoView: a light-weight client for visualization of genomic data PSICQUIC and PSISCORE: accessing and scoring molecular interactions. MyDas, an extensible Java DAS server Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers. DAS writeback: a collaborative annotation system easyDAS: automatic creation of DAS servers The Protein Feature Ontology: a tool for the unification of protein feature annotations Dasty2, an Ajax protein DAS client OntoDas - a tool for facilitating the construction of complex queries to the GO. Integrating biological data--the Distributed Annotation System 2013 2009 2010 2011 2012 UPV CIPFEMBL-EBIEMBL-EBI Publications
- 25. How
- 26. Quotes Good project management cannot guarantee success, but poor management on significant projects always leads to failure. A.A.Puntambekar The biggest single problem that afflicts software developing is that of underestimating resources required for a project. Mike Wooldridge Before, no one cared about standards. Now, people are very aware of their importance, so everyone is developing their own. ELIXIR WP12. Preparatory phase report Considerations for transitioning to open development (NCI): • Keep it simple. Make barriers to entry as low as possible, and reuse available resources. • Let the community decide. For an open-source development ecosystem to be successful, it needs to be truly owned • Purpose-driven requirements. The use of standards and any concept of “certification” should be established based on real needs and use cases. • Don’t over-think the process, and stop waiting to do something – fail early. Don’t wait for the code or process to be perfect. Put the applications out there and let them fail or succeed, as determined by the community.
- 28. Data integration problems Many data resources • Many to maintain • Databases change • New appearing • Some disappearing* • Not easy to find them Different query interfaces data integration? Variable results • Formats • Schemas • Controlled vocabularies • Minimum information guidelines * Merali Z. et all. Databases in peril. Nature 2005. • Inconsistency • Mapping problems • Records with not enough information • Redundancy
- 29. Data standards 13/12/2018 29 Integration AccessExchange Sharing Portability Interoperability Annotation Comparison Verification Reusability Representation Compliance Consistency Replication Web service API Submission Edition Conversion Comparison Visualization Analysis Integration Validation TOOLS
- 30. 1 3 5 Popular data integration approaches 4 6 2 ... Data centralization Data warehousing Dataset integration Hyperlinks Federated databases View integration
- 31. Heterogeneous data sources Same data types Homogeneous vs Heterogeneous data integration A B C 1 2 leverage B C A Teaching the fundamentals of biological data integration using classroom games. Schneider MV, Jimenez RC.
- 32. 184 molecular interactions Pathway resources 13 December 2018 32 132 9 43 73 62 51 38 20 14 Pathway resource list Protein-Protein Interactions Genetic Interaction Networks Protein-Compound Interactions Metabolic Pathways Signaling Pathways Gene Regulatory Networks Pathway Diagrams Protein Sequence Focused Other http://www.pathguide.org/ 442 pathway
- 33. Expertise to do this job • Software project management • Collaborative software development • Bioinformatics in multidisciplinary fields • Biological science • System administration • Writing • Interpersonal skills
- 34. Achievements (last 4 years) • Definition and implementation of standards like DAS and PSI • Start the BioJS community open source project • Participate as a Researcher Co-Investigator in a BBSRC grant proposal • Publish 17 publication (6 as a first or last author) • Write 2 book chapters • Report more than 10 deliverables • I supervised 5 students (3 of which are currently collaborating with our team) • Participate as speaker/trainer in almost 30 bioinformatics events • Co-organise 6 workshops about web services and visualisation • Participate in several projects including Biosapiends, ENFIN, COPa, IntAct, IMEx, PRIDE, Affinomics, LARK2-LEAPS, ELIXIR, BioMedBridges and AgedBrainSysBio